1
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Luo HY, Jiang C, Dou SX, Wang PY, Li H. Quantum Dot-Based Three-Dimensional Single-Particle Tracking Characterizes the Evolution of Spatiotemporal Heterogeneity in Necrotic Cells. Anal Chem 2024. [PMID: 38979688 DOI: 10.1021/acs.analchem.4c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Cell death is a fundamental biological process with different modes including apoptosis and necrosis. In contrast to programmed apoptosis, necrosis was previously considered disordered and passive, but it is now being realized to be under regulation by certain biological pathways. However, the intracellular dynamics that coordinates with cellular structure changes during necrosis remains unknown, limiting our understanding of the principles of necrosis. Here, we characterized the spatiotemporal intracellular diffusion dynamics in cells undergoing necrosis, using three-dimensional single-particle tracking of quantum dots. We found temporally increased diffusion rates in necrotic cells and spatially enhanced diffusion heterogeneity in the cell periphery, which could be attributed to the reduced molecular crowding resulting from cell swelling and peripheral blebbing, respectively. Moreover, the three-dimensional intracellular diffusion transits from strong anisotropy to nearly isotropy, suggesting a remodeling of the cytoarchitecture that relieves the axial constraint on intracellular diffusion during necrosis. Our results reveal the remarkable alterations of intracellular diffusion dynamics and biophysical properties in necrosis, providing insight into the well-organized nonequilibrium necrotic cell death from a biophysical perspective.
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Affiliation(s)
- 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, University of Chinese Academy of Sciences, Beijing 100049, China
| | - 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 Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China
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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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Chae SJ, Kim DW, Igoshin OA, Lee S, Kim JK. Beyond microtubules: The cellular environment at the endoplasmic reticulum attracts proteins to the nucleus, enabling nuclear transport. iScience 2024; 27:109235. [PMID: 38439967 PMCID: PMC10909898 DOI: 10.1016/j.isci.2024.109235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 01/03/2024] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
All proteins are translated in the cytoplasm, yet many, including transcription factors, play vital roles in the nucleus. While previous research has concentrated on molecular motors for the transport of these proteins to the nucleus, recent observations reveal perinuclear accumulation even in the absence of an energy source, hinting at alternative mechanisms. Here, we propose that structural properties of the cellular environment, specifically the endoplasmic reticulum (ER), can promote molecular transport to the perinucleus without requiring additional energy expenditure. Specifically, physical interaction between proteins and the ER impedes their diffusion and leads to their accumulation near the nucleus. This result explains why larger proteins, more frequently interacting with the ER membrane, tend to accumulate at the perinucleus. Interestingly, such diffusion in a heterogeneous environment follows Chapman's law rather than the popular Fick's law. Our findings suggest a novel protein transport mechanism arising solely from characteristics of the intracellular environment.
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Affiliation(s)
- Seok Joo Chae
- Department of Mathematical Sciences, KAIST, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Dae Wook Kim
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Oleg A. Igoshin
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Seunggyu Lee
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon 34126, Republic of Korea
- Division of Applied Mathematical Sciences, Korea University, Sejong 30019, Republic of Korea
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, KAIST, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon 34126, Republic of Korea
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4
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Pain C, Tynan C, Botchway SW, Kriechbaumer V. Variable-Angle Epifluorescence Microscopy for Single-Particle Tracking in the Plant ER. Methods Mol Biol 2024; 2772:273-283. [PMID: 38411821 DOI: 10.1007/978-1-0716-3710-4_20] [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] [Indexed: 02/28/2024]
Abstract
Single-particle tracking (SPT) of biomolecules in the plant endoplasmic reticulum has the potential to inform on the formation of protein-protein complexes, metabolons, and the transport of molecules through both the ER membrane and lumen. Plant cells are particularly challenging for observing and tracking single molecules due to their unique structure, size, and considerable autofluorescence. However, by using variable-angle or highly inclined epifluorescence microscopy (VAEM) and transient expression in tobacco, it is possible to observe single-particle dynamics in the ER. Selecting the appropriate fluorophore, and ensuring the correct fluorophore density in the ER, is essential for successful SPT. By using tuneable fluorophores, which can be photoconverted and photoactivated, it is possible to vary the density of visible fluorophores in the ER dynamically. Here we describe methods to prepare plant samples for VAEM and two methods for determining and analyzing single-particle tracks from VAEM time series.
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Affiliation(s)
- Charlotte Pain
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Christopher Tynan
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
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5
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Luo MB, Hua DY. Simulation Study on the Mechanism of Intermediate Subdiffusion of Diffusive Particles in Crowded Systems. ACS OMEGA 2023; 8:34188-34195. [PMID: 37744832 PMCID: PMC10515404 DOI: 10.1021/acsomega.3c05945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023]
Abstract
The intermediate subdiffusion of diffusive particles in crowded systems is studied for two model systems: the continuous time random walk (CTRW) model and the obstruction-binding model. For the CTRW model with an arbitrarily given longest waiting time τmax, we find that the diffusive particle exhibits subdiffusion below τmax and recovers normal diffusion above τmax. For the obstruction-binding model with randomly distributed attractive obstacles, the diffusion of the diffusive particle is dependent on the binding energy and the density of obstacles. Interestingly, diffusion curves for different binding strengths can be overlapped by rescaling the simulation time, indicating that the diffusive particle in the obstruction-binding model can change from the intermediate subdiffusion to the normal diffusion at a long-term simulation scale. The results of the two model systems show that the diffusive particles only exhibit intermediate subdiffusion below the longest waiting time. Therefore, long timescale subdiffusion would only be observed in the CTRW model with an infinitely long waiting time and in the obstruction-binding model with an infinitely large binding strength.
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Affiliation(s)
- Meng-Bo Luo
- School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Dao-Yang Hua
- School of Physics, Zhejiang University, Hangzhou 310027, China
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6
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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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7
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Itto Y. Conditional Entropic Approach to Nonequilibrium Complex Systems with Weak Fluctuation Correlation. ENTROPY (BASEL, SWITZERLAND) 2023; 25:e25040556. [PMID: 37190346 PMCID: PMC10137531 DOI: 10.3390/e25040556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 05/17/2023]
Abstract
A conditional entropic approach is discussed for nonequilibrium complex systems with a weak correlation between spatiotemporally fluctuating quantities on a large time scale. The weak correlation is found to constitute the fluctuation distribution that maximizes the entropy associated with the conditional fluctuations. The approach is illustrated in diffusion phenomenon of proteins inside bacteria. A further possible illustration is also presented for membraneless organelles in embryos and beads in cell extracts, which share common natures of fluctuations in their diffusion.
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Affiliation(s)
- Yuichi Itto
- Science Division, Center for General Education, Aichi Institute of Technology, Toyota 470-0392, Aichi, Japan
- Institut für Computerphysik, Universität Stuttgart, 70569 Stuttgart, Germany
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8
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Opioid-Modulated Receptor Localization and Erk1/2 Phosphorylation in Cells Coexpressing μ-Opioid and Nociceptin Receptors. Int J Mol Sci 2023; 24:ijms24021048. [PMID: 36674576 PMCID: PMC9865058 DOI: 10.3390/ijms24021048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
We attempted to examine the alterations elicited by opioids via coexpressed μ-opioid (MOP) and nociceptin/orphanin FQ (NOP) receptors for receptor localization and Erk1/2 (p44/42 MAPK) in human embryonic kidney (HEK) 293 cells. Through two-photon microscopy, the proximity of MOP and NOP receptors was verified by fluorescence resonance energy transfer (FRET), and morphine but not buprenorphine facilitated the process of MOP-NOP heterodimerization. Single-particle tracking (SPT) further revealed that morphine or buprenorphine hindered the movement of the MOP-NOP heterodimers. After exposure to morphine or buprenorphine, receptor localization on lipid rafts was detected by immunocytochemistry, and phosphorylation of Erk1/2 was determined by immunoblotting in HEK 293 cells expressing MOP, NOP, or MOP+NOP receptors. Colocalization of MOP and NOP on lipid rafts was enhanced by morphine but not buprenorphine. Morphine stimulated the phosphorylation of Erk1/2 with a similar potency in HEK 293 cells expressing MOP and MOP+NOP receptors, but buprenorphine appeared to activate Erk1/2 solely through NOP receptors. Our results suggest that opioids can fine-tune the cellular localization of opioid receptors and phosphorylation of Erk1/2 in MOP+NOP-expressing cells.
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9
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Jiang C, Dou SX, Wang PY, Li H. Quantifying transport dynamics with three-dimensional single-particle tracking in adherent cells. STAR Protoc 2022; 3:101790. [PMID: 36317175 PMCID: PMC9617199 DOI: 10.1016/j.xpro.2022.101790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Intracellular transport plays an important role in maintaining the physiological functions of cells. Here, we describe a protocol for 3D single-particle tracking within living cells. We detail the use of a two-focal imaging system and the analytical steps for quantifying 3D transport dynamics. This protocol can be used to characterize the intracellular diffusion and trafficking of macromolecules, nanoparticles, and endocytic vesicles in adherent cells. For complete details on the use and execution of this protocol, please refer to Jiang et al. (2022).
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Affiliation(s)
- Chao Jiang
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China; Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China.
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing 100875, China.
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10
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Venkatesh RB, Lee D. Interfacial Friction Controls the Motion of Confined Polymers in the Pores of Nanoparticle Packings. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Bharath Venkatesh
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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11
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Wójtowicz K, Antoniak MA, Trojnar M, Nyk M, Trombik T, Grzyb J. QD:Puf Nanohybrids Are Compatible with Studies in Cells. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3174. [PMID: 36144961 PMCID: PMC9506232 DOI: 10.3390/nano12183174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/10/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Colloidal semiconductor quantum dots (QD), as well as other nanoparticles, are useful in cell studies as fluorescent labels. They may also be used as more active components in various cellular assays, serving as sensors or effectors. However, not all QDs are biocompatible. One of the main problems is their outer coat, which needs to be stable and to sustain hydrophilicity. Here we show that purpose-designed CdSe QDs, covered with a Puf protein, can be efficiently accumulated by HeLa cells. The uptake was measurable after a few hours of incubation with nanoparticles and most of the fluorescence was localised in the internal membrane system of the cell, including the endoplasmic reticulum and the Golgi apparatus. The fluorescence properties of QDs were mostly preserved, although the maximum emission wavelength was slightly shifted, and the fluorescence lifetime was shortened, indicating partial sensitivity of the QDs to the cell microenvironment. QD accumulation resulted in a decrease in cell viability, which was attributed to disturbance of endoplasmic reticulum performance.
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Affiliation(s)
- Karolina Wójtowicz
- Department of Biotransformation, Faculty of Biotechnology, University of Wrocław, ul. F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Magda A. Antoniak
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Martyna Trojnar
- Department of Biophysics, Faculty of Biotechnology, University of Wrocław, ul. F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Marcin Nyk
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Tomasz Trombik
- Department of Biotransformation, Faculty of Biotechnology, University of Wrocław, ul. F. Joliot-Curie 14a, 50-383 Wrocław, Poland
- The Chair and Department of Biochemistry and Molecular Biology, Medical University of Lublin, ul. Chodzki 1, 20-093 Lublin, Poland
| | - Joanna Grzyb
- Department of Biophysics, Faculty of Biotechnology, University of Wrocław, ul. F. Joliot-Curie 14a, 50-383 Wrocław, Poland
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12
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Spatiotemporal three-dimensional transport dynamics of endocytic cargos and their physical regulations in cells. iScience 2022; 25:104210. [PMID: 35479412 PMCID: PMC9035719 DOI: 10.1016/j.isci.2022.104210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/14/2022] [Accepted: 04/04/2022] [Indexed: 11/21/2022] Open
Abstract
Intracellular transport, regulated by complex cytoarchitectures and active driving forces, is crucial for biomolecule translocations and relates to many cellular functions. Despite extensive knowledge obtained from two-dimensional (2D) experiments, the real three-dimensional (3D) spatiotemporal characteristics of intracellular transport is still unclear. With 3D single-particle tracking, we comprehensively studied the transport dynamics of endocytic cargos. With varying timescale, the intracellular transport changes from thermal-dominated 3D-constrained motion to active-dominated quasi-2D motion. Spatially, the lateral motion is heterogeneous with peripheral regions being faster than perinuclear regions, while the axial motion is homogeneous across the cells. We further confirmed that such anisotropy and heterogeneity of vesicle transport result from actively directed motion on microtubules. Strikingly, inside the vesicles, we observed endocytic nanoparticles make diffusive motions on their inner membranes when microtubules are absent, suggesting endocytic cargos are normally localized at the inner vesicle membranes through a physical connection to the microtubules outside during transport. Endocytic transport changes from 3D-constrained to quasi-2D motions with timescales Lateral motion is heterogeneous while axial motion is homogeneous across the cells Microtubules cause the anisotropy and heterogeneity of vesicle transport Endocytic particles make diffusive motion on the inner membrane of vesicles
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13
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Pradeep S, Zangle TA. Quantitative phase velocimetry measures bulk intracellular transport of cell mass during the cell cycle. Sci Rep 2022; 12:6074. [PMID: 35414087 PMCID: PMC9005622 DOI: 10.1038/s41598-022-10000-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/22/2022] [Indexed: 12/13/2022] Open
Abstract
Transport of mass within cells helps maintain homeostasis and is disrupted by disease and stress. Here, we develop quantitative phase velocimetry (QPV) as a label-free approach to make the invisible flow of mass within cells visible and quantifiable. We benchmark our approach against alternative image registration methods, a theoretical error model, and synthetic data. Our method tracks not just individual labeled particles or molecules, but the entire flow of bulk material through the cell. This enables us to measure diffusivity within distinct cell compartments using a single approach, which we use here for direct comparison of nuclear and cytoplasmic diffusivity. As a label-free method, QPV can be used for long-term tracking to capture dynamics through the cell cycle.
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Affiliation(s)
- Soorya Pradeep
- Department of Chemical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Thomas A Zangle
- Department of Chemical Engineering, University of Utah, Salt Lake City, UT, 84112, USA. .,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA.
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14
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Yuan JW, Zhang YN, Liu YR, Li W, Dou SX, Wei Y, Wang PY, Li H. Diffusion Behaviors of Integrins in Single Cells Altered by Epithelial to Mesenchymal Transition. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106498. [PMID: 34921576 DOI: 10.1002/smll.202106498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Cell morphology and migration depend critically on the adhesions on the extracellular matrix (ECM), determined by the transmembrane protein integrins. The epithelial to mesenchymal transition (EMT) is a prominent transformation process in which adherent cells acquire a mesenchymal phenotype and a promoted migration. EMT plays important roles in embryonic development and cancer metastasis, and its hallmarks include the acquisition of front-back cell polarity and loss of cell-cell contact. However, how integrins dynamically regulate cell-ECM adhesions and cellular behaviors during EMT is still unclear. Using single-particle tracking of β1-integrins labeled with quantum dots, the temporal-spatial on-membrane dynamics of integrins in the EMT of MCF10A cells is revealed. β1-integrins exhibit significantly enhanced dynamics, which temporally behave more diffusive and less immobilized, and spatially become distributed asymmetrically with front regions being more dynamic. These dynamic alterations are shown to arise from microtubule remodeling in EMT. The results shed new light on the EMT mechanism from the cell-ECM adhesion perspective, and suggest that the enhanced integrin diffusion may represent as a new hallmark of EMT.
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Affiliation(s)
- Jing-Wen Yuan
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Ning Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Yu-Ru Liu
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wei Li
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Wei
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Hui Li
- School of Systems Science and Institute of Nonequilibrium Systems, Beijing Normal University, Beijing, 100875, China
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15
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Abstract
Transport of intracellular components relies on a variety of active and passive mechanisms, ranging from the diffusive spreading of small molecules over short distances to motor-driven motion across long distances. The cell-scale behavior of these mechanisms is fundamentally dependent on the morphology of the underlying cellular structures. Diffusion-limited reaction times can be qualitatively altered by the presence of occluding barriers or by confinement in complex architectures, such as those of reticulated organelles. Motor-driven transport is modulated by the architecture of cytoskeletal filaments that serve as transport highways. In this review, we discuss the impact of geometry on intracellular transport processes that fulfill a broad range of functional objectives, including delivery, distribution, and sorting of cellular components. By unraveling the interplay between morphology and transport efficiency, we aim to elucidate key structure-function relationships that govern the architecture of transport systems at the cellular scale. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Anamika Agrawal
- Department of Physics, University of California, San Diego, La Jolla, California, USA;
| | - Zubenelgenubi C Scott
- Department of Physics, University of California, San Diego, La Jolla, California, USA;
| | - Elena F Koslover
- Department of Physics, University of California, San Diego, La Jolla, California, USA;
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16
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Wang Q, Feng Z, He H, Hu X, Mao J, Chen X, Liu L, Wei X, Liu D, Bi S, Wang X, Ge B, Yu D, Huang F. Nonblinking carbon dots for imaging and tracking receptors on a live cell membrane. Chem Commun (Camb) 2021; 57:5554-5557. [PMID: 33969837 DOI: 10.1039/d1cc01120k] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Blinking occurs with nearly all fluorophores including organic dyes, fluorescent proteins, semiconductor quantum dots and carbon dots (CDs). We developed non-blinking and photoresistant fluorescent CDs by introducing multiple aromatic domains onto a single carbon dot and demonstrated their great potential for imaging and tracking of receptors on a live cell membrane.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China.
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17
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Itto Y, Beck C. Superstatistical modelling of protein diffusion dynamics in bacteria. J R Soc Interface 2021; 18:20200927. [PMID: 33653112 PMCID: PMC8086855 DOI: 10.1098/rsif.2020.0927] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
A recent experiment (Sadoon AA, Wang Y. 2018 Phys. Rev. E98, 042411. (doi:10.1103/PhysRevE.98.042411)) has revealed that nucleoid-associated proteins (i.e. DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion constant but also the anomalous diffusion exponent fluctuates for the various proteins. The distribution of displacements of such proteins is observed to take a q-Gaussian form, which decays as a power law. Here, a statistical model is developed for the diffusive motion of the proteins within the bacterium, based on a superstatistics with two variables. This model hierarchically takes into account the joint fluctuations of both the anomalous diffusion exponents and the diffusion constants. A fractional Brownian motion is discussed as a possible local model. Good agreement with the experimental data is obtained.
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Affiliation(s)
- Yuichi Itto
- ICP, Universität Stuttgart, 70569 Stuttgart, Germany
- Science Division, Center for General Education, Aichi Institute of Technology, Aichi 470-0392, Japan
| | - Christian Beck
- School of Mathematical Sciences, Queen Mary University of London, London E1 4NS, UK
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18
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Wang Z, Wang X, Zhang Y, Xu W, Han X. Principles and Applications of Single Particle Tracking in Cell Research. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005133. [PMID: 33533163 DOI: 10.1002/smll.202005133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/24/2020] [Indexed: 06/12/2023]
Abstract
It is a tough challenge for many decades to decipher the complex relationships between cell behaviors and cellular physical properties. Single particle tracking (SPT) with high spatial and temporal resolution has been applied extensively in cell research to understand physicochemical properties of cells and their bio-functions by tracking endogenous or exogenous probes. This review describes the fundamental principles of SPT as well as its applications in intracellular mechanics, membrane dynamics, organelles distribution, and processes of internalization and transport. Finally, challenges and future directions of SPT are also discussed.
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Affiliation(s)
- Zhao Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xuejing Wang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, 310058, China
| | - Ying Zhang
- School of Materials and Chemical Engineering, Heilongjiang Institute of Technology, Harbin, 150027, China
| | - Weili Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
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19
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Pan Q, Sun D, Xue J, Hao J, Zhao H, Lin X, Yu L, He Y. Real-Time Study of Protein Phase Separation with Spatiotemporal Analysis of Single-Nanoparticle Trajectories. ACS NANO 2021; 15:539-549. [PMID: 33348982 DOI: 10.1021/acsnano.0c05486] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Liquid-liquid phase separation (LLPS) underlies the formation mechanism of membraneless biomolecular condensates locally to perform important physiological functions such as selective autophagy, but little is known about the relationship between their dynamic structural organization and biophysical properties. Here, a dark-field microscopy based single plasmonic nanoparticle tracking (DFSPT) technique was introduced to simultaneously monitor the diffusion dynamics of multiple gold nanorod (AuNR) probes in a protein LLPS system and to quantitatively characterize the spatiotemporal heterogeneity of the LLPS condensates during their phase transformation. Based on spatially and temporally resolved analysis of the diffusional behavior of the AuNRs, structure and material properties of p62 condensates, such as the viscoelasticity, the compartmentalization, and the recruitment of protein-covered nanoparticles into the large droplet, have been observed. Moreover, the nonsmooth droplet interface, its solidification after further phase transition or maturation, and the size effect of the inner vacuoles have also been revealed. Our method can be potentially applied to in vitro investigation of different reconstituted membrane-free biomolecular condensates and in vivo study of their dynamic evolution.
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Affiliation(s)
- Qi Pan
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Daxiao Sun
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianfeng Xue
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jie Hao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Hansen Zhao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Xijian Lin
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan He
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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20
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Harusawa K, Watanabe C, Kobori Y, Tomita K, Kitamura A, Kinjo M, Yanagisawa M. Membrane Surface Modulates Slow Diffusion in Small Crowded Droplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:437-444. [PMID: 33351626 DOI: 10.1021/acs.langmuir.0c03086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Membranes are ubiquitous structures in cells. The effects of membranes on various functional molecules have been reported, but their behaviors under macromolecular crowding and cell-sized confinement have not fully been understood. In this study, we model an intracellular environment by crowding micrometer-sized droplets and investigate the effects of membrane properties on molecular diffusion. The molecular diffusion inside small droplets covered with a lipid layer of phosphatidylcholine (PC) becomes slower compared with that of the corresponding bulk solutions under a crowding condition of polysaccharide dextran but not of its monomer unit, glucose. The addition of a poly(ethylene glycol) conjugated lipid (PEGylated lipid) to the PC membrane significantly alters the degree of slow diffusion observed inside small droplets of concentrated dextran. Interestingly, the change is not monotonic against dextran concentration; that is, the PEGylated membrane increases and decreases the degree of slow diffusion with increasing dextran concentration. We explain the nonmonotonic alternation from the increase in effective dextran concentration and the hindered temporal adsorption of dextran to the membrane. Because diffusion alteration by adding PEGylated lipid is observed for condensed small droplets of linear polymer PEG and hydrophilic protein bovine serum albumin, the phenomenon is general for other polymer systems as well. Furthermore, our findings may facilitate the understanding of intracellular molecular behaviors based on membrane effects as well as the development of numerous applications using polymer droplets.
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Affiliation(s)
- Kanae Harusawa
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Chiho Watanabe
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
| | - Yuta Kobori
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Kazuho Tomita
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Akira Kitamura
- Faculty of Advanced Life Science, Hokkaido University, Kita-21 Nishi-11 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Masataka Kinjo
- Faculty of Advanced Life Science, Hokkaido University, Kita-21 Nishi-11 Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Miho Yanagisawa
- Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department of Basic Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
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21
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Reveal heterogeneous motion states in single nanoparticle trajectory using its own history. Sci China Chem 2020. [DOI: 10.1007/s11426-020-9896-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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S Mogre S, Brown AI, Koslover EF. Getting around the cell: physical transport in the intracellular world. Phys Biol 2020; 17:061003. [PMID: 32663814 DOI: 10.1088/1478-3975/aba5e5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic cells face the challenging task of transporting a variety of particles through the complex intracellular milieu in order to deliver, distribute, and mix the many components that support cell function. In this review, we explore the biological objectives and physical mechanisms of intracellular transport. Our focus is on cytoplasmic and intra-organelle transport at the whole-cell scale. We outline several key biological functions that depend on physically transporting components across the cell, including the delivery of secreted proteins, support of cell growth and repair, propagation of intracellular signals, establishment of organelle contacts, and spatial organization of metabolic gradients. We then review the three primary physical modes of transport in eukaryotic cells: diffusive motion, motor-driven transport, and advection by cytoplasmic flow. For each mechanism, we identify the main factors that determine speed and directionality. We also highlight the efficiency of each transport mode in fulfilling various key objectives of transport, such as particle mixing, directed delivery, and rapid target search. Taken together, the interplay of diffusion, molecular motors, and flows supports the intracellular transport needs that underlie a broad variety of biological phenomena.
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Affiliation(s)
- Saurabh S Mogre
- Department of Physics, University of California, San Diego, San Diego, California 92093, United States of America
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23
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Luo L, Yi M. Quenched trap model on the extreme landscape: The rise of subdiffusion and non-Gaussian diffusion. Phys Rev E 2019; 100:042136. [PMID: 31770896 DOI: 10.1103/physreve.100.042136] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Indexed: 11/07/2022]
Abstract
Non-Gaussian diffusion has been intensively studied in recent years, which reflects the dynamic heterogeneity in the disordered media. The recent study on the non-Gaussian diffusion in a static disordered landscape suggests novel phenomena due to the quenched disorder. In this paper, we further investigate the random walk on this landscape under various effective temperatures μ, which continuously modulate the dynamic heterogeneity. We show in the long-time limit, the trap dynamics on the landscape is equivalent to the quenched trap model in which subdiffusion appears for μ<1. The non-Gaussian distribution of displacement has been analytically estimated for short t of which the stretched exponential tail is expected for μ≠1. Due to the localization in the ensemble of trajectory segments, an additional peak arises in P(x,t) around x=0 even for μ>1. Evolving in different timescales, the peak and the tail of P(x,t) are well split for a wide range of t. This theoretical paper reveals the connections among the subdiffusion, non-Gaussian diffusion, and the dynamic heterogeneity in the static disordered medium. It also offers an insight on how the cell would benefit from the quasistatic disordered structures.
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Affiliation(s)
- Liang Luo
- Department of Physics, Huazhong Agricultural University, Wuhan 430070, China.,Institute of Applied Physics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Yi
- School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China
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24
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Wang F, Chen B, Yan B, Yin Y, Hu L, Liang Y, Song M, Jiang G. Scattered Light Imaging Enables Real-Time Monitoring of Label-Free Nanoparticles and Fluorescent Biomolecules in Live Cells. J Am Chem Soc 2019; 141:14043-14047. [DOI: 10.1021/jacs.9b05894] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Fengbang Wang
- State Key Laboratory
of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
- Key Laboratory
of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Bolei Chen
- Hubei Key Laboratory
of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan 430056, People’s Republic of China
| | - Bing Yan
- Institute of Environmental
Research at Greater Bay, Key Laboratory for Water Quality and Conservation
of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, People’s Republic of China
| | - Yongguang Yin
- State Key Laboratory
of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
- Key Laboratory
of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
| | - Ligang Hu
- State Key Laboratory
of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
| | - Yong Liang
- Hubei Key Laboratory
of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan 430056, People’s Republic of China
- Institute
of Environment
and Health, Jianghan University, Wuhan 430056, People’s Republic of China
| | - Maoyong Song
- State Key Laboratory
of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
- Key Laboratory
of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Guibin Jiang
- State Key Laboratory
of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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25
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Ning L, Liu P, Zong Y, Liu R, Yang M, Chen K. Universal Scaling Law for Colloidal Diffusion in Complex Media. PHYSICAL REVIEW LETTERS 2019; 122:178002. [PMID: 31107097 DOI: 10.1103/physrevlett.122.178002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Using video microscopy and simulations, we study the diffusion of probe particles in a wide range of complex backgrounds, both crystalline and disordered, in quasi-2D colloidal systems. The dimensionless diffusion coefficients D^{*} from different systems collapse to a single master curve when plotted as a function of the structural entropy of the backgrounds, confirming the universal relation between diffusion dynamics and the structure of the medium. A new scaling equation is proposed with consideration for the viscous friction from the solvent, which is absent in previous theoretical models. This new universal law quantitatively predicts the diffusion coefficients from different systems over several orders of magnitude of D^{*}, with a single common fitting parameter.
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Affiliation(s)
- Luhui Ning
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Liu
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiwu Zong
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Rui Liu
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Mingcheng Yang
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Chen
- Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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26
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Qian C, Wu G, Jiang D, Zhao X, Chen HB, Yang Y, Liu XW. Identification of Nanoparticles via Plasmonic Scattering Interferometry. Angew Chem Int Ed Engl 2019; 58:4217-4220. [PMID: 30730602 DOI: 10.1002/anie.201813567] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/22/2019] [Indexed: 01/12/2023]
Abstract
The development of optical imaging techniques has led to significant advancements in single-nanoparticle tracking and analysis, but these techniques are incapable of label-free selective nanoparticle recognition. A label-free plasmonic imaging technology that is able to identify different kinds of nanoparticles in water is now presented. It quantifies the plasmonic interferometric scattering patterns of nanoparticles and establishes relationships among the refractive index, particle size, and pattern both numerically and experimentally. Using this approach, metallic and metallic oxide particles with different radii were distinguished without any calibration. The ability to optically identify and size different kinds of nanoparticles can provide a promising platform for investigating nanoparticles in complex environments to facilitate nanoscience studies, such as single-nanoparticle catalysis and nanoparticle-based drug delivery.
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Affiliation(s)
- Chen Qian
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Gang Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Di Jiang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Xiaona Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Hai-Bo Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
| | - Yunze Yang
- Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Xian-Wei Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science & Technology of China, Hefei, 230026, China
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27
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Qian C, Wu G, Jiang D, Zhao X, Chen H, Yang Y, Liu X. Identification of Nanoparticles via Plasmonic Scattering Interferometry. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chen Qian
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied ChemistryUniversity of Science & Technology of China Hefei 230026 China
| | - Gang Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied ChemistryUniversity of Science & Technology of China Hefei 230026 China
| | - Di Jiang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied ChemistryUniversity of Science & Technology of China Hefei 230026 China
| | - Xiaona Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied ChemistryUniversity of Science & Technology of China Hefei 230026 China
| | - Hai‐Bo Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied ChemistryUniversity of Science & Technology of China Hefei 230026 China
| | - Yunze Yang
- Center for Biosensors and Bioelectronics, Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Xian‐Wei Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied ChemistryUniversity of Science & Technology of China Hefei 230026 China
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28
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Schwarz J, J Leopold H, Leighton R, Miller RC, Aplin CP, Boersma AJ, Heikal AA, Sheets ED. Macromolecular crowding effects on energy transfer efficiency and donor-acceptor distance of hetero-FRET sensors using time-resolved fluorescence. Methods Appl Fluoresc 2019; 7:025002. [PMID: 30690439 DOI: 10.1088/2050-6120/ab0242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Living cells are crowded with macromolecules and organelles, which affect a myriad of biochemical processes. As a result, there is a need for sensitive molecular sensors for quantitative, site-specific assessment of macromolecular crowding. Here, we investigated the excited-state dynamics of recently developed hetero-FRET sensors (mCerulean3-linker-mCitrine) in homogeneous and heterogeneous environments using time-resolved fluorescence measurements, which are compatible with fluorescence lifetime imaging microscopy (FLIM). The linker in these FRET constructs, which tether the mCerulean3 (the donor) and mCitrine (the acceptor), vary in both length and flexibility. Glycerol and Ficoll-70 solutions were used for homogeneous and heterogeneous environments, respectively, at variable concentrations. The wavelength-dependent studies suggest that the 425-nm excitation and the 475-nm emission of the donor are best suited for quantitative assessment of the energy transfer efficiency and the donor-acceptor distance of these FRET probes. Under the same experimental conditions, the enzymatically cleaved counterpart of these probes was used as a control as well as a means to account for the changes in the environmental refractive indices. Our results indicate that the energy transfer efficiency of these FRET probes increases as the linker becomes shorter and more flexible in pure buffer at room temperature. In addition, the FRET probes favor a compact structure with enhanced energy transfer efficiency and a shorter donor-acceptor distance in the heterogeneous, polymer-crowded environment due to steric hindrance. In contrast, the stretched conformation of these FRET probes is more favorable in the viscous, homogeneous environment with a reduced energy transfer efficiency and relatively larger donor-acceptor distance as compared with those in pure buffer, which was attributed to a reduced structural fluctuation of the mCerulean3-mCitrine FRET pair in the viscous, more restrictive glycerol-enriched buffer. Our findings will help to advance the potential of these hetero-FRET probes using FLIM for spatio-temporal assessment of the compartmentalized crowding in living cells.
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Affiliation(s)
- Jacob Schwarz
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN, United States of America
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29
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Intracellular transport is accelerated in early apoptotic cells. Proc Natl Acad Sci U S A 2018; 115:12118-12123. [PMID: 30429318 DOI: 10.1073/pnas.1810017115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Intracellular transport of cellular proteins and organelles is critical for establishing and maintaining intracellular organization and cell physiology. Apoptosis is a process of programmed cell death with dramatic changes in cell morphology and organization, during which signaling molecules are transported between different organelles within the cells. However, how the intracellular transport changes in cells undergoing apoptosis remains unknown. Here, we study the dynamics of intracellular transport by using the single-particle tracking method and find that both directed and diffusive motions of endocytic vesicles are accelerated in early apoptotic cells. With careful elimination of other factors involved in the intracellular transport, the reason for the acceleration is attributed to the elevation of adenosine triphosphate (ATP) concentration. More importantly, we show that the accelerated intracellular transport is critical for apoptosis, and apoptosis is delayed when the dynamics of intracellular transport is regulated back to the normal level. Our results demonstrate the important role of transport dynamics in apoptosis and shed light on the apoptosis mechanism from a physical perspective.
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30
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Zhao H, Zhou Q, Xia M, Feng J, Chen Y, Zhang S, Zhang X. Characterize Collective Lysosome Heterogeneous Dynamics in Live Cell with a Space- and Time-Resolved Method. Anal Chem 2018; 90:9138-9147. [PMID: 29996056 DOI: 10.1021/acs.analchem.8b01563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
While studies of collective cell migration and bacteria swarming have tremendously promoted our fundamental knowledge of the complex systematic phenomena, the quantitative characterization of the collective organelles movement at subcellular level is yet to be fully explored. Here we tagged the lysosomes in live cells with fluorescent probe and imaged their spatial motion with wide field microscopy. To quantitatively characterize the collective lysosomal behavior with high spatiotemporal heterogeneity dynamics, we developed the particle collective analysis (PECAN) method based on the single particle tracking techniques. Thousands of trajectories were detected and analyzed in each single cell. The reliability was validated by comparing with traditional PIV method, simulated and experimental data sets. We show that the lysosomes in live cells move collectively with spatial heterogeneous and temporal long-term correlated dynamics. Furthermore, the continuous wavelet analysis suggested the existence of collective lysosomal oscillation in mouse neural cells. Generally, our method provides a practical workflow for characterizing the collective lysosomal motions which can benefit related areas such as organelles mediated drug delivery and cell activity profiling.
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Affiliation(s)
- Hansen Zhao
- Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Qiming Zhou
- Beijing National Research Center for Information Science and Technology, BNRist, School of Medicine , Tsinghua University , Beijing 100084 , China
| | - Mengchan Xia
- Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Jiaxin Feng
- Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yang Chen
- Beijing National Research Center for Information Science and Technology, BNRist, School of Medicine , Tsinghua University , Beijing 100084 , China.,Beijing National Research Center for Information Science and Technology, BNRist, Department of Automation , Tsinghua University , Beijing , 100084 , China
| | - Sichun Zhang
- Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Xinrong Zhang
- Department of Chemistry , Tsinghua University , Beijing 100084 , China
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31
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Li H, Ye F, Ren JY, Wang PY, Du LL, Liu JL. Active transport of cytoophidia in Schizosaccharomyces pombe. FASEB J 2018; 32:5891-5898. [PMID: 29782206 PMCID: PMC6292696 DOI: 10.1096/fj.201800045rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The metabolic enzyme cytidine triphosphate synthase has recently been found to form micrometer-sized filamentous structures termed cytoophidia, which are evolutionarily conserved across prokaryotes and eukaryotes. The cytoophidium represents a novel type of membraneless organelle and behaves dynamically inside the cell. The question of how cytoophidia transport is mediated, however, remains unanswered. For the first time, we detected in this study the active transport of cytoophidia, taking advantage of the fission yeast Schizosaccharomyces pombe as an excellent model for studying membraneless organelles. We demonstrated that actin filaments, not microtubules, are responsible for this transport. Furthermore, we determined that Myo52, a type of myosin V, is required for the active transport of cytoophidia. These results reveal the major players critical to the dynamics of cytoophidia and extend our understanding of intracellular transport of membraneless organelles.—Li, H., Ye, F., Ren, J.-Y., Wang, P.-Y., Du, L.-L., Liu, J.-L. Active transport of cytoophidia in Schizosaccharomyces pombe.
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Affiliation(s)
- Hui Li
- Department of Physiology, Anatomy, and Genetics, Medical Research Council Functional Genomics Unit, University of Oxford, Oxford, United Kingdom.,Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Fangfu Ye
- Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing-Yi Ren
- National Institute of Biological Sciences, Beijing, China; and
| | - Peng-Ye Wang
- Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China; and
| | - Ji-Long Liu
- Department of Physiology, Anatomy, and Genetics, Medical Research Council Functional Genomics Unit, University of Oxford, Oxford, United Kingdom.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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32
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Abstract
Non-Gaussian diffusion is commonly considered as a result of fluctuating diffusivity, which is correlated in time or in space or both. In this work, we investigate the non-Gaussian diffusion in static disordered media via a quenched trap model, where the diffusivity is spatially correlated. Several unique effects due to quenched disorder are reported. We analytically estimate the diffusion coefficient D_{dis} and its fluctuation over samples of finite size. We show a mechanism of population splitting in the non-Gaussian diffusion. It results in a sharp peak in the distribution of displacement P(x,t) around x=0, that has frequently been observed in experiments. We examine the fidelity of the coarse-grained diffusion map, which is reconstructed from particle trajectories. Finally, we propose a procedure to estimate the correlation length in static disordered environments, where the information stored in the sample-to-sample fluctuation has been utilized.
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Affiliation(s)
- Liang Luo
- Department of Physics, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Applied Physics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Yi
- Department of Physics, Huazhong Agricultural University, Wuhan 430070, China
- Institute of Applied Physics, Huazhong Agricultural University, Wuhan 430070, China
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33
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Watanabe C, Yanagisawa M. Cell-size confinement effect on protein diffusion in crowded poly(ethylene)glycol solution. Phys Chem Chem Phys 2018. [PMID: 29542748 DOI: 10.1039/c7cp08199e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Micrometric membrane confinements and macromolecular crowding of cytoplasm are key factors that regulate molecular diffusion in live cells. Previous studies have shown that macromolecular crowding delays molecular diffusion. However, the effect of cell-size confinement on diffusion in the crowding environment is yet to be elucidated. Using fluorescence correlation spectroscopy (FCS), we analyzed protein diffusion in microdroplets containing polymer solution covered with lipid membranes that mimic cells. As a result, we found that a synergistic condition of crowding and micrometric confinement results in accelerated protein diffusion on a sub-millisecond time scale. This acceleration rate strongly depended on the size of the confined space and the degree of crowding. These findings indicate that cell-size confinement supports protein diffusion in highly crowded cytoplasm.
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Affiliation(s)
- Chiho Watanabe
- Department of Applied Physics, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
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34
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Garland J. Unravelling the complexity of signalling networks in cancer: A review of the increasing role for computational modelling. Crit Rev Oncol Hematol 2017; 117:73-113. [PMID: 28807238 DOI: 10.1016/j.critrevonc.2017.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 02/06/2023] Open
Abstract
Cancer induction is a highly complex process involving hundreds of different inducers but whose eventual outcome is the same. Clearly, it is essential to understand how signalling pathways and networks generated by these inducers interact to regulate cell behaviour and create the cancer phenotype. While enormous strides have been made in identifying key networking profiles, the amount of data generated far exceeds our ability to understand how it all "fits together". The number of potential interactions is astronomically large and requires novel approaches and extreme computation methods to dissect them out. However, such methodologies have high intrinsic mathematical and conceptual content which is difficult to follow. This review explains how computation modelling is progressively finding solutions and also revealing unexpected and unpredictable nano-scale molecular behaviours extremely relevant to how signalling and networking are coherently integrated. It is divided into linked sections illustrated by numerous figures from the literature describing different approaches and offering visual portrayals of networking and major conceptual advances in the field. First, the problem of signalling complexity and data collection is illustrated for only a small selection of known oncogenes. Next, new concepts from biophysics, molecular behaviours, kinetics, organisation at the nano level and predictive models are presented. These areas include: visual representations of networking, Energy Landscapes and energy transfer/dissemination (entropy); diffusion, percolation; molecular crowding; protein allostery; quinary structure and fractal distributions; energy management, metabolism and re-examination of the Warburg effect. The importance of unravelling complex network interactions is then illustrated for some widely-used drugs in cancer therapy whose interactions are very extensive. Finally, use of computational modelling to develop micro- and nano- functional models ("bottom-up" research) is highlighted. The review concludes that computational modelling is an essential part of cancer research and is vital to understanding network formation and molecular behaviours that are associated with it. Its role is increasingly essential because it is unravelling the huge complexity of cancer induction otherwise unattainable by any other approach.
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Affiliation(s)
- John Garland
- Manchester Interdisciplinary Biocentre, Manchester University, Manchester, UK.
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35
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Osakada Y, Zhang K. Single-Particle Tracking Reveals a Dynamic Role of Actin Filaments in Assisting Long-Range Axonal Transport in Neurons. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yasuko Osakada
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
- The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047
| | - Kai Zhang
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, Illinois, 61801 (USA)
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36
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Probing cytoskeletal modulation of passive and active intracellular dynamics using nanobody-functionalized quantum dots. Nat Commun 2017; 8:14772. [PMID: 28322225 PMCID: PMC5364406 DOI: 10.1038/ncomms14772] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/27/2017] [Indexed: 11/08/2022] Open
Abstract
The cytoplasm is a highly complex and heterogeneous medium that is structured by the cytoskeleton. How local transport depends on the heterogeneous organization and dynamics of F-actin and microtubules is poorly understood. Here we use a novel delivery and functionalization strategy to utilize quantum dots (QDs) as probes for active and passive intracellular transport. Rapid imaging of non-functionalized QDs reveals two populations with a 100-fold difference in diffusion constant, with the faster fraction increasing upon actin depolymerization. When nanobody-functionalized QDs are targeted to different kinesin motor proteins, their trajectories do not display strong actin-induced transverse displacements, as suggested previously. Only kinesin-1 displays subtle directional fluctuations, because the subset of microtubules used by this motor undergoes prominent undulations. Using actin-targeting agents reveals that F-actin suppresses most microtubule shape remodelling, rather than promoting it. These results demonstrate how the spatial heterogeneity of the cytoskeleton imposes large variations in non-equilibrium intracellular dynamics.
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37
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Ding H, Jiang H, Zhao N, Hou Z. Diffusion of a Rouse chain in porous media: A mode-coupling-theory study. Phys Rev E 2017; 95:012121. [PMID: 28208313 DOI: 10.1103/physreve.95.012121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Indexed: 11/07/2022]
Abstract
We use a kinetic mode-coupling theory (MCT) combining with generalized Langevin equation (GLE) to study the diffusion and conformational dynamics of a bead-spring Rouse chain (RC) dissolved in porous media. The media contains fluid particles and immobile matrix ones wherein the latter leads to the lack of translational invariance. The friction kernel ζ(t) used in the GLE can be obtained directly by adopting a simple density-functional approach in which the density correlators calculated by MCT equations of porous media serve as inputs. Due to cage effects generated by surrounding particles, ζ(t) shows a very long tail memory in the high volume fraction of fluid and matrix. It is found that the long-time center-of-mass diffusion constant D_{CM} of the RC decreases with the increment of volume fraction, influencing more strongly by the matrix particles than by the fluid ones. The auto-correlation function (ACF) of the end-to-end distance fluctuation can also be calculated theoretically based on GLE. Of particular interest is that the power-law region of ACF has a nearly fixed length in logarithmic scale when it shifts to longer time range, with increasing the volume fraction of media particles. Moreover, the effect of lack of translational invariance has been investigated by comparing the results between fluid-matrix and pure fluid cases under identical total volume fraction.
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Affiliation(s)
- Huai Ding
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Huijun Jiang
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Zhonghuai Hou
- Department of Chemical Physics & Hefei National Laboratory for Physical Sciences at Microscales, University of Science and Technology of China, Hefei, Anhui 230026, China
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38
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Bio- chemical and physical characterizations of mesenchymal stromal cells along the time course of directed differentiation. Sci Rep 2016; 6:31547. [PMID: 27526936 PMCID: PMC4985743 DOI: 10.1038/srep31547] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 07/18/2016] [Indexed: 12/21/2022] Open
Abstract
Cellular biophysical properties are novel biomarkers of cell phenotypes which may reflect the status of differentiating stem cells. Accurate characterizations of cellular biophysical properties, in conjunction with the corresponding biochemical properties could help to distinguish stem cells from primary cells, cancer cells, and differentiated cells. However, the correlated evolution of these properties in the course of directed stem cells differentiation has not been well characterized. In this study, we applied video particle tracking microrheology (VPTM) to measure intracellular viscoelasticity of differentiating human mesenchymal stromal/stem cells (hMSCs). Our results showed that osteogenesis not only increased both elastic and viscous moduli, but also converted the intracellular viscoelasticity of differentiating hMSCs from viscous-like to elastic-like. In contrast, adipogenesis decreased both elastic and viscous moduli while hMSCs remained viscous-like during the differentiation. In conjunction with bio- chemical and physical parameters, such as gene expression profiles, cell morphology, and cytoskeleton arrangement, we demonstrated that VPTM is a unique approach to quantify, with high data throughput, the maturation level of differentiating hMSCs and to anticipate their fate decisions. This approach is well suited for time-lapsed study of the mechanobiology of differentiating stem cells especially in three dimensional physico-chemical biomimetic environments including porous scaffolds.
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39
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Arnold AM, Sevcsik E, Schütz GJ. Monte Carlo simulations of protein micropatterning in biomembranes: effects of immobile sticky obstacles. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2016; 49:10.1088/0022-3727/49/36/364002. [PMID: 30880837 PMCID: PMC6417683 DOI: 10.1088/0022-3727/49/36/364002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Single molecule trajectories of lipids and proteins can yield valuable information about the nanoscopic organization of the plasma membrane itself. The interpretation of such trajectories, however, is complicated, as the mobility of molecules can be affected by the presence of immobile obstacles, and the transient binding of the tracers to these obstacles. We have previously developed a micropatterning approach that allows for immobilizing a plasma membrane protein and probing the diffusional behavior of a putative interaction partner in living cells. Here, we provide guidelines on how this micropatterning approach can be extended to quantify interaction parameters between plasma membrane constituents in their natural environment. We simulated a patterned membrane system and evaluated the effect of different surface densities of patterned immobile obstacles on the relative mobility as well as the surface density of diffusing tracers. In the case of inert obstacles, the size of the obstacle can be assessed from its surface density at the percolation threshold, which in turn can be extracted from the diffusion behavior of the tracer. For sticky obstacles, two-dimensional dissociation constants can be determined from the tracer diffusion or surface density.
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Affiliation(s)
- Andreas M Arnold
- Institute of Applied Physics, Technische Universität Wien, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - Eva Sevcsik
- Institute of Applied Physics, Technische Universität Wien, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
| | - Gerhard J Schütz
- Institute of Applied Physics, Technische Universität Wien, Wiedner Hauptstrasse 8-10, 1040 Vienna, Austria
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40
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Guo X, Zhang Y, Liu J, Yang X, Huang J, Li L, Wan L, Wang K. Red blood cell membrane-mediated fusion of hydrophobic quantum dots with living cell membranes for cell imaging. J Mater Chem B 2016; 4:4191-4197. [PMID: 32264621 DOI: 10.1039/c6tb01067a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nanoparticle fusion with cell membranes is an interesting phenomenon that may have crucial implications for their biomedical applications. Here, we proposed a biomimetic and controlled route to fusion of hydrophobic quantum dots (QDs) with the cell membranes of living cells, while preserving their sensing and optical properties and thus their capability of membrane imaging and single-nanoparticle tracking. Red blood cell (RBC) membrane lipids were extracted to phase transfer hydrophobic QDs and the resulting RBC-encapsulated QDs (RBC-QDs) can be well fused within cell membranes as membrane markers. The fusion was validated through single-nanoparticle imaging and different movement behaviours were reliably discriminated. RBC-QDs possessed some novel features, such as controllable selective membrane staining, no invasion, and high photobleaching resistance, which allowed for long-term imaging, and single-nanoparticle tracking. This approach provides a versatile platform for controlled hydrophobic QD-based fluorescence investigation of living cell membranes.
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Affiliation(s)
- Xi Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
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41
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Manzo C, Garcia-Parajo MF. A review of progress in single particle tracking: from methods to biophysical insights. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:124601. [PMID: 26511974 DOI: 10.1088/0034-4885/78/12/124601] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Optical microscopy has for centuries been a key tool to study living cells with minimum invasiveness. The advent of single molecule techniques over the past two decades has revolutionized the field of cell biology by providing a more quantitative picture of the complex and highly dynamic organization of living systems. Amongst these techniques, single particle tracking (SPT) has emerged as a powerful approach to study a variety of dynamic processes in life sciences. SPT provides access to single molecule behavior in the natural context of living cells, thereby allowing a complete statistical characterization of the system under study. In this review we describe the foundations of SPT together with novel optical implementations that nowadays allow the investigation of single molecule dynamic events with increasingly high spatiotemporal resolution using molecular densities closer to physiological expression levels. We outline some of the algorithms for the faithful reconstruction of SPT trajectories as well as data analysis, and highlight biological examples where the technique has provided novel insights into the role of diffusion regulating cellular function. The last part of the review concentrates on different theoretical models that describe anomalous transport behavior and ergodicity breaking observed from SPT studies in living cells.
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Affiliation(s)
- Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
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42
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Zhou J, Yang Y, Zhang CY. Toward Biocompatible Semiconductor Quantum Dots: From Biosynthesis and Bioconjugation to Biomedical Application. Chem Rev 2015; 115:11669-717. [DOI: 10.1021/acs.chemrev.5b00049] [Citation(s) in RCA: 472] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Juan Zhou
- State
Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yong Yang
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chun-yang Zhang
- College
of Chemistry, Chemical Engineering and Materials Science, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Key Laboratory of Molecular and Nano Probes,
Ministry of Education, Shandong Provincial Key Laboratory of Clean
Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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43
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Luo L, Tang LH. Sample-dependent first-passage-time distribution in a disordered medium. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042137. [PMID: 26565198 DOI: 10.1103/physreve.92.042137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Indexed: 06/05/2023]
Abstract
Above two dimensions, diffusion of a particle in a medium with quenched random traps is believed to be well described by the annealed continuous-time random walk. We propose an approximate expression for the first-passage-time (FPT) distribution in a given sample that enables detailed comparison of the two problems. For a system of finite size, the number and spatial arrangement of deep traps yield significant sample-to-sample variations in the FPT statistics. Numerical simulations of a quenched trap model with power-law sojourn times confirm the existence of two characteristic time scales and a non-self-averaging FPT distribution, as predicted by our theory.
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Affiliation(s)
- Liang Luo
- Beijing Computational Science Research Center, Beijing 100094, China
| | - Lei-Han Tang
- Beijing Computational Science Research Center, Beijing 100094, China
- Department of Physics and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Hong Kong
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