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Yi H, Gong D, Daddysman MK, Renn M, Scherer NF. Distinct Sub- to Superdiffuse Insulin Granule Transport Behaviors in β-Cells Are Strongly Affected by Granule Age. J Phys Chem B 2024; 128:6246-6256. [PMID: 38861346 DOI: 10.1021/acs.jpcb.4c01403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Intracellular transport is a complex process that is difficult to describe by a single general model for motion. Here, we study the transport of insulin containing vesicles, termed granules, in live MIN6 cells. We characterize how the observed heterogeneity is affected by different intracellular factors by constructing a MIN6 cell line by CRISPR-CAS9 that constitutively expresses mCherry fused to insulin and is thus packaged in granules. Confocal microscopy imaging and single particle tracking of the granule transport provide long trajectories of thousands of single granule trajectories for statistical analysis. Mean squared displacement (MSD), angle correlation distribution, and step size distribution analysis allowed identifying five distinct granule transport subpopulations, from nearly immobile and subdiffusive to run-pause and superdiffusive. The subdiffusive subpopulation recapitulates the subordinated random walk we reported earlier (Tabei, 2013; ref 18). We show that the transport characteristics of the five subpopulations have a strong dependence on the age of insulin granules. The five subpopulations also reflect the effect of local microtubule and actin networks on transport in different cellular regions. Our results provide robust metrics to clarify the heterogeneity of granule transport and demonstrate the roles of microtubule versus actin networks with granule age since initial packaging in the Golgi.
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Affiliation(s)
- Hannah Yi
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Daozheng Gong
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
- Graduate Program in Biophysical Science, University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew K Daddysman
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Martha Renn
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Norbert F Scherer
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
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2
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Seckler H, Metzler R, Kelty-Stephen DG, Mangalam M. Multifractal spectral features enhance classification of anomalous diffusion. Phys Rev E 2024; 109:044133. [PMID: 38755826 DOI: 10.1103/physreve.109.044133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/19/2024] [Indexed: 05/18/2024]
Abstract
Anomalous diffusion processes, characterized by their nonstandard scaling of the mean-squared displacement, pose a unique challenge in classification and characterization. In a previous study [Mangalam et al., Phys. Rev. Res. 5, 023144 (2023)2643-156410.1103/PhysRevResearch.5.023144], we established a comprehensive framework for understanding anomalous diffusion using multifractal formalism. The present study delves into the potential of multifractal spectral features for effectively distinguishing anomalous diffusion trajectories from five widely used models: fractional Brownian motion, scaled Brownian motion, continuous-time random walk, annealed transient time motion, and Lévy walk. We generate extensive datasets comprising 10^{6} trajectories from these five anomalous diffusion models and extract multiple multifractal spectra from each trajectory to accomplish this. Our investigation entails a thorough analysis of neural network performance, encompassing features derived from varying numbers of spectra. We also explore the integration of multifractal spectra into traditional feature datasets, enabling us to assess their impact comprehensively. To ensure a statistically meaningful comparison, we categorize features into concept groups and train neural networks using features from each designated group. Notably, several feature groups demonstrate similar levels of accuracy, with the highest performance observed in groups utilizing moving-window characteristics and p varation features. Multifractal spectral features, particularly those derived from three spectra involving different timescales and cutoffs, closely follow, highlighting their robust discriminatory potential. Remarkably, a neural network exclusively trained on features from a single multifractal spectrum exhibits commendable performance, surpassing other feature groups. In summary, our findings underscore the diverse and potent efficacy of multifractal spectral features in enhancing the predictive capacity of machine learning to classify anomalous diffusion processes.
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Affiliation(s)
- Henrik Seckler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
- Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
| | - Damian G Kelty-Stephen
- Department of Psychology, State University of New York at New Paltz, New Paltz, New York 12561, USA
| | - Madhur Mangalam
- Department of Biomechanics and Center for Research in Human Movement Variability, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
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3
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Tang Y, Gharari F, Arias-Calluari K, Alonso-Marroquin F, Najafi MN. Variable-order porous media equations: Application on modeling the S&P500 and Bitcoin price return. Phys Rev E 2024; 109:024310. [PMID: 38491659 DOI: 10.1103/physreve.109.024310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/09/2024] [Indexed: 03/18/2024]
Abstract
This article reveals a specific category of solutions for the 1+1 variable order (VO) nonlinear fractional Fokker-Planck equations. These solutions are formulated using VO q-Gaussian functions, granting them significant versatility in their application to various real-world systems, such as financial economy areas spanning from conventional stock markets to cryptocurrencies. The VO q-Gaussian functions provide a more robust expression for the distribution function of price returns in real-world systems. Additionally, we analyzed the temporal evolution of the anomalous characteristic exponents derived from our study, which are associated with the long-term (power-law) memory in time series data and autocorrelation patterns.
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Affiliation(s)
- Yaoyue Tang
- Modelling and Simulation Research Group, The University of Sydney, Sydney NSW 2006, Australia
| | - Fatemeh Gharari
- Department of Statistics and Computer Science, University of Mohaghegh Ardabili, Ardabil 56199, Iran
| | - Karina Arias-Calluari
- School of Mathematics and Statistics, The University of Sydney, Sydney NSW 2006, Australia
| | | | - M N Najafi
- Department of Physics, University of Mohaghegh Ardabili, P.O. Box 179, Ardabil 11367, Iran
- Department of Mechanical Engineering, University of Akron, Akron, Ohio 44325, USA
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4
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Vasquez PA, Walker B, Bloom K, Kolbin D, Caughman N, Freeman R, Lysy M, Hult C, Newhall KA, Papanikolas M, Edelmaier C, Forest MG. The power of weak, transient interactions across biology: A paradigm of emergent behavior. PHYSICA D. NONLINEAR PHENOMENA 2023; 454:133866. [PMID: 38274029 PMCID: PMC10806540 DOI: 10.1016/j.physd.2023.133866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
A growing list of diverse biological systems and their equally diverse functionalities provides realizations of a paradigm of emergent behavior. In each of these biological systems, pervasive ensembles of weak, short-lived, spatially local interactions act autonomously to convey functionalities at larger spatial and temporal scales. In this article, a range of diverse systems and functionalities are presented in a cursory manner with literature citations for further details. Then two systems and their properties are discussed in more detail: yeast chromosome biology and human respiratory mucus.
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Affiliation(s)
- Paula A. Vasquez
- Department of Mathematics, University of South Carolina, United States of America
| | - Ben Walker
- Department of Mathematics, University of California at Irvine, United States of America
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Neall Caughman
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Martin Lysy
- Department of Statistics and Actuarial Science, University of Waterloo, Canada
| | - Caitlin Hult
- Department of Mathematics, Gettysburg College, United States of America
| | - Katherine A. Newhall
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Micah Papanikolas
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Christopher Edelmaier
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
- Center for Computational Biology, Flatiron Institute, United States of America
| | - M. Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
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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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Abelenda-Núñez I, Ortega F, Rubio RG, Guzmán E. Anomalous Colloidal Motion under Strong Confinement. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302115. [PMID: 37116105 DOI: 10.1002/smll.202302115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/13/2023] [Indexed: 06/19/2023]
Abstract
Diffusion of biological macromolecules in the cytoplasm is a paradigm of colloidal diffusion in an environment characterized by a strong restriction of the accessible volume. This makes of the understanding of the physical rules governing colloidal diffusion under conditions mimicking the reduction in accessible volume occurring in the cell cytoplasm, a problem of a paramount importance. This work aims to study how the thermal motion of spherical colloidal beads in the inner cavity of giant unilamellar vesicles (GUVs) is modified by strong confinement conditions, and the viscoelastic character of the medium. Using single particle tracking, it is found that both the confinement and the environmental viscoelasticity lead to the emergence of anomalous motion pathways for colloidal microbeads encapsulated in the aqueous inner cavity of GUVs. This anomalous diffusion is strongly dependent on the ratio between the volume of the colloidal particle and that of the GUV under consideration as well as on the viscosity of the particle's liquid environment. Therefore, the results evidence that the reduction of the free volume accessible to colloidal motion pushes the diffusion far from a standard Brownian pathway as a result of the change in the hydrodynamic boundary conditions driving the particle motion.
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Affiliation(s)
- Irene Abelenda-Núñez
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n., Madrid, 28040, Spain
| | - Francisco Ortega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n., Madrid, 28040, Spain
- Unidad de Materia Condensada, Instituto Pluridisciplinar, Universidad Complutense de Madrid, Paseo Juan XXIII 1., Madrid, 28040, Spain
| | - Ramón G Rubio
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n., Madrid, 28040, Spain
| | - Eduardo Guzmán
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n., Madrid, 28040, Spain
- Unidad de Materia Condensada, Instituto Pluridisciplinar, Universidad Complutense de Madrid, Paseo Juan XXIII 1., Madrid, 28040, Spain
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7
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Khan RAA, Luo M, Alsaad AM, Qattan IA, Abedrabbo S, Hua D, Zulfqar A. The Role of Polymer Chain Stiffness and Guest Nanoparticle Loading in Improving the Glass Transition Temperature of Polymer Nanocomposites. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1896. [PMID: 37446412 DOI: 10.3390/nano13131896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
The impact of polymer chain stiffness characterized by the bending modulus (kθ) on the glass transition temperature (Tg) of pure polymer systems, as well as polymer nanocomposites (PNCs), is investigated using molecular dynamics simulations. At small kθ values, the pure polymer system and respective PNCs are in an amorphous state, whereas at large kθ values, both systems are in a semicrystalline state with a glass transition at low temperature. For the pure polymer system, Tg initially increases with kθ and does not change obviously at large kθ. However, the Tg of PNCs shows interesting behaviors with the increasing volume fraction of nanoparticles (fNP) at different kθ values. Tg tends to increase with fNP at small kθ, whereas it becomes suppressed at large kθ.
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Affiliation(s)
- Raja Azhar Ashraaf Khan
- Department of Physics, Zhejiang Normal University, Jinhua 321004, China
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Mengbo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ahmad M Alsaad
- Department of Physics, Jordan University of Science & Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Issam A Qattan
- Department of Physics, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi 127788, United Arab Emirates
| | - Sufian Abedrabbo
- Department of Physics, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi 127788, United Arab Emirates
| | - Daoyang Hua
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Afsheen Zulfqar
- Department of Physics, Zhejiang Normal University, Jinhua 321004, China
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8
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Arbel-Goren R, McKeithen-Mead SA, Voglmaier D, Afremov I, Teza G, Grossman AD, Stavans J. Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer. Nucleic Acids Res 2023; 51:3116-3129. [PMID: 36762480 PMCID: PMC10123120 DOI: 10.1093/nar/gkad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that can transfer by conjugation to recipient cells. Some ICEs integrate into a unique site in the genome of their hosts. We studied quantitatively the process by which an ICE searches for its unique integration site in the Bacillus subtilis chromosome. We followed the motion of both ICEBs1 and the chromosomal integration site in real time within individual cells. ICEBs1 exhibited a wide spectrum of dynamical behaviors, ranging from rapid sub-diffusive displacements crisscrossing the cell, to kinetically trapped states. The chromosomal integration site moved sub-diffusively and exhibited pronounced dynamical asymmetry between longitudinal and transversal motions, highlighting the role of chromosomal structure and the heterogeneity of the bacterial interior in the search. The successful search for and subsequent recombination into the integration site is a key step in the acquisition of integrating mobile genetic elements. Our findings provide new insights into intracellular transport processes involving large DNA molecules.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Dominik Voglmaier
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idana Afremov
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gianluca Teza
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alan D Grossman
- Department of Biology Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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9
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Scott S, Weiss M, Selhuber-Unkel C, Barooji YF, Sabri A, Erler JT, Metzler R, Oddershede LB. Extracting, quantifying, and comparing dynamical and biomechanical properties of living matter through single particle tracking. Phys Chem Chem Phys 2023; 25:1513-1537. [PMID: 36546878 DOI: 10.1039/d2cp01384c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A panoply of new tools for tracking single particles and molecules has led to an explosion of experimental data, leading to novel insights into physical properties of living matter governing cellular development and function, health and disease. In this Perspective, we present tools to investigate the dynamics and mechanics of living systems from the molecular to cellular scale via single-particle techniques. In particular, we focus on methods to measure, interpret, and analyse complex data sets that are associated with forces, materials properties, transport, and emergent organisation phenomena within biological and soft-matter systems. Current approaches, challenges, and existing solutions in the associated fields are outlined in order to support the growing community of researchers at the interface of physics and the life sciences. Each section focuses not only on the general physical principles and the potential for understanding living matter, but also on details of practical data extraction and analysis, discussing limitations, interpretation, and comparison across different experimental realisations and theoretical frameworks. Particularly relevant results are introduced as examples. While this Perspective describes living matter from a physical perspective, highlighting experimental and theoretical physics techniques relevant for such systems, it is also meant to serve as a solid starting point for researchers in the life sciences interested in the implementation of biophysical methods.
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Affiliation(s)
- Shane Scott
- Institute of Physiology, Kiel University, Hermann-Rodewald-Straße 5, 24118 Kiel, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Christine Selhuber-Unkel
- Institute for Molecular Systems Engineering, Heidelberg University, D-69120 Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Younes F Barooji
- Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen, Denmark.
| | - Adal Sabri
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Janine T Erler
- BRIC, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Str. 24/25, D-14476 Potsdam, Germany.,Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
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10
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Punia B, Chaudhury S. Theoretical insights into the full description of DNA target search by subdiffusing proteins. Phys Chem Chem Phys 2022; 24:29074-29083. [PMID: 36440504 DOI: 10.1039/d2cp04934a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA binding proteins (DBPs) diffuse in the cytoplasm to recognise and bind with their respective target sites on the DNA to initiate several biologically important processes. The first passage time distributions (FPTDs) of DBPs are useful in quantifying the timescales of the most-probable search paths in addition to the mean value of the distribution which, strikingly, are decades of order apart in time. However, extremely crowded in vivo conditions or the viscoelasticity of the cellular medium among other factors causes biomolecules to exhibit anomalous diffusion which is usually overlooked in most theoretical studies. We have obtained approximate analytical expressions of a general FPTD and the two characteristic timescales that are valid for any single subdiffusing protein searching for its target in vivo. Our results can be applied to single-particle tracking experiments of target search.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune, Maharashtra, India.
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pune, Maharashtra, India.
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11
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Hua DY, Khan RAA, Luo MB. Langevin Dynamics Simulation on the Diffusivity of Polymers in Crowded Environments with Immobile Nanoparticles. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Dao-Yang Hua
- Department of Physics, Zhejiang University, Hangzhou310027, China
| | | | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou310027, China
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12
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Reiser M, Girelli A, Ragulskaya A, Das S, Berkowicz S, Bin M, Ladd-Parada M, Filianina M, Poggemann HF, Begam N, Akhundzadeh MS, Timmermann S, Randolph L, Chushkin Y, Seydel T, Boesenberg U, Hallmann J, Möller J, Rodriguez-Fernandez A, Rosca R, Schaffer R, Scholz M, Shayduk R, Zozulya A, Madsen A, Schreiber F, Zhang F, Perakis F, Gutt C. Resolving molecular diffusion and aggregation of antibody proteins with megahertz X-ray free-electron laser pulses. Nat Commun 2022; 13:5528. [PMID: 36130930 PMCID: PMC9490738 DOI: 10.1038/s41467-022-33154-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
X-ray free-electron lasers (XFELs) with megahertz repetition rate can provide novel insights into structural dynamics of biological macromolecule solutions. However, very high dose rates can lead to beam-induced dynamics and structural changes due to radiation damage. Here, we probe the dynamics of dense antibody protein (Ig-PEG) solutions using megahertz X-ray photon correlation spectroscopy (MHz-XPCS) at the European XFEL. By varying the total dose and dose rate, we identify a regime for measuring the motion of proteins in their first coordination shell, quantify XFEL-induced effects such as driven motion, and map out the extent of agglomeration dynamics. The results indicate that for average dose rates below 1.06 kGy μs-1 in a time window up to 10 μs, it is possible to capture the protein dynamics before the onset of beam induced aggregation. We refer to this approach as correlation before aggregation and demonstrate that MHz-XPCS bridges an important spatio-temporal gap in measurement techniques for biological samples.
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Affiliation(s)
- Mario Reiser
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Anastasia Ragulskaya
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Sudipta Das
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sharon Berkowicz
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Maddalena Bin
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Marjorie Ladd-Parada
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Mariia Filianina
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Hanna-Friederike Poggemann
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden.,Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | | | - Sonja Timmermann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072, Siegen, Germany
| | - Lisa Randolph
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072, Siegen, Germany
| | - Yuriy Chushkin
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, CS 40220, 38043, Grenoble Cedex 9, France
| | - Tilo Seydel
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Ulrike Boesenberg
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Jörg Hallmann
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Johannes Möller
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Robert Rosca
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Robert Schaffer
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Scholz
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Roman Shayduk
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Alexey Zozulya
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Anders Madsen
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072, Siegen, Germany.
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13
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Liu D, Qiu Y, Li Q, Zhang H. Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072110. [PMID: 35408509 PMCID: PMC9000840 DOI: 10.3390/molecules27072110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
The behavior of biomolecules in crowded environments remains largely unknown due to the accuracy of simulation models and the limited experimental data for comparison. Here we chose a small crowder of tetraethylene glycol (PEG-4) to investigate the self-crowding of PEG-4 solutions and molecular crowding effects on the structure and diffusion of lysozyme at varied concentrations from dilute water to pure PEG-4 liquid. Two Amber-like force fields of Amber14SB and a99SB-disp were examined with TIP3P (fast diffusivity and low viscosity) and a99SB-disp (slow diffusivity and high viscosity) water models, respectively. Compared to the Amber14SB protein simulations, the a99SB-disp model yields more coordinated water and less PEG-4 molecules, less intramolecular hydrogen bonds (HBs), more protein-water HBs, and less protein-PEG HBs as well as stronger interactions and more hydrophilic and less hydrophobic contacts with solvent molecules. The a99SB-disp model offers comparable protein-solvent interactions in concentrated PEG-4 solutions to that in pure water. The PEG-4 crowding leads to a slow-down in the diffusivity of water, PEG-4, and protein, and the decline in the diffusion from atomistic simulations is close to or faster than the hard sphere model that neglects attractive interactions. Despite these differences, the overall structure of lysozyme appears to be maintained well at different PEG-4 concentrations for both force fields, except a slightly large deviation at 370 K at low concentrations with the a99SB-disp model. This is mainly attributed to the strong intramolecular interactions of the protein in the Amber14SB force field and to the large viscosity of the a99SB-disp water model. The results indicate that the protein force fields and the viscosity of crowder solutions affect the simulation of biomolecules under crowding conditions.
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14
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van Steijn L, Wortel IMN, Sire C, Dupré L, Theraulaz G, Merks RMH. Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics. PLoS Comput Biol 2022; 18:e1009156. [PMID: 35157694 PMCID: PMC8880896 DOI: 10.1371/journal.pcbi.1009156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 02/25/2022] [Accepted: 01/18/2022] [Indexed: 11/18/2022] Open
Abstract
Lymphocytes have been described to perform different motility patterns such as Brownian random walks, persistent random walks, and Lévy walks. Depending on the conditions, such as confinement or the distribution of target cells, either Brownian or Lévy walks lead to more efficient interaction with the targets. The diversity of these motility patterns may be explained by an adaptive response to the surrounding extracellular matrix (ECM). Indeed, depending on the ECM composition, lymphocytes either display a floating motility without attaching to the ECM, or sliding and stepping motility with respectively continuous or discontinuous attachment to the ECM, or pivoting behaviour with sustained attachment to the ECM. Moreover, on the long term, lymphocytes either perform a persistent random walk or a Brownian-like movement depending on the ECM composition. How the ECM affects cell motility is still incompletely understood. Here, we integrate essential mechanistic details of the lymphocyte-matrix adhesions and lymphocyte intrinsic cytoskeletal induced cell propulsion into a Cellular Potts model (CPM). We show that the combination of de novo cell-matrix adhesion formation, adhesion growth and shrinkage, adhesion rupture, and feedback of adhesions onto cell propulsion recapitulates multiple lymphocyte behaviours, for different lymphocyte subsets and various substrates. With an increasing attachment area and increased adhesion strength, the cells’ speed and persistence decreases. Additionally, the model predicts random walks with short-term persistent but long-term subdiffusive properties resulting in a pivoting type of motility. For small adhesion areas, the spatial distribution of adhesions emerges as a key factor influencing cell motility. Small adhesions at the front allow for more persistent motility than larger clusters at the back, despite a similar total adhesion area. In conclusion, we present an integrated framework to simulate the effects of ECM proteins on cell-matrix adhesion dynamics. The model reveals a sufficient set of principles explaining the plasticity of lymphocyte motility. During immunosurveillance, lymphocytes patrol through tissues to interact with cancer cells, other immune cells, and pathogens. The efficiency of this process depends on the kinds of trajectories taken, ranging from simple Brownian walks to Lévy walks. The composition of the extracellular matrix (ECM), a network of macromolecules, affects the formation of cell-matrix adhesions, thus strongly influencing the way lymphocytes move. Here, we present a model of lymphocyte motility driven by adhesions that grow, shrink and rupture in response to the ECM and cellular forces. Compared to other models, our model is computationally light making it suitable for generating long term cell track data, while still capturing actin dynamics and adhesion turnover. Our model suggests that cell motility is affected by the force required to break adhesions and the rate at which new adhesions form. Adhesions can promote cell protrusion by inhibiting retrograde actin flow. After introducing this effect into the model, we found that it reduces the cellular diffusivity and that it promotes stick-slip behaviour. Furthermore, location and size of adhesion clusters determined cell persistence. Overall, our model explains the plasticity of lymphocyte behaviour in response to the ECM.
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Affiliation(s)
| | - Inge M. N. Wortel
- Data Science, Institute for Computing and Information Sciences, Radboud University, Nijmegen, The Netherlands
| | - Clément Sire
- Laboratoire de Physique Théorique, Centre National de la Recherche Scientifique (CNRS) & Université de Toulouse—Paul Sabatier, Toulouse, France
| | - Loïc Dupré
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Université de Toulouse, Toulouse, France
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Guy Theraulaz
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS) & Université de Toulouse—Paul Sabatier, Toulouse, France
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, India
| | - Roeland M. H. Merks
- Mathematical Institute, Leiden University, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- * E-mail:
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15
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Bellotto N, Agudo-Canalejo J, Colin R, Golestanian R, Malengo G, Sourjik V. Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth. eLife 2022; 11:82654. [PMID: 36468683 PMCID: PMC9810338 DOI: 10.7554/elife.82654] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here, we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli. For the faster-diffusing proteins, this size dependence is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.
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Affiliation(s)
- Nicola Bellotto
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | | | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany,Rudolf Peierls Centre for Theoretical Physics, University of OxfordOxfordUnited Kingdom
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
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16
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Zhang Z, Deng Q, Wang Z, Chen Y, Zhou T. Exact results for queuing models of stochastic transcription with memory and crosstalk. Phys Rev E 2021; 103:062414. [PMID: 34271765 DOI: 10.1103/physreve.103.062414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/03/2021] [Indexed: 11/07/2022]
Abstract
Gene transcription is a complex multistep biochemical process, which can create memory between individual reaction events. On the other hand, many inducible genes, when activated by external cues, are often coregulated by several competitive pathways with crosstalk. This raises an unexplored question: how do molecular memory and crosstalk together affect gene expressions? To address this question, we introduce a queuing model of stochastic transcription, where two crossing signaling pathways are used to direct gene activation in response to external signals and memory functions to model multistep reaction processes involved in transcription. We first establish, based on the total probability principle, the chemical master equation for this queuing model, and then we derive, based on the binomial moment approach, exact expressions for statistical quantities (including distributions) of mRNA, which provide insights into the roles of crosstalk and memory in controlling the mRNA level and noise. We find that molecular memory of gene activation decreases the mRNA level but increases the mRNA noise, and double activation pathways always reduce the mRNA noise in contrast to a single pathway. In addition, we find that molecular memory can make the mRNA bimodality disappear.
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Affiliation(s)
- Zhenquan Zhang
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Qiqi Deng
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Zihao Wang
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
| | - Yiren Chen
- College of Mathematics and Statistics, Shenzhen University, Shenzhen 518060, China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, School of Mathematics, Sun Yat-sen University, Guangzhou 510275, China
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17
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Bao JD, Wang XR, Liu WM. Ergodic time scale and transitive dynamics in single-particle tracking. Phys Rev E 2021; 103:032136. [PMID: 33862786 DOI: 10.1103/physreve.103.032136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/26/2021] [Indexed: 11/07/2022]
Abstract
We investigate ergodic time scales in single-particle tracking by introducing a covariance measure Ω(Δ;t) for the time-averaged relative square displacement recorded in lag-time Δ at elapsed time t. The present model is established in the generalized Langevin equation with a power-law memory function. The ratio Ω(Δ;Δ)/Ω(Δ;t) is shown to obey a universal scaling law for long but finite times and is used to extract the effective ergodic time. We derive a finite-time-averaged Green-Kubo relation and find that, to control the deviations in measurement results from ensemble averages, the ratio Δ/t must be neither too small nor close to unity. Our paper connects the experimental self-averaging property of a tracer with the theoretic velocity autocorrelation function and sheds light on the transition to ergodicity.
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Affiliation(s)
- Jing-Dong Bao
- Department of Physics, Beijing Normal University, Beijing 100875, China
| | - Xiang-Rong Wang
- Department of Physics, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Wu-Ming Liu
- Institute of Physics, Chinese Academy of Science, Beijing 100190, China
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18
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Levin M, Bel G, Roichman Y. Measurements and characterization of the dynamics of tracer particles in an actin network. J Chem Phys 2021; 154:144901. [PMID: 33858166 DOI: 10.1063/5.0045278] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The underlying physics governing the diffusion of a tracer particle in a viscoelastic material is a topic of some dispute. The long-term memory in the mechanical response of such materials should induce diffusive motion with a memory kernel, such as fractional Brownian motion (fBM). This is the reason that microrheology is able to provide the shear modulus of polymer networks. Surprisingly, the diffusion of a tracer particle in a network of a purified protein, actin, was found to conform to the continuous time random walk type (CTRW). We set out to resolve this discrepancy by studying the tracer particle diffusion using two different tracer particle sizes, in actin networks of different mesh sizes. We find that the ratio of tracer particle size to the characteristic length scale of a bio-polymer network plays a crucial role in determining the type of diffusion it performs. We find that the diffusion of the tracer particles has features of fBm when the particle is large compared to the mesh size, of normal diffusion when the particle is much smaller than the mesh size, and of the CTRW in between these two limits. Based on our findings, we propose and verify numerically a new model for the motion of the tracer in all regimes. Our model suggests that diffusion in actin networks consists of fBm of the tracer particle coupled with caging events with power-law distributed escape times.
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Affiliation(s)
- Maayan Levin
- Raymond and Beverly Sackler School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Golan Bel
- Department of Solar Energy and Environmental Physics, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 8499000, Israel
| | - Yael Roichman
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
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19
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Abstract
This account comprises personal reflections on the field of nanosystems primarily designed for the delivery of biologically active agents. It emphasises the colloidal nature of nanoparticles obeying the same physical laws that dictate the behaviour of disperse systems. Research reveals not only intrinsic complexities but a variety of possible trajectories in vivo and ex vivo, issues of stability, interactions and behaviour in a range of often constrained environments. Such are the variations in the chemical and physical nature of the nanosystems and the active agents they carry, their putative "targets" and the many biological systems and models in which they are employed, it is not possible to generalise. Stochastic events may exclude precise prediction or extrapolation of outcomes, but embracing and studying complexity lead to new insights, often aided by consideration of analogies in cognate areas. This is part of the process of illumination. Unexpected results provide the true essence and excitement of scientific endeavour. Simplification is perhaps its antithesis.
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20
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Qiu H, Zhang B, Zhou T. Explicit effect of stochastic reaction delay on gene expression. Phys Rev E 2020; 101:012405. [PMID: 32069597 DOI: 10.1103/physreve.101.012405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Indexed: 11/07/2022]
Abstract
Apart from intrinsic stochastic variability, gene expression also involves stochastic reaction delay arising from heterogeneity and fluctuation processes, which can affect the efficiency of reactants (e.g., mRNA or protein) in exploring their environments. In contrast to the former that has been extensively investigated, the impact of the latter on gene expression remains not fully understood. Here, we analyze a non-Markovian model of bursty gene expression with general delay distribution. We analytically find that the effect of stochastic reaction delay is equivalent to the introduction of negative feedback, and stationary protein distribution only depends on the mean of the delay and is independent of its distribution. We numerically show that the stochastic reaction delay always slightly amplifies the mean protein level but remarkably reduces the protein noise (quantified by the ratio of the variance over the squared average). Our analysis indicates that stochastic reaction delay is an important factor affecting gene expression.
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Affiliation(s)
- Huahai Qiu
- School of Mathematics and Computers, Wuhan Textile University, Wuhan 430200, People's Republic of China
| | - Bengong Zhang
- School of Mathematics and Computers, Wuhan Textile University, Wuhan 430200, People's Republic of China
| | - Tianshou Zhou
- School of Mathematics and Computers, Wuhan Textile University, Wuhan 430200, People's Republic of China.,Key Laboratory of Computational Mathematics, School of Mathematics, Sun Yat-sen University, Guangdong Province, Guangzhou 510275, People's Republic of China
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21
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Estrada E. Fractional diffusion on the human proteome as an alternative to the multi-organ damage of SARS-CoV-2. CHAOS (WOODBURY, N.Y.) 2020; 30:081104. [PMID: 32872802 PMCID: PMC7585451 DOI: 10.1063/5.0015626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/15/2020] [Indexed: 05/16/2023]
Abstract
The coronavirus 2019 (COVID-19) respiratory disease is caused by the novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), which uses the enzyme ACE2 to enter human cells. This disease is characterized by important damage at a multi-organ level, partially due to the abundant expression of ACE2 in practically all human tissues. However, not every organ in which ACE2 is abundant is affected by SARS-CoV-2, which suggests the existence of other multi-organ routes for transmitting the perturbations produced by the virus. We consider here diffusive processes through the protein-protein interaction (PPI) network of proteins targeted by SARS-CoV-2 as an alternative route. We found a subdiffusive regime that allows the propagation of virus perturbations through the PPI network at a significant rate. By following the main subdiffusive routes across the PPI network, we identify proteins mainly expressed in the heart, cerebral cortex, thymus, testis, lymph node, kidney, among others of the organs reported to be affected by COVID-19.
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Affiliation(s)
- Ernesto Estrada
- Instituto Universitario de Matemáticas y Aplicaciones, Universidad de Zaragoza, 50009 Zaragoza, Spain and ARAID Foundation, Government of Aragón, 50018 Zaragoza, Spain
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22
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Tateishi AA, Ribeiro HV, Sandev T, Petreska I, Lenzi EK. Quenched and annealed disorder mechanisms in comb models with fractional operators. Phys Rev E 2020; 101:022135. [PMID: 32168676 DOI: 10.1103/physreve.101.022135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
Recent experimental findings on anomalous diffusion have demanded novel models that combine annealed (temporal) and quenched (spatial or static) disorder mechanisms. The comb model is a simplified description of diffusion on percolation clusters, where the comblike structure mimics quenched disorder mechanisms and yields a subdiffusive regime. Here we extend the comb model to simultaneously account for quenched and annealed disorder mechanisms. To do so, we replace usual derivatives in the comb diffusion equation by different fractional time-derivative operators and the conventional comblike structure by a generalized fractal structure. Our hybrid comb models thus represent a diffusion where different comblike structures describe different quenched disorder mechanisms, and the fractional operators account for various annealed disorder mechanisms. We find exact solutions for the diffusion propagator and mean square displacement in terms of different memory kernels used for defining the fractional operators. Among other findings, we show that these models describe crossovers from subdiffusion to Brownian or confined diffusions, situations emerging in empirical results. These results reveal the critical role of interactions between geometrical restrictions and memory effects on modeling anomalous diffusion.
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Affiliation(s)
- A A Tateishi
- Departamento de Física, Universidade Tecnologica Federal de Pato Branco, Pato Branco, Paraná 85503-390, Brazil
| | - H V Ribeiro
- Departamento de Física, Universidade Estadual de Maringá, Maringá, Paraná 87020-900, Brazil
| | - T Sandev
- Research Center for Computer Science and Information Technologies, Macedonian Academy of Sciences and Arts, Bul. Krste Misirkov 2, 1000 Skopje, Macedonia
- Institute of Physics & Astronomy, University of Potsdam, D-14776 Potsdam-Golm, Germany
- Institute of Physics, Faculty of Natural Sciences and Mathematics, Ss Cyril and Methodius University, Arhimedova 3, 1000 Skopje, Macedonia
| | - I Petreska
- Institute of Physics, Faculty of Natural Sciences and Mathematics, Ss Cyril and Methodius University, Arhimedova 3, 1000 Skopje, Macedonia
| | - E K Lenzi
- Departamento de Física, Universidade Estadual de Ponta Grossa, Av. Carlos Cavalcanti 4748, 84030-900 Ponta Grossa, Paraná, Brazil
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23
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Dey P, Bhattacherjee A. Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu. Biophys J 2020; 118:505-517. [PMID: 31862109 PMCID: PMC6976804 DOI: 10.1016/j.bpj.2019.11.3388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/03/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Although the fast association between DNA-binding proteins (DBPs) and DNA is explained by a facilitated diffusion mechanism, in which DBPs adopt a weighted combination of three-dimensional diffusion and one-dimensional (1D) sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large-scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA-bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through, to our knowledge, novel 1D scanning mechanisms. In this one-dimensional scanning mode, the protein can float along the DNA under the influence of nonspecific interactions of bulk crowder molecules. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics in which protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedites the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder-concentration-dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.
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Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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24
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Warmenhoven JW, Henthorn NT, Ingram SP, Chadwick AL, Sotiropoulos M, Korabel N, Fedotov S, Mackay RI, Kirkby KJ, Merchant MJ. Insights into the non-homologous end joining pathway and double strand break end mobility provided by mechanistic in silico modelling. DNA Repair (Amst) 2020; 85:102743. [DOI: 10.1016/j.dnarep.2019.102743] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022]
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25
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Basak S, Sengupta S, Chattopadhyay K. Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells. Biophys Rev 2019; 11:851-872. [PMID: 31444739 PMCID: PMC6957588 DOI: 10.1007/s12551-019-00580-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/25/2019] [Indexed: 01/24/2023] Open
Abstract
In order to maintain cellular function, biomolecules like protein, DNA, and RNAs have to diffuse to the target spaces within the cell. Changes in the cytosolic microenvironment or in the nucleus during the fulfillment of these cellular processes affect their mobility, folding, and stability thereby impacting the transient or stable interactions with their adjacent neighbors in the organized and dynamic cellular interior. Using classical Brownian motion to elucidate the diffusion behavior of these biomolecules is hard considering their complex nature. The understanding of biomolecular diffusion inside cells still remains elusive due to the lack of a proper model that can be extrapolated to these cases. In this review, we have comprehensively addressed the progresses in this field, laying emphasis on the different aspects of anomalous diffusion in the different biochemical reactions in cell interior. These experiment-based models help to explain the diffusion behavior of biomolecules in the cytosolic and nuclear microenvironment. Moreover, since understanding of biochemical reactions within living cellular system is our main focus, we coupled the experimental observations with the concept of sub-diffusion from in vitro to in vivo condition. We believe that the pairing between the understanding of complex behavior and structure-function paradigm of biological molecules would take us forward by one step in order to solve the puzzle around diseases caused by cellular dysfunction.
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Affiliation(s)
- Sujit Basak
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.
| | - Sombuddha Sengupta
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Lab, Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology (CSIR-IICB), 4 Raja S.C Mullick Road, Jadavpur, Kolkata, West Bengal, 700032, India
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26
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Dey P, Bhattacherjee A. Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase. J Phys Chem B 2019; 123:10354-10364. [DOI: 10.1021/acs.jpcb.9b07342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
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27
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Impact of bacteria motility in the encounter rates with bacteriophage in mucus. Sci Rep 2019; 9:16427. [PMID: 31712565 PMCID: PMC6848219 DOI: 10.1038/s41598-019-52794-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 10/15/2019] [Indexed: 12/31/2022] Open
Abstract
Bacteriophages—or phages—are viruses that infect bacteria and are present in large concentrations in the mucosa that cover the internal organs of animals. Immunoglobulin (Ig) domains on the phage surface interact with mucin molecules, and this has been attributed to an increase in the encounter rates of phage with bacteria in mucus. However, the physical mechanism behind this phenomenon remains unclear. A continuous time random walk (CTRW) model simulating the diffusion due to mucin-T4 phage interactions was developed and calibrated to empirical data. A Langevin stochastic method for Escherichia coli (E. coli) run-and-tumble motility was combined with the phage CTRW model to describe phage-bacteria encounter rates in mucus for different mucus concentrations. Contrary to previous theoretical analyses, the emergent subdiffusion of T4 in mucus did not enhance the encounter rate of T4 against bacteria. Instead, for static E. coli, the diffusive T4 mutant lacking Ig domains outperformed the subdiffusive T4 wild type. E. coli’s motility dominated the encounter rates with both phage types in mucus. It is proposed, that the local fluid-flow generated by E. coli’s motility combined with T4 interacting with mucins may be the mechanism for increasing the encounter rates between the T4 phage and E. coli bacteria.
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28
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Furlan A, Gonzalez-Pisfil M, Leray A, Champelovier D, Henry M, Le Nézet C, Bensaude O, Lefranc M, Wohland T, Vandenbunder B, Bidaux G, Héliot L. HEXIM1 Diffusion in the Nucleus Is Regulated by Its Interactions with Both 7SK and P-TEFb. Biophys J 2019; 117:1615-1625. [PMID: 31590891 PMCID: PMC6838758 DOI: 10.1016/j.bpj.2019.09.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022] Open
Abstract
How nuclear proteins diffuse and find their targets remains a key question in the transcription field. Dynamic proteins in the nucleus are classically subdiffusive and undergo anomalous diffusion, yet the underlying physical mechanisms are still debated. In this study, we explore the contribution of interactions to the generation of anomalous diffusion by the means of fluorescence spectroscopy and simulation. Using interaction-deficient mutants, our study indicates that HEXIM1 interactions with both 7SK RNA and positive transcription elongation factor b are critical for HEXIM1 subdiffusion and thus provides evidence of the effects of protein-RNA interaction on molecular diffusion. Numerical simulations allowed us to establish that the proportions of distinct oligomeric HEXIM1 subpopulations define the apparent anomaly parameter of the whole population. Slight changes in the proportions of these oligomers can lead to significant shifts in the diffusive features and recapitulate the modifications observed in cells with the various interaction-deficient mutants. By combining simulations and experiments, our work opens new prospects in which the anomaly α coefficient in diffusion becomes a helpful tool to infer alterations in molecular interactions.
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Affiliation(s)
- Alessandro Furlan
- University of Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France.
| | - Mariano Gonzalez-Pisfil
- University of Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
| | - Aymeric Leray
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne Franche Comté, Dijon, France
| | - Dorian Champelovier
- University of Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
| | - Mélanie Henry
- University of Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
| | - Corentin Le Nézet
- University of Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
| | - Oliver Bensaude
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Marc Lefranc
- University of Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry, Center for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Bernard Vandenbunder
- University of Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
| | - Gabriel Bidaux
- University of Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France; INSERM UMR 1060, CarMeN laboratory, Univ Lyon1, IHU OPERA, Hôpital Louis Pradel, Hospices Civils de Lyon, Lyon, France
| | - Laurent Héliot
- University of Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France.
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29
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Traeger JC, Lamberty Z, Schwartz DK. Influence of Oligonucleotide Grafting Density on Surface-Mediated DNA Transport and Hybridization. ACS NANO 2019; 13:7850-7859. [PMID: 31244029 DOI: 10.1021/acsnano.9b02157] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Adsorption of soluble DNA to surfaces decorated with complementary DNA plays an important role in many bionanotechnology applications, and previous studies have reported complex dependencies of the surface density of immobilized DNA on hybridization. While these effects have been speculatively ascribed to steric or electrostatic effects, the influence of surface-mediated molecular transport (i.e., intermittent "hopping diffusion") has not been fully appreciated. Here, single-molecule tracking and Förster resonance energy transfer (FRET) were employed to characterize the mobility and the hybridization efficiency of adsorbed ssDNA oligonucleotides ("target") at solid-liquid interfaces exhibiting surface-immobilized ssDNA ("probe") over a wide range of surface grafting densities. Two distinct regimes were observed, with qualitatively different transport and hybridization behaviors. At dilute grafting density, only 1-3% of target molecules were observed to associate with probes (i.e., to hybridize). Adsorbing target molecules often searched unsuccessfully and "flew", via desorption-mediated diffusion, to secondary locations before hybridizing. In contrast, at high probe grafting density, approximately 20% of target DNA hybridized to immobilized probes, and almost always in the vicinity of initial adsorption. Moreover, following a dehybridization event, target molecules rehybridized at high probe density, but rehybridization was infrequent in the dilute density regime. Interestingly, the intermittent interfacial transport of mobile target molecules was suppressed by the presence of immobilized probe DNA, presumably due to an increased probability of readsorption following each "hop". Together, these findings suggested that many salient effects of grafting density on surface-mediated DNA hybridization can be directly related to the mechanisms of surface-mediated intermittent diffusion.
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Affiliation(s)
- Jeremiah C Traeger
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Zachary Lamberty
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
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30
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Ramadurai S, Sarangi NK, Maher S, MacConnell N, Bond AM, McDaid D, Flynn D, Keyes TE. Microcavity-Supported Lipid Bilayers; Evaluation of Drug-Lipid Membrane Interactions by Electrochemical Impedance and Fluorescence Correlation Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8095-8109. [PMID: 31120755 DOI: 10.1021/acs.langmuir.9b01028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Many drugs have intracellular or membrane-associated targets, thus understanding their interaction with the cell membrane is of value in drug development. Cell-free tools used to predict membrane interactions should replicate the molecular organization of the membrane. Microcavity array-supported lipid bilayer (MSLB) platforms are versatile biophysical models of the cell membrane that combine liposome-like membrane fluidity with stability and addressability. We used an MSLB herein to interrogate drug-membrane interactions across seven drugs from different classes, including nonsteroidal anti-inflammatories: ibuprofen (Ibu) and diclofenac (Dic); antibiotics: rifampicin (Rif), levofloxacin (Levo), and pefloxacin (Pef); and bisphosphonates: alendronate (Ale) and clodronate (Clo). Fluorescence lifetime correlation spectroscopy (FLCS) and electrochemical impedance spectroscopy (EIS) were used to evaluate the impact of drug on 1,2-dioleyl- sn-glycerophosphocholine and binary bilayers over physiologically relevant drug concentrations. Although FLCS data revealed Ibu, Levo, Pef, Ale, and Clo had no impact on lipid lateral mobility, EIS, which is more sensitive to membrane structural change, indicated modest but significant decreases to membrane resistivity consistent with adsorption but weak penetration of drugs at the membrane. Ale and Clo, evaluated at pH 5.25, did not impact the impedance of the membrane except at concentrations exceeding 4 mM. Conversely, Dic and Rif dramatically altered bilayer fluidity, suggesting their translocation through the bilayer, and EIS data showed that resistivity of the membrane decreased substantially with increasing drug concentration. Capacitance changes to the bilayer in most cases were insignificant. Using a Langmuir-Freundlich model to fit the EIS data, we propose Rsat as an empirical value that reflects permeation. Overall, the data indicate that Ibu, Levo, and Pef adsorb at the interface of the lipid membrane but Dic and Rif interact strongly, permeating the membrane core modifying the water/ion permeability of the bilayer structure. These observations are discussed in the context of previously reported data on drug permeability and log P.
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Affiliation(s)
- Sivaramakrishnan Ramadurai
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Nirod Kumar Sarangi
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Sean Maher
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Nicola MacConnell
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
| | - Alan M Bond
- School of Chemistry , Monash University , Clayton , Victoria 3800 , Australia
| | | | | | - Tia E Keyes
- School of Chemical Sciences and National Centre for Sensor Research , Dublin City University , Dublin 9 , Ireland
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31
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Carnaffan S, Kawai R. Analytic model for transient anomalous diffusion with highly persistent correlations. Phys Rev E 2019; 99:062120. [PMID: 31330708 DOI: 10.1103/physreve.99.062120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Indexed: 06/10/2023]
Abstract
In recent decades, many stochastic processes have been proposed as models for real world time series data with anomalous spreading, highly persistent correlations, and transient distributional characteristics. We introduce the higher order fractional tempered stable motion as the stochastic integral of the tempered stable motion with respect to a generalized higher order moving average kernel, which provides an analytic model for stochastic processes possessing these characteristics. This stochastic process provides a mathematical model for anomalous diffusion with a transient distribution resembling higher order fractional stable motion on short timescales and higher order fractional Brownian motion in the long run. The specifics of the crossover dynamics from the Lévy stable anomalous diffusion to the Gaussian anomalous diffusion are controlled by explicit parameter values that correspond to physical attributes of the process. It is well suited to modeling anomalous diffusion of any "type" (sub-, super-, regular, or hyperdiffusion) under appropriate parametrizations due to its power-law scaling of variance with respect to time. It is also a useful model for position-velocity-acceleration triples due to its convenient path differentiability and integrability properties. To highlight the potential physical relevance of this model for real world data, we outline its key statistical properties including its covariance structure, memory, and second order self-similarity. We also give an easy to implement elementary method for sample path generation which may be used as a basis for simulation and Monte Carlo studies.
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Affiliation(s)
- Sean Carnaffan
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia
| | - Reiichiro Kawai
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia
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32
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Macromolecular inversion-driven polymer insertion into model lipid bilayer membranes. J Colloid Interface Sci 2019; 542:483-494. [DOI: 10.1016/j.jcis.2019.01.093] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/17/2019] [Accepted: 01/22/2019] [Indexed: 11/22/2022]
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33
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Stolle MDN, Fradin C. Anomalous Diffusion in Inverted Variable-Lengthscale Fluorescence Correlation Spectroscopy. Biophys J 2019; 116:791-806. [PMID: 30782396 PMCID: PMC6400862 DOI: 10.1016/j.bpj.2019.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/12/2018] [Accepted: 01/14/2019] [Indexed: 11/24/2022] Open
Abstract
Using fluorescence correlation spectroscopy (FCS) to distinguish between different types of diffusion processes is often a perilous undertaking because the analysis of the resulting autocorrelation data is model dependant. Two recently introduced strategies, however, can help move toward a model-independent interpretation of FCS experiments: 1) the obtention of correlation data at different length scales and 2) their inversion to retrieve the mean-squared displacement associated with the process under study. We use computer simulations to examine the signature of several biologically relevant diffusion processes (simple diffusion, continuous-time random walk, caged diffusion, obstructed diffusion, two-state diffusion, and diffusing diffusivity) in variable-length-scale FCS. We show that, when used in concert, length-scale variation and data inversion permit us to identify non-Gaussian processes and, regardless of Gaussianity, to retrieve their mean-squared displacement over several orders of magnitude in time. This makes unbiased discrimination between different classes of diffusion models possible.
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Affiliation(s)
- Michael D N Stolle
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Cécile Fradin
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada.
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34
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Duarte D, Amarteifio S, Ang H, Kong IY, Ruivo N, Pruessner G, Hawkins ED, Lo Celso C. Defining the in vivo characteristics of acute myeloid leukemia cells behavior by intravital imaging. Immunol Cell Biol 2019; 97:229-235. [PMID: 30422351 PMCID: PMC6446728 DOI: 10.1111/imcb.12216] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/08/2018] [Accepted: 11/08/2018] [Indexed: 12/21/2022]
Abstract
The majority of acute myeloid leukemia (AML) patients have a poor response to conventional chemotherapy. The survival of chemoresistant cells is thought to depend on leukemia-bone marrow (BM) microenvironment interactions, which are not well understood. The CXCL12/CXCR4 axis has been proposed to support AML growth but was not studied at the single AML cell level. We recently showed that T-cell acute lymphoblastic leukemia (T-ALL) cells are highly motile in the BM; however, the characteristics of AML cell migration within the BM remain undefined. Here, we characterize the in vivo migratory behavior of AML cells and their response to chemotherapy and CXCR4 antagonism, using high-resolution 2-photon and confocal intravital microscopy of mouse calvarium BM and the well-established MLL-AF9-driven AML mouse model. We used the Notch1-driven T-ALL model as a benchmark comparison and AMD3100 for CXCR4 antagonism experiments. We show that AML cells are migratory, and in contrast with T-ALL, chemoresistant AML cells become less motile. Moreover, and in contrast with T-ALL, the in vivo exploratory behavior of expanding and chemoresistant AML cells is unaffected by AMD3100. These results expand our understanding of AML cells-BM microenvironment interactions, highlighting unique traits of leukemia of different lineages.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Benzylamines
- Bone Marrow/metabolism
- Bone Marrow/pathology
- Cell Line, Tumor
- Cell Movement
- Chemokine CXCL12/metabolism
- Cyclams
- Drug Resistance, Neoplasm/drug effects
- Heterocyclic Compounds/antagonists & inhibitors
- Heterocyclic Compounds/metabolism
- Intravital Microscopy
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Microscopy, Confocal
- Microscopy, Fluorescence, Multiphoton
- Receptors, CXCR4/metabolism
- Tumor Microenvironment
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Affiliation(s)
- Delfim Duarte
- Department of Life SciencesSir Alexander Fleming BuildingImperial College LondonLondonSW7 2AZUK
- Instituto de Investigação e Inovação em Saúde (i3S)University of PortoPorto4200‐135Portugal
- Department of BiomedicineFaculty of MedicineUniversity of PortoPorto4200‐319Portugal
- Department of Onco‐HematologyPortuguese Institute of Oncology (IPO)‐PortoPorto4200‐072Portugal
| | - Saoirse Amarteifio
- Department of MathematicsHuxley BuildingImperial College LondonLondonSW7 2AZUK
| | - Heather Ang
- Department of Life SciencesSir Alexander Fleming BuildingImperial College LondonLondonSW7 2AZUK
| | - Isabella Y Kong
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVIC3052Australia
- Department of Medical BiologyThe University of MelbourneParkvilleVIC3010Australia
| | - Nicola Ruivo
- Department of Life SciencesSir Alexander Fleming BuildingImperial College LondonLondonSW7 2AZUK
| | - Gunnar Pruessner
- Department of MathematicsHuxley BuildingImperial College LondonLondonSW7 2AZUK
| | - Edwin D Hawkins
- Department of Life SciencesSir Alexander Fleming BuildingImperial College LondonLondonSW7 2AZUK
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVIC3052Australia
- Department of Medical BiologyThe University of MelbourneParkvilleVIC3010Australia
| | - Cristina Lo Celso
- Department of Life SciencesSir Alexander Fleming BuildingImperial College LondonLondonSW7 2AZUK
- The Francis Crick InstituteLondonWC2A 3LYUK
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35
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Korabel N, Waigh TA, Fedotov S, Allan VJ. Non-Markovian intracellular transport with sub-diffusion and run-length dependent detachment rate. PLoS One 2018; 13:e0207436. [PMID: 30475848 PMCID: PMC6261056 DOI: 10.1371/journal.pone.0207436] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 10/31/2018] [Indexed: 11/19/2022] Open
Abstract
Intracellular transport of organelles is fundamental to cell function and health. The mounting evidence suggests that this transport is in fact anomalous. However, the reasons for the anomaly is still under debate. We examined experimental trajectories of organelles inside a living cell and propose a mathematical model that describes the previously reported transition from sub-diffusive to super-diffusive motion. In order to explain super-diffusive behaviour at long times, we introduce non-Markovian detachment kinetics of the cargo: the rate of detachment is inversely proportional to the time since the last attachment. Recently, we observed the non-Markovian detachment rate experimentally in eukaryotic cells. Here we further discuss different scenarios of how this effective non-Markovian detachment rate could arise. The non-Markovian model is successful in simultaneously describing the time averaged variance (the time averaged mean squared displacement corrected for directed motion), the mean first passage time of trajectories and the multiple peaks observed in the distributions of cargo velocities. We argue that non-Markovian kinetics could be biologically beneficial compared to the Markovian kinetics commonly used for modelling, by increasing the average distance the cargoes travel when a microtubule is blocked by other filaments. In turn, sub-diffusion allows cargoes to reach neighbouring filaments with higher probability, which promotes active motion along the microtubules.
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Affiliation(s)
- Nickolay Korabel
- School of Mathematics, University of Manchester, Manchester, United Kingdom
- * E-mail:
| | - Thomas A. Waigh
- Biological Physics, School of Physics and Astronomy, University of Manchester, Manchester, United Kingdom
- The Photon Science Institute, University of Manchester, Manchester, United Kingdom
| | - Sergei Fedotov
- School of Mathematics, University of Manchester, Manchester, United Kingdom
| | - Viki J. Allan
- Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
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36
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37
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Moran I, Nguyen A, Khoo WH, Butt D, Bourne K, Young C, Hermes JR, Biro M, Gracie G, Ma CS, Munier CML, Luciani F, Zaunders J, Parker A, Kelleher AD, Tangye SG, Croucher PI, Brink R, Read MN, Phan TG. Memory B cells are reactivated in subcapsular proliferative foci of lymph nodes. Nat Commun 2018; 9:3372. [PMID: 30135429 PMCID: PMC6105623 DOI: 10.1038/s41467-018-05772-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022] Open
Abstract
Vaccine-induced immunity depends on the generation of memory B cells (MBC). However, where and how MBCs are reactivated to make neutralising antibodies remain unknown. Here we show that MBCs are prepositioned in a subcapsular niche in lymph nodes where, upon reactivation by antigen, they rapidly proliferate and differentiate into antibody-secreting plasma cells in the subcapsular proliferative foci (SPF). This novel structure is enriched for signals provided by T follicular helper cells and antigen-presenting subcapsular sinus macrophages. Compared with contemporaneous secondary germinal centres, SPF have distinct single-cell molecular signature, cell migration pattern and plasma cell output. Moreover, SPF are found both in human and mouse lymph nodes, suggesting that they are conserved throughout mammalian evolution. Our data thus reveal that SPF is a seat of immunological memory that may be exploited to rapidly mobilise secondary antibody responses and improve vaccine efficacy.
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Affiliation(s)
- Imogen Moran
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - Akira Nguyen
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - Weng Hua Khoo
- Division of Bone Biology, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, NSW, 2052, Australia
| | - Danyal Butt
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,Biologics Research and Development, Teva Pharmaceuticals, Macquarie Park, NSW, 2113, Australia
| | - Katherine Bourne
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Clara Young
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Jana R Hermes
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Maté Biro
- EMBL Australia, Single Molecule Science Node, School of Medical Sciences, UNSW, Sydney, NSW, 2052, Australia
| | - Gary Gracie
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, NSW, 2010, Australia
| | - Cindy S Ma
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - C Mee Ling Munier
- The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, NSW, 2052, Australia
| | - Fabio Luciani
- The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, NSW, 2052, Australia.,School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW, 2052, Australia
| | - John Zaunders
- The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, NSW, 2052, Australia.,St Vincent's Hospital Sydney Centre for Applied Medical Research, Sydney, Australia
| | - Andrew Parker
- Department of Anatomical Pathology, St Vincent's Hospital, Sydney, NSW, 2010, Australia
| | - Anthony D Kelleher
- The Kirby Institute for Infection and Immunity in Society, UNSW, Sydney, NSW, 2052, Australia.,St Vincent's Hospital Sydney Centre for Applied Medical Research, Sydney, Australia
| | - Stuart G Tangye
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - Peter I Croucher
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia.,Division of Bone Biology, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, NSW, 2052, Australia
| | - Robert Brink
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia
| | - Mark N Read
- School of Life and Environmental Sciences and the Charles Perkins Centre, University of Sydney, Sydney, NSW, 2052, Australia
| | - Tri Giang Phan
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia. .,St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 2010, Australia.
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38
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Woringer M, Darzacq X. Protein motion in the nucleus: from anomalous diffusion to weak interactions. Biochem Soc Trans 2018; 46:945-956. [PMID: 30065106 PMCID: PMC6103463 DOI: 10.1042/bst20170310] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/02/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022]
Abstract
Understanding how transcription factors (TFs) regulate mammalian gene expression in space and time is a central topic in biology. To activate a gene, a TF has first to diffuse in the available space of the nucleus until it reaches a target DNA sequence or protein (target site). This eventually results in the recruitment of the whole transcriptional machinery. All these processes take place in the mammalian nucleoplasm, a highly organized and dynamic environment, in which some complexes transiently assemble and break apart, whereas others appear more stable. This diversity of dynamic behaviors arises from the number of biomolecules that make up the nucleoplasm and their pairwise interactions. Indeed, interactions energies that span several orders of magnitude, from covalent bounds to transient and dynamic interactions, can shape nuclear landscapes. Thus, the nuclear environment determines how frequently and how fast a TF contacts its target site, and it indirectly regulates gene expression. How exactly transient interactions are involved in the regulation of TF diffusion is unclear, but are reflected by live cell imaging techniques, including single-particle tracking (SPT). Overall, the macroscopic result of these microscopic interactions is almost always anomalous diffusion, a phenomenon widely studied and modeled. Here, we review the connections between the anomalous diffusion of a TF observed by SPT and the microscopic organization of the nucleus, including recently described topologically associated domains and dynamic phase-separated compartments. We propose that anomalous diffusion found in SPT data result from weak and transient interactions with dynamic nuclear substructures, and that SPT data analysis would benefit from a better description of such structures.
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Affiliation(s)
- Maxime Woringer
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, U.S.A.
- Unité Imagerie et Modélisation, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
- Sorbonne Universités, CNRS, F-75005 Paris, France
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, U.S.A.
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39
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Grebenkov DS, Krapf D. Steady-state reaction rate of diffusion-controlled reactions in sheets. J Chem Phys 2018; 149:064117. [DOI: 10.1063/1.5041074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Denis S. Grebenkov
- Laboratoire de Physique de la Matière Condensée (UMR 7643), CNRS–Ecole Polytechnique, University Paris-Saclay, 91128 Palaiseau, France
| | - Diego Krapf
- Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
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40
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Hancock R. Crowding, Entropic Forces, and Confinement: Crucial Factors for Structures and Functions in the Cell Nucleus. BIOCHEMISTRY (MOSCOW) 2018; 83:326-337. [PMID: 29626920 DOI: 10.1134/s0006297918040041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The view of the cell nucleus as a crowded system of colloid particles and that chromosomes are giant self-avoiding polymers is stimulating rapid advances in our understanding of its structure and activities, thanks to concepts and experimental methods from colloid, polymer, soft matter, and nano sciences and to increased computational power for simulating macromolecules and polymers. This review summarizes current understanding of some characteristics of the molecular environment in the nucleus, of how intranuclear compartments are formed, and of how the genome is highly but precisely compacted, and underlines the crucial, subtle, and sometimes unintuitive effects on structures and reactions of entropic forces caused by the high concentration of macromolecules in the nucleus.
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Affiliation(s)
- R Hancock
- Biosystems Group, Biotechnology Centre, Silesian University of Technology, Poland and Laval University Cancer Research Centre, Québec, G1R2J6, Canada.
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41
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Luzhansky ID, Schwartz AD, Cohen JD, MacMunn JP, Barney LE, Jansen LE, Peyton SR. Anomalously diffusing and persistently migrating cells in 2D and 3D culture environments. APL Bioeng 2018; 2:026112. [PMID: 31069309 PMCID: PMC6324209 DOI: 10.1063/1.5019196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/28/2018] [Indexed: 12/17/2022] Open
Abstract
Appropriately chosen descriptive models of cell migration in biomaterials will allow researchers to characterize and ultimately predict the movement of cells in engineered systems for a variety of applications in tissue engineering. The persistent random walk (PRW) model accurately describes cell migration on two-dimensional (2D) substrates. However, this model inherently cannot describe subdiffusive cell movement, i.e., migration paths in which the root mean square displacement increases more slowly than the square root of the time interval. Subdiffusivity is a common characteristic of cells moving in confined environments, such as three-dimensional (3D) porous scaffolds, hydrogel networks, and in vivo tissues. We demonstrate that a generalized anomalous diffusion (AD) model, which uses a simple power law to relate the mean square displacement to time, more accurately captures individual cell migration paths across a range of engineered 2D and 3D environments than does the more commonly used PRW model. We used the AD model parameters to distinguish cell movement profiles on substrates with different chemokinetic factors, geometries (2D vs 3D), substrate adhesivities, and compliances. Although the two models performed with equal precision for superdiffusive cells, we suggest a simple AD model, in lieu of PRW, to describe cell trajectories in populations with a significant subdiffusive fraction, such as cells in confined, 3D environments.
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Affiliation(s)
- Igor D. Luzhansky
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Alyssa D. Schwartz
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Joshua D. Cohen
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - John P. MacMunn
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Lauren E. Barney
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Lauren E. Jansen
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Shelly R. Peyton
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
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42
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Random Motion of Chromatin Is Influenced by Lamin A Interconnections. Biophys J 2018; 114:2465-2472. [PMID: 29759373 DOI: 10.1016/j.bpj.2018.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/11/2018] [Accepted: 04/19/2018] [Indexed: 01/30/2023] Open
Abstract
Using fluorescence correlation spectroscopy in single-plane illumination microscopy, we investigated the dynamics of chromatin in interphase mouse adult fibroblast cell nuclei under the influence of the intermediate filament protein lamin A. We find that 1) lamin A-eGFP and histone H2A-mRFP show significant comobility, indicating that their motions are clearly interconnected in the nucleus, and 2) that the random motion of histones H2A within the chromatin network is subdiffusive, i.e., the effective diffusion coefficient decreases for slow timescales. Knocking out lamin A changes the diffusion back to normal. Thus, lamin A influences the dynamics of the entire chromatin network. Our conclusion is that lamin A plays a central role in determining the viscoelasticity of the chromatin network and helping to maintain local ordering of interphase chromosomes.
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43
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Verma P, Dilley RL, Gyparaki MT, Greenberg RA. Direct Quantitative Monitoring of Homology-Directed DNA Repair of Damaged Telomeres. Methods Enzymol 2018; 600:107-134. [PMID: 29458755 DOI: 10.1016/bs.mie.2017.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Homology-directed DNA repair (HDR) is an evolutionary conserved mechanism that is required for genome integrity and organismal fitness across species. While a myriad of different factors and mechanisms are able to execute HDR, all forms necessitate common steps of DNA damage recognition, homology search and capture, and assembly of a DNA polymerase complex to conduct templated DNA synthesis. The central question of what determines HDR mechanism utilization in mammalian cells has been limited by an inability to directly monitor the DNA damage response and products of repair as they arise from a defined genomic lesion. In this chapter, we describe several methodologies to delineate major steps of HDR during alternative lengthening of telomeres in human cells. This includes procedures to visualize interchromosomal telomere homology searches in real time and quantitatively detect HDR synthesis of nascent telomeres emanating from synchronous activation of telomere DNA double-strand breaks. We highlight the critical details of these methods and their applicability to monitoring HDR at telomeres in a broad variety of mammalian cell types.
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Affiliation(s)
- Priyanka Verma
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Robert L Dilley
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Melina T Gyparaki
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Roger A Greenberg
- Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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44
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Aquino T, Dentz M. Chemical Continuous Time Random Walks. PHYSICAL REVIEW LETTERS 2017; 119:230601. [PMID: 29286686 DOI: 10.1103/physrevlett.119.230601] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Indexed: 06/07/2023]
Abstract
Kinetic Monte Carlo methods such as the Gillespie algorithm model chemical reactions as random walks in particle number space. The interreaction times are exponentially distributed under the assumption that the system is well mixed. We introduce an arbitrary interreaction time distribution, which may account for the impact of incomplete mixing on chemical reactions, and in general stochastic reaction delay, which may represent the impact of extrinsic noise. This process defines an inhomogeneous continuous time random walk in particle number space, from which we derive a generalized chemical master equation. This leads naturally to a generalization of the Gillespie algorithm. Based on this formalism, we determine the modified chemical rate laws for different interreaction time distributions. This framework traces Michaelis-Menten-type kinetics back to finite-mean delay times, and predicts time-nonlocal macroscopic reaction kinetics as a consequence of broadly distributed delays. Non-Markovian kinetics exhibit weak ergodicity breaking and show key features of reactions under local nonequilibrium.
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Affiliation(s)
- Tomás Aquino
- Spanish National Research Council (IDAEA-CSIC), 08034 Barcelona, Spain
| | - Marco Dentz
- Spanish National Research Council (IDAEA-CSIC), 08034 Barcelona, Spain
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45
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Trovato F, Fumagalli G. Molecular simulations of cellular processes. Biophys Rev 2017; 9:941-958. [PMID: 29185136 DOI: 10.1007/s12551-017-0363-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 11/19/2017] [Indexed: 12/12/2022] Open
Abstract
It is, nowadays, possible to simulate biological processes in conditions that mimic the different cellular compartments. Several groups have performed these calculations using molecular models that vary in performance and accuracy. In many cases, the atomistic degrees of freedom have been eliminated, sacrificing both structural complexity and chemical specificity to be able to explore slow processes. In this review, we will discuss the insights gained from computer simulations on macromolecule diffusion, nuclear body formation, and processes involving the genetic material inside cell-mimicking spaces. We will also discuss the challenges to generate new models suitable for the simulations of biological processes on a cell scale and for cell-cycle-long times, including non-equilibrium events such as the co-translational folding, misfolding, and aggregation of proteins. A prominent role will be played by the wise choice of the structural simplifications and, simultaneously, of a relatively complex energetic description. These challenging tasks will rely on the integration of experimental and computational methods, achieved through the application of efficient algorithms. Graphical abstract.
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Affiliation(s)
- Fabio Trovato
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany.
| | - Giordano Fumagalli
- Nephrology and Dialysis Unit, USL Toscana Nord Ovest, 55041, Lido di Camaiore, Lucca, Italy
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46
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Gura Sadovsky R, Brielle S, Kaganovich D, England JL. Measurement of Rapid Protein Diffusion in the Cytoplasm by Photo-Converted Intensity Profile Expansion. Cell Rep 2017; 18:2795-2806. [PMID: 28297680 PMCID: PMC5368347 DOI: 10.1016/j.celrep.2017.02.063] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 12/05/2016] [Accepted: 02/17/2017] [Indexed: 11/27/2022] Open
Abstract
The fluorescence microscopy methods presently used to characterize protein motion in cells infer protein motion from indirect observables, rather than measuring protein motion directly. Operationalizing these methods requires expertise that can constitute a barrier to their broad utilization. Here, we have developed PIPE (photo-converted intensity profile expansion) to directly measure the motion of tagged proteins and quantify it using an effective diffusion coefficient. PIPE works by pulsing photo-convertible fluorescent proteins, generating a peaked fluorescence signal at the pulsed region, and analyzing the spatial expansion of the signal. We demonstrate PIPE's success in measuring accurate diffusion coefficients in silico and in vitro and compare effective diffusion coefficients of native cellular proteins and free fluorophores in vivo. We apply PIPE to measure diffusion anomality in the cell and use it to distinguish free fluorophores from native cellular proteins. PIPE's direct measurement and ease of use make it appealing for cell biologists.
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Affiliation(s)
- Rotem Gura Sadovsky
- Physics of Living Systems Group, Massachusetts Institute of Technology, Cambridge, MA 02138, USA; Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Shlomi Brielle
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel; Alexander Grass Center for Bioengineering, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Daniel Kaganovich
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Jeremy L England
- Physics of Living Systems Group, Massachusetts Institute of Technology, Cambridge, MA 02138, USA.
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Mahfuz MU, Makrakis D, Mouftah HT. Concentration-Encoded Subdiffusive Molecular Communication: Theory, Channel Characteristics, and Optimum Signal Detection. IEEE Trans Nanobioscience 2017; 15:533-548. [PMID: 27824576 DOI: 10.1109/tnb.2016.2588323] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Unlike normal diffusion, in anomalous diffusion, the movement of a molecule is described by the correlated random walk model where the mean square displacement of a molecule depends on the power law of time. In molecular communication (MC), there are many scenarios when the propagation of molecules cannot be described by normal diffusion process, where anomalous diffusion is a better fit. In this paper, the effects of anomalous subdiffusion on concentration-encoded molecular communication (CEMC) are investigated. Although classical (i.e., normal) diffusion is a widely-used model of diffusion in molecular communication (MC) research, anomalous subdiffusion is quite common in biological media involving bio-nanomachines, yet inadequately addressed as a research issue so far. Using the fractional diffusion approach, the molecular propagation effects in the case of pure subdiffusion occurring in an unbounded three-dimensional propagation medium have been shown in detail in terms of temporal dispersion parameters of the impulse response of the subdiffusive channel. Correspondingly, the bit error rate (BER) performance of a CEMC system is investigated with sampling-based (SD) and strength (i.e., energy)-based (ED) signal detection methods. It is found that anomalous subdiffusion has distinctive time-dispersive properties that play a vital role in accurately designing a subdiffusive CEMC system. Unlike normal diffusion, to detect information symbols in subdiffusive CEMC, a receiver requires larger memory size to operate correctly and hence a more complex structure. An in-depth analysis has been made on the performances of SD and ED optimum receiver models under diffusion noise and intersymbol interference (ISI) scenarios when communication range, transmission data rate, and memory size vary. In subdiffusive CEMC, the SD method.
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48
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Liu L, Cherstvy AG, Metzler R. Facilitated Diffusion of Transcription Factor Proteins with Anomalous Bulk Diffusion. J Phys Chem B 2017; 121:1284-1289. [DOI: 10.1021/acs.jpcb.6b12413] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Lin Liu
- CAS
Key Laboratory of Soft Matter Chemistry, Dept. of Polymer Science
and Engineering, University of Science and Technology of China, Hefei, Anhui Province 230026, China
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Andrey G. Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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49
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Wagner T, Kroll A, Haramagatti CR, Lipinski HG, Wiemann M. Classification and Segmentation of Nanoparticle Diffusion Trajectories in Cellular Micro Environments. PLoS One 2017; 12:e0170165. [PMID: 28107406 PMCID: PMC5249096 DOI: 10.1371/journal.pone.0170165] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 12/30/2016] [Indexed: 11/24/2022] Open
Abstract
Darkfield and confocal laser scanning microscopy both allow for a simultaneous observation of live cells and single nanoparticles. Accordingly, a characterization of nanoparticle uptake and intracellular mobility appears possible within living cells. Single particle tracking allows to measure the size of a diffusing particle close to a cell. However, within the more complex system of a cell’s cytoplasm normal, confined or anomalous diffusion together with directed motion may occur. In this work we present a method to automatically classify and segment single trajectories into their respective motion types. Single trajectories were found to contain more than one motion type. We have trained a random forest with 9 different features. The average error over all motion types for synthetic trajectories was 7.2%. The software was successfully applied to trajectories of positive controls for normal- and constrained diffusion. Trajectories captured by nanoparticle tracking analysis served as positive control for normal diffusion. Nanoparticles inserted into a diblock copolymer membrane was used to generate constrained diffusion. Finally we segmented trajectories of diffusing (nano-)particles in V79 cells captured with both darkfield- and confocal laser scanning microscopy. The software called “TraJClassifier” is freely available as ImageJ/Fiji plugin via https://git.io/v6uz2.
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Affiliation(s)
- Thorsten Wagner
- Biomedical Imaging Group, Department of Informatics, University of Applied Sciences and Arts Dortmund, Dortmund, Germany
- * E-mail:
| | - Alexandra Kroll
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Chandrashekara R. Haramagatti
- Experimental Physics IV and Bayreuth Insitute for Macromolecular Research, University of Bayreuth, Bayreuth, Germany
| | - Hans-Gerd Lipinski
- Biomedical Imaging Group, Department of Informatics, University of Applied Sciences and Arts Dortmund, Dortmund, Germany
| | - Martin Wiemann
- IBE R&D gGmbH Institute for Lung Health, Münster, Germany
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50
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Lapeyre GJ, Dentz M. Reaction–diffusion with stochastic decay rates. Phys Chem Chem Phys 2017; 19:18863-18879. [DOI: 10.1039/c7cp02971c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Microscopic physical and chemical fluctuations in a reaction–diffusion system lead to anomalous chemical kinetics and transport on the mesoscopic scale. Emergent non-Markovian effects lead to power-law reaction times and localization of reacting species.
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Affiliation(s)
- G. John Lapeyre
- Spanish National Research Council (IDAEA-CSIC)
- E-08034 Barcelona
- Spain
- ICFO–Institut de Ciències Fotòniques
- Mediterranean Technology Park
| | - Marco Dentz
- Spanish National Research Council (IDAEA-CSIC)
- E-08034 Barcelona
- Spain
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