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Shiff CE, Kondev J, Mohapatra L. Ultrasensitivity of microtubule severing due to damage repair. iScience 2024; 27:108874. [PMID: 38327774 PMCID: PMC10847648 DOI: 10.1016/j.isci.2024.108874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
Abstract
Microtubule-based cytoskeletal structures aid in cell motility, cell polarization, and intracellular transport. These functions require a coordinated effort of regulatory proteins which interact with microtubule cytoskeleton distinctively. In-vitro experiments have shown that free tubulin can repair nanoscale damages of microtubules created by severing proteins. Based on this observation, we theoretically analyze microtubule severing as a competition between the processes of damage spreading and tubulin-induced repair. We demonstrate that this model is in quantitative agreement with in-vitro experiments and predict the existence of a critical tubulin concentration above which severing becomes rare, fast, and sensitive to concentration of free tubulin. We show that this sensitivity leads to a dramatic increase in the dynamic range of steady-state microtubule lengths when the free tubulin concentration is varied, and microtubule lengths are controlled by severing. Our work demonstrates how synergy between tubulin and microtubule-associated proteins can bring about specific dynamical properties of microtubules.
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Affiliation(s)
- Chloe E. Shiff
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Lishibanya Mohapatra
- School of Physics and Astronomy, College of Science, Rochester Institute of Technology, Rochester, NY 14623, USA
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2
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Linn S, Lawley SD. First-passage times under frequent stochastic resetting. Phys Rev E 2023; 108:024114. [PMID: 37723763 DOI: 10.1103/physreve.108.024114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/07/2023] [Indexed: 09/20/2023]
Abstract
We determine the full distribution and moments of the first passage time for a wide class of stochastic search processes in the limit of frequent stochastic resetting. Our results apply to any system whose short-time behavior of the search process without resetting can be estimated. In addition to the typical case of exponentially distributed resetting times, we prove our results for a variety of resetting time distributions. We illustrate our results in several examples and show that the errors of our approximations vanish exponentially fast in typical scenarios of diffusive search.
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Affiliation(s)
- Samantha Linn
- Department of Mathematics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Sean D Lawley
- Department of Mathematics, University of Utah, Salt Lake City, Utah 84112, USA
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Ma J, Do M, Gros MAL, Peskin CS, Larabell CA, Mori Y, Isaacson SA. Strong Intracellular Signal Inactivation Produces Sharper and More Robust Signaling from Cell Membrane to Nucleus. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1167. [PMID: 37613341 DOI: 10.1093/micmic/ozad067.598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Jingwei Ma
- Google, Mountain View, CA, United States
| | - Myan Do
- Department of Cellular and Molecular Medicine, University of California, San Diego Medical School, San Diego, CA, United States
| | - Mark A Le Gros
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, United States
- National Center for X-ray Tomography, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Charles S Peskin
- Courant Institute of Mathematical Sciences, New York University, New York, NY, United States
| | - Carolyn A Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, United States
- National Center for X-ray Tomography, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Yoichiro Mori
- Department of Mathematics, University of Pennsylvania, Philadelphia, PA, United States
| | - Samuel A Isaacson
- Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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Punia B, Chaudhury S. Influence of Nonspecific Interactions between Proteins and In Vivo Cytoplasmic Crowders in Facilitated Diffusion of Proteins: Theoretical Insights. J Phys Chem B 2022; 126:3037-3047. [PMID: 35438996 DOI: 10.1021/acs.jpcb.2c01021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The binding of proteins to their respective specific sites on the DNA through facilitated diffusion serves as the initial step of various important biological processes. While this search process has been thoroughly investigated via in vitro studies, the cellular environment is complex and may interfere with the protein's search dynamics. The cytosol is heavily crowded, which can potentially modify the search by nonspecifically interacting with the protein that has been mostly overlooked. In this work, we probe the target search dynamics in the presence of explicit crowding agents that have an affinity toward the protein. We theoretically investigate the role of such protein-crowder associations in the target search process using a discrete-state stochastic framework that allows for the analytical description of dynamic properties. It is found that stronger nonspecific associations between the crowder and proteins can accelerate the facilitated diffusion of proteins in comparison with a purely inert, rather weakly interacting cellular environment. This effect depends on how strong these associations are, the spatial positions of the target with respect to the crowders, and the size of the crowded region. Our theoretical results are also tested with Monte Carlo computer simulations. Our predictions are in qualitative agreement with existing experimental observations and computational studies.
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Affiliation(s)
- Bhawakshi Punia
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Srabanti Chaudhury
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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Li A, Zhang X, Singla J, White K, Loconte V, Hu C, Zhang C, Li S, Li W, Francis JP, Wang C, Sali A, Sun L, He X, Stevens RC. Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion. PLoS One 2022; 17:e0265567. [PMID: 35324950 PMCID: PMC8947144 DOI: 10.1371/journal.pone.0265567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/03/2022] [Indexed: 02/07/2023] Open
Abstract
The mesoscale description of the subcellular organization informs about cellular mechanisms in disease state. However, applications of soft X-ray tomography (SXT), an important approach for characterizing organelle organization, are limited by labor-intensive manual segmentation. Here we report a pipeline for automated segmentation and systematic analysis of SXT tomograms. Our approach combines semantic and first-applied instance segmentation to produce separate organelle masks with high Dice and Recall indexes, followed by analysis of organelle localization based on the radial distribution function. We demonstrated this technique by investigating the organization of INS-1E pancreatic β-cell organization under different treatments at multiple time points. Consistent with a previous analysis of a similar dataset, our results revealed the impact of glucose stimulation on the localization and molecular density of insulin vesicles and mitochondria. This pipeline can be extended to SXT tomograms of any cell type to shed light on the subcellular rearrangements under different drug treatments.
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Affiliation(s)
- Angdi Li
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangyi Zhang
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jitin Singla
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA, United States of America
| | - Kate White
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA, United States of America
| | - Valentina Loconte
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chuanyang Hu
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chuyu Zhang
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shuailin Li
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
| | - Weimin Li
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - John Paul Francis
- Department of Computer Science, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, United States of America
| | - Chenxi Wang
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Andrej Sali
- California Institute for Quantitative Biosciences, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
| | - Liping Sun
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- * E-mail: (LS); (XH); (RCS)
| | - Xuming He
- School of Information Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Engineering Research Center of Intelligent Vision and Imaging, Shanghai, China
- * E-mail: (LS); (XH); (RCS)
| | - Raymond C. Stevens
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA, United States of America
- * E-mail: (LS); (XH); (RCS)
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Loconte V, Chen JH, Cortese M, Ekman A, Le Gros MA, Larabell C, Bartenschlager R, Weinhardt V. Using soft X-ray tomography for rapid whole-cell quantitative imaging of SARS-CoV-2-infected cells. CELL REPORTS METHODS 2021; 1:100117. [PMID: 34729550 PMCID: PMC8552653 DOI: 10.1016/j.crmeth.2021.100117] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/10/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
High-resolution and rapid imaging of host cell ultrastructure can generate insights toward viral disease mechanism, for example for a severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Here, we employ full-rotation soft X-ray tomography (SXT) to examine organelle remodeling induced by SARS-CoV-2 at the whole-cell level with high spatial resolution and throughput. Most of the current SXT systems suffer from a restricted field of view due to use of flat sample supports and artifacts due to missing data. In this approach using cylindrical sample holders, a full-rotation tomogram of human lung epithelial cells is performed in less than 10 min. We demonstrate the potential of SXT imaging by visualizing aggregates of SARS-CoV-2 virions and virus-induced intracellular alterations. This rapid whole-cell imaging approach allows us to visualize the spatiotemporal changes of cellular organelles upon viral infection in a quantitative manner.
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Affiliation(s)
- Valentina Loconte
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Jian-Hua Chen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg, Germany
| | - Axel Ekman
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Mark A. Le Gros
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Carolyn Larabell
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology Heidelberg University, Heidelberg, Germany
- German Center for Infection Research, Heidelberg Partner Site, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Venera Weinhardt
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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