1
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Stein DB, Shelley MJ. Computational tools for cellular scale biophysics. Curr Opin Cell Biol 2024; 89:102379. [PMID: 38850680 DOI: 10.1016/j.ceb.2024.102379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/10/2024]
Abstract
Mathematical models are indispensable for disentangling the interactions through which biological components work together to generate the forces and flows that position, mix, and distribute proteins, nutrients, and organelles within the cell. To illuminate the ever more specific questions studied at the edge of biological inquiry, such models inevitably become more complex. Solving, simulating, and learning from these more realistic models requires the development of new analytic techniques, numerical methods, and scalable software. In this review, we discuss some recent developments in tools for understanding how large numbers of cytoskeletal filaments, driven by molecular motors and interacting with the cytoplasm and other structures in their environment, generate fluid flows, instabilities, and material deformations which help drive crucial cellular processes.
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Affiliation(s)
- David B Stein
- Center for Computational Biology, Flatiron Institute, 162 5th Ave, New York, 10010, NY, USA.
| | - Michael J Shelley
- Center for Computational Biology, Flatiron Institute, 162 5th Ave, New York, 10010, NY, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St, New York, 10012, NY, USA
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2
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Lemma B, Lemma LM, Ems-McClung SC, Walczak CE, Dogic Z, Needleman DJ. Structure and dynamics of motor-driven microtubule bundles. SOFT MATTER 2024; 20:5715-5723. [PMID: 38872426 PMCID: PMC11268426 DOI: 10.1039/d3sm01336g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
Connecting the large-scale emergent behaviors of active cytoskeletal materials to the microscopic properties of their constituents is a challenge due to a lack of data on the multiscale dynamics and structure of such systems. We approach this problem by studying the impact of depletion attraction on bundles of microtubules and kinesin-14 molecular motors. For all depletant concentrations, kinesin-14 bundles generate comparable extensile dynamics. However, this invariable mesoscopic behavior masks the transition in the microscopic motion of microtubules. Specifically, with increasing attraction, we observe a transition from bi-directional sliding with extension to pure extension with no sliding. Small-angle X-ray scattering shows that the transition in microtubule dynamics is concurrent with a structural rearrangement of microtubules from an open hexagonal to a compressed rectangular lattice. These results demonstrate that bundles of microtubules and molecular motors can display the same mesoscopic extensile behaviors despite having different internal structures and microscopic dynamics. They provide essential information for developing multiscale models of active matter.
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Affiliation(s)
- Bezia Lemma
- Physics Department, Harvard University, Cambridge, MA 02138, USA
- Physics Department, Brandeis University, Waltham, MA 02453, USA.
- Physics Department, University of California, Santa Barbara, CA 93106, USA
| | - Linnea M Lemma
- Physics Department, Brandeis University, Waltham, MA 02453, USA.
- Physics Department, University of California, Santa Barbara, CA 93106, USA
| | | | - Claire E Walczak
- Medical Sciences, Indiana University School of Medicine, Bloomington, IN 47405, USA
| | - Zvonimir Dogic
- Physics Department, Brandeis University, Waltham, MA 02453, USA.
- Physics Department, University of California, Santa Barbara, CA 93106, USA
- Biomolecular Science & Engineering Department, University of California, Santa Barbara, CA 93106, USA
| | - Daniel J Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Molecular & Cellular Biology Department, Harvard University, Cambridge, MA 02138, USA
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
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3
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Yeh LH, Ivanov IE, Chandler T, Byrum JR, Chhun BB, Guo SM, Foltz C, Hashemi E, Perez-Bermejo JA, Wang H, Yu Y, Kazansky PG, Conklin BR, Han MH, Mehta SB. Permittivity tensor imaging: modular label-free imaging of 3D dry mass and 3D orientation at high resolution. Nat Methods 2024; 21:1257-1274. [PMID: 38890427 PMCID: PMC11239526 DOI: 10.1038/s41592-024-02291-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 04/24/2024] [Indexed: 06/20/2024]
Abstract
The dry mass and the orientation of biomolecules can be imaged without a label by measuring their permittivity tensor (PT), which describes how biomolecules affect the phase and polarization of light. Three-dimensional (3D) imaging of PT has been challenging. We present a label-free computational microscopy technique, PT imaging (PTI), for the 3D measurement of PT. PTI encodes the invisible PT into images using oblique illumination, polarization-sensitive detection and volumetric sampling. PT is decoded from the data with a vectorial imaging model and a multi-channel inverse algorithm, assuming uniaxial symmetry in each voxel. We demonstrate high-resolution imaging of PT of isotropic beads, anisotropic glass targets, mouse brain tissue, infected cells and histology slides. PTI outperforms previous label-free imaging techniques such as vector tomography, ptychography and light-field imaging in resolving the 3D orientation and symmetry of organelles, cells and tissue. We provide open-source software and modular hardware to enable the adoption of the method.
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Affiliation(s)
- Li-Hao Yeh
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- ASML, San Jose, CA, USA
| | | | | | - Janie R Byrum
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- California's Stem Cell Agency, South San Francisco, CA, USA
| | - Bryant B Chhun
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Eikon Therapeutics, Hayward, CA, USA
| | - Syuan-Ming Guo
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Insitro, South San Francisco, CA, USA
| | - Cameron Foltz
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Quantinuum, Broomfield, CO, USA
| | | | - Juan A Perez-Bermejo
- Gladstone Institutes, San Francisco, CA, USA
- Genentech, South San Francisco, CA, USA
| | | | - Yanhao Yu
- University of Southampton, Southampton, UK
| | | | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA
- University of California San Francisco, San Francisco, CA, USA
| | - May H Han
- Stanford University, Palo Alto, CA, USA
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4
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Deng T, Lu W, Zhao X, Wang H, Zheng Y, Zheng A, Shen Z. Chondroitin sulfate/silk fibroin hydrogel incorporating graphene oxide quantum dots with photothermal-effect promotes type H vessel-related wound healing. Carbohydr Polym 2024; 334:121972. [PMID: 38553198 DOI: 10.1016/j.carbpol.2024.121972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 04/02/2024]
Abstract
Chronic wounds with bacterial infection present formidable clinical challenges. In this study, a versatile hydrogel dressing with antibacterial and angiogenic activity composite of silk fibroin (SF), chondroitin sulfate (CS), and graphene oxide quantum dots (GOQDs) is fabricated. GOQDs@SF/CS (GSC) hydrogel is rapidly formed through the enzyme catalytic action of horseradish peroxidase. With the incorporation of GOQDs both gelation speed and mechanical properties have been enhanced, and the photothermal characteristics of GOQDs in GSC hydrogel enabled bacterial killing through photothermal treatment (PTT) at ∼51 °C. In vitro studies show that the GSC hydrogels demonstrate excellent antibacterial performance and induce type H vessel differentiation of endothelial cells via the activated ERK1/2 signaling pathway and upregulated SLIT3 expression. In vivo results show that the hydrogel significantly promotes type H vessels formation, which is related to the collagen deposition, epithelialization and, ultimately, accelerates the regeneration of infected skin defects. Collectively, this multifunctional GSC hydrogel, with dual action of antibacterial efficacy and angiogenesis promotion, emerges as an innovative skin dressing with the potential for advancing in infected wound healing.
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Affiliation(s)
- Tanjun Deng
- Department of Dermatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Wenli Lu
- Department of Dermatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xiaoxian Zhao
- Department of Oral Mucosal Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University, Shanghai 200011, China
| | - Haoyu Wang
- Dermatology Center, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Yumeng Zheng
- Department of Dermatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Ao Zheng
- Department of Prosthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University, Shanghai 200011, China.
| | - Zhengyu Shen
- Department of Dermatology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
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5
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Paramanick S, Pal A, Soni H, Kumar N. Programming tunable active dynamics in a self-propelled robot. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:34. [PMID: 38782771 DOI: 10.1140/epje/s10189-024-00430-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024]
Abstract
We present a scheme for producing tunable active dynamics in a self-propelled robotic device. The robot moves using the differential drive mechanism where two wheels can vary their instantaneous velocities independently. These velocities are calculated by equating robot's equations of motion in two dimensions with well-established active particle models and encoded into the robot's microcontroller. We demonstrate that the robot can depict active Brownian, run and tumble, and Brownian dynamics with a wide range of parameters. The resulting motion analyzed using particle tracking shows excellent agreement with the theoretically predicted trajectories. Later, we show that its motion can be switched between different dynamics using light intensity as an external parameter. Intriguingly, we demonstrate that the robot can efficiently navigate through many obstacles by performing stochastic reorientations driven by the gradient in light intensity towards a desired location, namely the target. This work opens an avenue for designing tunable active systems with the potential of revealing the physics of active matter and its application for bio- and nature-inspired robotics.
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Affiliation(s)
- Somnath Paramanick
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Arnab Pal
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai, 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Harsh Soni
- School of Physical Sciences, Indian Institute of Technology Mandi, Mandi, 175001, India
| | - Nitin Kumar
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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6
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Nolte DD. Coherent light scattering from cellular dynamics in living tissues. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:036601. [PMID: 38433567 DOI: 10.1088/1361-6633/ad2229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
This review examines the biological physics of intracellular transport probed by the coherent optics of dynamic light scattering from optically thick living tissues. Cells and their constituents are in constant motion, composed of a broad range of speeds spanning many orders of magnitude that reflect the wide array of functions and mechanisms that maintain cellular health. From the organelle scale of tens of nanometers and upward in size, the motion inside living tissue is actively driven rather than thermal, propelled by the hydrolysis of bioenergetic molecules and the forces of molecular motors. Active transport can mimic the random walks of thermal Brownian motion, but mean-squared displacements are far from thermal equilibrium and can display anomalous diffusion through Lévy or fractional Brownian walks. Despite the average isotropic three-dimensional environment of cells and tissues, active cellular or intracellular transport of single light-scattering objects is often pseudo-one-dimensional, for instance as organelle displacement persists along cytoskeletal tracks or as membranes displace along the normal to cell surfaces, albeit isotropically oriented in three dimensions. Coherent light scattering is a natural tool to characterize such tissue dynamics because persistent directed transport induces Doppler shifts in the scattered light. The many frequency-shifted partial waves from the complex and dynamic media interfere to produce dynamic speckle that reveals tissue-scale processes through speckle contrast imaging and fluctuation spectroscopy. Low-coherence interferometry, dynamic optical coherence tomography, diffusing-wave spectroscopy, diffuse-correlation spectroscopy, differential dynamic microscopy and digital holography offer coherent detection methods that shed light on intracellular processes. In health-care applications, altered states of cellular health and disease display altered cellular motions that imprint on the statistical fluctuations of the scattered light. For instance, the efficacy of medical therapeutics can be monitored by measuring the changes they induce in the Doppler spectra of livingex vivocancer biopsies.
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Affiliation(s)
- David D Nolte
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, United States of America
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7
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Chauhan P, Lee HB, Goodbee N, Martin S, Branch R, Sahu S, Schwarz JM, Ross JL. Ionic strength alters crosslinker-driven self-organization of microtubules. Cytoskeleton (Hoboken) 2024. [PMID: 38385864 DOI: 10.1002/cm.21839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024]
Abstract
The microtubule cytoskeleton is a major structural element inside cells that directs self-organization using microtubule-associated proteins and motors. It has been shown that finite-sized, spindle-like microtubule organizations, called "tactoids," can form in vitro spontaneously from mixtures of tubulin and the antiparallel crosslinker, MAP65, from the MAP65/PRC1/Ase family. Here, we probe the ability of MAP65 to form tactoids as a function of the ionic strength of the buffer to attempt to break the electrostatic interactions binding MAP65 to microtubules and inter-MAP65 binding. We observe that, with increasing monovalent salts, the organizations change from finite tactoids to unbounded length bundles, yet the MAP65 binding and crosslinking appear to stay intact. We further explore the effects of ionic strength on the dissociation constant of MAP65 using both microtubule pelleting and single-molecule binding assays. We find that salt can reduce the binding, yet salt never negates it. Instead, we believe that the salt is affecting the ability of the MAP65 to form phase-separated droplets, which cause the nucleation and growth of tactoids, as recently demonstrated.
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Affiliation(s)
- Prashali Chauhan
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Hong Beom Lee
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Niaz Goodbee
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Sophia Martin
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Ruell Branch
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Sumon Sahu
- Department of Physics, New York University, New York, New York, USA
| | | | - Jennifer L Ross
- Physics Department, Syracuse University, Syracuse, New York, USA
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8
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Bonucci M, Shu T, Holt LJ. How it feels in a cell. Trends Cell Biol 2023; 33:924-938. [PMID: 37286396 PMCID: PMC10592589 DOI: 10.1016/j.tcb.2023.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Life emerges from thousands of biochemical processes occurring within a shared intracellular environment. We have gained deep insights from in vitro reconstitution of isolated biochemical reactions. However, the reaction medium in test tubes is typically simple and diluted. The cell interior is far more complex: macromolecules occupy more than a third of the space, and energy-consuming processes agitate the cell interior. Here, we review how this crowded, active environment impacts the motion and assembly of macromolecules, with an emphasis on mesoscale particles (10-1000 nm diameter). We describe methods to probe and analyze the biophysical properties of cells and highlight how changes in these properties can impact physiology and signaling, and potentially contribute to aging, and diseases, including cancer and neurodegeneration.
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Affiliation(s)
- Martina Bonucci
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA.
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9
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Valdez VA, Neahring L, Petry S, Dumont S. Mechanisms underlying spindle assembly and robustness. Nat Rev Mol Cell Biol 2023; 24:523-542. [PMID: 36977834 PMCID: PMC10642710 DOI: 10.1038/s41580-023-00584-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 03/30/2023]
Abstract
The microtubule-based spindle orchestrates chromosome segregation during cell division. Following more than a century of study, many components and pathways contributing to spindle assembly have been described, but how the spindle robustly assembles remains incompletely understood. This process involves the self-organization of a large number of molecular parts - up to hundreds of thousands in vertebrate cells - whose local interactions give rise to a cellular-scale structure with emergent architecture, mechanics and function. In this Review, we discuss key concepts in our understanding of spindle assembly, focusing on recent advances and the new approaches that enabled them. We describe the pathways that generate the microtubule framework of the spindle by driving microtubule nucleation in a spatially controlled fashion and present recent insights regarding the organization of individual microtubules into structural modules. Finally, we discuss the emergent properties of the spindle that enable robust chromosome segregation.
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Affiliation(s)
| | - Lila Neahring
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA, USA
- Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA, USA
| | - Sabine Petry
- Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Sophie Dumont
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA, USA.
- Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA, USA.
- Department of Biochemistry & Biophysics, UCSF, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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10
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Sahu S, Chauhan P, Lumen E, Moody K, Peddireddy K, Mani N, Subramanian R, Robertson-Anderson R, Wolfe AJ, Ross JL. Interplay of self-organization of microtubule asters and crosslinking protein condensates. PNAS NEXUS 2023; 2:pgad231. [PMID: 37497046 PMCID: PMC10367440 DOI: 10.1093/pnasnexus/pgad231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/28/2023]
Abstract
The cytoskeleton is a major focus of physical studies to understand organization inside cells given its primary role in cell motility, cell division, and cell mechanics. Recently, protein condensation has been shown to be another major intracellular organizational strategy. Here, we report that the microtubule crosslinking proteins, MAP65-1 and PRC1, can form phase separated condensates at physiological salt and temperature without additional crowding agents in vitro. The size of the droplets depends on the concentration of protein. MAP65 condensates are liquid at first and can gelate over time. We show that these condensates can nucleate and grow microtubule bundles that form asters, regardless of the viscoelasticity of the condensate. The droplet size directly controls the number of projections in the microtubule asters, demonstrating that the MAP65 concentration can control the organization of microtubules. When gel-like droplets nucleate and grow asters from a shell of tubulin at the surface, the microtubules are able to re-fluidize the MAP65 condensate, returning the MAP65 molecules to solution. This work implies that there is an interplay between condensate formation from microtubule-associated proteins, microtubule organization, and condensate dissolution that could be important for the dynamics of intracellular organization.
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Affiliation(s)
- Sumon Sahu
- Physics Department, Syracuse University, Syracuse, NY 13244, USA
- Department of Physics, New York University, New York, NY 10003, USA
| | - Prashali Chauhan
- Physics Department, Syracuse University, Syracuse, NY 13244, USA
- The Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Ellie Lumen
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY 13084, USA
| | - Kelsey Moody
- The Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | | | - Nandini Mani
- Massachusetts General Hospital, Boston, MA 02115, USA
| | | | | | - Aaron J Wolfe
- The Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA
- Ichor Life Sciences, Inc., 2561 US Route 11, LaFayette, NY 13084, USA
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Jennifer L Ross
- Physics Department, Syracuse University, Syracuse, NY 13244, USA
- The Bioinspired Institute, Syracuse University, Syracuse, NY 13244, USA
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11
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Müller S. Assessment of Spindle Shape Control by Spindle Poleward Flux Measurements and FRAP Bulk Analysis. Methods Mol Biol 2023; 2604:113-125. [PMID: 36773229 DOI: 10.1007/978-1-0716-2867-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
In plants, the segregation of genetic material is achieved by an acentrosomal, mitotic spindle. This macromolecular machinery consists of different microtubule subpopulations and interacting proteins. The majority of what we know about the assembly and shape control of the mitotic spindle arose from vertebrate model systems. The dynamic properties of the individual tubulin polymers are crucial for the accurate assembly of the spindle array and are modulated by microtubule-associated motor and non-motor proteins. The mitotic spindle relies on a phenomenon called poleward microtubule flux that is critical to establish spindle shape, chromosome alignment, and segregation. This flux is under control of the non-motor microtubule-associated proteins and force-generating motors. Despite the large number of (plant-specific) kinesin motor proteins expressed during mitosis, their mitotic roles remain largely elusive. Moreover, reports on mitotic spindle formation and shape control in higher plants are scarce. In this chapter, an overview of the basic principles and methods concerning live imaging of prometa- and metaphase spindles and the analysis of spindle microtubule flux using fluorescence recovery after photobleaching is provided.
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Affiliation(s)
- Sabine Müller
- Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany.
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12
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Soujanya M, Bihani A, Hajirnis N, Pathak RU, Mishra RK. Nuclear architecture and the structural basis of mitotic memory. CHROMOSOME RESEARCH : AN INTERNATIONAL JOURNAL ON THE MOLECULAR, SUPRAMOLECULAR AND EVOLUTIONARY ASPECTS OF CHROMOSOME BIOLOGY 2023; 31:8. [PMID: 36725757 DOI: 10.1007/s10577-023-09714-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/13/2022] [Accepted: 12/19/2022] [Indexed: 02/03/2023]
Abstract
The nucleus is a complex organelle that hosts the genome and is essential for vital processes like DNA replication, DNA repair, transcription, and splicing. The genome is non-randomly organized in the three-dimensional space of the nucleus. This functional sub-compartmentalization was thought to be organized on the framework of nuclear matrix (NuMat), a non-chromatin scaffold that functions as a substratum for various molecular processes of the nucleus. More recently, nuclear bodies or membrane-less subcompartments of the nucleus are thought to arise due to phase separation of chromatin, RNA, and proteins. The nuclear architecture is an amalgamation of the relative organization of chromatin, epigenetic landscape, the nuclear bodies, and the nucleoskeleton in the three-dimensional space of the nucleus. During mitosis, the nucleus undergoes drastic changes in morphology to the degree that it ceases to exist as such; various nuclear components, including the envelope that defines the nucleus, disintegrate, and the chromatin acquires mitosis-specific epigenetic marks and condenses to form chromosome. Upon mitotic exit, chromosomes are decondensed, re-establish hierarchical genome organization, and regain epigenetic and transcriptional status similar to that of the mother cell. How this mitotic memory is inherited during cell division remains a puzzle. NuMat components that are a part of the mitotic chromosome in the form of mitotic chromosome scaffold (MiCS) could potentially be the seeds that guide the relative re-establishment of the epigenome, chromosome territories, and the nuclear bodies. Here, we synthesize the advances towards understanding cellular memory of nuclear architecture across mitosis and propose a hypothesis that a subset of NuMat proteome essential for nucleation of various nuclear bodies are retained in MiCS to serve as seeds of mitotic memory, thus ensuring the daughter cells re-establish the complex status of nuclear architecture similar to that of the mother cells, thereby maintaining the pre-mitotic transcriptional status.
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Affiliation(s)
- Mamilla Soujanya
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
- AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Ashish Bihani
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
| | - Nikhil Hajirnis
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
- Department of Anatomy and Neurobiology, University of Maryland, Baltimore, USA
| | - Rashmi U Pathak
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India
| | - Rakesh K Mishra
- CSIR - Centre for Cellular & Molecular Biology, Hyderabad, India.
- AcSIR - Academy of Scientific and Innovative Research, Ghaziabad, India.
- TIGS - Tata Institute for Genetics and Society, Bangalore, India.
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13
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Harrison D, Rorot W, Laukaityte U. Mind the matter: Active matter, soft robotics, and the making of bio-inspired artificial intelligence. Front Neurorobot 2022; 16:880724. [PMID: 36620483 PMCID: PMC9815774 DOI: 10.3389/fnbot.2022.880724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022] Open
Abstract
Philosophical and theoretical debates on the multiple realisability of the cognitive have historically influenced discussions of the possible systems capable of instantiating complex functions like memory, learning, goal-directedness, and decision-making. These debates have had the corollary of undermining, if not altogether neglecting, the materiality and corporeality of cognition-treating material, living processes as "hardware" problems that can be abstracted out and, in principle, implemented in a variety of materials-in particular on digital computers and in the form of state-of-the-art neural networks. In sum, the matter in se has been taken not to matter for cognition. However, in this paper, we argue that the materiality of cognition-and the living, self-organizing processes that it enables-requires a more detailed assessment when understanding the nature of cognition and recreating it in the field of embodied robotics. Or, in slogan form, that the matter matters for cognitive form and function. We pull from the fields of Active Matter Physics, Soft Robotics, and Basal Cognition literature to suggest that the imbrication between material and cognitive processes is closer than standard accounts of multiple realisability suggest. In light of this, we propose upgrading the notion of multiple realisability from the standard version-what we call 1.0-to a more nuanced conception 2.0 to better reflect the recent empirical advancements, while at the same time averting many of the problems that have been raised for it. These fields are actively reshaping the terrain in which we understand materiality and how it enables, mediates, and constrains cognition. We propose that taking the materiality of our embodied, precarious nature seriously furnishes an important research avenue for the development of embodied robots that autonomously value, engage, and interact with the environment in a goal-directed manner, in response to existential needs of survival, persistence, and, ultimately, reproduction. Thus, we argue that by placing further emphasis on the soft, active, and plastic nature of the materials that constitute cognitive embodiment, we can move further in the direction of autonomous embodied robots and Artificial Intelligence.
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Affiliation(s)
- David Harrison
- Department of History and Philosophy of Science, University of Cambridge, Cambridge, United Kingdom,Leverhulme Centre for the Future of Intelligence, Cambridge, United Kingdom,Konrad Lorenz Institute for Evolution and Cognition Research, Vienna, Austria,*Correspondence: David Harrison
| | - Wiktor Rorot
- Human Interactivity and Language Lab, Faculty of Psychology, University of Warsaw, Warsaw, Poland,Wiktor Rorot
| | - Urte Laukaityte
- Department of Philosophy, University of California, Berkeley, Berkeley, CA, United States
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14
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Kiewisz R, Fabig G, Conway W, Baum D, Needleman DJ, Müller-Reichert T. Three-dimensional structure of kinetochore-fibers in human mitotic spindles. eLife 2022; 11:75459. [PMID: 35894209 PMCID: PMC9365394 DOI: 10.7554/elife.75459] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/24/2022] [Indexed: 11/13/2022] Open
Abstract
During cell division, kinetochore microtubules (KMTs) provide a physical linkage between the chromosomes and the rest of the spindle. KMTs in mammalian cells are organized into bundles, so-called kinetochore-fibers (k-fibers), but the ultrastructure of these fibers is currently not well characterized. Here, we show by large-scale electron tomography that each k-fiber in HeLa cells in metaphase is composed of approximately nine KMTs, only half of which reach the spindle pole. Our comprehensive reconstructions allowed us to analyze the three-dimensional (3D) morphology of k-fibers and their surrounding MTs in detail. We found that k-fibers exhibit remarkable variation in circumference and KMT density along their length, with the pole-proximal side showing a broadening. Extending our structural analysis then to other MTs in the spindle, we further observed that the association of KMTs with non-KMTs predominantly occurs in the spindle pole regions. Our 3D reconstructions have implications for KMT growth and k-fiber self-organization models as covered in a parallel publication applying complementary live-cell imaging in combination with biophysical modeling (Conway et al., 2022). Finally, we also introduce a new visualization tool allowing an interactive display of our 3D spindle data that will serve as a resource for further structural studies on mitosis in human cells.
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Affiliation(s)
- Robert Kiewisz
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - William Conway
- Department of Physics, Harvard University, Cambridge, United States
| | - Daniel Baum
- Department of Visual and Data-Centric Computing, Zuse Institute Berlin, Berlin, Germany
| | - Daniel J Needleman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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15
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Conway W, Kiewisz R, Fabig G, Kelleher CP, Wu HY, Anjur-Dietrich M, Müller-Reichert T, Needleman DJ. Self-organization of kinetochore-fibers in human mitotic spindles. eLife 2022; 11:75458. [PMID: 35876665 PMCID: PMC9398449 DOI: 10.7554/elife.75458] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/24/2022] [Indexed: 11/22/2022] Open
Abstract
During eukaryotic cell division, chromosomes are linked to microtubules (MTs) in the spindle by a macromolecular complex called the kinetochore. The bound kinetochore microtubules (KMTs) are crucial to ensuring accurate chromosome segregation. Recent reconstructions by electron tomography (Kiewisz et al., 2022) captured the positions and configurations of every MT in human mitotic spindles, revealing that roughly half the KMTs in these spindles do not reach the pole. Here, we investigate the processes that give rise to this distribution of KMTs using a combination of analysis of large-scale electron tomography, photoconversion experiments, quantitative polarized light microscopy, and biophysical modeling. Our results indicate that in metaphase, KMTs grow away from the kinetochores along well-defined trajectories, with the speed of the KMT minus ends continually decreasing as the minus ends approach the pole, implying that longer KMTs grow more slowly than shorter KMTs. The locations of KMT minus ends, and the turnover and movements of tubulin in KMTs, are consistent with models in which KMTs predominately nucleate de novo at kinetochores in metaphase and are inconsistent with substantial numbers of non-KMTs being recruited to the kinetochore in metaphase. Taken together, this work leads to a mathematical model of the self-organization of kinetochore-fibers in human mitotic spindles.
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Affiliation(s)
- William Conway
- Department of Physics, Harvard University, Cambridge, United States
| | - Robert Kiewisz
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Colm P Kelleher
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Hai-Yin Wu
- Department of Physics, Harvard University, Cambridge, United States
| | - Maya Anjur-Dietrich
- John A Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Daniel J Needleman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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16
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Extensile to contractile transition in active microtubule-actin composites generates layered asters with programmable lifetimes. Proc Natl Acad Sci U S A 2022; 119:2115895119. [PMID: 35086931 PMCID: PMC8812548 DOI: 10.1073/pnas.2115895119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
We study a reconstituted composite system consisting of an active microtubule network interdigitated with a passive network of entangled F-actin filaments. Increasing the concentration of filamentous actin controls the emergent dynamics, inducing a transition from turbulent-like flows to bulk contractions. At intermediate concentrations, where the active stresses change their symmetry from anisotropic extensile to isotropic contracting, the composite separates into layered asters that coexist with the background turbulent fluid. Contracted onion-like asters have a radially extending microtubule-rich cortex that envelops alternating layers of microtubules and F-actin. These self-regulating structures undergo internal reorganization, which appears to minimize the surface area and maintain the ordered layering, even when undergoing aster merging events. Finally, the layered asters are metastable structures. Their lifetime, which ranges from minutes to hours, is encoded in the material properties of the composite. These results challenge the current models of active matter. They demonstrate self-organized dynamical states and patterns evocative of those observed in the cytoskeleton do not require precise biochemical regulation, but can arise from purely mechanical interactions of actively driven filamentous materials.
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17
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Neahring L, Cho NH, Dumont S. Opposing motors provide mechanical and functional robustness in the human spindle. Dev Cell 2021; 56:3006-3018.e5. [PMID: 34614397 DOI: 10.1016/j.devcel.2021.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/27/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
At each cell division, the spindle self-organizes from microtubules and motors. In human spindles, the motors dynein and Eg5 generate contractile and extensile stress, respectively. Inhibiting dynein or its targeting factor NuMA leads to unfocused, turbulent spindles, and inhibiting Eg5 leads to monopoles; yet, bipolar spindles form when both are inhibited together. What, then, are the roles of these opposing motors? Here, we generate NuMA/dynein- and Eg5-doubly inhibited spindles that not only attain a typical metaphase shape and size but also undergo anaphase. However, these spindles have reduced microtubule dynamics and are mechanically fragile, fracturing under force. Furthermore, they exhibit lagging chromosomes and a dramatic left-handed twist at anaphase. Thus, although these opposing motors are not required for spindle shape, they are essential to its mechanical and functional robustness. This work suggests a design principle whereby opposing active stresses provide robustness to force-generating cellular structures.
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Affiliation(s)
- Lila Neahring
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA; Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA 94143, USA.
| | - Nathan H Cho
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA; Tetrad Graduate Program, UCSF, San Francisco, CA 94158, USA
| | - Sophie Dumont
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA 94158, USA; Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA 94143, USA; Tetrad Graduate Program, UCSF, San Francisco, CA 94158, USA; Department of Biochemistry & Biophysics, UCSF, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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18
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Dierichs K, Menges A. Designing architectural materials: from granular form to functional granular material. BIOINSPIRATION & BIOMIMETICS 2021; 16:065010. [PMID: 34555826 DOI: 10.1088/1748-3190/ac2987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Designed granular materials are a novel class of architectural material system. Following one of the key paradigms of designed matter, material form and material function are closely interrelated in these systems. In this context, the article aims to contribute a parametric particle design model as an interface for this interrelation. A granular material is understood as an aggregation of large numbers of individual particles between which only short-range repulsive contact forces are acting. Granular materials are highly pertinent material systems for architecture. Due to the fact that they can act both as a solid and a liquid, they can be recycled and reconfigured multiple times and are thus highly sustainable. Designed granular materials have the added potential that the function of the granular material can be calibrated through the definition of the particles' form. Research on the design of granular materials in architecture is nascent. In physics they have been explored mainly with respect to different particle shapes. However, no coherent parametric particle design model of designed particle shapes for granular material systems in architecture has yet been established which considers both fabrication constraints and simulation requirements. The parametric particle design model proposed in this article has been based on a design system which has been developed through feasibility tests and simulations conducted in research and teaching. Based on this design system the parametric particle design model is developed integrating both fabrication constraints for architecture-scale particle systems and the geometric requirements of established simulation methods for granular materials. Initially the design system and related feasibility tests are presented. The parametric particle design model resulting from that is then described in detail. Directions of further research are discussed especially with respect to the integration of the parametric particle design model in 'inverse' design methods.
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Affiliation(s)
- Karola Dierichs
- Institute for Computational Design and Construction (ICD), University of Stuttgart, Stuttgart, Germany
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces (MPICI), Potsdam, Germany
- weißensee school of art and design berlin (khb), Berlin, Germany
- Cluster of Excellence Matters of Activity (MoA), Humboldt-Universität zu Berlin, Berlin, Germany
| | - Achim Menges
- Institute for Computational Design and Construction (ICD), University of Stuttgart, Stuttgart, Germany
- Cluster of Excellence Integrative Computational Design and Construction for Architecture (IntCDC), University of Stuttgart, Stuttgart, Germany
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19
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Fan Y, Wu KT, Aghvami SA, Fraden S, Breuer KS. Effects of confinement on the dynamics and correlation scales in kinesin-microtubule active fluids. Phys Rev E 2021; 104:034601. [PMID: 34654122 DOI: 10.1103/physreve.104.034601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/09/2021] [Indexed: 11/06/2022]
Abstract
We study the influence of solid boundaries on dynamics and structure of kinesin-driven microtubule active fluids as the height of the container, H, increases from hundreds of micrometers to several millimeters. By three-dimensional tracking of passive tracers dispersed in the active fluid, we observe that the activity level, characterized by velocity fluctuations, increases as system size increases and retains a small-scale isotropy. Concomitantly, as the confinement level decreases, the velocity-velocity temporal correlation develops a strong positive correlation at longer times, suggesting the establishment of a "memory". We estimate the characteristic size of the flow structures from the spatial correlation function and find that, as the confinement becomes weaker, the correlation length, l_{c}, saturates at approximately 400 microns. This saturation suggests an intrinsic length scale which, along with the small-scale isotropy, demonstrates the multiscale nature of this kinesin-driven bundled microtubule active system.
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Affiliation(s)
- Yi Fan
- Center for Fluid Mechanics, School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Kun-Ta Wu
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
| | - S Ali Aghvami
- School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Seth Fraden
- School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Kenneth S Breuer
- Center for Fluid Mechanics, School of Engineering, Brown University, Providence, Rhode Island 02912, USA
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20
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Mofatteh M, Echegaray-Iturra F, Alamban A, Dalla Ricca F, Bakshi A, Aydogan MG. Autonomous clocks that regulate organelle biogenesis, cytoskeletal organization, and intracellular dynamics. eLife 2021; 10:e72104. [PMID: 34586070 PMCID: PMC8480978 DOI: 10.7554/elife.72104] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/14/2021] [Indexed: 12/27/2022] Open
Abstract
How do cells perceive time? Do cells use temporal information to regulate the production/degradation of their enzymes, membranes, and organelles? Does controlling biological time influence cytoskeletal organization and cellular architecture in ways that confer evolutionary and physiological advantages? Potential answers to these fundamental questions of cell biology have historically revolved around the discussion of 'master' temporal programs, such as the principal cyclin-dependent kinase/cyclin cell division oscillator and the circadian clock. In this review, we provide an overview of the recent evidence supporting an emerging concept of 'autonomous clocks,' which under normal conditions can be entrained by the cell cycle and/or the circadian clock to run at their pace, but can also run independently to serve their functions if/when these major temporal programs are halted/abrupted. We begin the discussion by introducing recent developments in the study of such clocks and their roles at different scales and complexities. We then use current advances to elucidate the logic and molecular architecture of temporal networks that comprise autonomous clocks, providing important clues as to how these clocks may have evolved to run independently and, sometimes at the cost of redundancy, have strongly coupled to run under the full command of the cell cycle and/or the circadian clock. Next, we review a list of important recent findings that have shed new light onto potential hallmarks of autonomous clocks, suggestive of prospective theoretical and experimental approaches to further accelerate their discovery. Finally, we discuss their roles in health and disease, as well as possible therapeutic opportunities that targeting the autonomous clocks may offer.
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Affiliation(s)
- Mohammad Mofatteh
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Fabio Echegaray-Iturra
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Andrew Alamban
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Francesco Dalla Ricca
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Anand Bakshi
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Mustafa G Aydogan
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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21
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Paparini S, Virga EG. Shape bistability in 2D chromonic droplets. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:495101. [PMID: 34517353 DOI: 10.1088/1361-648x/ac2645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
An extensive experimental study of the shapes of two-dimensional bipolar droplets of the chromonic nematic phase of disodium cromoglycate (DSCG) sandwiched between glass plates, by Kimet alwas published in (2013J. Phys.: Condens. Matter25404202). The paper includes a mathematical model of this system. We have extended this study by further theoretical modelling. Our results are in good, quantitative agreement with the experimental data. The model has produced what promises to be a more accurate estimate for the isotropic surface tension at the nematic/isotropic solution interface-and predicts a regime of shape bistability (which has not yet been observed) for larger droplets, where tactoids (pointed, zeppelin-shaped droplets) and smooth-edged discoids can coexist in equilibrium. The general method presented in this paper is also applied to the tactoids formed by F-actin filaments in solution, for which an estimate is given for the value of the isotropic surface tension at the nematic/isotropic interface.
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Affiliation(s)
- Silvia Paparini
- Dipartimento di Matematica, Università di Pavia, Via Ferrata 5, 27100 Pavia, Italy
| | - Epifanio G Virga
- Dipartimento di Matematica, Università di Pavia, Via Ferrata 5, 27100 Pavia, Italy
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22
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Biswas A, Kim K, Cojoc G, Guck J, Reber S. The Xenopus spindle is as dense as the surrounding cytoplasm. Dev Cell 2021; 56:967-975.e5. [PMID: 33823135 DOI: 10.1016/j.devcel.2021.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/11/2021] [Accepted: 03/08/2021] [Indexed: 12/22/2022]
Abstract
The mitotic spindle is a self-organizing molecular machine, where hundreds of different molecules continuously interact to maintain a dynamic steady state. While our understanding of key molecular players in spindle assembly is significant, it is still largely unknown how the spindle's material properties emerge from molecular interactions. Here, we use correlative fluorescence imaging and label-free three-dimensional optical diffraction tomography (ODT) to measure the Xenopus spindle's mass density distribution. While the spindle has been commonly referred to as a denser phase of the cytoplasm, we find that it has the same density as its surrounding, which makes it neutrally buoyant. Molecular perturbations suggest that spindle mass density can be modulated by tuning microtubule nucleation and dynamics. Together, ODT provides direct, unbiased, and quantitative information of the spindle's emergent physical properties-essential to advance predictive frameworks of spindle assembly and function.
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Affiliation(s)
- Abin Biswas
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Max-Planck-Institute for the Science of Light, 91058 Erlangen, Germany
| | - Kyoohyun Kim
- Max-Planck-Institute for the Science of Light, 91058 Erlangen, Germany; BIOTEC, Technische Universität Dresden, 01307 Dresden, Germany
| | - Gheorghe Cojoc
- BIOTEC, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jochen Guck
- Max-Planck-Institute for the Science of Light, 91058 Erlangen, Germany; BIOTEC, Technische Universität Dresden, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
| | - Simone Reber
- IRI Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; University of Applied Sciences Berlin, 13353 Berlin, Germany.
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23
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Abstract
Cytoskeletal active nematics exhibit striking nonequilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which kinesin motors are linked by a double-stranded DNA linker. The efficiency by which DNA-based clusters power active nematics depends on both the stepping dynamics of the kinesin motors and the chemical structure of the polymeric linker. Fluorescence anisotropy measurements reveal that the motor clusters, like filamentous microtubules, exhibit local nematic order. The properties of the DNA linker enable the design of force-sensing clusters. When the load across the linker exceeds a critical threshold, the clusters fall apart, ceasing to generate active stresses and slowing the system dynamics. Fluorescence readout reveals the fraction of bound clusters that generate interfilament sliding. In turn, this yields the average load experienced by the kinesin motors as they step along the microtubules. DNA-motor clusters provide a foundation for understanding the molecular mechanism by which nanoscale molecular motors collectively generate mesoscopic active stresses, which in turn power macroscale nonequilibrium dynamics of active nematics.
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24
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Physical bioenergetics: Energy fluxes, budgets, and constraints in cells. Proc Natl Acad Sci U S A 2021; 118:2026786118. [PMID: 34140336 DOI: 10.1073/pnas.2026786118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What are the constraints and limits energy flows impose on cellular processes? Do cells operate near these limits, and if so how do energetic constraints impact cellular functions? Physics has provided many tools to study nonequilibrium systems and to define physical limits, but applying these tools to cell biology remains a challenge. Physical bioenergetics, which resides at the interface of nonequilibrium physics, energy metabolism, and cell biology, seeks to understand how much energy cells are using, how they partition this energy between different cellular processes, and the associated energetic constraints. Here we review recent advances and discuss open questions and challenges in physical bioenergetics.
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25
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Sahu S, Herbst L, Quinn R, Ross JL. Crowder and surface effects on self-organization of microtubules. Phys Rev E 2021; 103:062408. [PMID: 34271669 DOI: 10.1103/physreve.103.062408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 05/14/2021] [Indexed: 12/30/2022]
Abstract
Microtubules are an essential physical building block of cellular systems. They are organized using specific crosslinkers, motors, and influencers of nucleation and growth. With the addition of antiparallel crosslinkers, microtubule self-organization patterns go through a transition from fanlike structures to homogeneous tactoid condensates in vitro. Tactoids are reminiscent of biological mitotic spindles, the cell division machinery. To create these organizations, we previously used polymer crowding agents. Here we study how altering the properties of the crowders, such as type, size, and molecular weight, affects microtubule organization. Comparing simulations with experiments, we observe a scaling law associated with the fanlike patterns in the absence of crosslinkers. Tactoids formed in the presence of crosslinkers show variable length, depending on the crowders. We correlate the subtle differences to filament contour length changes, affected by nucleation and growth rate changes induced by the polymers in solution. Using quantitative image analysis, we deduce that the tactoids differ from traditional liquid crystal organization, as they are limited in width irrespective of crowders and surfaces, and behave as solidlike condensates.
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Affiliation(s)
- Sumon Sahu
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA
| | - Lena Herbst
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Ryan Quinn
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Jennifer L Ross
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA
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26
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Mechanical Mechanisms of Chromosome Segregation. Cells 2021; 10:cells10020465. [PMID: 33671543 PMCID: PMC7926803 DOI: 10.3390/cells10020465] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
Chromosome segregation—the partitioning of genetic material into two daughter cells—is one of the most crucial processes in cell division. In all Eukaryotes, chromosome segregation is driven by the spindle, a microtubule-based, self-organizing subcellular structure. Extensive research performed over the past 150 years has identified numerous commonalities and contrasts between spindles in different systems. In this review, we use simple coarse-grained models to organize and integrate previous studies of chromosome segregation. We discuss sites of force generation in spindles and fundamental mechanical principles that any understanding of chromosome segregation must be based upon. We argue that conserved sites of force generation may interact differently in different spindles, leading to distinct mechanical mechanisms of chromosome segregation. We suggest experiments to determine which mechanical mechanism is operative in a particular spindle under study. Finally, we propose that combining biophysical experiments, coarse-grained theories, and evolutionary genetics will be a productive approach to enhance our understanding of chromosome segregation in the future.
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27
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Wiegand T, Hyman AA. Drops and fibers - how biomolecular condensates and cytoskeletal filaments influence each other. Emerg Top Life Sci 2020; 4:247-261. [PMID: 33048111 PMCID: PMC7733666 DOI: 10.1042/etls20190174] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
The cellular cytoskeleton self-organizes by specific monomer-monomer interactions resulting in the polymerization of filaments. While we have long thought about the role of polymerization in cytoskeleton formation, we have only begun to consider the role of condensation in cytoskeletal organization. In this review, we highlight how the interplay between polymerization and condensation leads to the formation of the cytoskeleton.
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Affiliation(s)
- Tina Wiegand
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
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28
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Gagnon DA, Dessi C, Berezney JP, Boros R, Chen DTN, Dogic Z, Blair DL. Shear-Induced Gelation of Self-Yielding Active Networks. PHYSICAL REVIEW LETTERS 2020; 125:178003. [PMID: 33156652 DOI: 10.1103/physrevlett.125.178003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
An enticing feature of active materials is the possibility of controlling macroscale rheological properties through the activity of the microscopic constituents. Using a unique combination of microscopy and rheology we study three dimensional microtubule-based active materials whose autonomous flows are powered by a continually rearranging connected network. We quantify the relationship between the microscopic dynamics and the bulk mechanical properties of these nonequilibrium networks. Experiments reveal a surprising nonmonotonic viscosity that strongly depends on the relative magnitude of the rate of internally generated activity and the externally applied shear. A simple two-state mechanical model that accounts for both the solidlike and yielded fluidlike elements of the network accurately describes the rheological measurements.
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Affiliation(s)
- David A Gagnon
- Department of Physics and Institute for Soft Matter Synthesis & Metrology, Georgetown University, 3700 O Street NW, Washington, D.C. 20057, USA
| | - Claudia Dessi
- Department of Physics and Institute for Soft Matter Synthesis & Metrology, Georgetown University, 3700 O Street NW, Washington, D.C. 20057, USA
| | - John P Berezney
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Remi Boros
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Daniel T-N Chen
- Department of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Zvonimir Dogic
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Daniel L Blair
- Department of Physics and Institute for Soft Matter Synthesis & Metrology, Georgetown University, 3700 O Street NW, Washington, D.C. 20057, USA
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29
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Chen L, Lee CF, Toner J. Universality class for a nonequilibrium state of matter: A d=4-ε expansion study of Malthusian flocks. Phys Rev E 2020; 102:022610. [PMID: 32942483 DOI: 10.1103/physreve.102.022610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/17/2020] [Indexed: 02/02/2023]
Abstract
We show that "Malthusian flocks"-i.e., coherently moving collections of self-propelled entities (such as living creatures) which are being "born" and "dying" during their motion-belong to a new universality class in spatial dimensions d>2. We calculate the universal exponents and scaling laws of this new universality class to O(ε) in a d=4-ε expansion and find these are different from the "canonical" exponents previously conjectured to hold for "immortal" flocks (i.e., those without birth and death) and shown to hold for incompressible flocks with spatial dimensions in the range of 2<d≤4. We also obtain a universal amplitude ratio relating the damping of transverse and longitudinal velocity and density fluctuations in these systems. Furthermore, we find a universal separatrix in real space (r) between two regions in which the equal-time density correlation 〈δρ(r,t)δρ(0,t)〉 has opposite signs. Our expansion should be quite accurate in d=3, allowing precise quantitative comparisons between our theory, simulations, and experiments.
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Affiliation(s)
- Leiming Chen
- School of Materials Science and Physics, China University of Mining and Technology, Xuzhou Jiangsu 221116, People's Republic of China
| | - Chiu Fan Lee
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - John Toner
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, USA
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30
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Chen L, Lee CF, Toner J. Moving, Reproducing, and Dying Beyond Flatland: Malthusian Flocks in Dimensions d>2. PHYSICAL REVIEW LETTERS 2020; 125:098003. [PMID: 32915622 DOI: 10.1103/physrevlett.125.098003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
We show that "Malthusian flocks"-i.e., coherently moving collections of self-propelled entities (such as living creatures) which are being "born" and "dying" during their motion-belong to a new universality class in spatial dimensions d>2. We calculate the universal exponents and scaling laws of this new universality class to O(ε) in an ε=4-d expansion, and find these are different from the "canonical" exponents previously conjectured to hold for "immortal" flocks (i.e., those without birth and death) and shown to hold for incompressible flocks in d>2. Our expansion should be quite accurate in d=3, allowing precise quantitative comparisons between our theory, simulations, and experiments.
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Affiliation(s)
- Leiming Chen
- School of Materials Science and Physics, China University of Mining and Technology, Xuzhou, Jiangsu 221116, People's Republic of China
| | - Chiu Fan Lee
- Department of Bioengineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - John Toner
- Department of Physics and Institute for Fundamental Science, University of Oregon, Eugene, Oregon 97403, USA
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31
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Ong JY, Torres JZ. Phase Separation in Cell Division. Mol Cell 2020; 80:9-20. [PMID: 32860741 DOI: 10.1016/j.molcel.2020.08.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/10/2020] [Accepted: 08/07/2020] [Indexed: 02/08/2023]
Abstract
Cell division requires the assembly and organization of a microtubule spindle for the proper separation of chromosomes in mitosis and meiosis. Phase separation is an emerging paradigm for understanding spatial and temporal regulation of a variety of cellular processes, including cell division. Phase-separated condensates have been recently discovered at many structures during cell division as a possible mechanism for properly localizing, organizing, and activating proteins involved in cell division. Here, we review how these condensates play roles in regulating microtubule density and organization and spindle assembly and function and in activating some of the key players in cell division. We conclude with perspectives on areas of future research for this exciting and rapidly advancing field.
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Affiliation(s)
- Joseph Y Ong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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32
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Nazockdast E, Redemann S. Mechanics of the spindle apparatus. Semin Cell Dev Biol 2020; 107:91-102. [PMID: 32747191 DOI: 10.1016/j.semcdb.2020.06.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/02/2020] [Accepted: 06/30/2020] [Indexed: 12/01/2022]
Abstract
During mitosis microtubules self-organize to form a bipolar mitotic spindle structure, which positions the sister chromatids on the spindle mid-plane and separates them afterwards. Previous studies have identified many spindle associated proteins. Yet, we do not fully understand how these nanoscopic proteins lead to force generation through interactions of individual microtubules, motor proteins and chromosomes, and how a large number of these local interactions ultimately determine the structure and mechanics of the spindle in micron scale. Here we review the current understanding and open questions related to the structure and mechanics of the mitotic spindle. We then discuss how a combination of electron microscopy and computational modeling can be used to tackle some of these open questions.
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Affiliation(s)
- Ehssan Nazockdast
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3250, USA.
| | - Stefanie Redemann
- Center for Membrane and Cell Physiology & Department of Molecular Physiology and Biological Physics, University of Virginia, School of Medicine, Charlottesville, VA, USA.
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33
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Active forces shape the metaphase spindle through a mechanical instability. Proc Natl Acad Sci U S A 2020; 117:16154-16159. [PMID: 32601228 DOI: 10.1073/pnas.2002446117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The metaphase spindle is a dynamic structure orchestrating chromosome segregation during cell division. Recently, soft matter approaches have shown that the spindle behaves as an active liquid crystal. Still, it remains unclear how active force generation contributes to its characteristic spindle-like shape. Here we combine theory and experiments to show that molecular motor-driven forces shape the structure through a barreling-type instability. We test our physical model by titrating dynein activity in Xenopus egg extract spindles and quantifying the shape and microtubule orientation. We conclude that spindles are shaped by the interplay between surface tension, nematic elasticity, and motor-driven active forces. Our study reveals how motor proteins can mold liquid crystalline droplets and has implications for the design of active soft materials.
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34
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Scheff DR, Weirich KL, Dasbiswas K, Patel A, Vaikuntanathan S, Gardel ML. Tuning shape and internal structure of protein droplets via biopolymer filaments. SOFT MATTER 2020; 16:5659-5668. [PMID: 32519715 DOI: 10.1039/c9sm02462j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Macromolecules can phase separate to form liquid condensates, which are emerging as critical compartments in fields as diverse as intracellular organization and soft materials design. A myriad of macromolecules, including the protein FUS, form condensates which behave as isotropic liquids. Here, we investigate the influence of filament dopants on the material properties of protein liquids. We find that the short, biopolymer filaments of actin spontaneously partition into FUS droplets to form composite liquid droplets. As the concentration of the filament dopants increases, the coalescence time decreases, indicating that the dopants control viscosity relative to surface tension. The droplet shape is tunable and ranges from spherical to tactoid as the filament length or concentration is increased. We find that the tactoids are well described by a model of a quasi bipolar liquid crystal droplet, where nematic order from the anisotropic actin filaments competes with isotropic interfacial energy from the FUS, controlling droplet shape in a size-dependent manner. Our results demonstrate a versatile approach to construct tunable, anisotropic macromolecular liquids.
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Affiliation(s)
- Danielle R Scheff
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and Department of Physics, University of Chicago, Chicago, IL 60637, USA
| | - Kimberly L Weirich
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and HHMI HCIA Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Kinjal Dasbiswas
- Department of Physics, University of California, Merced, CA 95343, USA
| | - Avinash Patel
- HHMI HCIA Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA and Dewpoint Therapeutics GmbH, Pfotenhauer Strasse 108, Dresden 01307, USA
| | - Suriyanarayanan Vaikuntanathan
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Margaret L Gardel
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and Department of Physics, University of Chicago, Chicago, IL 60637, USA and HHMI HCIA Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
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35
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Geisterfer ZM, Zhu DY, Mitchison TJ, Oakey J, Gatlin JC. Microtubule Growth Rates Are Sensitive to Global and Local Changes in Microtubule Plus-End Density. Curr Biol 2020; 30:3016-3023.e3. [PMID: 32531285 DOI: 10.1016/j.cub.2020.05.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/14/2020] [Accepted: 05/18/2020] [Indexed: 01/02/2023]
Abstract
The microtubule cytoskeleton plays critically important roles in numerous cellular functions in eukaryotes, and it does so across a functionally diverse and morphologically disparate range of cell types [1]. In these roles, microtubule assemblies must adopt distinct morphologies and physical dimensions to perform specific functions [2-5]. As such, these macromolecular assemblies-as well as the dynamics of the individual microtubule polymers from which they are made-must scale and change in accordance with cell size, geometry, and function. Microtubules in cells typically assemble to a steady state in mass, leaving enough of their tubulin subunits soluble to allow rapid growth and turnover. This suggests some negative feedback that limits the extent of assembly, for example, decrease in growth rate, or increase in catastrophe rate, as the soluble subunit pool decreases. Although these ideas have informed the field for decades, they have not been observed experimentally. Here, we describe the application of an experimental approach that combines cell-free extracts with photo-patterned hydrogel micro-enclosures as a means to investigate microtubule dynamics in cytoplasmic volumes of defined size and shape. Our measurements reveal a negative correlation between microtubule plus-end density and microtubule growth rates and suggest that these rates are sensitive to the presence of nearby growing ends.
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Affiliation(s)
- Zachary M Geisterfer
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA.
| | - Daniel Y Zhu
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA
| | - Timothy J Mitchison
- Department of Systems Biology, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Marine Biological Laboratory, Cell Division and Organization Group, 7 MBL Street, Woods Hole, MA 02543, USA
| | - John Oakey
- Marine Biological Laboratory, Cell Division and Organization Group, 7 MBL Street, Woods Hole, MA 02543, USA; Department of Chemical Engineering, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA
| | - Jesse C Gatlin
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82070, USA; Marine Biological Laboratory, Cell Division and Organization Group, 7 MBL Street, Woods Hole, MA 02543, USA.
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36
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Suresh P, Long AF, Dumont S. Microneedle manipulation of the mammalian spindle reveals specialized, short-lived reinforcement near chromosomes. eLife 2020; 9:e53807. [PMID: 32191206 PMCID: PMC7117910 DOI: 10.7554/elife.53807] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/18/2020] [Indexed: 12/21/2022] Open
Abstract
The spindle generates force to segregate chromosomes at cell division. In mammalian cells, kinetochore-fibers connect chromosomes to the spindle. The dynamic spindle anchors kinetochore-fibers in space and time to move chromosomes. Yet, how it does so remains poorly understood as we lack tools to directly challenge this anchorage. Here, we adapt microneedle manipulation to exert local forces on the spindle with spatiotemporal control. Pulling on kinetochore-fibers reveals the preservation of local architecture in the spindle-center over seconds. Sister, but not neighbor, kinetochore-fibers remain tightly coupled, restricting chromosome stretching. Further, pulled kinetochore-fibers pivot around poles but not chromosomes, retaining their orientation within 3 μm of chromosomes. This local reinforcement has a 20 s lifetime, and requires the microtubule crosslinker PRC1. Together, these observations indicate short-lived, specialized reinforcement in the spindle center. This could help protect chromosome attachments from transient forces while allowing spindle remodeling, and chromosome movements, over longer timescales.
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Affiliation(s)
- Pooja Suresh
- Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Alexandra F Long
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Sophie Dumont
- Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Cell and Tissue Biology, University of California, San FranciscoSan FranciscoUnited States
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
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37
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Edelmaier C, Lamson AR, Gergely ZR, Ansari S, Blackwell R, McIntosh JR, Glaser MA, Betterton MD. Mechanisms of chromosome biorientation and bipolar spindle assembly analyzed by computational modeling. eLife 2020; 9:48787. [PMID: 32053104 PMCID: PMC7311174 DOI: 10.7554/elife.48787] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 02/12/2020] [Indexed: 01/19/2023] Open
Abstract
The essential functions required for mitotic spindle assembly and chromosome biorientation and segregation are not fully understood, despite extensive study. To illuminate the combinations of ingredients most important to align and segregate chromosomes and simultaneously assemble a bipolar spindle, we developed a computational model of fission-yeast mitosis. Robust chromosome biorientation requires progressive restriction of attachment geometry, destabilization of misaligned attachments, and attachment force dependence. Large spindle length fluctuations can occur when the kinetochore-microtubule attachment lifetime is long. The primary spindle force generators are kinesin-5 motors and crosslinkers in early mitosis, while interkinetochore stretch becomes important after biorientation. The same mechanisms that contribute to persistent biorientation lead to segregation of chromosomes to the poles after anaphase onset. This model therefore provides a framework to interrogate key requirements for robust chromosome biorientation, spindle length regulation, and force generation in the spindle. Before a cell divides, it must make a copy of its genetic material and then promptly split in two. This process, called mitosis, is coordinated by many different molecular machines. The DNA is copied, then the duplicated chromosomes line up at the middle of the cell. Next, an apparatus called the mitotic spindle latches onto the chromosomes before pulling them apart. The mitotic spindle is a bundle of long, thin filaments called microtubules. It attaches to chromosomes at the kinetochore, the point where two copied chromosomes are cinched together in their middle. Proper cell division is vital for the healthy growth of all organisms, big and small, and yet some parts of the process remain poorly understood despite extensive study. Specifically, there is more to learn about how the mitotic spindle self-assembles, and how microtubules and kinetochores work together to correctly orient and segregate chromosomes into two sister cells. These nanoscale processes are happening a hundred times a minute, so computer simulations are a good way to test what we know. Edelmaier et al. developed a computer model to simulate cell division in fission yeast, a species of yeast often used to study fundamental processes in the cell. The model simulates how the mitotic spindle assembles, how its microtubules attach to the kinetochore and the force required to pull two sister chromosomes apart. Building the simulation involved modelling interactions between the mitotic spindle and kinetochore, their movement and forces applied. To test its accuracy, model simulations were compared to recordings of the mitotic spindle – including its length, structure and position – imaged from dividing yeast cells. Running the simulation, Edelmaier et al. found that several key effects are essential for the proper movement of chromosomes in mitosis. This includes holding chromosomes in the correct orientation as the mitotic spindle assembles and controlling the relative position of microtubules as they attach to the kinetochore. Misaligned attachments must also be readily deconstructed and corrected to prevent any errors. The simulations also showed that kinetochores must begin to exert more force (to separate the chromosomes) once the mitotic spindle is attached correctly. Altogether, these findings improve the current understanding of how the mitotic spindle and its counterparts control cell division. Errors in chromosome segregation are associated with birth defects and cancer in humans, and this new simulation could potentially now be used to help make predictions about how to correct mistakes in the process.
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Affiliation(s)
| | - Adam R Lamson
- Department of Physics, University of Colorado Boulder, Boulder, United States
| | - Zachary R Gergely
- Department of Physics, University of Colorado Boulder, Boulder, United States.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Saad Ansari
- Department of Physics, University of Colorado Boulder, Boulder, United States
| | - Robert Blackwell
- Department of Physics, University of Colorado Boulder, Boulder, United States
| | - J Richard McIntosh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
| | - Matthew A Glaser
- Department of Physics, University of Colorado Boulder, Boulder, United States
| | - Meredith D Betterton
- Department of Physics, University of Colorado Boulder, Boulder, United States.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, United States
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38
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Numerical Parameter Space Compression and Its Application to Biophysical Models. Biophys J 2020; 118:1455-1465. [PMID: 32070477 DOI: 10.1016/j.bpj.2020.01.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/07/2019] [Accepted: 01/14/2020] [Indexed: 11/20/2022] Open
Abstract
Physical models of biological systems can become difficult to interpret when they have a large number of parameters. But the models themselves actually depend on (i.e., are sensitive to) only a subset of those parameters. This phenomenon is due to parameter space compression (PSC), in which a subset of parameters emerges as "stiff" as a function of time or space. PSC has only been used to explain analytically solvable physics models. We have generalized this result by developing a numerical approach to PSC that can be applied to any computational model. We validated our method against analytically solvable models of a random walk with drift and protein production and degradation. We then applied our method to a simple computational model of microtubule dynamic instability. We propose that numerical PSC has the potential to identify the low-dimensional structure of many computational models in biophysics. The low-dimensional structure of a model is easier to interpret and identifies the mechanisms and experiments that best characterize the system.
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39
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Gârlea IC, Dammone O, Alvarado J, Notenboom V, Jia Y, Koenderink GH, Aarts DGAL, Lettinga MP, Mulder BM. Colloidal Liquid Crystals Confined to Synthetic Tactoids. Sci Rep 2019; 9:20391. [PMID: 31892707 PMCID: PMC6938498 DOI: 10.1038/s41598-019-56729-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/22/2019] [Indexed: 11/24/2022] Open
Abstract
When a liquid crystal forming particles are confined to a spatial volume with dimensions comparable to that of their own size, they face a complex trade-off between their global tendency to align and the local constraints imposed by the boundary conditions. This interplay may lead to a non-trivial orientational patterns that strongly depend on the geometry of the confining volume. This novel regime of liquid crystalline behavior can be probed with colloidal particles that are macro-aggregates of biomolecules. Here we study director fields of filamentous fd-viruses in quasi-2D lens-shaped chambers that mimic the shape of tactoids, the nematic droplets that form during isotropic-nematic phase separation. By varying the size and aspect ratio of the chambers we force these particles into confinements that vary from circular to extremely spindle-like shapes and observe the director field using fluorescence microscopy. In the resulting phase diagram, next to configurations predicted earlier for 3D tactoids, we find a number of novel configurations. Using Monte Carlo Simulations, we show that these novel states are metastable, yet long-lived. Their multiplicity can be explained by the co-existence of multiple dynamic relaxation pathways leading to the final stable states.
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Affiliation(s)
- Ioana C Gârlea
- AMOLF, Department of Living Matter, Amsterdam, 1098XG, The Netherlands. .,University of Vienna, Faculty of Physics, Vienna, A-1090, Austria.
| | - Oliver Dammone
- University of Oxford, Department of Chemistry, Oxford, OX1 3QZ, UK
| | - José Alvarado
- AMOLF, Department of Living Matter, Amsterdam, 1098XG, The Netherlands
| | - Valerie Notenboom
- AMOLF, Department of Living Matter, Amsterdam, 1098XG, The Netherlands
| | - Yunfei Jia
- Forschungszentrum Jülich, Institute of Complex Systems (ICS-3), Jülich, 52425, Germany
| | - Gijsje H Koenderink
- AMOLF, Department of Living Matter, Amsterdam, 1098XG, The Netherlands.,Kavli Institute of Nanoscience, Delft University of Technology, Department of Bionanoscience, Delft, 2629HZ, The Netherlands
| | - Dirk G A L Aarts
- University of Oxford, Department of Chemistry, Oxford, OX1 3QZ, UK
| | - M Paul Lettinga
- Forschungszentrum Jülich, Institute of Complex Systems (ICS-3), Jülich, 52425, Germany. .,KU Leuven, Laboratory for Soft Matter and Biophysics, Leuven, B-300, Belgium.
| | - Bela M Mulder
- AMOLF, Department of Living Matter, Amsterdam, 1098XG, The Netherlands
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40
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Fürthauer S, Lemma B, Foster PJ, Ems-McClung SC, Yu CH, Walczak CE, Dogic Z, Needleman DJ, Shelley MJ. Self-straining of actively crosslinked microtubule networks. NATURE PHYSICS 2019; 15:1295-1300. [PMID: 32322291 PMCID: PMC7176317 DOI: 10.1038/s41567-019-0642-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 07/17/2019] [Indexed: 05/26/2023]
Abstract
Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks are active and densely crosslinked. Relating their large-scale dynamics to the properties of their constituents remains an unsolved problem. Here, we study an in vitro active gel made from aligned microtubules and XCTK2 kinesin motors. Using photobleaching, we demonstrate that the gel's aligned microtubules, driven by motors, continually slide past each other at a speed independent of the local microtubule polarity and motor concentration. This phenomenon is also observed, and remains unexplained, in spindles. We derive a general framework for coarse graining microtubule gels crosslinked by molecular motors from microscopic considerations. Using microtubule-microtubule coupling through a force-velocity relationship for kinesin, this theory naturally explains the experimental results: motors generate an active strain rate in regions of changing polarity, which allows microtubules of opposite polarities to slide past each other without stressing the material.
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Affiliation(s)
| | - Bezia Lemma
- Department of Physics, Harvard University, Cambridge, MA, USA
- Department of Physics, Brandeis University, Waltham, MA, USA
- Department of Physics, University of California, Santa Barbara, CA, USA
| | - Peter J Foster
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Che-Hang Yu
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA, USA
| | | | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, MA, USA
- Department of Physics, University of California, Santa Barbara, CA, USA
| | - Daniel J Needleman
- Paulson School of Engineering & Applied Science and Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Michael J Shelley
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Courant Institute, New York University, New York, NY, USA
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41
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Sone K, Ashida Y. Anomalous Topological Active Matter. PHYSICAL REVIEW LETTERS 2019; 123:205502. [PMID: 31809111 DOI: 10.1103/physrevlett.123.205502] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Active systems exhibit spontaneous flows induced by self-propulsion of microscopic constituents and can reach a nonequilibrium steady state without an external drive. Constructing the analogy between the quantum anomalous Hall insulators and active matter with spontaneous flows, we show that topologically protected sound modes can arise in a steady-state active system in continuum space. We point out that the net vorticity of the steady-state flow, which acts as a counterpart of the gauge field in condensed-matter settings, must vanish under realistic conditions for active systems. The quantum anomalous Hall effect thus provides design principles for realizing topological metamaterials. We propose and analyze the concrete minimal model and numerically calculate its band structure and eigenvectors, demonstrating the emergence of nonzero bulk topological invariants with the corresponding edge sound modes. This new type of topological active systems can potentially expand possibilities for their experimental realizations and may have broad applications to practical active metamaterials. Possible realization of non-Hermitian topological phenomena in active systems is also discussed.
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Affiliation(s)
- Kazuki Sone
- Department of Applied Physics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuto Ashida
- Department of Applied Physics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Physics, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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42
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Nazockdast E. Hydrodynamic interactions of filaments polymerizing against obstacles. Cytoskeleton (Hoboken) 2019; 76:586-599. [DOI: 10.1002/cm.21570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Ehssan Nazockdast
- Department of Applied Physical SciencesUniversity of North Carolina Chapel Hill North Carolina
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43
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Mura F, Gradziuk G, Broedersz CP. Mesoscopic non-equilibrium measures can reveal intrinsic features of the active driving. SOFT MATTER 2019; 15:8067-8076. [PMID: 31576897 DOI: 10.1039/c9sm01169b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biological assemblies such as chromosomes, membranes, and the cytoskeleton are driven out of equilibrium at the nanoscale by enzymatic activity and molecular motors. Similar non-equilibrium dynamics can be realized in synthetic systems, such as chemically fueled colloidal particles. Characterizing the stochastic non-equilibrium dynamics of such active soft assemblies still remains a challenge. Recently, new non-invasive approaches have been proposed to determine the non-equilibrium behavior, which are based on detecting broken detailed balance in the stochastic trajectories of several coordinates of the system. Inspired by the method of two-point microrheology, in which the equilibrium fluctuations of a pair of probe particles reveal the viscoelastic response of an equilibrium system, here, we investigate whether we can extend such an approach to non-equilibrium assemblies: can one extract information on the nature of the active driving in a system from the analysis of a two-point non-equilibrium measure? We address this question theoretically in the context of a class of elastic systems, driven out of equilibrium by a spatially heterogeneous stochastic internal driving. We consider several scenarios for the spatial features of the internal driving that may be relevant in biological and synthetic systems, and investigate how such features of the active noise may be reflected in the long-range scaling behavior of two-point non-equilibrium measures.
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Affiliation(s)
- Federica Mura
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany.
| | - Grzegorz Gradziuk
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany.
| | - Chase P Broedersz
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany.
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44
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Redemann S, Fürthauer S, Shelley M, Müller-Reichert T. Current approaches for the analysis of spindle organization. Curr Opin Struct Biol 2019; 58:269-277. [DOI: 10.1016/j.sbi.2019.05.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 01/06/2023]
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45
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Krmpot AJ, Nikolić SN, Oasa S, Papadopoulos DK, Vitali M, Oura M, Mikuni S, Thyberg P, Tisa S, Kinjo M, Nilsson L, Terenius L, Rigler R, Vukojević V. Functional Fluorescence Microscopy Imaging: Quantitative Scanning-Free Confocal Fluorescence Microscopy for the Characterization of Fast Dynamic Processes in Live Cells. Anal Chem 2019; 91:11129-11137. [PMID: 31364842 DOI: 10.1021/acs.analchem.9b01813] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Functional fluorescence microscopy imaging (fFMI), a time-resolved (21 μs/frame) confocal fluorescence microscopy imaging technique without scanning, is developed for quantitative characterization of fast reaction-transport processes in solution and in live cells. The method is based on massively parallel fluorescence correlation spectroscopy (FCS). Simultaneous excitation of fluorescent molecules in multiple spots in the focal plane is achieved using a diffractive optical element (DOE). Fluorescence from the DOE-generated 1024 illuminated spots is detected in a confocal arrangement by a matching matrix detector comprising 32 × 32 single-photon avalanche photodiodes (SPADs). Software for data acquisition and fast auto- and cross-correlation analysis by parallel signal processing using a graphic processing unit (GPU) allows temporal autocorrelation across all pixels in the image frame in 4 s and cross-correlation between first- and second-order neighbor pixels in 45 s. We present here this quantitative, time-resolved imaging method with single-molecule sensitivity and demonstrate its usefulness for mapping in live cell location-specific differences in the concentration and translational diffusion of molecules in different subcellular compartments. In particular, we show that molecules without a specific biological function, e.g., the enhanced green fluorescent protein (eGFP), exhibit uniform diffusion. In contrast, molecules that perform specialized biological functions and bind specifically to their molecular targets show location-specific differences in their concentration and diffusion, exemplified here for two transcription factor molecules, the glucocorticoid receptor (GR) before and after nuclear translocation and the Sex combs reduced (Scr) transcription factor in the salivary gland of Drosophila ex vivo.
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Affiliation(s)
- Aleksandar J Krmpot
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden.,Institute of Physics Belgrade , University of Belgrade , Belgrade 11080 , Serbia
| | - Stanko N Nikolić
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden.,Institute of Physics Belgrade , University of Belgrade , Belgrade 11080 , Serbia
| | - Sho Oasa
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden
| | | | | | - Makoto Oura
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science , Hokkaido University , Sapporo , Hokkaido 001-0021 , Japan
| | - Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science , Hokkaido University , Sapporo , Hokkaido 001-0021 , Japan
| | - Per Thyberg
- Department of Applied Physics , AlbaNova University Center, Royal Institute of Technology , Stockholm 10691 , Sweden
| | - Simone Tisa
- Micro Photon Devices (MPD) , Bolzano 39100 , Italy
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science , Hokkaido University , Sapporo , Hokkaido 001-0021 , Japan
| | - Lennart Nilsson
- Department of Biosciences and Nutrition , Karolinska Institutet , Huddinge 14183 , Sweden
| | - Lars Terenius
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden
| | - Rudolf Rigler
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden.,Department of Medical Biochemistry and Biophysics (MBB) , Karolinska Institutet , Stockholm 17177 , Sweden
| | - Vladana Vukojević
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM) , Karolinska Institutet , Stockholm 17176 , Sweden
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46
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Maryshev I, Goryachev AB, Marenduzzo D, Morozov A. Dry active turbulence in a model for microtubule-motor mixtures. SOFT MATTER 2019; 15:6038-6043. [PMID: 31298679 DOI: 10.1039/c9sm00558g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We study the dynamics and phase behaviour of a dry suspension of microtubules and molecular motors. We obtain a set of continuum equations by rigorously coarse graining a microscopic model where motor-induced interactions lead to parallel or antiparallel ordering. Through numerical simulations, we show that this model generically creates either stable stripes, or a never-settling pattern where stripes periodically form, rotate and then split up. We derive a minimal model which displays the same instability as the full model, and clarifies the underlying physical mechanism. The necessary ingredients are an extensile flux arising from microtubule sliding and an interfacial torque favouring ordering along density gradients. We argue that our minimal model unifies various previous observations of chaotic behaviour in dry active matter into a general universality class.
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Affiliation(s)
- Ivan Maryshev
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Andrew B Goryachev
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK.
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Alexander Morozov
- SUPA, School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
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47
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Ramananarivo S, Ducrot E, Palacci J. Activity-controlled annealing of colloidal monolayers. Nat Commun 2019; 10:3380. [PMID: 31358762 PMCID: PMC6662715 DOI: 10.1038/s41467-019-11362-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/04/2019] [Indexed: 11/26/2022] Open
Abstract
Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium.
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Affiliation(s)
- Sophie Ramananarivo
- Department of Physics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0319, USA
- Ladhyx, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau Cedex, France
| | - Etienne Ducrot
- Center for Soft Matter Research, Department of Physics, New York University, 726 Broadway, New York, NY, 10003, USA
| | - Jeremie Palacci
- Department of Physics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0319, USA.
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48
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Prelogović M, Winters L, Milas A, Tolić IM, Pavin N. Pivot-and-bond model explains microtubule bundle formation. Phys Rev E 2019; 100:012403. [PMID: 31499770 DOI: 10.1103/physreve.100.012403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 06/10/2023]
Abstract
During mitosis, microtubules form a spindle, which is responsible for proper segregation of the genetic material. A common structural element in a mitotic spindle is a parallel bundle, consisting of two or more microtubules growing from the same origin and held together by cross-linking proteins. An interesting question is what are the physical principles underlying the formation and stability of such microtubule bundles. Here we show, by introducing the pivot-and-bond model, that random angular movement of microtubules around the spindle pole and forces exerted by cross-linking proteins can explain the formation of microtubule bundles as observed in our experiments. The model predicts that stable parallel bundles can form in the presence of either passive crosslinkers or plus-end directed motors, but not minus-end directed motors. In the cases where bundles form, the time needed for their formation depends mainly on the concentration of cross-linking proteins and the angular diffusion of the microtubule. In conclusion, the angular motion drives the alignment of microtubules, which in turn allows the cross-linking proteins to connect the microtubules into a stable bundle.
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Affiliation(s)
- Marcel Prelogović
- Department of Physics, Faculty of Science, University of Zagreb, Bijenička cesta 32, 10000 Zagreb, Croatia
| | - Lora Winters
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Ana Milas
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Iva M Tolić
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Nenad Pavin
- Department of Physics, Faculty of Science, University of Zagreb, Bijenička cesta 32, 10000 Zagreb, Croatia
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49
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Andorfer R, Alper JD. From isolated structures to continuous networks: A categorization of cytoskeleton-based motile engineered biological microstructures. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1553. [PMID: 30740918 PMCID: PMC6881777 DOI: 10.1002/wnan.1553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 11/06/2022]
Abstract
As technology at the small scale is advancing, motile engineered microstructures are becoming useful in drug delivery, biomedicine, and lab-on-a-chip devices. However, traditional engineering methods and materials can be inefficient or functionally inadequate for small-scale applications. Increasingly, researchers are turning to the biology of the cytoskeleton, including microtubules, actin filaments, kinesins, dyneins, myosins, and associated proteins, for both inspiration and solutions. They are engineering structures with components that range from being entirely biological to being entirely synthetic mimics of biology and on scales that range from isotropic continuous networks to single isolated structures. Motile biological microstructures trace their origins from the development of assays used to study the cytoskeleton to the array of structures currently available today. We define 12 types of motile biological microstructures, based on four categories: entirely biological, modular, hybrid, and synthetic, and three scales: networks, clusters, and isolated structures. We highlight some key examples, the unique functionalities, and the potential applications of each microstructure type, and we summarize the quantitative models that enable engineering them. By categorizing the diversity of motile biological microstructures in this way, we aim to establish a framework to classify these structures, define the gaps in current research, and spur ideas to fill those gaps. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Nanotechnology Approaches to Biology > Cells at the Nanoscale Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Rachel Andorfer
- Department of Bioengineering, Clemson University, Clemson, South Carolina
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
| | - Joshua D. Alper
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina
- Department of Biological Sciences, Clemson University, Clemson, South Carolina
- Eukaryotic Pathogen Innovations Center, Clemson University, Clemson, South Carolina
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50
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Pamula MC, Carlini L, Forth S, Verma P, Suresh S, Legant WR, Khodjakov A, Betzig E, Kapoor TM. High-resolution imaging reveals how the spindle midzone impacts chromosome movement. J Cell Biol 2019; 218:2529-2544. [PMID: 31248912 PMCID: PMC6683753 DOI: 10.1083/jcb.201904169] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/21/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022] Open
Abstract
Microtubule bundles in the spindle midzone have been reported to either promote or hinder chromosome movement. Pamula et al. examine the assembly dynamics of midzone microtubule bundles during anaphase and how chromosome segregation is impacted by aberrant bundle assembly. In the spindle midzone, microtubules from opposite half-spindles form bundles between segregating chromosomes. Microtubule bundles can either push or restrict chromosome movement during anaphase in different cellular contexts, but how these activities are achieved remains poorly understood. Here, we use high-resolution live-cell imaging to analyze individual microtubule bundles, growing filaments, and chromosome movement in dividing human cells. Within bundles, filament overlap length marked by the cross-linking protein PRC1 decreases during anaphase as chromosome segregation slows. Filament ends within microtubule bundles appear capped despite dynamic PRC1 turnover and submicrometer proximity to growing microtubules. Chromosome segregation distance and rate are increased in two human cell lines when microtubule bundle assembly is prevented via PRC1 knockdown. Upon expressing a mutant PRC1 with reduced microtubule affinity, bundles assemble but chromosome hypersegregation is still observed. We propose that microtubule overlap length reduction, typically linked to pushing forces generated within filament bundles, is needed to properly restrict spindle elongation and position chromosomes within daughter cells.
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Affiliation(s)
- Melissa C Pamula
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
| | - Lina Carlini
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
| | - Scott Forth
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY
| | - Priyanka Verma
- Department of Cancer Biology, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Subbulakshmi Suresh
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
| | - Wesley R Legant
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC.,Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, and North Carolina State University, Raleigh, NC
| | - Alexey Khodjakov
- Wadsworth Center, New York State Department of Health, Albany, NY
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA.,Department of Physics and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
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