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Andreu-Carbó M, Egoldt C, Velluz MC, Aumeier C. Microtubule damage shapes the acetylation gradient. Nat Commun 2024; 15:2029. [PMID: 38448418 PMCID: PMC10918088 DOI: 10.1038/s41467-024-46379-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
The properties of single microtubules within the microtubule network can be modulated through post-translational modifications (PTMs), including acetylation within the lumen of microtubules. To access the lumen, the enzymes could enter through the microtubule ends and at damage sites along the microtubule shaft. Here we show that the acetylation profile depends on damage sites, which can be caused by the motor protein kinesin-1. Indeed, the entry of the deacetylase HDAC6 into the microtubule lumen can be modulated by kinesin-1-induced damage sites. In contrast, activity of the microtubule acetylase αTAT1 is independent of kinesin-1-caused shaft damage. On a cellular level, our results show that microtubule acetylation distributes in an exponential gradient. This gradient results from tight regulation of microtubule (de)acetylation and scales with the size of the cells. The control of shaft damage represents a mechanism to regulate PTMs inside the microtubule by giving access to the lumen.
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Affiliation(s)
| | - Cornelia Egoldt
- Department of Biochemistry, University of Geneva, 1211, Geneva, Switzerland
| | | | - Charlotte Aumeier
- Department of Biochemistry, University of Geneva, 1211, Geneva, Switzerland.
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2
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Miesch J, Wimbish RT, Velluz MC, Aumeier C. Phase separation of +TIP networks regulates microtubule dynamics. Proc Natl Acad Sci U S A 2023; 120:e2301457120. [PMID: 37603768 PMCID: PMC10469336 DOI: 10.1073/pnas.2301457120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/12/2023] [Indexed: 08/23/2023] Open
Abstract
Regulation of microtubule dynamics is essential for diverse cellular functions, and proteins that bind to dynamic microtubule ends can regulate network dynamics. Here, we show that two conserved microtubule end-binding proteins, CLIP-170 and EB3, undergo phase separation and form dense liquid networks. When CLIP-170 and EB3 act together, the multivalency of the network increases, which synergistically increases the amount of protein in the dense phase. In vitro and in cells, these liquid networks can concentrate tubulin. In vitro, in the presence of microtubules, phase separation of EB3/CLIP-170 can enrich tubulin all along the microtubule. In this condition, microtubule growth speed increases up to twofold and the frequency of depolymerization events are strongly reduced compared to conditions in which there is no phase separation. Our data show that phase separation of EB3/CLIP-170 adds an additional layer of regulation to the control of microtubule growth dynamics.
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Affiliation(s)
- Julie Miesch
- Department of Biochemistry, University of Geneva, Geneva1211, Switzerland
| | - Robert T. Wimbish
- Department of Biochemistry, University of Geneva, Geneva1211, Switzerland
| | | | - Charlotte Aumeier
- Department of Biochemistry, University of Geneva, Geneva1211, Switzerland
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3
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Ebberink E, Fernandes S, Hatzopoulos G, Agashe N, Chang PH, Guidotti N, Reichart TM, Reymond L, Velluz MC, Schneider F, Pourroy C, Janke C, Gönczy P, Fierz B, Aumeier C. Tubulin engineering by semi-synthesis reveals that polyglutamylation directs detyrosination. Nat Chem 2023:10.1038/s41557-023-01228-8. [PMID: 37386282 DOI: 10.1038/s41557-023-01228-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 04/28/2023] [Indexed: 07/01/2023]
Abstract
Microtubules, a critical component of the cytoskeleton, carry post-translational modifications (PTMs) that are important for the regulation of key cellular processes. Long-lived microtubules, in neurons particularly, exhibit both detyrosination of α-tubulin and polyglutamylation. Dysregulation of these PTMs can result in developmental defects and neurodegeneration. Owing to a lack of tools to study the regulation and function of these PTMs, the mechanisms that govern such PTM patterns are not well understood. Here we produce fully functional tubulin carrying precisely defined PTMs within its C-terminal tail. We ligate synthetic α-tubulin tails-which are site-specifically glutamylated-to recombinant human tubulin heterodimers by applying a sortase- and intein-mediated tandem transamidation strategy. Using microtubules reconstituted with these designer tubulins, we find that α-tubulin polyglutamylation promotes its detyrosination by enhancing the activity of the tubulin tyrosine carboxypeptidase vasohibin/small vasohibin-binding protein in a manner dependent on the length of polyglutamyl chains. We also find that modulating polyglutamylation levels in cells results in corresponding changes in detyrosination, corroborating the link between the detyrosination cycle to polyglutamylation.
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Affiliation(s)
- Eduard Ebberink
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Simon Fernandes
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Georgios Hatzopoulos
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Ninad Agashe
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Po-Han Chang
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Nora Guidotti
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Timothy M Reichart
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Luc Reymond
- Biomolecular Screening Facility, EPFL, Lausanne, Switzerland
| | | | - Fabian Schneider
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Cédric Pourroy
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland
| | - Carsten Janke
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France
- Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LCBM, Lausanne, Switzerland.
| | - Charlotte Aumeier
- Department of Biochemistry, University of Geneva, Geneva, Switzerland.
- National Center for Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.
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4
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Schaer J, Andreu-Carbó M, Kruse K, Aumeier C. The effect of motor-induced shaft dynamics on microtubule stability and length. Biophys J 2023; 122:346-359. [PMID: 36502273 PMCID: PMC9892620 DOI: 10.1016/j.bpj.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/17/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Control of microtubule abundance, stability, and length is crucial to regulate intracellular transport as well as cell polarity and division. How microtubule stability depends on tubulin addition or removal at the dynamic ends is well studied. However, microtubule rescue, the event when a microtubule switches from shrinking to growing, occurs at tubulin exchange sites along the shaft. Molecular motors have recently been shown to promote such exchanges. Using a stochastic theoretical description, we study how microtubule stability and length depend on motor-induced tubulin exchange and thus rescue. Our theoretical description matches our in vitro experiments on microtubule dynamics in the presence of kinesin-1 molecular motors. Although the overall dynamics of a population of microtubules can be captured by an effective rescue rate, by assigning rescue to exchange sites, we reveal that the dynamics of individual microtubules within the population differ dramatically. Furthermore, we study in detail a transition from bounded to unbounded microtubule growth. Our results provide novel insights into how molecular motors imprint information of microtubule stability on the microtubule network.
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Affiliation(s)
- Joël Schaer
- Department of Biochemistry, University of Geneva, Geneva, Switzerland; Department of Theoretical Physics, University of Geneva, Geneva, Switzerland
| | | | - Karsten Kruse
- Department of Biochemistry, University of Geneva, Geneva, Switzerland; Department of Theoretical Physics, University of Geneva, Geneva, Switzerland; National Center for Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.
| | - Charlotte Aumeier
- Department of Biochemistry, University of Geneva, Geneva, Switzerland; National Center for Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.
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5
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Andreu-Carbó M, Fernandes S, Aumeier C. Two-color in vitro assay to visualize and quantify microtubule shaft dynamics. STAR Protoc 2022; 3:101320. [PMID: 35496777 PMCID: PMC9043774 DOI: 10.1016/j.xpro.2022.101320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Microtubules are dynamic polymers where tubulin exchanges not only at the ends but also all along the microtubule shaft. In vitro reconstitutions are a vital approach to study microtubule tip dynamics, while direct observation of shaft dynamics is challenging. Here, we describe a dual-color in vitro assay to visualize microtubule shaft dynamics using purified, labeled bovine brain tubulin. With this assay, we can quantitatively address how proteins or small molecules impact the dynamics at the microtubule shaft. For complete details on the use and execution of this protocol, please refer to Andreu-Carbó et al. (2022).
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Affiliation(s)
| | - Simon Fernandes
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Charlotte Aumeier
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
- National Center for Competence in Research Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
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6
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Triclin S, Inoue D, Gaillard J, Htet ZM, DeSantis ME, Portran D, Derivery E, Aumeier C, Schaedel L, John K, Leterrier C, Reck-Peterson SL, Blanchoin L, Théry M. Self-repair protects microtubules from destruction by molecular motors. Nat Mater 2021; 20:883-891. [PMID: 33479528 PMCID: PMC7611741 DOI: 10.1038/s41563-020-00905-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 12/09/2020] [Indexed: 05/30/2023]
Abstract
Microtubule instability stems from the low energy of tubulin dimer interactions, which sets the growing polymer close to its disassembly conditions. Molecular motors use ATP hydrolysis to produce mechanical work and move on microtubules. This raises the possibility that the mechanical work produced by walking motors can break dimer interactions and trigger microtubule disassembly. We tested this hypothesis by studying the interplay between microtubules and moving molecular motors in vitro. Our results show that molecular motors can remove tubulin dimers from the lattice and rapidly destroy microtubules. We also found that dimer removal by motors was compensated for by the insertion of free tubulin dimers into the microtubule lattice. This self-repair mechanism allows microtubules to survive the damage induced by molecular motors as they move along their tracks. Our study reveals the existence of coupling between the motion of molecular motors and the renewal of the microtubule lattice.
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Affiliation(s)
- Sarah Triclin
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Daisuke Inoue
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
- Department of Human Science, Faculty of Design, Kyushu University, Fukuoka, Japan
| | - Jérémie Gaillard
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Zaw Min Htet
- Deptartment of Cellular and Molecular Medicine, and Cell and Developmental Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Morgan E DeSantis
- Deptartment of Cellular and Molecular Medicine, and Cell and Developmental Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Didier Portran
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | - Emmanuel Derivery
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Charlotte Aumeier
- Department of Biochemistry, University of Geneva, Genève, Switzerland
| | - Laura Schaedel
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Karin John
- Laboratoire Interdisciplinaire de Physique, University of Grenoble-Alpes, CNRS, Grenoble, France
| | | | - Samara L Reck-Peterson
- Deptartment of Cellular and Molecular Medicine, and Cell and Developmental Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Laurent Blanchoin
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France.
- Institut de Recherche Saint Louis, U976 Human Immunology Pathophysiology Immunotherapy (HIPI), CytoMorpho Lab, University of Paris, INSERM, CEA, Paris, France.
| | - Manuel Théry
- Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, University of Grenoble-Alpes, CEA, CNRS, INRA, Grenoble, France.
- Institut de Recherche Saint Louis, U976 Human Immunology Pathophysiology Immunotherapy (HIPI), CytoMorpho Lab, University of Paris, INSERM, CEA, Paris, France.
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7
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Angerani S, Lindberg E, Klena N, Bleck CKE, Aumeier C, Winssinger N. Kinesin-1 activity recorded in living cells with a precipitating dye. Nat Commun 2021; 12:1463. [PMID: 33674590 PMCID: PMC7935933 DOI: 10.1038/s41467-021-21626-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/03/2021] [Indexed: 01/15/2023] Open
Abstract
Kinesin-1 is a processive motor protein that uses ATP-derived energy to transport a variety of intracellular cargoes toward the cell periphery. The ability to visualize and monitor kinesin transport in live cells is critical to study the myriad of functions associated with cargo trafficking. Herein we report the discovery of a fluorogenic small molecule substrate (QPD-OTf) for kinesin-1 that yields a precipitating dye along its walking path on microtubules (MTs). QPD-OTf enables to monitor native kinesin-1 transport activity in cellulo without external modifications. In vitro assays show that kinesin-1 and MTs are sufficient to yield fluorescent crystals; in cells, kinesin-1 specific transport of cargo from the Golgi appears as trails of fluorescence over time. These findings are further supported by docking studies, which suggest the binding of the activity-based substrate in the nucleotide binding site of kinesin-1.
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Affiliation(s)
- Simona Angerani
- School of Chemistry and Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Eric Lindberg
- School of Chemistry and Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Nikolai Klena
- Department of Cell Biology, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Christopher K E Bleck
- Electron Microscopy Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charlotte Aumeier
- School of Chemistry and Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.
| | - Nicolas Winssinger
- School of Chemistry and Biochemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.
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Schaedel L, Triclin S, Chrétien D, Abrieu A, Aumeier C, Gaillard J, Blanchoin L, Théry M, John K. Lattice defects induce microtubule self-renewal. Nat Phys 2019; 15:830-838. [PMID: 31867047 PMCID: PMC6924994 DOI: 10.1038/s41567-019-0542-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Microtubules are dynamic polymers, which grow and shrink by addition and removal of tubulin dimers at their extremities. Within the microtubule shaft, dimers adopt a densely packed and highly ordered crystal-like lattice structure, which is generally not considered to be dynamic. Here we report that thermal forces are sufficient to remodel the microtubule shaft, despite its apparent stability. Our combined experimental data and numerical simulations on lattice dynamics and structure suggest that dimers can spontaneously leave and be incorporated into the lattice at structural defects. We propose a model mechanism, where the lattice dynamics is initiated via a passive breathing mechanism at dislocations, which are frequent in rapidly growing microtubules. These results show that we may need to extend the concept of dissipative dynamics, previously established for microtubule extremities, to the entire shaft, instead of considering it as a passive material.
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Affiliation(s)
- Laura Schaedel
- Univ. Grenoble-Alpes, CEA, CNRS, INRA, Biosciences & Biotechnology Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
| | - Sarah Triclin
- Univ. Grenoble-Alpes, CEA, CNRS, INRA, Biosciences & Biotechnology Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
| | - Denis Chrétien
- Univ. Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes) - UMR 6290, F-35000 Rennes, France
| | - Ariane Abrieu
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | - Charlotte Aumeier
- Univ. Grenoble-Alpes, CEA, CNRS, INRA, Biosciences & Biotechnology Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
| | - Jérémie Gaillard
- Univ. Grenoble-Alpes, CEA, CNRS, INRA, Biosciences & Biotechnology Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
| | - Laurent Blanchoin
- Univ. Grenoble-Alpes, CEA, CNRS, INRA, Biosciences & Biotechnology Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
- Univ. Paris Diderot, INSERM, CEA, Hôpital Saint Louis, Institut Universitaire d’Hematologie, UMRS1160, CytoMorpho Lab, 75010 Paris, France
- Address correspondence to: , ,
| | - Manuel Théry
- Univ. Grenoble-Alpes, CEA, CNRS, INRA, Biosciences & Biotechnology Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
- Univ. Paris Diderot, INSERM, CEA, Hôpital Saint Louis, Institut Universitaire d’Hematologie, UMRS1160, CytoMorpho Lab, 75010 Paris, France
- Address correspondence to: , ,
| | - Karin John
- Univ. Grenoble-Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, 38000 Grenoble, France
- Address correspondence to: , ,
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Aumeier C, Kasdorf B, Gruber M, Busse H, Wiese C, Zink W, Graf B, Zausig Y. Lipid emulsion pretreatment has different effects on mepivacaine and bupivacaine cardiac toxicity in an isolated rat heart model †. Br J Anaesth 2014; 112:735-41. [DOI: 10.1093/bja/aet353] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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