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Lee CT, Bell M, Bonilla-Quintana M, Rangamani P. Biophysical Modeling of Synaptic Plasticity. Annu Rev Biophys 2024; 53:397-426. [PMID: 38382115 DOI: 10.1146/annurev-biophys-072123-124954] [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: 02/23/2024]
Abstract
Dendritic spines are small, bulbous compartments that function as postsynaptic sites and undergo intense biochemical and biophysical activity. The role of the myriad signaling pathways that are implicated in synaptic plasticity is well studied. A recent abundance of quantitative experimental data has made the events associated with synaptic plasticity amenable to quantitative biophysical modeling. Spines are also fascinating biophysical computational units because spine geometry, signal transduction, and mechanics work in a complex feedback loop to tune synaptic plasticity. In this sense, ideas from modeling cell motility can inspire us to develop multiscale approaches for predictive modeling of synaptic plasticity. In this article, we review the key steps in postsynaptic plasticity with a specific focus on the impact of spine geometry on signaling, cytoskeleton rearrangement, and membrane mechanics. We summarize the main experimental observations and highlight how theory and computation can aid our understanding of these complex processes.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Miriam Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Mayte Bonilla-Quintana
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
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2
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Sharma A, Hill KE, Schwarzbauer JE. Extracellular matrix composition affects outgrowth of dendrites and dendritic spines on cortical neurons. Front Cell Neurosci 2023; 17:1177663. [PMID: 37388410 PMCID: PMC10300442 DOI: 10.3389/fncel.2023.1177663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/29/2023] [Indexed: 07/01/2023] Open
Abstract
The composition of the extracellular matrix (ECM) in nervous tissue plays an important role in controlling neuronal outgrowth and synapse development. Changes in both protein and glycosaminoglycan components of the ECM occur with tissue injury and may affect neuron growth. To investigate neuron responses to alterations in fibronectin (FN), a major component of the wound ECM, we grew cortical neurons on cell-derived decellularized matrices composed of wild type FN (FN+/+) or of a mutant form of FN (FNΔ/+) from which the III13 heparin-binding site had been deleted by CRISPR-Cas 9 gene editing. The most significant effect of the mutant FN was a reduction in dendrite outgrowth. Not only were dendrites shorter on mutant FNΔ/+-collagen (COL) matrix than on wild type (FN+/+-COL) matrix, but the number of dendrites and dendritic spines per neuron and the spine densities were also dramatically reduced on FNΔ/+-COL matrices. Mass spectrometry and immunostaining identified a reduction in tenascin-C (TN-C) levels in the mutant matrix. TN-C is an ECM protein that binds to the III13 site of FN and modulates cell-matrix interactions and has been linked to dendrite development. We propose that TN-C binding to FN in the wound matrix supports dendrite and spine development during repair of damaged neural tissue. Overall, these results show that changes in ECM composition can dramatically affect elaboration of neurites and support the idea that the ECM microenvironment controls neuron morphology and connectivity.
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Affiliation(s)
| | | | - Jean E. Schwarzbauer
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
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3
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Mercaldo V, Vidimova B, Gastaldo D, Fernández E, Lo AC, Cencelli G, Pedini G, De Rubeis S, Longo F, Klann E, Smit AB, Grant SGN, Achsel T, Bagni C. Altered striatal actin dynamics drives behavioral inflexibility in a mouse model of fragile X syndrome. Neuron 2023; 111:1760-1775.e8. [PMID: 36996810 DOI: 10.1016/j.neuron.2023.03.008] [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: 02/01/2022] [Revised: 12/21/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023]
Abstract
The proteome of glutamatergic synapses is diverse across the mammalian brain and involved in neurodevelopmental disorders (NDDs). Among those is fragile X syndrome (FXS), an NDD caused by the absence of the functional RNA-binding protein FMRP. Here, we demonstrate how the brain region-specific composition of postsynaptic density (PSD) contributes to FXS. In the striatum, the FXS mouse model shows an altered association of the PSD with the actin cytoskeleton, reflecting immature dendritic spine morphology and reduced synaptic actin dynamics. Enhancing actin turnover with constitutively active RAC1 ameliorates these deficits. At the behavioral level, the FXS model displays striatal-driven inflexibility, a typical feature of FXS individuals, which is rescued by exogenous RAC1. Striatal ablation of Fmr1 is sufficient to recapitulate behavioral impairments observed in the FXS model. These results indicate that dysregulation of synaptic actin dynamics in the striatum, a region largely unexplored in FXS, contributes to the manifestation of FXS behavioral phenotypes.
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Affiliation(s)
- Valentina Mercaldo
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Barbora Vidimova
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Denise Gastaldo
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Esperanza Fernández
- VIB & UGent Center for Medical Biotechnology, Universiteit Gent, 9052 Ghent, Belgium
| | - Adrian C Lo
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland
| | - Giulia Cencelli
- Department of Biomedicine and Prevention, Università degli Studi di Roma "Tor Vergata", 00133 Rome, Italy; Institute of Neurosurgery, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Giorgia Pedini
- Department of Biomedicine and Prevention, Università degli Studi di Roma "Tor Vergata", 00133 Rome, Italy
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesco Longo
- Center for Neural Science, New York University, New York, NY 10029, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY 10029, USA
| | - August B Smit
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Seth G N Grant
- Center for the Clinical Brain Sciences and Simons Initiatives for the Developing Brain, The University of Edinburgh, Edinburgh EH16 4SB, Scotland
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland.
| | - Claudia Bagni
- Department of Fundamental Neurosciences, Université de Lausanne, 1005 Lausanne, Switzerland; Department of Biomedicine and Prevention, Università degli Studi di Roma "Tor Vergata", 00133 Rome, Italy.
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4
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Rasia-Filho AA, Calcagnotto ME, von Bohlen Und Halbach O. Introduction: What Are Dendritic Spines? ADVANCES IN NEUROBIOLOGY 2023; 34:1-68. [PMID: 37962793 DOI: 10.1007/978-3-031-36159-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Dendritic spines are cellular specializations that greatly increase the connectivity of neurons and modulate the "weight" of most postsynaptic excitatory potentials. Spines are found in very diverse animal species providing neural networks with a high integrative and computational possibility and plasticity, enabling the perception of sensorial stimuli and the elaboration of a myriad of behavioral displays, including emotional processing, memory, and learning. Humans have trillions of spines in the cerebral cortex, and these spines in a continuum of shapes and sizes can integrate the features that differ our brain from other species. In this chapter, we describe (1) the discovery of these small neuronal protrusions and the search for the biological meaning of dendritic spines; (2) the heterogeneity of shapes and sizes of spines, whose structure and composition are associated with the fine-tuning of synaptic processing in each nervous area, as well as the findings that support the role of dendritic spines in increasing the wiring of neural circuits and their functions; and (3) within the intraspine microenvironment, the integration and activation of signaling biochemical pathways, the compartmentalization of molecules or their spreading outside the spine, and the biophysical properties that can affect parent dendrites. We also provide (4) examples of plasticity involving dendritic spines and neural circuits relevant to species survival and comment on (5) current research advancements and challenges in this exciting research field.
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Affiliation(s)
- Alberto A Rasia-Filho
- Department of Basic Sciences/Physiology and Graduate Program in Biosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
- Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Elisa Calcagnotto
- Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Department of Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Graduate Program in Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Graduate Program in Psychiatry and Behavioral Science, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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5
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Tran PD, Blanpied TA, Atzberger PJ. Protein drift-diffusion dynamics and phase separation in curved cell membranes and dendritic spines: Hybrid discrete-continuum methods. Phys Rev E 2022; 106:044402. [PMID: 36397472 DOI: 10.1103/physreve.106.044402] [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: 10/04/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine discrete particle descriptions with continuum-level models for tracking the individual protein drift-diffusion dynamics when coupled to continuum fields. We show how our approaches can be used to investigate phenomena motivated by protein kinetics within dendritic spines. The spine geometry is hypothesized to play an important biological role regulating synaptic strength, protein kinetics, and self-assembly of clusters. We perform simulation studies for model spine geometries varying the neck size to investigate how phase-separation and protein organization is influenced by different shapes. We also show how our methods can be used to study the roles of geometry in reaction-diffusion systems including Turing instabilities. Our methods provide general approaches for investigating protein kinetics and drift-diffusion dynamics within curved membrane structures.
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Affiliation(s)
- Patrick D Tran
- Physics, College of Creative Studies, University of California, Santa Barbara, Santa Barbara, California 93106-3080, USA
| | - Thomas A Blanpied
- Department of Physiology, University of Maryland, Baltimore, Maryland 21201, USA
| | - Paul J Atzberger
- Department of Mathematics and Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106-3080, USA
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6
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Bell MK, Holst MV, Lee CT, Rangamani P. Dendritic spine morphology regulates calcium-dependent synaptic weight change. J Gen Physiol 2022; 154:e202112980. [PMID: 35819365 PMCID: PMC9280073 DOI: 10.1085/jgp.202112980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 01/14/2023] Open
Abstract
Dendritic spines act as biochemical computational units and must adapt their responses according to their activation history. Calcium influx acts as the first signaling step during postsynaptic activation and is a determinant of synaptic weight change. Dendritic spines also come in a variety of sizes and shapes. To probe the relationship between calcium dynamics and spine morphology, we used a stochastic reaction-diffusion model of calcium dynamics in idealized and realistic geometries. We show that despite the stochastic nature of the various calcium channels, receptors, and pumps, spine size and shape can modulate calcium dynamics and subsequently synaptic weight updates in a deterministic manner. Through a series of exhaustive simulations and analyses, we found that the calcium dynamics and synaptic weight change depend on the volume-to-surface area of the spine. The relationships between calcium dynamics and spine morphology identified in idealized geometries also hold in realistic geometries, suggesting that there are geometrically determined deterministic relationships that may modulate synaptic weight change.
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Affiliation(s)
- Miriam K. Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
| | - Maven V. Holst
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
| | - Christopher T. Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA
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7
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Li JM, Yang FH, Chao MW, Tseng CY. Swimming exercise prevents hippocampal dendritic spine changes and memory loss caused by aging: An application of a new semi-automated spine analysis software. Mol Cell Neurosci 2022; 121:103755. [PMID: 35850447 DOI: 10.1016/j.mcn.2022.103755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 11/17/2022] Open
Abstract
Dendritic spines are small, ratchet-like protrusions on neuronal dendrites that form synapses for receiving neuronal messages. Dendritic spine morphology is associated with synapse function. If neurons degrade or are damaged, the spine morphology of neurons changes. Given that most commercially available spine analysis software is expensive and complex, this study investigated a semi-automated spine analysis software, CTSpine, and used previously published data to verify the accuracy of the analysis results of this software. We also applied CTSpine to understand whether aging causes alterations in the hippocampal spine morphology and whether physical exercise can impede dendritic spine changes in 20 male Sprague Dawley rats. The spines of pyramidal cells in the hippocampal Cornu Ammonis 1 (CA1) region in the aging group were more enriched in filopodium type pattern than those in the control group, whereas the spines of the exercised aging group showed a similar pattern to that of the control. No significant changes were observed in neuronal dendritic spines in other hippocampal regions. However, long-term hippocampal memory was considerably decreased in the aging group, which was reversed to some extent in the exercised aging group. CTSpine, a self-developed semi-automatic spine analysis software, showed results similar to those noted in published data and can be effectively applied to the study of dendritic patterns, including neurodevelopment and disease.
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Affiliation(s)
- Jun-Ming Li
- Psychiatry Department, Taoyuan Armed Forces General Hospital, No. 168, Zhongxing Rd., Longtan Dist, Taoyuan City 32551, Taiwan.
| | - Fu-Hua Yang
- Department of Biomedical Engineering, Chung Yuan Christian University, Zhongli District, Taoyuan 320, Taiwan.
| | - Ming-Wei Chao
- Department of Bioscience Technology, Chung Yuan Christian University, Zhongli District, Taoyuan 320, Taiwan.
| | - Chia-Yi Tseng
- Department of Biomedical Engineering, Chung Yuan Christian University, Zhongli District, Taoyuan 320, Taiwan.
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8
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Bonilla-Quintana M, Rangamani P. Can biophysical models of dendritic spines be used to explore synaptic changes associated with addiction? Phys Biol 2022; 19. [PMID: 35508164 DOI: 10.1088/1478-3975/ac6cbe] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/04/2022] [Indexed: 11/11/2022]
Abstract
Effective treatments that prevent or reduce drug relapse vulnerability should be developed to relieve the high burden of drug addiction on society. This will only be possible by enhancing the understanding of the molecular mechanisms underlying the neurobiology of addiction. Recent experimental data have shown that dendritic spines, small protrusions from the dendrites that receive excitatory input, of spiny neurons in the nucleus accumbens exhibit morphological changes during drug exposure and withdrawal. Moreover, these changes relate to the characteristic drug-seeking behavior of addiction. However, due to the complexity of the dendritic spines, we do not yet fully understand the processes underlying their structural changes in response to different inputs. We propose that biophysical models can enhance the current understanding of these processes by incorporating different, and sometimes, discrepant experimental data to identify the shared underlying mechanisms and generate experimentally testable hypotheses. This review aims to give an up-to-date report on biophysical models of dendritic spines, focusing on those models that describe their shape changes, which are well-known to relate to learning and memory. Moreover, it examines how these models can enhance our understanding of the effect of the drugs and the synaptic changes during withdrawal, as well as during neurodegenerative disease progression such as Alzheimer's disease.
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Affiliation(s)
- Mayte Bonilla-Quintana
- Mechanical Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0021, UNITED STATES
| | - Padmini Rangamani
- Mechanical Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0021, UNITED STATES
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9
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Kim SJ, Woo Y, Kim HJ, Goo BS, Nhung TTM, Lee SA, Suh BK, Mun DJ, Kim JH, Park SK. Retinoic acid-induced protein 14 controls dendritic spine dynamics associated with depressive-like behaviors. eLife 2022; 11:77755. [PMID: 35467532 PMCID: PMC9068211 DOI: 10.7554/elife.77755] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/24/2022] [Indexed: 11/24/2022] Open
Abstract
Dendritic spines are the central postsynaptic machinery that determines synaptic function. The F-actin within dendritic spines regulates their dynamic formation and elimination. Rai14 is an F-actin-regulating protein with a membrane-shaping function. Here, we identified the roles of Rai14 for the regulation of dendritic spine dynamics associated with stress-induced depressive-like behaviors. Rai14-deficient neurons exhibit reduced dendritic spine density in the Rai14+/- mouse brain, resulting in impaired functional synaptic activity. Rai14 was protected from degradation by complex formation with Tara, and accumulated in the dendritic spine neck, thereby enhancing spine maintenance. Concurrently, Rai14 deficiency in mice altered gene expression profile relevant to depressive conditions and increased depressive-like behaviors. Moreover, Rai14 expression was reduced in the prefrontal cortex of the mouse stress model, which was blocked by antidepressant treatment. Thus, we propose that Rai14-dependent regulation of dendritic spines may underlie the plastic changes of neuronal connections relevant to depressive-like behaviors.
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Affiliation(s)
- Soo Jeong Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Youngsik Woo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Hyun Jin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Bon Seong Goo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Truong Thi My Nhung
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seol-Ae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Bo Kyoung Suh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Dong Jin Mun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Joung-Hun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
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10
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Rasia-Filho AA. Unraveling Brain Microcircuits, Dendritic Spines, and Synaptic Processing Using Multiple Complementary Approaches. Front Physiol 2022; 13:831568. [PMID: 35295578 PMCID: PMC8918670 DOI: 10.3389/fphys.2022.831568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/26/2022] [Indexed: 12/21/2022] Open
Affiliation(s)
- Alberto A. Rasia-Filho
- Department of Basic Sciences/Physiology, Graduate Program in Biosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
- Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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11
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Park Y, Singh P, Fai TG. Coarse-grained Stochastic Model of Myosin-Driven Vesicles into Dendritic Spines. SIAM JOURNAL ON APPLIED MATHEMATICS 2022; 82:793-820. [PMID: 36314039 PMCID: PMC9603279 DOI: 10.1137/21m1434180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We study the dynamics of membrane vesicle motor transport into dendritic spines, which are bulbous intracellular compartments in neurons that play a key role in transmitting signals between neurons. We consider the stochastic analog of the vesicle transport model in [Park and Fai, The Dynamics of Vesicles Driven Into Closed Constrictions by Molecular Motors. Bull. Math. Biol. 82, 141 (2020)]. The stochastic version, which may be considered as an agent-based model, relies mostly on the action of individual myosin motors to produce vesicle motion. To aid in our analysis, we coarse-grain this agent-based model using a master equation combined with a partial differential equation describing the probability of local motor positions. We confirm through convergence studies that the coarse-graining captures the essential features of bistability in velocity (observed in experiments) and waiting-time distributions to switch between steady-state velocities. Interestingly, these results allow us to reformulate the translocation problem in terms of conditional mean first passage times for a run-and-tumble particle moving on a finite domain with absorbing boundaries at the two ends. We conclude by presenting numerical and analytical calculations of vesicle translocation.
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Affiliation(s)
- Youngmin Park
- Department of Mathematics, Brandeis University, Waltham, MA 02453, USA
- Corresponding author
| | - Prashant Singh
- International Centre for Theoretical Sciences, TIFR, Bengaluru 560089, India
| | - Thomas G. Fai
- Department of Mathematics, Brandeis University, Waltham, MA 02453, USA
- Volen Center for Complex Systems, Waltham, MA 02453, USA
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12
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Dutta P, Bharti P, Kumar J, Maiti S. Role of actin cytoskeleton in the organization and function of ionotropic glutamate receptors. Curr Res Struct Biol 2021; 3:277-289. [PMID: 34766008 PMCID: PMC8569634 DOI: 10.1016/j.crstbi.2021.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 09/04/2021] [Accepted: 10/09/2021] [Indexed: 12/22/2022] Open
Abstract
Neural networks with precise connection are compulsory for learning and memory. Various cellular events occur during the genesis of dendritic spines to their maturation, synapse formation, stabilization of the synapse, and proper signal transmission. The cortical actin cytoskeleton and its multiple regulatory proteins are crucial for the above cellular events. The different types of ionotropic glutamate receptors (iGluRs) present on the postsynaptic density (PSD) are also essential for learning and memory. Interaction of the iGluRs in association of their auxiliary proteins with actin cytoskeleton regulated by actin-binding proteins (ABPs) are required for precise long-term potentiation (LTP) and long-term depression (LTD). There has been a quest to understand the mechanistic detail of synapse function involving these receptors with dynamic actin cytoskeleton. A major, emerging area of investigation is the relationship between ABPs and iGluRs in synapse development. In this review we have summarized the current understanding of iGluRs functioning with respect to the actin cytoskeleton, scaffolding proteins, and their regulators. The AMPA, NMDA, Delta and Kainate receptors need the stable underlying actin cytoskeleton to anchor through synaptic proteins for precise synapse formation. The different types of ABPs present in neurons play a critical role in dynamizing/stabilizing the actin cytoskeleton needed for iGluRs function.
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Affiliation(s)
- Priyanka Dutta
- National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Pratibha Bharti
- National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Janesh Kumar
- National Centre for Cell Science, Pune, Maharashtra, 411007, India
| | - Sankar Maiti
- Indian Institute of Science Education and Research, Kolkata, 741246, India
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13
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Pulikkottil VV, Somashekar BP, Bhalla US. Computation, wiring, and plasticity in synaptic clusters. Curr Opin Neurobiol 2021; 70:101-112. [PMID: 34509808 DOI: 10.1016/j.conb.2021.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 07/28/2021] [Accepted: 08/09/2021] [Indexed: 01/19/2023]
Abstract
Synaptic clusters on dendrites are extraordinarily compact computational building blocks. They contribute to key local computations through biophysical and biochemical signaling that utilizes convergence in space and time as an organizing principle. However, these computations can only arise in very special contexts. Dendritic cluster computations, their highly organized input connectivity, and the mechanisms for their formation are closely linked, yet these have not been analyzed as parts of a single process. Here, we examine these linkages. The sheer density of axonal and dendritic arborizations means that there are far more potential connections (close enough for a spine to reach an axon) than actual ones. We see how dendritic clusters draw upon electrical, chemical, and mechano-chemical signaling to implement the rules for formation of connections and subsequent computations. Crucially, the same mechanisms that underlie their functions also underlie their formation.
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Affiliation(s)
| | - Bhanu Priya Somashekar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Upinder S Bhalla
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
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14
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Alimohamadi H, Bell MK, Halpain S, Rangamani P. Mechanical Principles Governing the Shapes of Dendritic Spines. Front Physiol 2021; 12:657074. [PMID: 34220531 PMCID: PMC8242199 DOI: 10.3389/fphys.2021.657074] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/13/2021] [Indexed: 02/04/2023] Open
Abstract
Dendritic spines are small, bulbous protrusions along the dendrites of neurons and are sites of excitatory postsynaptic activity. The morphology of spines has been implicated in their function in synaptic plasticity and their shapes have been well-characterized, but the potential mechanics underlying their shape development and maintenance have not yet been fully understood. In this work, we explore the mechanical principles that could underlie specific shapes using a minimal biophysical model of membrane-actin interactions. Using this model, we first identify the possible force regimes that give rise to the classic spine shapes-stubby, filopodia, thin, and mushroom-shaped spines. We also use this model to investigate how the spine neck might be stabilized using periodic rings of actin or associated proteins. Finally, we use this model to predict that the cooperation between force generation and ring structures can regulate the energy landscape of spine shapes across a wide range of tensions. Thus, our study provides insights into how mechanical aspects of actin-mediated force generation and tension can play critical roles in spine shape maintenance.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Miriam K. Bell
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Shelley Halpain
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, United States
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, United States
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15
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Jia Y, Zhao Q, Yin H, Guo S, Sun M, Yang Z, Zhao X. Reaction-Diffusion Model-Based Research on Formation Mechanism of Neuron Dendritic Spine Patterns. Front Neurorobot 2021; 15:563682. [PMID: 34194309 PMCID: PMC8236519 DOI: 10.3389/fnbot.2021.563682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
The pattern abnormalities of dendritic spine, tiny protrusions on neuron dendrites, have been found related to multiple nervous system diseases, such as Parkinson's disease and schizophrenia. The determination of the factors affecting spine patterns is of vital importance to explore the pathogenesis of these diseases, and further, search the treatment method for them. Although the study of dendritic spines is a hot topic in neuroscience in recent years, there is still a lack of systematic study on the formation mechanism of its pattern. This paper provided a reinterpretation of reaction-diffusion model to simulate the formation process of dendritic spine, and further, study the factors affecting spine patterns. First, all four classic shapes of spines, mushroom-type, stubby-type, thin-type, and branched-type were reproduced using the model. We found that the consumption rate of substrates by the cytoskeleton is a key factor to regulate spine shape. Moreover, we found that the density of spines can be regulated by the amount of an exogenous activator and inhibitor, which is in accordance with the anatomical results found in hippocampal CA1 in SD rats with glioma. Further, we analyzed the inner mechanism of the above model parameters regulating the dendritic spine pattern through Turing instability analysis and drew a conclusion that an exogenous inhibitor and activator changes Turing wavelength through which to regulate spine densities. Finally, we discussed the deep regulation mechanisms of several reported regulators of dendritic spine shape and densities based on our simulation results. Our work might evoke attention to the mathematic model-based pathogenesis research for neuron diseases which are related to the dendritic spine pattern abnormalities and spark inspiration in the treatment research for these diseases.
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Affiliation(s)
- Yiqing Jia
- Institute of Robotics and Automatic Information Systems, College of Artificial Intelligence, Nankai University, Tianjin, China
| | - Qili Zhao
- Institute of Robotics and Automatic Information Systems, College of Artificial Intelligence, Nankai University, Tianjin, China
| | - Hongqiang Yin
- State Key Laboratory of Medicinal Chemical Biology, School of Medicine, Nankai University, Tianjin, China
| | - Shan Guo
- Institute of Robotics and Automatic Information Systems, College of Artificial Intelligence, Nankai University, Tianjin, China
| | - Mingzhu Sun
- Institute of Robotics and Automatic Information Systems, College of Artificial Intelligence, Nankai University, Tianjin, China
| | - Zhuo Yang
- State Key Laboratory of Medicinal Chemical Biology, School of Medicine, Nankai University, Tianjin, China
| | - Xin Zhao
- Institute of Robotics and Automatic Information Systems, College of Artificial Intelligence, Nankai University, Tianjin, China
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16
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Hagan MF, Grason GM. Equilibrium mechanisms of self-limiting assembly. REVIEWS OF MODERN PHYSICS 2021; 93:025008. [PMID: 35221384 PMCID: PMC8880259 DOI: 10.1103/revmodphys.93.025008] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of equilibrium assembly processes give rise to two states: one consisting of dispersed disassociated subunits, and the other, a bulk-condensed state of unlimited size. This review focuses on the more specialized class of self-limiting assembly, which describes equilibrium assembly processes resulting in finite-size structures. These systems pose a generic and basic question, how do thermodynamic processes involving non-covalent interactions between identical subunits "measure" and select the size of assembled structures? In this review, we begin with an introduction to the basic statistical mechanical framework for assembly thermodynamics, and use this to highlight the key physical ingredients that ensure equilibrium assembly will terminate at finite dimensions. Then, we introduce examples of self-limiting assembly systems, and classify them within this framework based on two broad categories: self-closing assemblies and open-boundary assemblies. These include well-known cases in biology and synthetic soft matter - micellization of amphiphiles and shell/tubule formation of tapered subunits - as well as less widely known classes of assemblies, such as short-range attractive/long-range repulsive systems and geometrically-frustrated assemblies. For each of these self-limiting mechanisms, we describe the physical mechanisms that select equilibrium assembly size, as well as potential limitations of finite-size selection. Finally, we discuss alternative mechanisms for finite-size assemblies, and draw contrasts with the size-control that these can achieve relative to self-limitation in equilibrium, single-species assemblies.
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Affiliation(s)
- Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
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17
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Bonilla-Quintana M, Wörgötter F. Exploring new roles for actin upon LTP induction in dendritic spines. Sci Rep 2021; 11:7072. [PMID: 33782451 PMCID: PMC8007616 DOI: 10.1038/s41598-021-86367-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/15/2021] [Indexed: 01/21/2023] Open
Abstract
Dendritic spines, small protrusions of the dendrites, enlarge upon LTP induction, linking morphological and functional properties. Although the role of actin in spine enlargement has been well studied, little is known about its relationship with mechanical membrane properties, such as membrane tension, which is involved in many cell processes, like exocytosis. Here, we use a 3D model of the dendritic spine to investigate how polymerization of actin filaments can effectively elevate the membrane tension to trigger exocytosis in a domain close to the tip of the spine. Moreover, we show that the same pool of actin promotes full membrane fusion after exocytosis and spine stabilization.
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18
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Reproducing asymmetrical spine shape fluctuations in a model of actin dynamics predicts self-organized criticality. Sci Rep 2021; 11:4012. [PMID: 33597561 PMCID: PMC7889935 DOI: 10.1038/s41598-021-83331-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/29/2021] [Indexed: 12/19/2022] Open
Abstract
Dendritic spines change their size and shape spontaneously, but the function of this remains unclear. Here, we address this in a biophysical model of spine fluctuations, which reproduces experimentally measured spine fluctuations. For this, we characterize size- and shape fluctuations from confocal microscopy image sequences using autoregressive models and a new set of shape descriptors derived from circular statistics. Using the biophysical model, we extrapolate into longer temporal intervals and find the presence of 1/f noise. When investigating its origins, the model predicts that the actin dynamics underlying shape fluctuations self-organizes into a critical state, which creates a fine balance between static actin filaments and free monomers. In a comparison against a non-critical model, we show that this state facilitates spine enlargement, which happens after LTP induction. Thus, ongoing spine shape fluctuations might be necessary to react quickly to plasticity events.
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19
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Tamada H, Blanc J, Korogod N, Petersen CC, Knott GW. Ultrastructural comparison of dendritic spine morphology preserved with cryo and chemical fixation. eLife 2020; 9:56384. [PMID: 33274717 PMCID: PMC7748412 DOI: 10.7554/elife.56384] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 12/04/2020] [Indexed: 12/25/2022] Open
Abstract
Previously, we showed that cryo fixation of adult mouse brain tissue gave a truer representation of brain ultrastructure in comparison with a standard chemical fixation method (Korogod et al., 2015). Extracellular space matched physiological measurements, there were larger numbers of docked vesicles and less glial coverage of synapses and blood capillaries. Here, using the same preservation approaches, we compared the morphology of dendritic spines. We show that the length of the spine and the volume of its head is unchanged; however, the spine neck width is thinner by more than 30% after cryo fixation. In addition, the weak correlation between spine neck width and head volume seen after chemical fixation was not present in cryo-fixed spines. Our data suggest that spine neck geometry is independent of the spine head volume, with cryo fixation showing enhanced spine head compartmentalization and a higher predicted electrical resistance between spine head and parent dendrite.
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Affiliation(s)
- Hiromi Tamada
- Laboratory of Sensory Processing, Brain Mind Institute, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Biological Electron Microscopy Facility, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Functional Anatomy and Neuroscience, Graduate School of Medicine, Nagoya University, Nagoya, Japan.,Japan Society of the Promotion of Sciences (JSPS), Tokyo, Japan
| | - Jerome Blanc
- Biological Electron Microscopy Facility, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Natalya Korogod
- Biological Electron Microscopy Facility, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,School of Health Sciences (HESAV), University of Applied Sciences and Arts Western Switzerland (HES-SO), Lausanne, Switzerland
| | - Carl Ch Petersen
- Laboratory of Sensory Processing, Brain Mind Institute, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Graham W Knott
- Biological Electron Microscopy Facility, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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20
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Regulation of actin dynamics in dendritic spines: Nanostructure, molecular mobility, and signaling mechanisms. Mol Cell Neurosci 2020; 109:103564. [DOI: 10.1016/j.mcn.2020.103564] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/04/2020] [Indexed: 12/16/2022] Open
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21
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Ben Zablah Y, Merovitch N, Jia Z. The Role of ADF/Cofilin in Synaptic Physiology and Alzheimer's Disease. Front Cell Dev Biol 2020; 8:594998. [PMID: 33282872 PMCID: PMC7688896 DOI: 10.3389/fcell.2020.594998] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/23/2020] [Indexed: 12/21/2022] Open
Abstract
Actin-depolymerization factor (ADF)/cofilin, a family of actin-binding proteins, are critical for the regulation of actin reorganization in response to various signals. Accumulating evidence indicates that ADF/cofilin also play important roles in neuronal structure and function, including long-term potentiation and depression. These are the most extensively studied forms of long-lasting synaptic plasticity and are widely regarded as cellular mechanisms underlying learning and memory. ADF/cofilin regulate synaptic function through their effects on dendritic spines and the trafficking of glutamate receptors, the principal mediator of excitatory synaptic transmission in vertebrates. Regulation of ADF/cofilin involves various signaling pathways converging on LIM domain kinases and slingshot phosphatases, which phosphorylate/inactivate and dephosphorylate/activate ADF/cofilin, respectively. Actin-depolymerization factor/cofilin activity is also regulated by other actin-binding proteins, activity-dependent subcellular distribution and protein translation. Abnormalities in ADF/cofilin have been associated with several neurodegenerative disorders such as Alzheimer’s disease. Therefore, investigating the roles of ADF/cofilin in the brain is not only important for understanding the fundamental processes governing neuronal structure and function, but also may provide potential therapeutic strategies to treat brain disorders.
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Affiliation(s)
- Youssif Ben Zablah
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Neil Merovitch
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Zhengping Jia
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada.,Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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22
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Costa JF, Dines M, Lamprecht R. The Role of Rac GTPase in Dendritic Spine Morphogenesis and Memory. Front Synaptic Neurosci 2020; 12:12. [PMID: 32362820 PMCID: PMC7182350 DOI: 10.3389/fnsyn.2020.00012] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/04/2020] [Indexed: 11/21/2022] Open
Abstract
The ability to form memories in the brain is needed for daily functions, and its impairment is associated with human mental disorders. Evidence indicates that long-term memory (LTM)-related processes such as its consolidation, extinction and forgetting involve changes of synaptic efficacy produced by alterations in neural transmission and morphology. Modulation of the morphology and number of dendritic spines has been proposed to contribute to changes in neuronal transmission mediating such LTM-related processes. Rac GTPase activity is regulated by synaptic activation and it can affect spine morphology by controlling actin-regulatory proteins. Recent evidence shows that changes in Rac GTPase activity affect memory consolidation, extinction, erasure and forgetting and can affect spine morphology in brain areas that mediate these behaviors. Altered Rac GTPase activity is associated with abnormal spine morphology and brain disorders. By affecting Rac GTPase activity we can further understand the roles of spine morphogenesis in memory. Moreover, manipulation of Rac GTPase activity may serve as a therapeutic tool for the treatment of memory-related brain diseases.
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Affiliation(s)
| | | | - Raphael Lamprecht
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
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23
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Bonilla-Quintana M, Wörgötter F, Tetzlaff C, Fauth M. Modeling the Shape of Synaptic Spines by Their Actin Dynamics. Front Synaptic Neurosci 2020; 12:9. [PMID: 32218728 PMCID: PMC7078677 DOI: 10.3389/fnsyn.2020.00009] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/24/2020] [Indexed: 01/05/2023] Open
Abstract
Dendritic spines are the morphological basis of excitatory synapses in the cortex and their size and shape correlates with functional synaptic properties. Recent experiments show that spines exhibit large shape fluctuations that are not related to activity-dependent plasticity but nonetheless might influence memory storage at their synapses. To investigate the determinants of such spontaneous fluctuations, we propose a mathematical model for the dynamics of the spine shape and analyze it in 2D-related to experimental microscopic imagery-and in 3D. We show that the spine shape is governed by a local imbalance between membrane tension and the expansive force from actin bundles that originates from discrete actin polymerization foci. Experiments have shown that only few such polymerization foci co-exist at any time in a spine, each having limited life time. The model shows that the momentarily existing set of such foci pushes the membrane along certain directions until foci are replaced and other directions may now be affected. We explore these relations in depth and use our model to predict shape and temporal characteristics of spines from the different biophysical parameters involved in actin polymerization. Approximating the model by a single recursive equation we finally demonstrate that the temporal evolution of the number of active foci is sufficient to predict the size of the model-spines. Thus, our model provides the first platform to study the relation between molecular and morphological properties of the spine with a high degree of biophysical detail.
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Affiliation(s)
- Mayte Bonilla-Quintana
- Department for Computational Neuroscience, Third Institute of Physics-Biophysics, Georg-August-University, Göttingen, Germany
| | - Florentin Wörgötter
- Department for Computational Neuroscience, Third Institute of Physics-Biophysics, Georg-August-University, Göttingen, Germany
- Bernstein Center for Computational Neuroscience, Georg-August-University, Göttingen, Germany
| | - Christian Tetzlaff
- Department for Computational Neuroscience, Third Institute of Physics-Biophysics, Georg-August-University, Göttingen, Germany
- Bernstein Center for Computational Neuroscience, Georg-August-University, Göttingen, Germany
| | - Michael Fauth
- Department for Computational Neuroscience, Third Institute of Physics-Biophysics, Georg-August-University, Göttingen, Germany
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24
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Miermans CA, Broedersz CP. A lattice kinetic Monte-Carlo method for simulating chromosomal dynamics and other (non-)equilibrium bio-assemblies. SOFT MATTER 2020; 16:544-556. [PMID: 31808764 DOI: 10.1039/c9sm01835b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biological assemblies in living cells such as chromosomes constitute large many-body systems that operate in a fluctuating, out-of-equilibrium environment. Since a brute-force simulation of that many degrees of freedom is currently computationally unfeasible, it is necessary to perform coarse-grained stochastic simulations. Here, we develop all tools necessary to write a lattice kinetic Monte-Carlo (LKMC) algorithm capable of performing such simulations. We discuss the validity and limits of this approach by testing the results of the simulation method in simple settings. Importantly, we illustrate how at large external forces Metropolis-Hastings kinetics violate the fluctuation-dissipation and steady-state fluctuation theorems and discuss better alternatives. Although this simulation framework is rather general, we demonstrate our approach using a DNA polymer with interacting SMC condensin loop-extruding enzymes. Specifically, we show that the scaling behavior of the loop-size distributions that we obtain in our LKMC simulations of this SMC-DNA system is consistent with that reported in other studies using Brownian dynamics simulations and analytic approaches. Moreover, we find that the irreversible dynamics of these enzymes under certain conditions result in frozen, sterically jammed polymer configurations, highlighting a potential pitfall of this approach.
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Affiliation(s)
- Christiaan A Miermans
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany.
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25
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Chen M, Pritchard C, Fortune D, Kodi P, Grados M. Hydrogen sulfide: a target to modulate oxidative stress and neuroplasticity for the treatment of pathological anxiety. Expert Rev Neurother 2019; 20:109-121. [DOI: 10.1080/14737175.2019.1668270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mary Chen
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Diandra Fortune
- Department of Psychiatry and Behavioral Neuroscience, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Priyadurga Kodi
- Department of Internal Medicine, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - Marco Grados
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
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26
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Si Z, Wang X, Zhang Z, Wang J, Li J, Li J, Li L, Li Y, Peng Y, Sun C, Hui Y, Gao X. Heme Oxygenase 1 Induces Tau Oligomer Formation and Synapse Aberrations in Hippocampal Neurons. J Alzheimers Dis 2019; 65:409-419. [PMID: 30040734 DOI: 10.3233/jad-180451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by behavioral changes and cognitive decline. Recent evidence suggests that it is the soluble forms of tau oligomers (Tau-O) and Aβ oligomers (oAβ) rather than the well-studied insoluble protein aggregates that possess the neurotoxicity, infectivity, and amplification underlying disease progression. Heme oxygenase 1 (HO-1), an inducible enzyme upregulated in the cortex and hippocampus of AD brains, was reported to damage neural structures and disrupt brain function, suggesting possible contributions to Tau-O-mediated neurodegeneration. In this study, we focused on the effects of HO-1 on Tau-O formation. In hippocampus of HO-1-overexpressing transgenic mice and neural 2a (N2a) cells, Tau-O was co-localized with HO-1 as visualized by immunofluorescence staining. Furthermore, primary cultured hippocampal neurons from HO-1 transgenic mice showed elevated Tau-O and concomitant reductions in spine density and length as well as dendritic length, diameter, and arborization. Blocking Tau-O formation by isoprenaline reversed these HO-1-induced morphological changes. These results indicated that HO-1 contributes to Tau-O formation and ensuing synaptic damage. Thus, HO-1 is a promising target for AD drug development.
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27
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Bell M, Bartol T, Sejnowski T, Rangamani P. Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium. J Gen Physiol 2019; 151:1017-1034. [PMID: 31324651 PMCID: PMC6683673 DOI: 10.1085/jgp.201812261] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 05/10/2019] [Accepted: 06/17/2019] [Indexed: 01/27/2023] Open
Abstract
Dendritic spines are small subcompartments that protrude from the dendrites of neurons and are important for signaling activity and synaptic communication. These subcompartments have been characterized to have different shapes. While it is known that these shapes are associated with spine function, the specific nature of these shape-function relationships is not well understood. In this work, we systematically investigated the relationship between the shape and size of both the spine head and spine apparatus, a specialized endoplasmic reticulum compartment within the spine head, in modulating rapid calcium dynamics using mathematical modeling. We developed a spatial multicompartment reaction-diffusion model of calcium dynamics in three dimensions with various flux sources, including N-methyl-D-aspartate receptors (NMDARs), voltage-sensitive calcium channels (VSCCs), and different ion pumps on the plasma membrane. Using this model, we make several important predictions. First, the volume to surface area ratio of the spine regulates calcium dynamics. Second, membrane fluxes impact calcium dynamics temporally and spatially in a nonlinear fashion. Finally, the spine apparatus can act as a physical buffer for calcium by acting as a sink and rescaling the calcium concentration. These predictions set the stage for future experimental investigations of calcium dynamics in dendritic spines.
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Affiliation(s)
- Miriam Bell
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA
| | - Tom Bartol
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA
| | - Terrence Sejnowski
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA
- Division of Biological Sciences, University of California, San Diego, San Diego, CA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA
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28
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Telles-Longui M, Mourelle D, Schöwe NM, Cipolli GC, Malerba HN, Buck HS, Viel TA. α7 nicotinic ACh receptors are necessary for memory recovery and neuroprotection promoted by attention training in amyloid-β-infused mice. Br J Pharmacol 2019; 176:3193-3205. [PMID: 31144293 DOI: 10.1111/bph.14744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 05/04/2019] [Accepted: 05/10/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND AND PURPOSE Attention training reverses the neurodegeneration and memory loss promoted by infusion of amyloid-β (Aβ) peptide in rats and increases the density of α7 nicotinic ACh receptors (α7nAChRs) in brain areas related to memory. Hence, we aimed to assess the role of α7nAChRs in the memory recovery promoted by attention training. EXPERIMENTAL APPROACH C57Bl/6 mice were chronically infused with Aβ, Aβ plus the α7 antagonist methyllycaconitine (MLA), or MLA alone. Control animals were infused with vehicle. Animals were subjected weekly to the active avoidance shuttle box for 4 weeks (attention training). The brain and serum were collected for biochemical and histological analysis. KEY RESULTS Aβ caused cognitive impairment, which was reversed by the weekly training, whereas Aβ + MLA also promoted memory loss but with no reversal with weekly training. MLA alone also promoted memory loss but with only partial reversal with the training. Animals infused with Aβ alone showed senile plaques in hippocampus, no change in BDNF levels in cortex, hippocampus, and serum, but increased AChE activity in cortex and hippocampus. Co-treatment with MLA increased AChE activity and senile plaque deposition in hippocampus as well as reducing BDNF in hippocampus and serum, suggesting a lack of α7nAChR function leads to a loss of neuroprotection mechanisms. CONCLUSIONS AND IMPLICATIONS The α7nAChR has a determinant role in memory recovery and brain resilience in the presence of neurodegeneration promoted by Aβ peptide. These data support further studies concerning these receptors as pharmacological targets for future therapies.
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Affiliation(s)
- Milena Telles-Longui
- Graduate Course on Pharmacology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Danilo Mourelle
- Graduate Course on Pharmacology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Natalia Mendes Schöwe
- Graduate Course on Pharmacology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.,Research Group on Neuropharmacology of Aging, São Paulo, Brazil
| | | | - Helena Nascimento Malerba
- Graduate Course on Pharmacology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.,Research Group on Neuropharmacology of Aging, São Paulo, Brazil
| | - Hudson Sousa Buck
- Department of Physiological Sciences, Santa Casa de São Paulo School of Medical Sciences, São Paulo, Brazil.,Research Group on Neuropharmacology of Aging, São Paulo, Brazil
| | - Tania Araujo Viel
- Graduate Course on Pharmacology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.,School of Arts, Sciences and Humanities, Universidade de São Paulo, São Paulo, Brazil
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29
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Urban P, Rezaei V, Bokota G, Denkiewicz M, Basu S, Plewczyński D. Dendritic Spines Taxonomy: The Functional and Structural Classification • Time-Dependent Probabilistic Model of Neuronal Activation. J Comput Biol 2019; 26:322-335. [PMID: 30810368 DOI: 10.1089/cmb.2018.0155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Categorizing spines into four subpopulations, stubby, mushroom, thin, or filopodia, is one of the common approaches in morphological analysis. Most cellular models describing synaptic plasticity, long-term potentiation (LTP), and long-term depression associate synaptic strength with either spine enlargement or spine shrinkage. Unfortunately, although we have a lot of available software with automatic spine segmentation and feature extraction methods, at present none of them allows for automatic and unbiased distinction between dendritic spine subpopulations, or for the detailed computational models of spine behavior. Therefore, we propose structural classification based on two different mathematical approaches: unsupervised construction of spine shape taxonomy based on arbitrary features (SpineTool) and supervised classification exploiting convolution kernels theory (2dSpAn). We compared two populations of spines in a form of static and dynamic data sets gathered at three time points. The dynamic data contain two sets of spines: the active set and the control set. The first population was stimulated with LTP, and the other population in its resting state was used as a control population. We propose one equation describing the distribution of variables that best fits all dendritic spine parameters.
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Affiliation(s)
- Paulina Urban
- 1 Center of New Technologies, University of Warsaw, Warsaw, Poland.,2 College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Vahid Rezaei
- 3 Department of Statistics, Faculty of Mathematics and Computer Sciences, Allameh Tabataba'i University, Tehran, Iran.,4 School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Grzegorz Bokota
- 1 Center of New Technologies, University of Warsaw, Warsaw, Poland.,5 Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Michał Denkiewicz
- 1 Center of New Technologies, University of Warsaw, Warsaw, Poland.,2 College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Subhadip Basu
- 6 Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
| | - Dariusz Plewczyński
- 1 Center of New Technologies, University of Warsaw, Warsaw, Poland.,7 Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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A key function for microtubule-associated-protein 6 in activity-dependent stabilisation of actin filaments in dendritic spines. Nat Commun 2018; 9:3775. [PMID: 30224655 PMCID: PMC6141585 DOI: 10.1038/s41467-018-05869-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/27/2018] [Indexed: 11/09/2022] Open
Abstract
Emerging evidence indicates that microtubule-associated proteins (MAPs) are implicated in synaptic function; in particular, mice deficient for MAP6 exhibit striking deficits in plasticity and cognition. How MAP6 connects to plasticity mechanisms is unclear. Here, we address the possible role of this protein in dendritic spines. We find that in MAP6-deficient cortical and hippocampal neurons, maintenance of mature spines is impaired, and can be restored by expressing a stretch of the MAP6 sequence called Mc modules. Mc modules directly bind actin filaments and mediate activity-dependent stabilisation of F-actin in dendritic spines, a key event of synaptic plasticity. In vitro, Mc modules enhance actin filament nucleation and promote the formation of stable, highly ordered filament bundles. Activity-induced phosphorylation of MAP6 likely controls its transfer to the spine cytoskeleton. These results provide a molecular explanation for the role of MAP6 in cognition, enlightening the connection between cytoskeletal dysfunction, synaptic impairment and neuropsychiatric illnesses. Microtubule-associated protein 6 (MAP6) is known to be important for synaptic plasticity and cognition, supposedly via interaction with microtubules. Here, the authors found that MAP6 is crucial for the stabilisation of enlarged synapses through its association with a different cytoskeletal element, actin.
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Kawabata Galbraith K, Fujishima K, Mizuno H, Lee SJ, Uemura T, Sakimura K, Mishina M, Watanabe N, Kengaku M. MTSS1 Regulation of Actin-Nucleating Formin DAAM1 in Dendritic Filopodia Determines Final Dendritic Configuration of Purkinje Cells. Cell Rep 2018; 24:95-106.e9. [DOI: 10.1016/j.celrep.2018.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 05/01/2018] [Accepted: 06/01/2018] [Indexed: 10/28/2022] Open
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Evidence for altered dendritic spine compartmentalization in Alzheimer's disease and functional effects in a mouse model. Acta Neuropathol 2018; 135:839-854. [PMID: 29696365 DOI: 10.1007/s00401-018-1847-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/30/2018] [Accepted: 04/05/2018] [Indexed: 12/23/2022]
Abstract
Alzheimer's disease (AD) is associated with a progressive loss of synapses and neurons. Studies in animal models indicate that morphological alterations of dendritic spines precede synapse loss, increasing the proportion of large and short ("stubby") spines. Whether similar alterations occur in human patients, and what their functional consequences could be, is not known. We analyzed biopsies from AD patients and APP x presenilin 1 knock-in mice that were previously shown to present a loss of pyramidal neurons in the CA1 area of the hippocampus. We observed that the proportion of stubby spines and the width of spine necks are inversely correlated with synapse density in frontal cortical biopsies from non-AD and AD patients. In mice, the reduction in the density of synapses in the stratum radiatum was preceded by an alteration of spine morphology, with a reduction of their length and an enlargement of their neck. Serial sectioning examined with electron microscopy allowed us to precisely measure spine parameters. Mathematical modeling indicated that the shortening and widening of the necks should alter the electrical compartmentalization of the spines, leading to reduced postsynaptic potentials in spine heads, but not in soma. Accordingly, there was no alteration in basal synaptic transmission, but long-term potentiation and spatial memory were impaired. These results indicate that an alteration of spine morphology could be involved in the early cognitive deficits associated with AD.
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Basu S, Lamprecht R. The Role of Actin Cytoskeleton in Dendritic Spines in the Maintenance of Long-Term Memory. Front Mol Neurosci 2018; 11:143. [PMID: 29765302 PMCID: PMC5938600 DOI: 10.3389/fnmol.2018.00143] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Abstract
Evidence indicates that long-term memory formation involves alterations in synaptic efficacy produced by modifications in neural transmission and morphology. However, it is not clear how such alterations induced by learning, that encode memory, are maintained over long period of time to preserve long-term memory. This is especially intriguing as the half-life of most of the proteins that underlie such changes is usually in the range of hours to days and these proteins may change their location over time. In this review we describe studies that indicate the involvement of dendritic spines in memory formation and its maintenance. These studies show that learning leads to changes in the number and morphology of spines. Disruption in spines morphology or manipulations that lead to alteration in their number after consolidation are associated with impairment in memory maintenance. We further ask how changes in dendritic spines morphology, induced by learning and reputed to encode memory, are maintained to preserve long-term memory. We propose a mechanism, based on studies described in the review, whereby the actin cytoskeleton and its regulatory proteins involved in the initial alteration in spine morphology induced by learning are also essential for spine structural stabilization that maintains long-term memory. In this model glutamate receptors and other synaptic receptors activation during learning leads to the creation of new actin cytoskeletal scaffold leading to changes in spines morphology and memory formation. This new actin cytoskeletal scaffold is preserved beyond actin and its regulatory proteins turnover and dynamics by active stabilization of the level and activity of actin regulatory proteins within these memory spines.
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Affiliation(s)
- Sreetama Basu
- Sagol Departmant of Neurobiology, Faculty of Natural Sciences, The Integrated Brain and Behavior Research Center, University of Haifa, Haifa, Israel
| | - Raphael Lamprecht
- Sagol Departmant of Neurobiology, Faculty of Natural Sciences, The Integrated Brain and Behavior Research Center, University of Haifa, Haifa, Israel
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Du J, Zhang X, Cao H, Jiang D, Wang X, Zhou W, Chen K, Zhou J, Jiang H, Ba L. MiR-194 is involved in morphogenesis of spiral ganglion neurons in inner ear by rearranging actin cytoskeleton via targeting RhoB. Int J Dev Neurosci 2017; 63:16-26. [PMID: 28941704 DOI: 10.1016/j.ijdevneu.2017.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/17/2017] [Accepted: 09/19/2017] [Indexed: 02/05/2023] Open
Abstract
Many microRNAs participate in the development, differentiation and function preservation of the embryonic and adult inner ear, but many details still need to be elucidated regarding the numerous microRNAs in the inner ear. Based on previous investigations on the microRNA profile in the inner ear, we confirmed that several microRNAs are expressed in the inner ear, and we detected the spatial expression of these microRNAs in the neonatal mouse inner ear. Then we focused on miR-194 for its specific expression with a dynamic spatiotemporal pattern during inner ear development. Overexpression of miR-194 in cultured spiral ganglion cells significantly affected the dendrites of differentiated neurons, with more branching and obviously dispersed nerve fibres. Furthermore, the cytoskeleton of cultured cells was markedly affected, as disordered actin filaments resulting from miR-194 overexpression and enhanced filaments resulting from miR-194 knockdown were observed. Together with the bioinformatic methods, the RT-qPCR and western blot results showed that RhoB is a candidate target of miR-194 in the morphogenesis of spiral ganglion neurons. Additionally, the double luciferase reporter system was used to identify RhoB as a novel target of miR-194. Finally, the inhibition of RhoB activation by Clostridium difficile toxin B disturbed the organization of the actin filament, similar to the effects of miR-194 overexpression. In summary, we investigated microRNA expression in the mouse inner ear, and demonstrated that miR-194 is dynamically expressed during inner ear development; importantly, we found that miR-194 affects neuron morphogenesis positively through Rho B-mediated F-actin rearrangement.
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Affiliation(s)
- Jintao Du
- Department of Otorhinolaryngology Head & Neck Surgery, West China Hospital, Sichuan University, 37 Guoxue Lane, Chengdu, 610041, China
| | - Xuemei Zhang
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Hui Cao
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Di Jiang
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Xianren Wang
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Wei Zhou
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China; Department of Otolaryngology, People's Hospital of Meishan, Meishan, Sichuan, 620010, China
| | - Kaitian Chen
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China
| | - Jiao Zhou
- Department of Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hongyan Jiang
- Department of Otorhinolaryngology, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, 510080, China.
| | - Luo Ba
- Department of Otolaryngology, People's Hospital of the Tibet Autonomous Region, Lasha, China.
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Bertling E, Hotulainen P. New waves in dendritic spine actin cytoskeleton: From branches and bundles to rings, from actin binding proteins to post-translational modifications. Mol Cell Neurosci 2017; 84:77-84. [PMID: 28479292 DOI: 10.1016/j.mcn.2017.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/24/2017] [Accepted: 05/03/2017] [Indexed: 12/21/2022] Open
Abstract
Dendritic spines are small actin-rich protrusions from neuronal dendrites that form the postsynaptic part of most excitatory synapses. Changes in the number or strength of synapses are physiological mechanisms behind learning. The growth and maturation of dendritic spines and the activity-induced changes to their morphology are all based on changes to the actin cytoskeleton. In this review, we will discuss the regulation of the actin cytoskeleton in dendritic spine formation and maturation, as well as in synaptic strengthening. Concerning spine formation, we will focus on spine initiation, which has received less attention in the literature. We will also examine the recently revealed regulation of the actin cytoskeleton through post-translational modifications of actin monomers, in addition to the conventional regulation of actin via actin-binding proteins.
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Affiliation(s)
- Enni Bertling
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Pirta Hotulainen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland.
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