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Facchini G, Rathery A, Douady S, Sillam-Dussès D, Perna A. Substrate evaporation drives collective construction in termites. eLife 2024; 12:RP86843. [PMID: 38597934 PMCID: PMC11006414 DOI: 10.7554/elife.86843] [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] [Indexed: 04/11/2024] Open
Abstract
Termites build complex nests which are an impressive example of self-organization. We know that the coordinated actions involved in the construction of these nests by multiple individuals are primarily mediated by signals and cues embedded in the structure of the nest itself. However, to date there is still no scientific consensus about the nature of the stimuli that guide termite construction, and how they are sensed by termites. In order to address these questions, we studied the early building behavior of Coptotermes gestroi termites in artificial arenas, decorated with topographic cues to stimulate construction. Pellet collections were evenly distributed across the experimental setup, compatible with a collection mechanism that is not affected by local topography, but only by the distribution of termite occupancy (termites pick pellets at the positions where they are). Conversely, pellet depositions were concentrated at locations of high surface curvature and at the boundaries between different types of substrate. The single feature shared by all pellet deposition regions was that they correspond to local maxima in the evaporation flux. We can show analytically and we confirm experimentally that evaporation flux is directly proportional to the local curvature of nest surfaces. Taken together, our results indicate that surface curvature is sufficient to organize termite building activity and that termites likely sense curvature indirectly through substrate evaporation. Our findings reconcile the apparently discordant results of previous studies.
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Affiliation(s)
- Giulio Facchini
- Life Sciences Department, University of RoehamptonLondonUnited Kingdom
- Service de Chimie et Physique Non Linéaire, Université Libre de BruxellesBrusselsBelgium
- Laboratoire Matière et Systèmes Complexe, CNRS, Université Paris CitéParisFrance
| | - Alann Rathery
- Life Sciences Department, University of RoehamptonLondonUnited Kingdom
| | - Stéphane Douady
- Laboratoire Matière et Systèmes Complexe, CNRS, Université Paris CitéParisFrance
| | - David Sillam-Dussès
- Laboratoire d’Ethologie Expérimentale et Comparée, LEEC, UR 4443, Université Sorbonne Paris NordVilletaneuseFrance
| | - Andrea Perna
- Life Sciences Department, University of RoehamptonLondonUnited Kingdom
- Networks Unit, IMT School for Advanced Studies LuccaLuccaItaly
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2
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Duveau F, Cordier C, Chiron L, Le Bec M, Pouzet S, Séguin J, Llamosi A, Sorre B, Di Meglio JM, Hersen P. Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability. eLife 2024; 12:RP88750. [PMID: 38568203 PMCID: PMC10990491 DOI: 10.7554/elife.88750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Indexed: 04/05/2024] Open
Abstract
Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting factors, we quantified the effects of dual fluctuations of osmotic stress and glucose deprivation on yeast cells using microfluidics and time-lapse microscopy. Strikingly, we observed that cell proliferation, survival, and signaling depend on the phasing of the two periodic stresses. Cells divided faster, survived longer, and showed decreased transcriptional response when fluctuations of hyperosmotic stress and glucose deprivation occurred in phase than when the two stresses occurred alternatively. Therefore, glucose availability regulates yeast responses to dynamic osmotic stress, showcasing the key role of metabolic fluctuations in cellular responses to dynamic stress. We also found that mutants with impaired osmotic stress response were better adapted to alternating stresses than wild-type cells, showing that genetic mechanisms of adaptation to a persistent stress factor can be detrimental under dynamically interacting conditions.
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Affiliation(s)
- Fabien Duveau
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364LyonFrance
| | - Céline Cordier
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Lionel Chiron
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Matthias Le Bec
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Sylvain Pouzet
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Julie Séguin
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Artémis Llamosi
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Benoit Sorre
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
| | - Jean-Marc Di Meglio
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
| | - Pascal Hersen
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université Paris Diderot, 10 rue Alice Domon et Léonie DuquetParisFrance
- Laboratoire Physico Chimie Curie, UMR168, Institut Curie, 16 rue Pierre et Marie Curie, 75005ParisFrance
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3
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Challita EJ, Bhamla MS. Unifying fluidic excretion across life from cicadas to elephants. Proc Natl Acad Sci U S A 2024; 121:e2317878121. [PMID: 38466877 PMCID: PMC10990113 DOI: 10.1073/pnas.2317878121] [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: 10/22/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024] Open
Abstract
Can insects weighing mere grams challenge our current understanding of fluid dynamics in urination, jetting fluids like their larger mammalian counterparts? Current fluid urination models, predominantly formulated for mammals, suggest that jetting is confined to animals over 3 kg, owing to viscous and surface tension constraints at microscales. Our findings defy this paradigm by demonstrating that cicadas-weighing just 2 g-possess the capability for jetting fluids through remarkably small orifices. Using dimensional analysis, we introduce a unifying fluid dynamics scaling framework that accommodates a broad range of taxa, from surface-tension-dominated insects to inertia and gravity-reliant mammals. This study not only refines our understanding of fluid excretion across various species but also highlights its potential relevance in diverse fields such as ecology, evolutionary biology, and biofluid dynamics.
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Affiliation(s)
- Elio J. Challita
- Chemical & Biomolecular Engineering, Georgia Institute of Technology, Georgia30332, Atlanta
| | - M. Saad Bhamla
- Chemical & Biomolecular Engineering, Georgia Institute of Technology, Georgia30332, Atlanta
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4
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Morel C, Lemerle E, Tsai FC, Obadia T, Srivastava N, Marechal M, Salles A, Albert M, Stefani C, Benito Y, Vandenesch F, Lamaze C, Vassilopoulos S, Piel M, Bassereau P, Gonzalez-Rodriguez D, Leduc C, Lemichez E. Caveolin-1 protects endothelial cells from extensive expansion of transcellular tunnel by stiffening the plasma membrane. eLife 2024; 12:RP92078. [PMID: 38517935 PMCID: PMC10959525 DOI: 10.7554/elife.92078] [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] [Indexed: 03/24/2024] Open
Abstract
Large transcellular pores elicited by bacterial mono-ADP-ribosyltransferase (mART) exotoxins inhibiting the small RhoA GTPase compromise the endothelial barrier. Recent advances in biophysical modeling point toward membrane tension and bending rigidity as the minimal set of mechanical parameters determining the nucleation and maximal size of transendothelial cell macroaperture (TEM) tunnels induced by bacterial RhoA-targeting mART exotoxins. We report that cellular depletion of caveolin-1, the membrane-embedded building block of caveolae, and depletion of cavin-1, the master regulator of caveolae invaginations, increase the number of TEMs per cell. The enhanced occurrence of TEM nucleation events correlates with a reduction in cell height due to the increase in cell spreading and decrease in cell volume, which, together with the disruption of RhoA-driven F-actin meshwork, favor membrane apposition for TEM nucleation. Strikingly, caveolin-1 specifically controls the opening speed of TEMs, leading to their dramatic 5.4-fold larger widening. Consistent with the increase in TEM density and width in siCAV1 cells, we record a higher lethality in CAV1 KO mice subjected to a catalytically active mART exotoxin targeting RhoA during staphylococcal bloodstream infection. Combined theoretical modeling with independent biophysical measurements of plasma membrane bending rigidity points toward a specific contribution of caveolin-1 to membrane stiffening in addition to the role of cavin-1/caveolin-1-dependent caveolae in the control of membrane tension homeostasis.
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Affiliation(s)
- Camille Morel
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Inserm U1306, Unité des Toxines Bactériennes, Département de MicrobiologieParisFrance
| | - Eline Lemerle
- Sorbonne Université, INSERM UMR974, Institut de Myologie, Centre de Recherche en MyologieParisFrance
| | - Feng-Ching Tsai
- Institut Curie, PSL Research University, CNRS UMR168, Physics of Cells and Cancer LaboratoryParisFrance
| | - Thomas Obadia
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HubParisFrance
- Institut Pasteur, Université Paris Cité, G5 Infectious Diseases Epidemiology and AnalyticsParisFrance
| | - Nishit Srivastava
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, Sorbonne UniversityParisFrance
| | - Maud Marechal
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Inserm U1306, Unité des Toxines Bactériennes, Département de MicrobiologieParisFrance
| | - Audrey Salles
- Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT)ParisFrance
| | - Marvin Albert
- Institut Pasteur, Université Paris Cité, Image Analysis HubParisFrance
| | - Caroline Stefani
- Benaroya Research Institute at Virginia Mason, Department of ImmunologySeattleUnited States
| | - Yvonne Benito
- Centre National de Référence des Staphylocoques, Hospices Civiles de LyonLyonFrance
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, FranceLyonFrance
| | - Christophe Lamaze
- Institut Curie, PSL Research University, INSERM U1143, CNRS UMR3666, Membrane Mechanics and Dynamics of Intracellular Signaling LaboratoryParisFrance
| | - Stéphane Vassilopoulos
- Sorbonne Université, INSERM UMR974, Institut de Myologie, Centre de Recherche en MyologieParisFrance
| | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, Sorbonne UniversityParisFrance
| | - Patricia Bassereau
- Institut Curie, PSL Research University, CNRS UMR168, Physics of Cells and Cancer LaboratoryParisFrance
| | | | - Cecile Leduc
- Université Paris Cité, Institut Jacques Monod, CNRS UMR7592ParisFrance
| | - Emmanuel Lemichez
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Inserm U1306, Unité des Toxines Bactériennes, Département de MicrobiologieParisFrance
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5
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Jeong D, Shi G, Li X, Thirumalai D. Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion. eLife 2024; 12:RP88564. [PMID: 38502563 PMCID: PMC10950330 DOI: 10.7554/elife.88564] [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] [Indexed: 03/21/2024] Open
Abstract
Compartment formation in interphase chromosomes is a result of spatial segregation between euchromatin and heterochromatin on a few megabase pairs (Mbp) scale. On the sub-Mbp scales, topologically associating domains (TADs) appear as interacting domains along the diagonal in the ensemble averaged Hi-C contact map. Hi-C experiments showed that most of the TADs vanish upon deleting cohesin, while the compartment structure is maintained, and perhaps even enhanced. However, closer inspection of the data reveals that a non-negligible fraction of TADs is preserved (P-TADs) after cohesin loss. Imaging experiments show that, at the single-cell level, TAD-like structures are present even without cohesin. To provide a structural basis for these findings, we first used polymer simulations to show that certain TADs with epigenetic switches across their boundaries survive after depletion of loops. More importantly, the three-dimensional structures show that many of the P-TADs have sharp physical boundaries. Informed by the simulations, we analyzed the Hi-C maps (with and without cohesin) in mouse liver and human colorectal carcinoma cell lines, which affirmed that epigenetic switches and physical boundaries (calculated using the predicted 3D structures using the data-driven HIPPS method that uses Hi-C as the input) explain the origin of the P-TADs. Single-cell structures display TAD-like features in the absence of cohesin that are remarkably similar to the findings in imaging experiments. Some P-TADs, with physical boundaries, are relevant to the retention of enhancer-promoter/promoter-promoter interactions. Overall, our study shows that preservation of a subset of TADs upon removing cohesin is a robust phenomenon that is valid across multiple cell lines.
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Affiliation(s)
- Davin Jeong
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - Guang Shi
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - Xin Li
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - D Thirumalai
- Department of Chemistry, University of Texas at AustinAustinUnited States
- Department of Physics, University of Texas at AustinAustinUnited States
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6
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Jafarinia H, van der Giessen E, Onck PR. C9orf72 polyPR directly binds to various nuclear transport components. eLife 2024; 12:RP89694. [PMID: 38483313 PMCID: PMC10939497 DOI: 10.7554/elife.89694] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
The disruption of nucleocytoplasmic transport (NCT) is an important mechanism in neurodegenerative diseases. In the case of C9orf72-ALS, trafficking of macromolecules through the nuclear pore complex (NPC) might get frustrated by the binding of C9orf72-translated arginine-containing dipeptide repeat proteins (R-DPRs) to the Kapβ family of nuclear transport receptors. Besides Kapβs, several other types of transport components have been linked to NCT impairments in R-DPR-expressed cells, but the molecular origin of these observations has not been clarified. Here, we adopt a coarse-grained molecular dynamics model at amino acid resolution to study the direct interaction between polyPR, the most toxic DPR, and various nuclear transport components to elucidate the binding mechanisms and provide a complete picture of potential polyPR-mediated NCT defects. We found polyPR to directly bind to several isoforms of the Impα family, CAS (the specific exporter of Impα) and RanGAP. We observe no binding between polyPR and Ran. Longer polyPRs at lower salt concentrations also make contact with RanGEF and NTF2. Analyzing the polyPR contact sites on the transport components reveals that polyPR potentially interferes with RanGTP/RanGDP binding, with nuclear localization signal (NLS)-containing cargoes (cargo-NLS) binding to Impα, with cargo-NLS release from Impα, and with Impα export from the nucleus. The abundance of polyPR-binding sites on multiple transport components combined with the inherent polyPR length dependence makes direct polyPR interference of NCT a potential mechanistic pathway of C9orf72 toxicity.
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Affiliation(s)
- Hamidreza Jafarinia
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Erik van der Giessen
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
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7
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Morrell MC, Nemenman I, Sederberg A. Neural criticality from effective latent variables. eLife 2024; 12:RP89337. [PMID: 38470471 PMCID: PMC10957169 DOI: 10.7554/elife.89337] [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] [Indexed: 03/13/2024] Open
Abstract
Observations of power laws in neural activity data have raised the intriguing notion that brains may operate in a critical state. One example of this critical state is 'avalanche criticality', which has been observed in various systems, including cultured neurons, zebrafish, rodent cortex, and human EEG. More recently, power laws were also observed in neural populations in the mouse under an activity coarse-graining procedure, and they were explained as a consequence of the neural activity being coupled to multiple latent dynamical variables. An intriguing possibility is that avalanche criticality emerges due to a similar mechanism. Here, we determine the conditions under which latent dynamical variables give rise to avalanche criticality. We find that populations coupled to multiple latent variables produce critical behavior across a broader parameter range than those coupled to a single, quasi-static latent variable, but in both cases, avalanche criticality is observed without fine-tuning of model parameters. We identify two regimes of avalanches, both critical but differing in the amount of information carried about the latent variable. Our results suggest that avalanche criticality arises in neural systems in which activity is effectively modeled as a population driven by a few dynamical variables and these variables can be inferred from the population activity.
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Affiliation(s)
- Mia C Morrell
- Department of Physics, New York UniversityNew YorkUnited States
| | - Ilya Nemenman
- Department of Physics, Department of Biology, Initiative in Theory and Modeling of Living Systems, Emory UniversityAtlantaUnited States
| | - Audrey Sederberg
- Department of Neuroscience, University of Minnesota Medical SchoolMinneapolisUnited States
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8
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de-Carvalho J, Tlili S, Saunders TE, Telley IA. The positioning mechanics of microtubule asters in Drosophila embryo explants. eLife 2024; 12:RP90541. [PMID: 38426416 PMCID: PMC10911390 DOI: 10.7554/elife.90541] [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] [Indexed: 03/02/2024] Open
Abstract
Microtubule asters are essential in localizing the action of microtubules in processes including mitosis and organelle positioning. In large cells, such as the one-cell sea urchin embryo, aster dynamics are dominated by hydrodynamic pulling forces. However, in systems with more densely positioned nuclei such as the early Drosophila embryo, which packs around 6000 nuclei within the syncytium in a crystalline-like order, it is unclear what processes dominate aster dynamics. Here, we take advantage of a cell cycle regulation Drosophila mutant to generate embryos with multiple asters, independent from nuclei. We use an ex vivo assay to further simplify this biological system to explore the forces generated by and between asters. Through live imaging, drug and optical perturbations, and theoretical modeling, we demonstrate that these asters likely generate an effective pushing force over short distances.
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Affiliation(s)
- Jorge de-Carvalho
- Instituto Gulbenkian de Ciência, Fundação Calouste GulbenkianOeirasPortugal
| | - Sham Tlili
- Mechanobiology Institute and Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Timothy E Saunders
- Mechanobiology Institute and Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Institute of Molecular and Cellular Biology, A*Star, ProteosSingaporeSingapore
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of WarwickWarwickUnited Kingdom
| | - Ivo A Telley
- Instituto Gulbenkian de Ciência, Fundação Calouste GulbenkianOeirasPortugal
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9
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Abstract
Microsporidia are eukaryotic, obligate intracellular parasites that infect a wide range of hosts, leading to health and economic burdens worldwide. Microsporidia use an unusual invasion organelle called the polar tube (PT), which is ejected from a dormant spore at ultra-fast speeds, to infect host cells. The mechanics of PT ejection are impressive. Anncaliia algerae microsporidia spores (3-4 μm in size) shoot out a 100-nm-wide PT at a speed of 300 μm/s, creating a shear rate of 3000 s-1. The infectious cargo, which contains two nuclei, is shot through this narrow tube for a distance of ∼60-140 μm (Jaroenlak et al, 2020) and into the host cell. Considering the large hydraulic resistance in an extremely thin tube and the low-Reynolds-number nature of the process, it is not known how microsporidia can achieve this ultrafast event. In this study, we use Serial Block-Face Scanning Electron Microscopy to capture 3-dimensional snapshots of A. algerae spores in different states of the PT ejection process. Grounded in these data, we propose a theoretical framework starting with a systematic exploration of possible topological connectivity amongst organelles, and assess the energy requirements of the resulting models. We perform PT firing experiments in media of varying viscosity, and use the results to rank our proposed hypotheses based on their predicted energy requirement. We also present a possible mechanism for cargo translocation, and quantitatively compare our predictions to experimental observations. Our study provides a comprehensive biophysical analysis of the energy dissipation of microsporidian infection process and demonstrates the extreme limits of cellular hydraulics.
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Affiliation(s)
- Ray Chang
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Ari Davydov
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Pattana Jaroenlak
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Breane Budaitis
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
- Department of Microbiology, New York University School of MedicineNew YorkUnited States
| | - Gira Bhabha
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Manu Prakash
- Department of Bioengineering, Stanford UniversityStanfordUnited States
- Woods Institute for the Environment, Stanford UniversityStanfordUnited States
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10
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Boffi NM, Guo Y, Rycroft CH, Amir A. How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution. eLife 2024; 12:RP87895. [PMID: 38376390 PMCID: PMC10942580 DOI: 10.7554/elife.87895] [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] [Indexed: 02/21/2024] Open
Abstract
The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population's mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of a simulated evolving population subject to a standard serial dilution protocol. Through extensive numerical experimentation, we find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that increasing the level of clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but leaves the rate of growth invariant when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape. The simulation package for this work may be found at https://github.com/nmboffi/spin_glass_evodyn.
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Affiliation(s)
- Nicholas M Boffi
- Courant Institute of Mathematical Sciences, New York UniversityNew YorkUnited States
| | - Yipei Guo
- Janelia Research CampusAshburnUnited States
| | - Chris H Rycroft
- Department of Mathematics, University of Wisconsin–MadisonMadisonUnited States
- Mathematics Group, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Ariel Amir
- Weizmann Institute of ScienceRehovotIsrael
- John A. Paulson School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
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11
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Klughammer N, Barth A, Dekker M, Fragasso A, Onck PR, Dekker C. Diameter dependence of transport through nuclear pore complex mimics studied using optical nanopores. eLife 2024; 12:RP87174. [PMID: 38376900 PMCID: PMC10942607 DOI: 10.7554/elife.87174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Indexed: 02/21/2024] Open
Abstract
The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single-molecule translocations through individual pores using optical detection. We probe the selectivity of Nsp1-coated pores by quantitatively comparing the translocation rates of the nuclear transport receptor Kap95 to the inert probe BSA over a wide range of pore sizes from 35 nm to 160 nm. Pores below 55 ± 5 nm show significant selectivity that gradually decreases for larger pores. This finding is corroborated by coarse-grained molecular dynamics simulations of the Nsp1 mesh within the pore, which suggest that leakage of BSA occurs by diffusion through transient openings within the dynamic mesh. Furthermore, we experimentally observe a modulation of the BSA permeation when varying the concentration of Kap95. The results demonstrate the potential of single-molecule fluorescence measurements on biomimetic NPCs to elucidate the principles of nuclear transport.
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Affiliation(s)
- Nils Klughammer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Maurice Dekker
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
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12
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Zhang Y, Lauder GV. Energy conservation by collective movement in schooling fish. eLife 2024; 12:RP90352. [PMID: 38375853 PMCID: PMC10942612 DOI: 10.7554/elife.90352] [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] [Indexed: 02/21/2024] Open
Abstract
Many animals moving through fluids exhibit highly coordinated group movement that is thought to reduce the cost of locomotion. However, direct energetic measurements demonstrating the energy-saving benefits of fluid-mediated collective movements remain elusive. By characterizing both aerobic and anaerobic metabolic energy contributions in schools of giant danio (Devario aequipinnatus), we discovered that fish schools have a concave upward shaped metabolism-speed curve, with a minimum metabolic cost at ~1 body length s-1. We demonstrate that fish schools reduce total energy expenditure (TEE) per tail beat by up to 56% compared to solitary fish. When reaching their maximum sustained swimming speed, fish swimming in schools had a 44% higher maximum aerobic performance and used 65% less non-aerobic energy compared to solitary individuals, which lowered the TEE and total cost of transport by up to 53%, near the lowest recorded for any aquatic organism. Fish in schools also recovered from exercise 43% faster than solitary fish. The non-aerobic energetic savings that occur when fish in schools actively swim at high speed can considerably improve both peak and repeated performance which is likely to be beneficial for evading predators. These energetic savings may underlie the prevalence of coordinated group locomotion in fishes.
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Affiliation(s)
- Yangfan Zhang
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - George V Lauder
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
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13
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Goetz A, Akl H, Dixit P. The ability to sense the environment is heterogeneously distributed in cell populations. eLife 2024; 12:RP87747. [PMID: 38293960 PMCID: PMC10942581 DOI: 10.7554/elife.87747] [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] [Indexed: 02/01/2024] Open
Abstract
Channel capacity of signaling networks quantifies their fidelity in sensing extracellular inputs. Low estimates of channel capacities for several mammalian signaling networks suggest that cells can barely detect the presence/absence of environmental signals. However, given the extensive heterogeneity and temporal stability of cell state variables, we hypothesize that the sensing ability itself may depend on the state of the cells. In this work, we present an information-theoretic framework to quantify the distribution of sensing abilities from single-cell data. Using data on two mammalian pathways, we show that sensing abilities are widely distributed in the population and most cells achieve better resolution of inputs compared to an 'average cell'. We verify these predictions using live-cell imaging data on the IGFR/FoxO pathway. Importantly, we identify cell state variables that correlate with cells' sensing abilities. This information-theoretic framework will significantly improve our understanding of how cells sense in their environment.
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Affiliation(s)
- Andrew Goetz
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
| | - Hoda Akl
- Department of Physics, University of FloridaGainesvilleUnited States
| | - Purushottam Dixit
- Department of Biomedical Engineering, Yale UniversityNew HavenUnited States
- Systems Biology Institute, Yale UniversityWest HavenUnited States
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14
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Kæstel-Hansen J, Hatzakis NS. Everything, everywhere, almost at once. eLife 2024; 13:e95362. [PMID: 38285015 PMCID: PMC10824506 DOI: 10.7554/elife.95362] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024] Open
Abstract
A new platform that can follow the movement of individual proteins inside millions of cells in a single day will help contribute to existing knowledge of cell biology and identify new therapeutics.
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Affiliation(s)
- Jacob Kæstel-Hansen
- Department of Chemistry, Novo Nordisk Foundation Center for Optimized Oligo Escape and Control of Disease, University of CopenhagenCopenhagenDenmark
| | - Nikos S Hatzakis
- Department of Chemistry, Novo Nordisk Foundation Center for Optimized Oligo Escape and Control of Disease, University of CopenhagenCopenhagenDenmark
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15
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Peercy BE, Hodson DJ. Synchronizing beta cells in the pancreas. eLife 2024; 13:e95103. [PMID: 38270512 PMCID: PMC10810605 DOI: 10.7554/elife.95103] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
The secretion of insulin from the pancreas relies on both gap junctions and subpopulations of beta cells with specific intrinsic properties.
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Affiliation(s)
- Bradford E Peercy
- Department of Mathematics and Statistics, University of Maryland Baltimore County (UMBC)BaltimoreUnited States
| | - David J Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM), NIHR Oxford Biomedical Research Centre, Churchill Hospital, Radcliffe Department of Medicine, University of OxfordOxfordUnited Kingdom
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16
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Shoemaker WR, Grilli J. Investigating macroecological patterns in coarse-grained microbial communities using the stochastic logistic model of growth. eLife 2024; 12:RP89650. [PMID: 38251984 PMCID: PMC10945690 DOI: 10.7554/elife.89650] [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] [Indexed: 01/23/2024] Open
Abstract
The structure and diversity of microbial communities are intrinsically hierarchical due to the shared evolutionary history of their constituents. This history is typically captured through taxonomic assignment and phylogenetic reconstruction, sources of information that are frequently used to group microbes into higher levels of organization in experimental and natural communities. Connecting community diversity to the joint ecological dynamics of the abundances of these groups is a central problem of community ecology. However, how microbial diversity depends on the scale of observation at which groups are defined has never been systematically examined. Here, we used a macroecological approach to quantitatively characterize the structure and diversity of microbial communities among disparate environments across taxonomic and phylogenetic scales. We found that measures of biodiversity at a given scale can be consistently predicted using a minimal model of ecology, the Stochastic Logistic Model of growth (SLM). This result suggests that the SLM is a more appropriate null-model for microbial biodiversity than alternatives such as the Unified Neutral Theory of Biodiversity. Extending these within-scale results, we examined the relationship between measures of biodiversity calculated at different scales (e.g. genus vs. family), an empirical pattern previously evaluated in the context of the Diversity Begets Diversity (DBD) hypothesis (Madi et al., 2020). We found that the relationship between richness estimates at different scales can be quantitatively predicted assuming independence among community members, demonstrating that the DBD can be sufficiently explained using the SLM as a null model of ecology. Contrastingly, only by including correlations between the abundances of community members (e.g. as the consequence of interactions) can we predict the relationship between estimates of diversity at different scales. The results of this study characterize novel microbial patterns across scales of organization and establish a sharp demarcation between recently proposed macroecological patterns that are not and are affected by ecological interactions.
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Affiliation(s)
- William R Shoemaker
- Quantitative Life Sciences, The Abdus Salam International Centre for Theoretical Physics (ICTP)TriesteItaly
| | - Jacopo Grilli
- Quantitative Life Sciences, The Abdus Salam International Centre for Theoretical Physics (ICTP)TriesteItaly
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17
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Lameira AR, Hardus ME, Ravignani A, Raimondi T, Gamba M. Recursive self-embedded vocal motifs in wild orangutans. eLife 2024; 12:RP88348. [PMID: 38252123 PMCID: PMC10945596 DOI: 10.7554/elife.88348] [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] [Indexed: 01/23/2024] Open
Abstract
Recursive procedures that allow placing a vocal signal inside another of a similar kind provide a neuro-computational blueprint for syntax and phonology in spoken language and human song. There are, however, no known vocal sequences among nonhuman primates arranged in self-embedded patterns that evince vocal recursion or potential incipient or evolutionary transitional forms thereof, suggesting a neuro-cognitive transformation exclusive to humans. Here, we uncover that wild flanged male orangutan long calls feature rhythmically isochronous call sequences nested within isochronous call sequences, consistent with two hierarchical strata. Remarkably, three temporally and acoustically distinct call rhythms in the lower stratum were not related to the overarching rhythm at the higher stratum by any low multiples, which suggests that these recursive structures were neither the result of parallel non-hierarchical procedures nor anatomical artifacts of bodily constraints or resonances. Findings represent a case of temporally recursive hominid vocal combinatorics in the absence of syntax, semantics, phonology, or music. Second-order combinatorics, 'sequences within sequences', involving hierarchically organized and cyclically structured vocal sounds in ancient hominids may have preluded the evolution of recursion in modern language-able humans.
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Affiliation(s)
- Adriano R Lameira
- Department of Psychology, University of WarwickCoventryUnited Kingdom
| | | | - Andrea Ravignani
- Comparative Bioacoustics Group, Max Planck Institute for PsycholinguisticsNijmegenNetherlands
- Center for Music in the Brain, Department of Clinical Medicine, Aarhus University & The Royal Academy of Music Aarhus/AalborgAarhusDenmark
- Department of Human Neurosciences, Sapienza University of RomeRomeItaly
| | - Teresa Raimondi
- Department of Life Sciences and Systems Biology, University of TurinoTorinoItaly
| | - Marco Gamba
- Department of Life Sciences and Systems Biology, University of TurinoTorinoItaly
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18
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Das R, Sinha S, Li X, Kirkpatrick TR, Thirumalai D. Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis. eLife 2024; 12:RP87966. [PMID: 38241331 PMCID: PMC10945604 DOI: 10.7554/elife.87966] [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] [Indexed: 01/21/2024] Open
Abstract
A recent experiment on zebrafish blastoderm morphogenesis showed that the viscosity (η) of a non-confluent embryonic tissue grows sharply until a critical cell packing fraction (ϕS). The increase in η up to ϕS is similar to the behavior observed in several glass-forming materials, which suggests that the cell dynamics is sluggish or glass-like. Surprisingly, η is a constant above ϕS. To determine the mechanism of this unusual dependence of η on ϕ, we performed extensive simulations using an agent-based model of a dense non-confluent two-dimensional tissue. We show that polydispersity in the cell size, and the propensity of the cells to deform, results in the saturation of the available free area per cell beyond a critical packing fraction. Saturation in the free space not only explains the viscosity plateau above ϕS but also provides a relationship between equilibrium geometrical packing to the dramatic increase in the relaxation dynamics.
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Affiliation(s)
- Rajsekhar Das
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - Sumit Sinha
- Department of Physics, University of Texas at AustinAustinUnited States
| | - Xin Li
- Department of Chemistry, University of Texas at AustinAustinUnited States
| | - TR Kirkpatrick
- Institute for Physical Science and Technology, University of MarylandCollege ParkUnited States
| | - D Thirumalai
- Department of Chemistry, University of Texas at AustinAustinUnited States
- Department of Physics, University of Texas at AustinAustinUnited States
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19
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Seelbinder B, Wagner S, Jain M, Erben E, Klykov S, Stoev ID, Krishnaswamy VR, Kreysing M. Probe-free optical chromatin deformation and measurement of differential mechanical properties in the nucleus. eLife 2024; 13:e76421. [PMID: 38214505 PMCID: PMC10786458 DOI: 10.7554/elife.76421] [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: 12/15/2021] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
The nucleus is highly organized to facilitate coordinated gene transcription. Measuring the rheological properties of the nucleus and its sub-compartments will be crucial to understand the principles underlying nuclear organization. Here, we show that strongly localized temperature gradients (approaching 1°C/µm) can lead to substantial intra-nuclear chromatin displacements (>1 µm), while nuclear area and lamina shape remain unaffected. Using particle image velocimetry (PIV), intra-nuclear displacement fields can be calculated and converted into spatio-temporally resolved maps of various strain components. Using this approach, we show that chromatin displacements are highly reversible, indicating that elastic contributions are dominant in maintaining nuclear organization on the time scale of seconds. In genetically inverted nuclei, centrally compacted heterochromatin displays high resistance to deformation, giving a rigid, solid-like appearance. Correlating spatially resolved strain maps with fluorescent reporters in conventional interphase nuclei reveals that various nuclear compartments possess distinct mechanical identities. Surprisingly, both densely and loosely packed chromatin showed high resistance to deformation, compared to medium dense chromatin. Equally, nucleoli display particularly high resistance and strong local anchoring to heterochromatin. Our results establish how localized temperature gradients can be used to drive nuclear compartments out of mechanical equilibrium to obtain spatial maps of their material responses.
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Affiliation(s)
- Benjamin Seelbinder
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | - Susan Wagner
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
| | - Manavi Jain
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | - Elena Erben
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | - Sergei Klykov
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | - Iliya Dimitrov Stoev
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
| | | | - Moritz Kreysing
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Centre for Systems BiologyDresdenGermany
- Institute of Biological and Chemical Systems-Biological Information Processing, Karlsruhe Institute of TechnologyEggenstein-LeopoldshafenGermany
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20
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Armengol-Collado JM, Carenza LN, Giomi L. Hydrodynamics and multiscale order in confluent epithelia. eLife 2024; 13:e86400. [PMID: 38189410 PMCID: PMC10963026 DOI: 10.7554/elife.86400] [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: 01/24/2023] [Accepted: 01/05/2024] [Indexed: 01/09/2024] Open
Abstract
We formulate a hydrodynamic theory of confluent epithelia: i.e. monolayers of epithelial cells adhering to each other without gaps. Taking advantage of recent progresses toward establishing a general hydrodynamic theory of p-atic liquid crystals, we demonstrate that collectively migrating epithelia feature both nematic (i.e. p = 2) and hexatic (i.e. p = 6) orders, with the former being dominant at large and the latter at small length scales. Such a remarkable multiscale liquid crystal order leaves a distinct signature in the system's structure factor, which exhibits two different power-law scaling regimes, reflecting both the hexagonal geometry of small cells clusters and the uniaxial structure of the global cellular flow. We support these analytical predictions with two different cell-resolved models of epithelia - i.e. the self-propelled Voronoi model and the multiphase field model - and highlight how momentum dissipation and noise influence the range of fluctuations at small length scales, thereby affecting the degree of cooperativity between cells. Our construction provides a theoretical framework to conceptualize the recent observation of multiscale order in layers of Madin-Darby canine kidney cells and pave the way for further theoretical developments.
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Affiliation(s)
| | | | - Luca Giomi
- Instituut-Lorentz, Leiden UniversityLeidenNetherlands
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21
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Toker D, Müller E, Miyamoto H, Riga MS, Lladó-Pelfort L, Yamakawa K, Artigas F, Shine JM, Hudson AE, Pouratian N, Monti MM. Criticality supports cross-frequency cortical-thalamic information transfer during conscious states. eLife 2024; 13:e86547. [PMID: 38180472 PMCID: PMC10805384 DOI: 10.7554/elife.86547] [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: 01/31/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
Consciousness is thought to be regulated by bidirectional information transfer between the cortex and thalamus, but the nature of this bidirectional communication - and its possible disruption in unconsciousness - remains poorly understood. Here, we present two main findings elucidating mechanisms of corticothalamic information transfer during conscious states. First, we identify a highly preserved spectral channel of cortical-thalamic communication that is present during conscious states, but which is diminished during the loss of consciousness and enhanced during psychedelic states. Specifically, we show that in humans, mice, and rats, information sent from either the cortex or thalamus via δ/θ/α waves (∼1-13 Hz) is consistently encoded by the other brain region by high γ waves (52-104 Hz); moreover, unconsciousness induced by propofol anesthesia or generalized spike-and-wave seizures diminishes this cross-frequency communication, whereas the psychedelic 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) enhances this low-to-high frequency interregional communication. Second, we leverage numerical simulations and neural electrophysiology recordings from the thalamus and cortex of human patients, rats, and mice to show that these changes in cross-frequency cortical-thalamic information transfer may be mediated by excursions of low-frequency thalamocortical electrodynamics toward/away from edge-of-chaos criticality, or the phase transition from stability to chaos. Overall, our findings link thalamic-cortical communication to consciousness, and further offer a novel, mathematically well-defined framework to explain the disruption to thalamic-cortical information transfer during unconscious states.
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Affiliation(s)
- Daniel Toker
- Department of Neurology, University of California, Los AngelesLos AngelesUnited States
- Department of Psychology, University of California, Los AngelesLos AngelesUnited States
| | - Eli Müller
- Brain and Mind Centre, University of SydneySydneyAustralia
| | - Hiroyuki Miyamoto
- Laboratory for Neurogenetics, RIKEN Center for Brain ScienceSaitamaJapan
- PRESTO, Japan Science and Technology AgencySaitamaJapan
- International Research Center for Neurointelligence, University of TokyoNagoyaJapan
| | - Maurizio S Riga
- Andalusian Center for Molecular Biology and Regenerative MedicineSevilleSpain
| | - Laia Lladó-Pelfort
- Departament de Ciències Bàsiques, Universitat de Vic-Universitat Central de CatalunyaBarcelonaSpain
| | - Kazuhiro Yamakawa
- Laboratory for Neurogenetics, RIKEN Center for Brain ScienceSaitamaJapan
- Department of Neurodevelopmental Disorder Genetics, Institute of Brain Science, Nagoya City University Graduate School of Medical ScienceNagoyaJapan
| | - Francesc Artigas
- Departament de Neurociències i Terapèutica Experimental, CSIC-Institut d’Investigacions Biomèdiques de BarcelonaBarcelonaSpain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos IIIMadridSpain
| | - James M Shine
- Brain and Mind Centre, University of SydneySydneyAustralia
| | - Andrew E Hudson
- Department of Anesthesiology, Veterans Affairs Greater Los Angeles Healthcare SystemLos AngelesUnited States
- Department of Anesthesiology and Perioperative Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Nader Pouratian
- Department of Neurological Surgery, UT Southwestern Medical CenterDallasUnited States
| | - Martin M Monti
- Department of Psychology, University of California, Los AngelesLos AngelesUnited States
- Department of Neurosurgery, University of California, Los AngelesLos AngelesUnited States
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22
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Leeds BK, Kostello KF, Liu YY, Nelson CR, Biggins S, Asbury CL. Mechanical coupling coordinates microtubule growth. eLife 2023; 12:RP89467. [PMID: 38150374 PMCID: PMC10752587 DOI: 10.7554/elife.89467] [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] [Indexed: 12/29/2023] Open
Abstract
During mitosis, kinetochore-attached microtubules form bundles (k-fibers) in which many filaments grow and shorten in near-perfect unison to align and segregate each chromosome. However, individual microtubules grow at intrinsically variable rates, which must be tightly regulated for a k-fiber to behave as a single unit. This exquisite coordination might be achieved biochemically, via selective binding of polymerases and depolymerases, or mechanically, because k-fiber microtubules are coupled through a shared load that influences their growth. Here, we use a novel dual laser trap assay to show that microtubule pairs growing in vitro are coordinated by mechanical coupling. Kinetic analyses show that microtubule growth is interrupted by stochastic, force-dependent pauses and indicate persistent heterogeneity in growth speed during non-pauses. A simple model incorporating both force-dependent pausing and persistent growth speed heterogeneity explains the measured coordination of microtubule pairs without any free fit parameters. Our findings illustrate how microtubule growth may be synchronized during mitosis and provide a basis for modeling k-fiber bundles with three or more microtubules, as found in many eukaryotes.
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Affiliation(s)
- Bonnibelle K Leeds
- Department of Physiology & Biophysics, University of WashingtonSeattleUnited States
| | - Katelyn F Kostello
- Department of Physiology & Biophysics, University of WashingtonSeattleUnited States
| | - Yuna Y Liu
- Department of Physiology & Biophysics, University of WashingtonSeattleUnited States
| | - Christian R Nelson
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Sue Biggins
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Charles L Asbury
- Department of Physiology & Biophysics, University of WashingtonSeattleUnited States
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23
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Piscitello-Gómez R, Gruber FS, Krishna A, Duclut C, Modes CD, Popović M, Jülicher F, Dye NA, Eaton S. Core PCP mutations affect short-time mechanical properties but not tissue morphogenesis in the Drosophila pupal wing. eLife 2023; 12:e85581. [PMID: 38117039 PMCID: PMC10843330 DOI: 10.7554/elife.85581] [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: 12/15/2022] [Accepted: 12/18/2023] [Indexed: 12/21/2023] Open
Abstract
How morphogenetic movements are robustly coordinated in space and time is a fundamental open question in biology. We study this question using the wing of Drosophila melanogaster, an epithelial tissue that undergoes large-scale tissue flows during pupal stages. Previously, we showed that pupal wing morphogenesis involves both cellular behaviors that allow relaxation of mechanical tissue stress, as well as cellular behaviors that appear to be actively patterned (Etournay et al., 2015). Here, we show that these active cellular behaviors are not guided by the core planar cell polarity (PCP) pathway, a conserved signaling system that guides tissue development in many other contexts. We find no significant phenotype on the cellular dynamics underlying pupal morphogenesis in mutants of core PCP. Furthermore, using laser ablation experiments, coupled with a rheological model to describe the dynamics of the response to laser ablation, we conclude that while core PCP mutations affect the fast timescale response to laser ablation they do not significantly affect overall tissue mechanics. In conclusion, our work shows that cellular dynamics and tissue shape changes during Drosophila pupal wing morphogenesis do not require core PCP as an orientational guiding cue.
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Affiliation(s)
- Romina Piscitello-Gómez
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- DFG Excellence Cluster Physics of Life, Technische Universität DresdenDresdenGermany
| | - Franz S Gruber
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- National Phenotypic Screening Centre, University of DundeeDundeeUnited Kingdom
| | - Abhijeet Krishna
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- DFG Excellence Cluster Physics of Life, Technische Universität DresdenDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Charlie Duclut
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, Université PSL, Sorbonne UniversitéParisFrance
- Max Planck Institute for Physics of Complex SystemsDresdenGermany
- Université Paris Cité, Laboratoire Matière et Systèmes ComplexesParisFrance
| | - Carl D Modes
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- DFG Excellence Cluster Physics of Life, Technische Universität DresdenDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
| | - Marko Popović
- DFG Excellence Cluster Physics of Life, Technische Universität DresdenDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Max Planck Institute for Physics of Complex SystemsDresdenGermany
| | - Frank Jülicher
- DFG Excellence Cluster Physics of Life, Technische Universität DresdenDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Max Planck Institute for Physics of Complex SystemsDresdenGermany
| | - Natalie A Dye
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- DFG Excellence Cluster Physics of Life, Technische Universität DresdenDresdenGermany
- Mildred Scheel Nachwuchszentrum P2, Medical Faculty, Technische Universität DresdenDresdenGermany
| | - Suzanne Eaton
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- DFG Excellence Cluster Physics of Life, Technische Universität DresdenDresdenGermany
- Center for Systems Biology DresdenDresdenGermany
- Biotechnologisches Zentrum, Technische Universität DresdenDresdenGermany
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24
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Abstract
Nucleotide and force-dependent mechanisms control how the viral genome of lambda bacteriophage is inserted into capsids.
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Affiliation(s)
- Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis UniversityBudapestHungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis UniversityBudapestHungary
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25
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Noetscher GM, Serano PJ, Horner M, Prokop A, Hanson J, Fujimoto K, Brown J, Nazarian A, Ackerman J, Makaroff SN. An in silico testbed for fast and accurate MR labeling of orthopedic implants. eLife 2023; 12:RP90440. [PMID: 38096104 PMCID: PMC10721214 DOI: 10.7554/elife.90440] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
One limitation on the ability to monitor health in older adults using magnetic resonance (MR) imaging is the presence of implants, where the prevalence of implantable devices (orthopedic, cardiac, neuromodulation) increases in the population, as does the pervasiveness of conditions requiring MRI studies for diagnosis (musculoskeletal diseases, infections, or cancer). The present study describes a novel multiphysics implant modeling testbed using the following approaches with two examples: (1) an in silico human model based on the widely available Visible Human Project (VHP) cryo-section dataset; (2) a finite element method (FEM) modeling software workbench from Ansys (Electronics Desktop/Mechanical) to model MR radio frequency (RF) coils and the temperature rise modeling in heterogeneous media. The in silico VHP-Female model (250 parts with an additional 40 components specifically characterizing embedded implants and resultant surrounding tissues) corresponds to a 60-year-old female with a body mass index of 36. The testbed includes the FEM-compatible in silico human model, an implant embedding procedure, a generic parameterizable MRI RF birdcage two-port coil model, a workflow for computing heat sources on the implant surface and in adjacent tissues, and a thermal FEM solver directly linked to the MR coil simulator to determine implant heating based on an MR imaging study protocol. The primary target is MR labeling of large orthopedic implants. The testbed has very recently been approved by the US Food and Drug Administration (FDA) as a medical device development tool for 1.5 T orthopedic implant examinations.
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Affiliation(s)
- Gregory M Noetscher
- Electrical & Computer Eng. Dept, Worcester Polytechnic InstituteWorcesterUnited States
| | | | | | | | | | | | - James Brown
- Micro Systems Enigineering, Inc, an affiliate of BiotronikLake OswegoUnited States
| | - Ara Nazarian
- Musculoskeletal Translational Innovation Initiative, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center and Harvard Medical SchoolBostonUnited States
| | - Jerome Ackerman
- Harvard Medical SchoolBostonUnited States
- Athinoula A Martinos Center for Biomed. Imaging, Massachusetts General HospitalCharlestownUnited States
| | - Sergey N Makaroff
- Electrical & Computer Eng. Dept, Worcester Polytechnic InstituteWorcesterUnited States
- Athinoula A Martinos Center for Biomed. Imaging, Massachusetts General HospitalCharlestownUnited States
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26
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Ramesh V, Krishnan J. A unified approach to dissecting biphasic responses in cell signaling. eLife 2023; 13:e86520. [PMID: 38054655 DOI: 10.7554/elife.86520] [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: 01/30/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023] Open
Abstract
Biphasic responses are encountered at all levels in biological systems. At the cellular level, biphasic dose-responses are widely encountered in cell signaling and post-translational modification systems and represent safeguards against overactivation or overexpression of species. In this paper, we provide a unified theoretical synthesis of biphasic responses in cell signaling systems, by assessing signaling systems ranging from basic biochemical building blocks to canonical network structures to well-characterized exemplars on one hand, and examining different types of doses on the other. By using analytical and computational approaches applied to a range of systems across levels (described by broadly employed models), we reveal (i) design principles enabling the presence of biphasic responses, including in almost all instances, an explicit characterization of the parameter space (ii) structural factors which preclude the possibility of biphasic responses (iii) different combinations of the presence or absence of enzyme-biphasic and substrate-biphasic responses, representing safeguards against overactivation and overexpression, respectively (iv) the possibility of broadly robust biphasic responses (v) the complete alteration of signaling behavior in a network due to biphasic interactions between species (biphasic regulation) (vi) the propensity of different co-existing biphasic responses in the Erk signaling network. These results both individually and in totality have a number of important consequences for systems and synthetic biology.
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Affiliation(s)
- Vaidhiswaran Ramesh
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London, London, United Kingdom
| | - J Krishnan
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London, London, United Kingdom
- Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London, United Kingdom
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27
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Briggs JK, Gresch A, Marinelli I, Dwulet JM, Albers DJ, Kravets V, Benninger RKP. β-cell intrinsic dynamics rather than gap junction structure dictates subpopulations in the islet functional network. eLife 2023; 12:e83147. [PMID: 38018905 PMCID: PMC10803032 DOI: 10.7554/elife.83147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/31/2022] [Accepted: 11/27/2023] [Indexed: 11/30/2023] Open
Abstract
Diabetes is caused by the inability of electrically coupled, functionally heterogeneous β-cells within the pancreatic islet to provide adequate insulin secretion. Functional networks have been used to represent synchronized oscillatory [Ca2+] dynamics and to study β-cell subpopulations, which play an important role in driving islet function. The mechanism by which highly synchronized β-cell subpopulations drive islet function is unclear. We used experimental and computational techniques to investigate the relationship between functional networks, structural (gap junction) networks, and intrinsic β-cell dynamics in slow and fast oscillating islets. Highly synchronized subpopulations in the functional network were differentiated by intrinsic dynamics, including metabolic activity and KATP channel conductance, more than structural coupling. Consistent with this, intrinsic dynamics were more predictive of high synchronization in the islet functional network as compared to high levels of structural coupling. Finally, dysfunction of gap junctions, which can occur in diabetes, caused decreases in the efficiency and clustering of the functional network. These results indicate that intrinsic dynamics rather than structure drive connections in the functional network and highly synchronized subpopulations, but gap junctions are still essential for overall network efficiency. These findings deepen our interpretation of functional networks and the formation of functional subpopulations in dynamic tissues such as the islet.
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Affiliation(s)
- Jennifer K Briggs
- Department of Bioengineering, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Anne Gresch
- Department of Bioengineering, University of Colorado Anschutz Medical CampusAuroraUnited States
- Barbara Davis Center for Childhood Diabetes, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Isabella Marinelli
- Centre for Systems Modelling and Quantitative Biomedicine, University of BirminghamBirminghamUnited Kingdom
| | - JaeAnn M Dwulet
- Department of Bioengineering, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - David J Albers
- Department of Bioengineering, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Biomedical Informatics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Vira Kravets
- Department of Bioengineering, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Richard KP Benninger
- Department of Bioengineering, University of Colorado Anschutz Medical CampusAuroraUnited States
- Barbara Davis Center for Childhood Diabetes, University of Colorado Anschutz Medical CampusAuroraUnited States
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28
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Berne A, Zhang T, Shomar J, Ferrer AJ, Valdes A, Ohyama T, Klein M. Mechanical vibration patterns elicit behavioral transitions and habituation in crawling Drosophila larvae. eLife 2023; 12:e69205. [PMID: 37855833 PMCID: PMC10586805 DOI: 10.7554/elife.69205] [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: 04/07/2021] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
How animals respond to repeatedly applied stimuli, and how animals respond to mechanical stimuli in particular, are important questions in behavioral neuroscience. We study adaptation to repeated mechanical agitation using the Drosophila larva. Vertical vibration stimuli elicit a discrete set of responses in crawling larvae: continuation, pause, turn, and reversal. Through high-throughput larva tracking, we characterize how the likelihood of each response depends on vibration intensity and on the timing of repeated vibration pulses. By examining transitions between behavioral states at the population and individual levels, we investigate how the animals habituate to the stimulus patterns. We identify time constants associated with desensitization to prolonged vibration, with re-sensitization during removal of a stimulus, and additional layers of habituation that operate in the overall response. Known memory-deficient mutants exhibit distinct behavior profiles and habituation time constants. An analogous simple electrical circuit suggests possible neural and molecular processes behind adaptive behavior.
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Affiliation(s)
- Alexander Berne
- Department of Physics, Department of Biology, University of MiamiCoral GablesUnited States
| | - Tom Zhang
- Department of Physics, Department of Biology, University of MiamiCoral GablesUnited States
| | - Joseph Shomar
- Department of Physics, Department of Biology, University of MiamiCoral GablesUnited States
| | - Anggie J Ferrer
- Department of Physics, Department of Biology, University of MiamiCoral GablesUnited States
| | - Aaron Valdes
- Department of Physics, Department of Biology, University of MiamiCoral GablesUnited States
| | - Tomoko Ohyama
- Department of Biology, McGill UniversityMontrealCanada
| | - Mason Klein
- Department of Physics, Department of Biology, University of MiamiCoral GablesUnited States
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29
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Bellegarda C, Zavard G, Moisan L, Brochard-Wyart F, Joanny JF, Gray RS, Cantaut-Belarif Y, Wyart C. The Reissner fiber under tension in vivo shows dynamic interaction with ciliated cells contacting the cerebrospinal fluid. eLife 2023; 12:e86175. [PMID: 37772792 PMCID: PMC10617989 DOI: 10.7554/elife.86175] [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: 01/14/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023] Open
Abstract
The Reissner fiber (RF) is an acellular thread positioned in the midline of the central canal that aggregates thanks to the beating of numerous cilia from ependymal radial glial cells (ERGs) generating flow in the central canal of the spinal cord. RF together with cerebrospinal fluid (CSF)-contacting neurons (CSF-cNs) form an axial sensory system detecting curvature. How RF, CSF-cNs and the multitude of motile cilia from ERGs interact in vivo appears critical for maintenance of RF and sensory functions of CSF-cNs to keep a straight body axis, but is not well-understood. Using in vivo imaging in larval zebrafish, we show that RF is under tension and resonates dorsoventrally. Focal RF ablations trigger retraction and relaxation of the fiber's cut ends, with larger retraction speeds for rostral ablations. We built a mechanical model that estimates RF stress diffusion coefficient D at 5 mm2/s and reveals that tension builds up rostrally along the fiber. After RF ablation, spontaneous CSF-cN activity decreased and ciliary motility changed, suggesting physical interactions between RF and cilia projecting into the central canal. We observed that motile cilia were caudally-tilted and frequently interacted with RF. We propose that the numerous ependymal motile monocilia contribute to RF's heterogenous tension via weak interactions. Our work demonstrates that under tension, the Reissner fiber dynamically interacts with motile cilia generating CSF flow and spinal sensory neurons.
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Affiliation(s)
- Celine Bellegarda
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique–Hôpitaux de Paris, Campus Hospitalier Pitié-SalpêtrièreParisFrance
| | - Guillaume Zavard
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique–Hôpitaux de Paris, Campus Hospitalier Pitié-SalpêtrièreParisFrance
| | | | | | - Jean-François Joanny
- Paris Sciences et Lettres (PSL) University, Institut Curie, Sorbonne UniversitéParisFrance
- Paris Sciences et Lettres (PSL) University, Collège de FranceParisFrance
| | - Ryan S Gray
- Dell Pediatrics Research Institute, The University of Texas at AustinAustinUnited States
| | - Yasmine Cantaut-Belarif
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique–Hôpitaux de Paris, Campus Hospitalier Pitié-SalpêtrièreParisFrance
| | - Claire Wyart
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique–Hôpitaux de Paris, Campus Hospitalier Pitié-SalpêtrièreParisFrance
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30
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Quiroga X, Walani N, Disanza A, Chavero A, Mittens A, Tebar F, Trepat X, Parton RG, Geli MI, Scita G, Arroyo M, Le Roux AL, Roca-Cusachs P. A mechanosensing mechanism controls plasma membrane shape homeostasis at the nanoscale. eLife 2023; 12:e72316. [PMID: 37747150 PMCID: PMC10569792 DOI: 10.7554/elife.72316] [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: 07/19/2021] [Accepted: 09/24/2023] [Indexed: 09/26/2023] Open
Abstract
As cells migrate and experience forces from their surroundings, they constantly undergo mechanical deformations which reshape their plasma membrane (PM). To maintain homeostasis, cells need to detect and restore such changes, not only in terms of overall PM area and tension as previously described, but also in terms of local, nanoscale topography. Here, we describe a novel phenomenon, by which cells sense and restore mechanically induced PM nanoscale deformations. We show that cell stretch and subsequent compression reshape the PM in a way that generates local membrane evaginations in the 100 nm scale. These evaginations are recognized by I-BAR proteins, which triggers a burst of actin polymerization mediated by Rac1 and Arp2/3. The actin polymerization burst subsequently re-flattens the evagination, completing the mechanochemical feedback loop. Our results demonstrate a new mechanosensing mechanism for PM shape homeostasis, with potential applicability in different physiological scenarios.
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Affiliation(s)
- Xarxa Quiroga
- Institute for Bioengineering of Catalonia, the Barcelona Institute of Technology (BIST)BarcelonaSpain
- Departament de Biomedicina, Unitat de Biofísica i Bioenginyeria, Facultat de Medicina i Ciències de la Salut, Universitat de BarcelonaBarcelonaSpain
| | - Nikhil Walani
- Department of Applied Mechanics, IIT DelhiNew DelhiIndia
| | - Andrea Disanza
- IFOM ETS - The AIRC Institute of Molecular OncologyMilanItaly
| | - Albert Chavero
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Centre de Recerca Biomèdica CELLEX, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de BarcelonaBarcelonaSpain
| | - Alexandra Mittens
- Institute for Bioengineering of Catalonia, the Barcelona Institute of Technology (BIST)BarcelonaSpain
| | - Francesc Tebar
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Centre de Recerca Biomèdica CELLEX, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de BarcelonaBarcelonaSpain
| | - Xavier Trepat
- Institute for Bioengineering of Catalonia, the Barcelona Institute of Technology (BIST)BarcelonaSpain
| | - Robert G Parton
- Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis, University of QueenslandBrisbaneAustralia
| | | | - Giorgio Scita
- IFOM ETS - The AIRC Institute of Molecular OncologyMilanItaly
- Department of Oncology and Haemato-Oncology, University of MilanMilanItaly
| | - Marino Arroyo
- Institute for Bioengineering of Catalonia, the Barcelona Institute of Technology (BIST)BarcelonaSpain
- Universitat Politècnica de Catalunya (UPC), Campus Nord, Carrer de Jordi GironaBarcelonaSpain
- Centre Internacional de Mètodes Numèrics en Enginyeria (CIMNE)BarcelonaSpain
| | - Anabel-Lise Le Roux
- Institute for Bioengineering of Catalonia, the Barcelona Institute of Technology (BIST)BarcelonaSpain
| | - Pere Roca-Cusachs
- Institute for Bioengineering of Catalonia, the Barcelona Institute of Technology (BIST)BarcelonaSpain
- Departament de Biomedicina, Unitat de Biofísica i Bioenginyeria, Facultat de Medicina i Ciències de la Salut, Universitat de BarcelonaBarcelonaSpain
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31
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Ruppel A, Wörthmüller D, Misiak V, Kelkar M, Wang I, Moreau P, Méry A, Révilloud J, Charras G, Cappello G, Boudou T, Schwarz US, Balland M. Force propagation between epithelial cells depends on active coupling and mechano-structural polarization. eLife 2023; 12:e83588. [PMID: 37548995 PMCID: PMC10511242 DOI: 10.7554/elife.83588] [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: 09/20/2022] [Accepted: 08/07/2023] [Indexed: 08/08/2023] Open
Abstract
Cell-generated forces play a major role in coordinating the large-scale behavior of cell assemblies, in particular during development, wound healing, and cancer. Mechanical signals propagate faster than biochemical signals, but can have similar effects, especially in epithelial tissues with strong cell-cell adhesion. However, a quantitative description of the transmission chain from force generation in a sender cell, force propagation across cell-cell boundaries, and the concomitant response of receiver cells is missing. For a quantitative analysis of this important situation, here we propose a minimal model system of two epithelial cells on an H-pattern ('cell doublet'). After optogenetically activating RhoA, a major regulator of cell contractility, in the sender cell, we measure the mechanical response of the receiver cell by traction force and monolayer stress microscopies. In general, we find that the receiver cells show an active response so that the cell doublet forms a coherent unit. However, force propagation and response of the receiver cell also strongly depend on the mechano-structural polarization in the cell assembly, which is controlled by cell-matrix adhesion to the adhesive micropattern. We find that the response of the receiver cell is stronger when the mechano-structural polarization axis is oriented perpendicular to the direction of force propagation, reminiscent of the Poisson effect in passive materials. We finally show that the same effects are at work in small tissues. Our work demonstrates that cellular organization and active mechanical response of a tissue are key to maintain signal strength and lead to the emergence of elasticity, which means that signals are not dissipated like in a viscous system, but can propagate over large distances.
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Affiliation(s)
- Artur Ruppel
- Université Grenoble Alpes, CNRS, LIPhyGrenobleFrance
| | - Dennis Wörthmüller
- Institute for Theoretical Physics, Heidelberg UniversityHeidelbergGermany
- BioQuant–Center for Quantitative Biology, Heidelberg UniversityHeidelbergGermany
| | | | - Manasi Kelkar
- London Centre for Nanotechnology, University College LondonLondonUnited Kingdom
| | - Irène Wang
- Université Grenoble Alpes, CNRS, LIPhyGrenobleFrance
| | | | - Adrien Méry
- Université Grenoble Alpes, CNRS, LIPhyGrenobleFrance
| | | | - Guillaume Charras
- London Centre for Nanotechnology, University College LondonLondonUnited Kingdom
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
- Institute for the Physics of Living Systems, University College LondonLondonUnited Kingdom
| | | | - Thomas Boudou
- Université Grenoble Alpes, CNRS, LIPhyGrenobleFrance
| | - Ulrich S Schwarz
- Institute for Theoretical Physics, Heidelberg UniversityHeidelbergGermany
- BioQuant–Center for Quantitative Biology, Heidelberg UniversityHeidelbergGermany
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32
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Yu J, Dancausse S, Paz M, Faderin T, Gaviria M, Shomar JW, Zucker D, Venkatachalam V, Klein M. Continuous, long-term crawling behavior characterized by a robotic transport system. eLife 2023; 12:e86585. [PMID: 37535068 PMCID: PMC10400072 DOI: 10.7554/elife.86585] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023] Open
Abstract
Detailed descriptions of behavior provide critical insight into the structure and function of nervous systems. In Drosophila larvae and many other systems, short behavioral experiments have been successful in characterizing rapid responses to a range of stimuli at the population level. However, the lack of long-term continuous observation makes it difficult to dissect comprehensive behavioral dynamics of individual animals and how behavior (and therefore the nervous system) develops over time. To allow for long-term continuous observations in individual fly larvae, we have engineered a robotic instrument that automatically tracks and transports larvae throughout an arena. The flexibility and reliability of its design enables controlled stimulus delivery and continuous measurement over developmental time scales, yielding an unprecedented level of detailed locomotion data. We utilize the new system's capabilities to perform continuous observation of exploratory search behavior over a duration of 6 hr with and without a thermal gradient present, and in a single larva for over 30 hr. Long-term free-roaming behavior and analogous short-term experiments show similar dynamics that take place at the beginning of each experiment. Finally, characterization of larval thermotaxis in individuals reveals a bimodal distribution in navigation efficiency, identifying distinct phenotypes that are obfuscated when only analyzing population averages.
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Affiliation(s)
- James Yu
- Department of Physics, Northeastern University, Boston, United States
| | - Stephanie Dancausse
- Department of Physics and Department of Biology, University of Miami, Coral Gables, United States
| | - Maria Paz
- Department of Physics, Northeastern University, Boston, United States
| | - Tolu Faderin
- Department of Physics, Northeastern University, Boston, United States
| | - Melissa Gaviria
- Department of Physics and Department of Biology, University of Miami, Coral Gables, United States
| | - Joseph W Shomar
- Department of Physics and Department of Biology, University of Miami, Coral Gables, United States
| | | | | | - Mason Klein
- Department of Physics and Department of Biology, University of Miami, Coral Gables, United States
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33
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Chen KS, Wu R, Gershow MH, Leifer AM. Continuous odor profile monitoring to study olfactory navigation in small animals. eLife 2023; 12:e85910. [PMID: 37489570 PMCID: PMC10425172 DOI: 10.7554/elife.85910] [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: 01/03/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023] Open
Abstract
Olfactory navigation is observed across species and plays a crucial role in locating resources for survival. In the laboratory, understanding the behavioral strategies and neural circuits underlying odor-taxis requires a detailed understanding of the animal's sensory environment. For small model organisms like Caenorhabditis elegans and larval Drosophila melanogaster, controlling and measuring the odor environment experienced by the animal can be challenging, especially for airborne odors, which are subject to subtle effects from airflow, temperature variation, and from the odor's adhesion, adsorption, or reemission. Here, we present a method to control and measure airborne odor concentration in an arena compatible with an agar substrate. Our method allows continuous controlling and monitoring of the odor profile while imaging animal behavior. We construct stationary chemical landscapes in an odor flow chamber through spatially patterned odorized air. The odor concentration is measured with a spatially distributed array of digital gas sensors. Careful placement of the sensors allows the odor concentration across the arena to be continuously inferred in space and monitored through time. We use this approach to measure the odor concentration that each animal experiences as it undergoes chemotaxis behavior and report chemotaxis strategies for C. elegans and D. melanogaster larvae populations as they navigate spatial odor landscapes.
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Affiliation(s)
- Kevin S Chen
- Princeton Neuroscience Institute, Princeton UniversityPrincetonUnited States
| | - Rui Wu
- Department of Physics, New York UniversityNew YorkUnited States
| | - Marc H Gershow
- Department of Physics, New York UniversityNew YorkUnited States
- Center for Neural Science, New York UniversityNew YorkUnited States
| | - Andrew M Leifer
- Princeton Neuroscience Institute, Princeton UniversityPrincetonUnited States
- Department of Physics, Princeton UniversityPrincetonUnited States
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34
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Stehnach MR, Henshaw RJ, Floge SA, Guasto JS. Multiplexed microfluidic screening of bacterial chemotaxis. eLife 2023; 12:e85348. [PMID: 37486823 PMCID: PMC10365836 DOI: 10.7554/elife.85348] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 06/15/2023] [Indexed: 07/26/2023] Open
Abstract
Microorganism sensing of and responding to ambient chemical gradients regulates a myriad of microbial processes that are fundamental to ecosystem function and human health and disease. The development of efficient, high-throughput screening tools for microbial chemotaxis is essential to disentangling the roles of diverse chemical compounds and concentrations that control cell nutrient uptake, chemorepulsion from toxins, and microbial pathogenesis. Here, we present a novel microfluidic multiplexed chemotaxis device (MCD) which uses serial dilution to simultaneously perform six parallel bacterial chemotaxis assays that span five orders of magnitude in chemostimulant concentration on a single chip. We first validated the dilution and gradient generation performance of the MCD, and then compared the measured chemotactic response of an established bacterial chemotaxis system (Vibrio alginolyticus) to a standard microfluidic assay. Next, the MCD's versatility was assessed by quantifying the chemotactic responses of different bacteria (Psuedoalteromonas haloplanktis, Escherichia coli) to different chemoattractants and chemorepellents. The MCD vastly accelerates the chemotactic screening process, which is critical to deciphering the complex sea of chemical stimuli underlying microbial responses.
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Affiliation(s)
- Michael R Stehnach
- Department of Mechanical Engineering, Tufts University, Medford, United States
| | - Richard J Henshaw
- Department of Mechanical Engineering, Tufts University, Medford, United States
| | - Sheri A Floge
- Department of Biology, Wake Forest University, Winston-Salem, United States
| | - Jeffrey S Guasto
- Department of Mechanical Engineering, Tufts University, Medford, United States
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35
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Sampaio P, Pestana S, Bota C, Guerrero A, Telley IA, Smith D, Lopes SS. Fluid extraction from the left-right organizer uncovers mechanical properties needed for symmetry breaking. eLife 2023; 12:e83861. [PMID: 37477290 PMCID: PMC10361723 DOI: 10.7554/elife.83861] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/27/2023] [Indexed: 07/22/2023] Open
Abstract
Humans and other vertebrates define body axis left-right asymmetry in the early stages of embryo development. The mechanism behind left-right establishment is not fully understood. Symmetry breaking occurs in a dedicated organ called the left-right organizer (LRO) and involves motile cilia generating fluid-flow therein. However, it has been a matter of debate whether the process of symmetry breaking relies on a chemosensory or a mechanosensory mechanism (Shinohara et al., 2012). Novel tailored manipulations for LRO fluid extraction in living zebrafish embryos allowed us to pinpoint a physiological developmental period for breaking left-right symmetry during development. The shortest critical time-window was narrowed to one hour and characterized by a mild counterclockwise flow. The experimental challenge consisted in emptying the LRO of its fluid, abrogating simultaneously flow force and chemical determinants. Our findings revealed an unprecedented recovery capacity of the embryo to re-fil and re-circulate new LRO fluid. The embryos that later developed laterality problems were found to be those that had lower anterior angular velocity and thus less anterior-posterior heterogeneity. Next, aiming to test the presence of any secreted determinant, we replaced the extracted LRO fluid by a physiological buffer. Despite some transitory flow homogenization, laterality defects were absent unless viscosity was altered, demonstrating that symmetry breaking does not depend on the nature of the fluid content but is rather sensitive to fluid mechanics. Altogether, we conclude that the zebrafish LRO is more sensitive to fluid dynamics for symmetry breaking.
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Affiliation(s)
- Pedro Sampaio
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School. Faculdade de8 Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Sara Pestana
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School. Faculdade de8 Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Catarina Bota
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School. Faculdade de8 Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Adán Guerrero
- Laboratorio Nacional de Microscopía Avanzada. Departamento de Genética del Desarrollo y Fisiología Molecular. Instituto de Biotecnología. Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Ivo A Telley
- Instituto Gulbenkian de Ciência, Fundação Calouste Gulbenkian, Oeiras, Portugal
| | - David Smith
- School of Mathematics, University of Birmingham, Birmingham, United Kingdom
- Institute for Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Susana Santos Lopes
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School. Faculdade de8 Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
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36
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Polyansky AA, Gallego LD, Efremov RG, Köhler A, Zagrovic B. Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales. eLife 2023; 12:e80038. [PMID: 37470705 PMCID: PMC10406433 DOI: 10.7554/elife.80038] [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: 05/06/2022] [Accepted: 07/18/2023] [Indexed: 07/21/2023] Open
Abstract
Non-membrane-bound biomolecular condensates have been proposed to represent an important mode of subcellular organization in diverse biological settings. However, the fundamental principles governing the spatial organization and dynamics of condensates at the atomistic level remain unclear. The Saccharomyces cerevisiae Lge1 protein is required for histone H2B ubiquitination and its N-terminal intrinsically disordered fragment (Lge11-80) undergoes robust phase separation. This study connects single- and multi-chain all-atom molecular dynamics simulations of Lge11-80 with the in vitro behavior of Lge11-80 condensates. Analysis of modeled protein-protein interactions elucidates the key determinants of Lge11-80 condensate formation and links configurational entropy, valency, and compactness of proteins inside the condensates. A newly derived analytical formalism, related to colloid fractal cluster formation, describes condensate architecture across length scales as a function of protein valency and compactness. In particular, the formalism provides an atomistically resolved model of Lge11-80 condensates on the scale of hundreds of nanometers starting from individual protein conformers captured in simulations. The simulation-derived fractal dimensions of condensates of Lge11-80 and its mutants agree with their in vitro morphologies. The presented framework enables a multiscale description of biomolecular condensates and embeds their study in a wider context of colloid self-organization.
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Affiliation(s)
- Anton A Polyansky
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational BiologyViennaAustria
| | - Laura D Gallego
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
| | - Roman G Efremov
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussian Federation
| | - Alwin Köhler
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
- University of Vienna, Center for Molecular Biology, Department of Biochemistry and Cell BiologyViennaAustria
| | - Bojan Zagrovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational BiologyViennaAustria
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37
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Adame-Arana O, Bajpai G, Lorber D, Volk T, Safran S. Regulation of chromatin microphase separation by binding of protein complexes. eLife 2023; 12:e82983. [PMID: 37436818 DOI: 10.7554/elife.82983] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
We show evidence of the association of RNA polymerase II (RNAP) with chromatin in a core-shell organization, reminiscent of microphase separation where the cores comprise dense chromatin and the shell, RNAP and chromatin with low density. These observations motivate our physical model for the regulation of core-shell chromatin organization. Here, we model chromatin as a multiblock copolymer, comprising active and inactive regions (blocks) that are both in poor solvent and tend to be condensed in the absence of binding proteins. However, we show that the solvent quality for the active regions of chromatin can be regulated by the binding of protein complexes (e.g., RNAP and transcription factors). Using the theory of polymer brushes, we find that such binding leads to swelling of the active chromatin regions which in turn modifies the spatial organization of the inactive regions. In addition, we use simulations to study spherical chromatin micelles, whose cores comprise inactive regions and shells comprise active regions and bound protein complexes. In spherical micelles the swelling increases the number of inactive cores and controls their size. Thus, genetic modifications affecting the binding strength of chromatin-binding protein complexes may modulate the solvent quality experienced by chromatin and regulate the physical organization of the genome.
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Affiliation(s)
- Omar Adame-Arana
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Gaurav Bajpai
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Dana Lorber
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Talila Volk
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Samuel Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
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38
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Richter M, Neahring L, Tao J, Sutanto R, Cho NH, Dumont S. Kinetochore-fiber lengths are maintained locally but coordinated globally by polesin the mammalian spindle. eLife 2023; 12:e85208. [PMID: 37395732 DOI: 10.7554/elife.85208] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/02/2023] [Indexed: 07/04/2023] Open
Abstract
At each cell division, nanometer-scale components self-organize to build a micron-scale spindle. In mammalian spindles, microtubule bundles called kinetochore-fibers attach to chromosomes and focus into spindle poles. Despite evidence suggesting that poles can set spindle length, their role remains poorly understood. In fact, many species do not have spindle poles. Here, we probe the pole's contribution to mammalian spindle length, dynamics, and function by inhibiting dynein to generate spindles whose kinetochore-fibers do not focus into poles, yet maintain a metaphase steady-state length. We find that unfocused kinetochore-fibers have a mean length indistinguishable from control, but a broader length distribution, and reduced length coordination between sisters and neighbors. Further, we show that unfocused kinetochore-fibers, like control, can grow back to their steady-state length if acutely shortened by drug treatment or laser ablation: they recover their length by tuning their end dynamics, albeit slower due to their reduced baseline dynamics. Thus, kinetochore-fiber dynamics are regulated by their length, not just pole-focusing forces. Finally, we show that spindles with unfocused kinetochore-fibers can segregate chromosomes but fail to correctly do so. We propose that mammalian spindle length emerges locally from individual k-fibers while spindle poles globally coordinate k-fibers across space and time.
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Affiliation(s)
- Manuela Richter
- Tetrad Graduate Program, University of California - San Francisco, San Francisco, United States
| | - Lila Neahring
- Department of Bioengineering and Therapeutic Sciences, University of California - San Francisco, San Francisco, United States
| | - Jinghui Tao
- Department of Bioengineering and Therapeutic Sciences, University of California - San Francisco, San Francisco, United States
| | - Renaldo Sutanto
- Department of Bioengineering and Therapeutic Sciences, University of California - San Francisco, San Francisco, United States
| | - Nathan H Cho
- Tetrad Graduate Program, University of California - San Francisco, San Francisco, United States
| | - Sophie Dumont
- Department of Cell and Tissue Biology, University of California - San Francisco, San Francisco, United States
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39
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Nawroth JC, Giez C, Klimovich A, Kanso E, Bosch TCG. Spontaneous body wall contractions stabilize the fluid microenvironment that shapes host-microbe associations. eLife 2023; 12:e83637. [PMID: 37399060 PMCID: PMC10396340 DOI: 10.7554/elife.83637] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 06/30/2023] [Indexed: 07/04/2023] Open
Abstract
The freshwater polyp Hydra is a popular biological model system; however, we still do not understand one of its most salient behaviours, the generation of spontaneous body wall contractions. Here, by applying experimental fluid dynamics analysis and mathematical modelling, we provide functional evidence that spontaneous contractions of body walls enhance the transport of chemical compounds from and to the tissue surface where symbiotic bacteria reside. Experimentally, a reduction in the frequency of spontaneous body wall contractions is associated with a changed composition of the colonizing microbiota. Together, our findings suggest that spontaneous body wall contractions create an important fluid transport mechanism that (1) may shape and stabilize specific host-microbe associations and (2) create fluid microhabitats that may modulate the spatial distribution of the colonizing microbes. This mechanism may be more broadly applicable to animal-microbe interactions since research has shown that rhythmic spontaneous contractions in the gastrointestinal tracts are essential for maintaining normal microbiota.
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Affiliation(s)
| | | | | | - Eva Kanso
- Aerospace and Mechanical Engineering, University of Southern California, Los Angeles, United States
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40
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Ye Y, Lin J. Putting scaling laws on a physical foundation. eLife 2023; 12:e89415. [PMID: 37314067 DOI: 10.7554/elife.89415] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023] Open
Abstract
As a cell changes size during the cell cycle, why does its density remain constant?
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Affiliation(s)
- Yiyang Ye
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Jie Lin
- Center for Quantitative Biology and the Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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41
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Shimizu TS, Kiers ET, Stone HA. Exploring the dynamics of vascular adaptation. eLife 2023; 12:88052. [PMID: 37227267 DOI: 10.7554/elife.88052] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
A combination of in toto imaging and theory suggests a new mechanism for the remodeling of veins in vascular networks.
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Affiliation(s)
| | - E Toby Kiers
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, United States
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42
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Gomez S, Bureau L, John K, Chêne EN, Débarre D, Lecuyer S. Substrate stiffness impacts early biofilm formation by modulating Pseudomonas aeruginosa twitching motility. eLife 2023; 12:81112. [PMID: 37158596 DOI: 10.7554/elife.81112] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
Surface-associated lifestyles dominate in the bacterial world. Large multicellular assemblies, called biofilms, are essential to the survival of bacteria in harsh environments, and are closely linked to antibiotic resistance in pathogenic strains. Biofilms stem from the surface colonization of a wide variety of substrates encountered by bacteria, from living tissues to inert materials. Here, we demonstrate experimentally that the promiscuous opportunistic pathogen Pseudomonas aeruginosa explores substrates differently based on their rigidity, leading to striking variations in biofilm structure, exopolysaccharides (EPS) distribution, strain mixing during co-colonization and phenotypic expression. Using simple kinetic models, we show that these phenotypes arise through a mechanical interaction between the elasticity of the substrate and the type IV pilus (T4P) machinery, that mediates the surface-based motility called twitching. Together, our findings reveal a new role for substrate softness in the spatial organization of bacteria in complex microenvironments, with far-reaching consequences on efficient biofilm formation.
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Affiliation(s)
- Sofia Gomez
- Université Grenoble Alpes, CNRS, Grenoble, France
| | | | - Karin John
- Université Grenoble Alpes, CNRS, Grenoble, France
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43
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Rollin R, Joanny JF, Sens P. Physical basis of the cell size scaling laws. eLife 2023; 12:82490. [PMID: 37129354 DOI: 10.7554/elife.82490] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 04/28/2023] [Indexed: 05/03/2023] Open
Abstract
Cellular growth is the result of passive physical constraints and active biological processes. Their interplay leads to the appearance of robust and ubiquitous scaling laws relating linearly cell size, dry mass, and nuclear size. Despite accumulating experimental evidence, their origin is still unclear. Here, we show that these laws can be explained quantitatively by a single model of size regulation based on three simple, yet generic, physical constraints defining altogether the Pump-Leak model. Based on quantitative estimates, we clearly map the Pump-Leak model coarse-grained parameters with the dominant cellular components. We propose that dry mass density homeostasis arises from the scaling between proteins and small osmolytes, mainly amino-acids and ions. Our model predicts this scaling to naturally fail, both at senescence when DNA and RNAs are saturated by RNA polymerases and ribosomes respectively, and at mitotic entry due to the counterion release following histone tail modifications. Based on the same physical laws, we further show that nuclear scaling results from a osmotic balance at the nuclear envelope and a large pool of metabolites, which dilutes chromatin counterions that do not scale during growth.
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Affiliation(s)
- Romain Rollin
- PSL Research University, Institut Curie, CNRS UMR168, Paris, France
| | | | - Pierre Sens
- PSL Research University, Institut Curie, CNRS UMR168, Paris, France
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44
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Ng BWL, Scheeff S, Xeque Amada J. Making it hard to replicate. eLife 2023; 12:88044. [PMID: 37114773 PMCID: PMC10147374 DOI: 10.7554/elife.88044] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Understanding how to harden liquid condensates produced by influenza A virus could accelerate the development of novel antiviral drugs.
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45
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Rao L, Horn N, Meister N, Preiss S, Taylor WR, Santuz A, Schütz P. Comparable in vivo joint kinematics between self-reported stable and unstable knees after TKA can be explained by muscular adaptation strategies: a retrospective observational study. eLife 2023; 12:85136. [PMID: 37159500 DOI: 10.7554/elife.85136] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/25/2023] [Indexed: 05/11/2023] Open
Abstract
Background: Postoperative knee instability is one of the major reasons accounting for unsatisfactory outcomes, as well as a major failure mechanism leading to total knee arthroplasty (TKA) revision. Nevertheless, subjective knee instability is not well defined clinically, plausibly because the relationships between instability and implant kinematics during functional activities of daily living remain unclear. Although muscles play a critical role in supporting the dynamic stability of the knee joint, the influence of joint instability on muscle synergy patterns is poorly understood. Therefore, this study aimed to understand the impact of self-reported joint instability on tibiofemoral kinematics and muscle synergy patterns after TKA during functional gait activities of daily living. Methods: Tibiofemoral kinematics and muscle synergy patterns were examined during level walking, downhill walking, and stair descent in eight self-reported unstable knees after TKA (3M:5F, 68.9±8.3 years, BMI 26.1±3.2 kg/m2, 31.9±20.4 months postoperatively), and compared against ten stable TKA knees (7M:3F, 62.6±6.8 years, 33.9±8.5 months postoperatively, BMI 29.4±4.8 kg/m2). For each knee joint, clinical assessments of postoperative outcome were performed, while joint kinematics were evaluated using moving video-fluoroscopy, and muscle synergy patterns were recorded using electromyography. Results: Our results reveal that average condylar A-P translations, rotations, as well as their ranges of motion were comparable between stable and unstable groups. However, the unstable group exhibited more heterogeneous muscle synergy patterns and prolonged activation of knee flexors compared to the stable group. In addition, subjects who reported instability events during measurement showed distinct, subject-specific tibiofemoral kinematic patterns in the early/mid-swing phase of gait. Conclusions: Our findings suggest that accurate movement analysis is sensitive for detecting acute instability events, but might be less robust in identifying general joint instability. Conversely, muscle synergy patterns seem to be able to identify muscular adaptation associated with underlying chronic knee instability. Funding: This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
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Affiliation(s)
- Longfeng Rao
- Laboratory for Movement Biomechanics, ETH Zurich, Zurich, Switzerland
| | - Nils Horn
- Department of lower extremities, Schulthess-Klinik, Zurich, Switzerland
| | - Nadja Meister
- Laboratory for Movement Biomechanics, ETH Zurich, Zurich, Switzerland
| | - Stefan Preiss
- Department of lower extremities, Schulthess-Klinik, Zurich, Switzerland
| | - William R Taylor
- Laboratory for Movement Biomechanics, ETH Zurich, Zurich, Switzerland
| | | | - Pascal Schütz
- Laboratory for Movement Biomechanics, ETH Zurich, Zurich, Switzerland
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46
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Bhat D, Hauf S, Plessy C, Yokobayashi Y, Pigolotti S. Correction: Speed variations of bacterial replisomes. eLife 2023; 12:88685. [PMID: 37074130 PMCID: PMC10115438 DOI: 10.7554/elife.88685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
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47
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Monfared S, Ravichandran G, Andrade J, Doostmohammadi A. Mechanical basis and topological routes to cell elimination. eLife 2023; 12:82435. [PMID: 37070647 PMCID: PMC10112887 DOI: 10.7554/elife.82435] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/22/2023] [Indexed: 04/19/2023] Open
Abstract
Cell layers eliminate unwanted cells through the extrusion process, which underlines healthy versus flawed tissue behaviors. Although several biochemical pathways have been identified, the underlying mechanical basis including the forces involved in cellular extrusion remains largely unexplored. Utilizing a phase-field model of a three-dimensional cell layer, we study the interplay of cell extrusion with cell-cell and cell-substrate interactions in a flat monolayer. Independent tuning of cell-cell versus cell-substrate adhesion forces reveals that extrusion events can be distinctly linked to defects in nematic and hexatic orders associated with cellular arrangements. Specifically, we show that by increasing relative cell-cell adhesion forces the cell monolayer can switch between the collective tendency towards fivefold, hexatic, disclinations relative to half-integer, nematic, defects for extruding a cell. We unify our findings by accessing three-dimensional mechanical stress fields to show that an extrusion event acts as a mechanism to relieve localized stress concentration.
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Affiliation(s)
- Siavash Monfared
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, United States
| | - Guruswami Ravichandran
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, United States
| | - José Andrade
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, United States
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48
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Sknepnek R, Djafer-Cherif I, Chuai M, Weijer C, Henkes S. Generating active T1 transitions through mechanochemical feedback. eLife 2023; 12:79862. [PMID: 37039463 PMCID: PMC10156166 DOI: 10.7554/elife.79862] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 04/09/2023] [Indexed: 04/12/2023] Open
Abstract
Convergence-extension in embryos is controlled by chemical and mechanical signalling. A key cellular process is the exchange of neighbours via T1 transitions. We propose and analyse a model with positive feedback between recruitment of myosin motors and mechanical tension in cell junctions. The model produces active T1 events, which act to elongate the tissue perpendicular to the main direction of tissue stress. Using an idealized tissue patch comprising several active cells embedded in a matrix of passive hexagonal cells we identified an optimal range of mechanical stresses to trigger an active T1 event. We show that directed stresses also generate tension chains in a realistic patch made entirely of active cells of random shapes, and leads to convergence-extension over a range of parameters. Our findings show that active intercalations can generate stress that activates T1 events in neighbouring cells resulting in tension dependent tissue reorganisation, in qualitative agreement with experiments on gastrulation in chick embryos.
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Affiliation(s)
- Rastko Sknepnek
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | | | - Manli Chuai
- School of Life Sciences, University of Dundee, Dundee, United States
| | - Cornelis Weijer
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Silke Henkes
- Leiden Institute of Physics, Leiden University, Leiden, Netherlands
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49
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Etibor TA, Vale-Costa S, Sridharan S, Brás D, Becher I, Mello VH, Ferreira F, Alenquer M, Savitski MM, Amorim MJ. Defining basic rules for hardening influenza A virus liquid condensates. eLife 2023; 12:85182. [PMID: 37013374 PMCID: PMC10154025 DOI: 10.7554/elife.85182] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/16/2023] [Indexed: 04/05/2023] Open
Abstract
In biological systems, liquid and solid-like biomolecular condensates may contain the same molecules but their behaviour, including movement, elasticity and viscosity, is different on account of distinct physicochemical properties. As such, it is known that phase transitions affect the function of biological condensates and that material properties can be tuned by several factors including temperature, concentration and valency. It is, however, unclear if some factors are more efficient than others at regulating their behaviour. Viral infections are good systems to address this question as they form condensates de novo as part of their replication programmes. Here, we used influenza A virus liquid cytosolic condensates, A.K.A viral inclusions, to provide a proof of concept that liquid condensate hardening via changes in the valency of its components is more efficient than altering their concentration or the temperature of the cell. Liquid IAV inclusions may be hardened by targeting vRNP interactions via the known NP oligomerizing molecule, nucleozin, both in vitro and in vivo without affecting host proteome abundance nor solubility. This study is a starting point for understanding how to pharmacologically modulate the material properties of IAV inclusions and may offer opportunities for alternative antiviral strategies.
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Affiliation(s)
| | - Silvia Vale-Costa
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Daniela Brás
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Victor Hugo Mello
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Filipe Ferreira
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Marta Alenquer
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Maria-João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
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50
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Couzin ID, Li L. The benefits of swimming together. eLife 2023; 12:86807. [PMID: 36947111 PMCID: PMC10032650 DOI: 10.7554/elife.86807] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
When a fish beats its tail, it produces vortices in the water that other fish could take advantage of to save energy while swimming.
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Affiliation(s)
- Iain D Couzin
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Liang Li
- Department of Collective Behaviour, Max Planck Institute of Animal Behavior, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
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