Pub Date : 2024-07-25DOI: 10.1103/prxlife.2.033004
Ameya G. Prabhune, A. S. García-Gordillo, Igor S. Aranson, Thomas R. Powers, Nuris Figueroa-Morales
Bacteria thrive in anisotropic media such as biofilms, biopolymer solutions, and soil pores. In strongly mechanically anisotropic media, physical interactions force bacteria to swim along a preferred direction rather than to execute the three-dimensional random walk due to their run-and-tumble behavior. Despite their ubiquity in nature and importance for human health, there is little understanding of bacterial mechanisms to navigate these media while constrained to one-dimensional motion. Using a biocompatible liquid crystal, we discovered two mechanisms used by bacteria to switch directions in anisotropic media. First, the flagella assemble in bundles that work against each other from opposite ends of the cell body, and the dominating side in this flagellar “Tug-of-Oars” propels the bacterium along the nematic direction. Bacteria frequently revert their swimming direction 180∘ by a mechanism of flagellar buckling and reorganization on the opposite side of the cell. The Frank elastic energies of the liquid crystal dictate the minimum compression for the Euler buckling of a flagellum. Beyond a critical elasticity of the medium, flagellar motors cannot generate the necessary torque for flagellar buckling, and bacteria are stuck in their configuration. However, we found that bacteria can still switch swimming directions using a second mechanism where individual bundles alternate their rotation. Our results shed light on bacterial strategies to navigate anisotropic media and give rise to questions about sensing environmental cues and adapting at the level of flagellar bundles. The two adaptation mechanisms found here support the use of biocompatible liquid crystals as a synthetic model for bacterial natural environments. Published by the American Physical Society 2024
{"title":"Bacteria Navigate Anisotropic Media using a Flagellar Tug-of-Oars","authors":"Ameya G. Prabhune, A. S. García-Gordillo, Igor S. Aranson, Thomas R. Powers, Nuris Figueroa-Morales","doi":"10.1103/prxlife.2.033004","DOIUrl":"https://doi.org/10.1103/prxlife.2.033004","url":null,"abstract":"Bacteria thrive in anisotropic media such as biofilms, biopolymer solutions, and soil pores. In strongly mechanically anisotropic media, physical interactions force bacteria to swim along a preferred direction rather than to execute the three-dimensional random walk due to their run-and-tumble behavior. Despite their ubiquity in nature and importance for human health, there is little understanding of bacterial mechanisms to navigate these media while constrained to one-dimensional motion. Using a biocompatible liquid crystal, we discovered two mechanisms used by bacteria to switch directions in anisotropic media. First, the flagella assemble in bundles that work against each other from opposite ends of the cell body, and the dominating side in this flagellar “Tug-of-Oars” propels the bacterium along the nematic direction. Bacteria frequently revert their swimming direction 180∘ by a mechanism of flagellar buckling and reorganization on the opposite side of the cell. The Frank elastic energies of the liquid crystal dictate the minimum compression for the Euler buckling of a flagellum. Beyond a critical elasticity of the medium, flagellar motors cannot generate the necessary torque for flagellar buckling, and bacteria are stuck in their configuration. However, we found that bacteria can still switch swimming directions using a second mechanism where individual bundles alternate their rotation. Our results shed light on bacterial strategies to navigate anisotropic media and give rise to questions about sensing environmental cues and adapting at the level of flagellar bundles. The two adaptation mechanisms found here support the use of biocompatible liquid crystals as a synthetic model for bacterial natural environments.\u0000 \u0000 \u0000 \u0000 \u0000 Published by the American Physical Society\u0000 2024\u0000 \u0000 \u0000","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"58 47","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141804732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-25DOI: 10.1103/prxlife.2.030001
S. Bradde, Margaret Gardel
{"title":"Editorial: PRX Life Celebrates Its First Anniversary","authors":"S. Bradde, Margaret Gardel","doi":"10.1103/prxlife.2.030001","DOIUrl":"https://doi.org/10.1103/prxlife.2.030001","url":null,"abstract":"","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"14 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141804211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-06DOI: 10.1103/prxlife.2.023011
Subhadip Biswas, D. Potoyan
Biomolecular condensates are dynamic intracellular entities defined by their sequence- and composition-encoded material properties. During aging, these properties can change dramatically, potentially leading to pathological solidlike states, the mechanisms of which remain poorly understood. Recent experiments reveal that the aging of condensates involves a complex interplay of solvent depletion, strengthening of sticker links, and the formation of rigid structural segments such as beta fibrils. In this study, we use various coarse-grained models to investigate how solvent expulsion, biopolymer chain rigidity, and the lifetimes of sticker contacts influence the viscoelastic properties and aging dynamics of condensates. We find that the rigidity of the biopolymer backbone is essential for replicating the predominant elastic behavior observed in experiments. In contrast, models using fully flexible chains—an assumption common in simulations of intrinsically disordered proteins—fail to exhibit a dominant elastic regime. We also demonstrate that altering the solvent content within condensates affects the crossover between storage and loss moduli. This suggests that desolvation plays a significant role in condensate aging by promoting the transition from a viscous to an elastic state. Furthermore, the lifetime of sticker pairs profoundly influences the mature state of the condensates; short-lived stickers lead to a Maxwell fluid behavior, while longer-lived, irreversibly cross-linked stickers result in solidlike properties, consistent with the Kelvin-Voigt model. Finally, by incorporating the chain rigidification, desolvation, and sticker pair formation into a nonequilibrium dynamic aging simulation, we show the molecular mechanism of forming solid shells around the condensate surfaces observed in a recent experimental report. Published by the American Physical Society 2024
{"title":"Molecular Drivers of Aging in Biomolecular Condensates: Desolvation, Rigidification, and Sticker Lifetimes","authors":"Subhadip Biswas, D. Potoyan","doi":"10.1103/prxlife.2.023011","DOIUrl":"https://doi.org/10.1103/prxlife.2.023011","url":null,"abstract":"Biomolecular condensates are dynamic intracellular entities defined by their sequence- and composition-encoded material properties. During aging, these properties can change dramatically, potentially leading to pathological solidlike states, the mechanisms of which remain poorly understood. Recent experiments reveal that the aging of condensates involves a complex interplay of solvent depletion, strengthening of sticker links, and the formation of rigid structural segments such as beta fibrils. In this study, we use various coarse-grained models to investigate how solvent expulsion, biopolymer chain rigidity, and the lifetimes of sticker contacts influence the viscoelastic properties and aging dynamics of condensates. We find that the rigidity of the biopolymer backbone is essential for replicating the predominant elastic behavior observed in experiments. In contrast, models using fully flexible chains—an assumption common in simulations of intrinsically disordered proteins—fail to exhibit a dominant elastic regime. We also demonstrate that altering the solvent content within condensates affects the crossover between storage and loss moduli. This suggests that desolvation plays a significant role in condensate aging by promoting the transition from a viscous to an elastic state. Furthermore, the lifetime of sticker pairs profoundly influences the mature state of the condensates; short-lived stickers lead to a Maxwell fluid behavior, while longer-lived, irreversibly cross-linked stickers result in solidlike properties, consistent with the Kelvin-Voigt model. Finally, by incorporating the chain rigidification, desolvation, and sticker pair formation into a nonequilibrium dynamic aging simulation, we show the molecular mechanism of forming solid shells around the condensate surfaces observed in a recent experimental report.\u0000 \u0000 \u0000 \u0000 \u0000 Published by the American Physical Society\u0000 2024\u0000 \u0000 \u0000","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"22 42","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141380178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-14DOI: 10.1103/prxlife.2.013013
Moritz Layer, M. Helias, David Dahmen
{"title":"Effect of Synaptic Heterogeneity on Neuronal Coordination","authors":"Moritz Layer, M. Helias, David Dahmen","doi":"10.1103/prxlife.2.013013","DOIUrl":"https://doi.org/10.1103/prxlife.2.013013","url":null,"abstract":"","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"18 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140243723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-13DOI: 10.1103/prxlife.2.013008
Dan Gorbonos, N. Gov, I. Couzin
{"title":"Geometrical Structure of Bifurcations during Spatial Decision-Making","authors":"Dan Gorbonos, N. Gov, I. Couzin","doi":"10.1103/prxlife.2.013008","DOIUrl":"https://doi.org/10.1103/prxlife.2.013008","url":null,"abstract":"","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"8 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139779775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-13DOI: 10.1103/prxlife.2.013008
Dan Gorbonos, N. Gov, I. Couzin
{"title":"Geometrical Structure of Bifurcations during Spatial Decision-Making","authors":"Dan Gorbonos, N. Gov, I. Couzin","doi":"10.1103/prxlife.2.013008","DOIUrl":"https://doi.org/10.1103/prxlife.2.013008","url":null,"abstract":"","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"55 13","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139839791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-30DOI: 10.1103/prxlife.2.013006
Rabia Laghmach, Michele Di Pierro, D. Potoyan
{"title":"Four-Dimensional Mesoscale Liquid Model of Nucleus Resolves Chromatin's Radial Organization","authors":"Rabia Laghmach, Michele Di Pierro, D. Potoyan","doi":"10.1103/prxlife.2.013006","DOIUrl":"https://doi.org/10.1103/prxlife.2.013006","url":null,"abstract":"","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"171 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140484135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-25DOI: 10.1103/prxlife.2.013005
Agathe Nidriche, Martine Moulin, Philippe Oger, J. R. Stewart, Lucile Mangin-Thro, Wolfgang Schmidt, Gerald Kneller, Judith Peters
{"title":"Impact of Isotopic Exchange on Hydrated Protein Dynamics Revealed by Polarized Neutron Scattering","authors":"Agathe Nidriche, Martine Moulin, Philippe Oger, J. R. Stewart, Lucile Mangin-Thro, Wolfgang Schmidt, Gerald Kneller, Judith Peters","doi":"10.1103/prxlife.2.013005","DOIUrl":"https://doi.org/10.1103/prxlife.2.013005","url":null,"abstract":"","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139596077","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-23DOI: 10.1103/prxlife.2.013004
K. Y. Guerra Santillán, Christian Dahmann, E. Fischer-Friedrich
{"title":"Elastic Contractile Stress in the Basement Membrane Generates Basal Tension in Epithelia","authors":"K. Y. Guerra Santillán, Christian Dahmann, E. Fischer-Friedrich","doi":"10.1103/prxlife.2.013004","DOIUrl":"https://doi.org/10.1103/prxlife.2.013004","url":null,"abstract":"","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"56 19","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139603441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-18DOI: 10.1103/prxlife.2.013003
Verónica Puerto-Belda, J. Ruz, Carmen Millá, Álvaro Cano, M. L. Yubero, Sergio García, P. Kosaka, M. Calleja, Javier Tamayo
{"title":"Measuring Vibrational Modes in Living Human Cells","authors":"Verónica Puerto-Belda, J. Ruz, Carmen Millá, Álvaro Cano, M. L. Yubero, Sergio García, P. Kosaka, M. Calleja, Javier Tamayo","doi":"10.1103/prxlife.2.013003","DOIUrl":"https://doi.org/10.1103/prxlife.2.013003","url":null,"abstract":"","PeriodicalId":500583,"journal":{"name":"PRX Life","volume":"104 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139616064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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