1
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Cacho-Navas C, López-Pujante C, Reglero-Real N, Colás-Algora N, Cuervo A, Conesa JJ, Barroso S, de Rivas G, Ciordia S, Paradela A, D'Agostino G, Manzo C, Feito J, Andrés G, Molina-Jiménez F, Majano P, Correas I, Carazo JM, Nourshargh S, Huch M, Millán J. ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin. eLife 2024; 12:RP89261. [PMID: 38597186 PMCID: PMC11006420 DOI: 10.7554/elife.89261] [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
Epithelial intercellular adhesion molecule (ICAM)-1 is apically polarized, interacts with, and guides leukocytes across epithelial barriers. Polarized hepatic epithelia organize their apical membrane domain into bile canaliculi and ducts, which are not accessible to circulating immune cells but that nevertheless confine most of ICAM-1. Here, by analyzing ICAM-1_KO human hepatic cells, liver organoids from ICAM-1_KO mice and rescue-of-function experiments, we show that ICAM-1 regulates epithelial apicobasal polarity in a leukocyte adhesion-independent manner. ICAM-1 signals to an actomyosin network at the base of canalicular microvilli, thereby controlling the dynamics and size of bile canalicular-like structures. We identified the scaffolding protein EBP50/NHERF1/SLC9A3R1, which connects membrane proteins with the underlying actin cytoskeleton, in the proximity interactome of ICAM-1. EBP50 and ICAM-1 form nano-scale domains that overlap in microvilli, from which ICAM-1 regulates EBP50 nano-organization. Indeed, EBP50 expression is required for ICAM-1-mediated control of BC morphogenesis and actomyosin. Our findings indicate that ICAM-1 regulates the dynamics of epithelial apical membrane domains beyond its role as a heterotypic cell-cell adhesion molecule and reveal potential therapeutic strategies for preserving epithelial architecture during inflammatory stress.
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Affiliation(s)
| | | | - Natalia Reglero-Real
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | | | - Ana Cuervo
- Centro Nacional de Biotecnologia (CSIC)MadridSpain
| | | | - Susana Barroso
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | - Gema de Rivas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | | | | | | | - Carlo Manzo
- Facultat de Ciències, Tecnologia i Enginyeries, Universitat de Vic – Universitat Central de Catalunya (UVic-UCC)VicSpain
| | - Jorge Feito
- Servicio de Anatomía Patológica, Hospital Universitario de SalamancaSalamancaSpain
| | - Germán Andrés
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | - Francisca Molina-Jiménez
- Molecular Biology Unit, Hospital Universitario de la PrincesaMadridSpain
- Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa)MadridSpain
| | - Pedro Majano
- Molecular Biology Unit, Hospital Universitario de la PrincesaMadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)MadridSpain
- Department of Cellular Biology, Universidad Complutense de MadridMadridSpain
| | - Isabel Correas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
| | | | - Sussan Nourshargh
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | - Meritxell Huch
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Jaime Millán
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAMMadridSpain
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2
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Manzo C, Isetta M, Castagna A. Did the first description of patients with polymyalgia rheumatica take place in Scotland or in Denmark? Reumatismo 2024; 76. [PMID: 38523578 DOI: 10.4081/reumatismo.2024.1673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 12/22/2023] [Indexed: 03/26/2024] Open
Abstract
The first description of polymyalgia rheumatica (PMR) is generally attributed to Dr. Bruce. In an 1888 article entitled Senile rheumatic gout, he described five male patients aged from 60 to 74 years whom he had visited at the Strathpeffer spa in Scotland. In 1945, Dr. Holst and Dr. Johansen reported on five female patients examined over several months at the Medical Department of Roskilde County Hospital in Denmark. These patients suffered from hip, upper arms, and neck pain associated with elevated ESR and constitutional manifestations such as low-grade fever or loss of weight. In the same year, Meulengracht, another Danish physician, reported on two patients with shoulder pain and stiffness associated with fever, weight loss, and an increased erythrocyte sedimentation rate. As in the five patients reported by Dr. Holst and Dr. Johansen, a prolonged recovery time was recorded. On reading and comparing these three accounts, we question whether it is correct to attribute the first description of PMR to Dr. Bruce and put forward shifting this accolade to the three Danish physicians.
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Affiliation(s)
- C Manzo
- Internal and Geriatric Medicine Department, Rheumatology Outpatient Clinic, Health Authority Napoli 3 sud, Sant'Agnello.
| | - M Isetta
- Central and North West London NHS Trust, London.
| | - A Castagna
- Primary Care Department, Catanzaro Provincial Health Authority, Soverato.
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3
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Kumar V, Shepard Bryan J, Rojewski A, Manzo C, Pressé S. Learning Continuous 2D Diffusion Maps from Particle Trajectories without Data Binning. bioRxiv 2024:2024.02.27.582378. [PMID: 38464131 PMCID: PMC10925201 DOI: 10.1101/2024.02.27.582378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Diffusion coefficients often vary across regions, such as cellular membranes, and quantifying their variation can provide valuable insight into local membrane properties such as composition and stiffness. Toward quantifying diffusion coefficient spatial maps and uncertainties from particle tracks, we use a Bayesian method and place Gaussian Process (GP) Priors on the maps. For the sake of computational efficiency, we leverage inducing point methods on GPs arising from the mathematical structure of the data giving rise to non-conjugate likelihood-prior pairs. We analyze both synthetic data, where ground truth is known, as well as data drawn from live-cell single-molecule imaging of membrane proteins. The resulting tool provides an unsupervised method to rigorously map diffusion coefficients continuously across membranes without data binning.
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Affiliation(s)
- Vishesh Kumar
- Center for Biological Physics, Arizona State University, USA
- Department of Physics, Arizona State University, USA
| | - J. Shepard Bryan
- Center for Biological Physics, Arizona State University, USA
- Department of Physics, Arizona State University, USA
| | - Alex Rojewski
- Center for Biological Physics, Arizona State University, USA
- Department of Physics, Arizona State University, USA
| | - Carlo Manzo
- Facultat de Ciéncies, Tecnologia i Enginyeries, Universitat de Vic – Universitat Central de Catalunya (UVic-UCC), C. de la Laura,13, 08500 Vic, Barcelona, Spain
- Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), 08500 Vic, Barcelona, Spain
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, USA
- Department of Physics, Arizona State University, USA
- School of Molecular Sciences, Arizona State University
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4
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Requena B, Masó-Orriols S, Bertran J, Lewenstein M, Manzo C, Muñoz-Gil G. Inferring pointwise diffusion properties of single trajectories with deep learning. Biophys J 2023; 122:4360-4369. [PMID: 37853693 PMCID: PMC10698275 DOI: 10.1016/j.bpj.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023] Open
Abstract
To characterize the mechanisms governing the diffusion of particles in biological scenarios, it is essential to accurately determine their diffusive properties. To do so, we propose a machine-learning method to characterize diffusion processes with time-dependent properties at the experimental time resolution. Our approach operates at the single-trajectory level predicting the properties of interest, such as the diffusion coefficient or the anomalous diffusion exponent, at every time step of the trajectory. In this way, changes in the diffusive properties occurring along the trajectory emerge naturally in the prediction and thus allow the characterization without any prior knowledge or assumption about the system. We first benchmark the method on synthetic trajectories simulated under several conditions. We show that our approach can successfully characterize both abrupt and continuous changes in the diffusion coefficient or the anomalous diffusion exponent. Finally, we leverage the method to analyze experiments of single-molecule diffusion of two membrane proteins in living cells: the pathogen-recognition receptor DC-SIGN and the integrin α5β1. The analysis allows us to characterize physical parameters and diffusive states with unprecedented accuracy, shedding new light on the underlying mechanisms.
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Affiliation(s)
- Borja Requena
- ICFO - Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain
| | - Sergi Masó-Orriols
- Facultat de Ciències, Tecnologia I Enginyeries, Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain; Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), Vic, Barcelona, Spain
| | - Joan Bertran
- Facultat de Ciències, Tecnologia I Enginyeries, Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain; Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), Vic, Barcelona, Spain
| | - Maciej Lewenstein
- ICFO - Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels (Barcelona), Spain; ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | - Carlo Manzo
- Facultat de Ciències, Tecnologia I Enginyeries, Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain; Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), Vic, Barcelona, Spain.
| | - Gorka Muñoz-Gil
- Institute for Theoretical Physics, University of Innsbruck, Innsbruck, Austria.
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5
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Sanz-Paz M, van Zanten TS, Manzo C, Mivelle M, Garcia-Parajo MF. Broadband Plasmonic Nanoantennas for Multi-Color Nanoscale Dynamics in Living Cells. Small 2023:e2207977. [PMID: 36999791 DOI: 10.1002/smll.202207977] [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] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Recently, the implementation of plasmonic nanoantennas has opened new possibilities to investigate the nanoscale dynamics of individual biomolecules in living cells. However, studies so far have been restricted to single molecular species as the narrow wavelength resonance of gold-based nanostructures precludes the simultaneous interrogation of different fluorescently labeled molecules. Here, broadband aluminum-based nanoantennas carved at the apex of near-field probes are exploited to resolve nanoscale-dynamic molecular interactions on living cell membranes. Through multicolor excitation, the authors simultaneously recorded fluorescence fluctuations of dual-color labeled transmembrane receptors known to form nanoclusters. Fluorescence cross-correlation studies revealed transient interactions between individual receptors in regions of ≈60 nm. Moreover, the high signal-to-background ratio provided by the antenna illumination allowed the authors to directly detect fluorescent bursts arising from the passage of individual receptors underneath the antenna. Remarkably, by reducing the illumination volume below the characteristic receptor nanocluster sizes, the molecular diffusion within nanoclusters is resolved and distinguished from nanocluster diffusion. Spatiotemporal characterization of transient interactions between molecules is crucial to understand how they communicate with each other to regulate cell function. This work demonstrates the potential of broadband photonic antennas to study multi-molecular events and interactions in living cell membranes with unprecedented spatiotemporal resolution.
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Affiliation(s)
- Maria Sanz-Paz
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute for Science and Technology, Barcelona, 08860, Spain
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg, CH-1700, Switzerland
| | - Thomas S van Zanten
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute for Science and Technology, Barcelona, 08860, Spain
- National Centre for Biological Sciences, Bangalore, 560065, India
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute for Science and Technology, Barcelona, 08860, Spain
- Facultat de Ciéncies, Tecnologia i Enginyeries, Universitat de Vic - Universitat Central de Catalunya, C. de la Laura 13, Vic, 08500, Spain
| | - Mathieu Mivelle
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, UMR 7588, Paris, 75005, France
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute for Science and Technology, Barcelona, 08860, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain
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6
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Gutiérrez-Martínez E, Benet Garrab S, Mateos N, Erkiziac I, Nieto-Garai JA, Lorizate M, Borgman KJE, Manzo C, Campelo F, Izquierdo-Useros N, Martinez-Picado J, Garcia-Parajo MF. Actin-regulated Siglec-1 nanoclustering influences HIV-1 capture and virus-containing compartment formation in dendritic cells. eLife 2023; 12:78836. [PMID: 36940134 PMCID: PMC10065798 DOI: 10.7554/elife.78836] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/19/2023] [Indexed: 03/21/2023] Open
Abstract
The immunoglobulin-like lectin receptor CD169 (Siglec-1) mediates the capture of HIV-1 by activated dendritic cells (DC) through binding to sialylated ligands. These interactions result in a more efficient virus capture as compared to resting DCs, although the underlying mechanisms are poorly understood. Using a combination of super-resolution microscopy, single particle tracking and biochemical perturbations we studied the nanoscale organization of Siglec-1 on activated DCs and its impact on viral capture and its trafficking to a single viral-containing compartment. We found that activation of DCs leads to Siglec-1 basal nanoclustering at specific plasma membrane regions where receptor diffusion is constrained by Rho-ROCK activation and formin-dependent actin polymerization. Using liposomes with varying ganglioside concentrations, we further demonstrate that Siglec-1 nanoclustering enhances the receptor avidity to limiting concentrations of gangliosides carrying sialic ligands. Binding to either HIV-1 particles or ganglioside-bearing liposomes lead to enhanced Siglec-1 nanoclustering and global actin rearrangements characterized by a drop in RhoA activity, facilitating the final accumulation of viral particles in a single sac-like compartment. Overall, our work provides new insights on the role of the actin machinery of activated DCs in regulating the formation of basal Siglec-1 nanoclustering, being decisive for the capture and actin-dependent trafficking of HIV-1 into the virus-containing compartment.
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Affiliation(s)
- Enric Gutiérrez-Martínez
- Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Susana Benet Garrab
- Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Nicolas Mateos
- Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Kyra J E Borgman
- Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carlo Manzo
- Facultat de Ciències i Tecnologia, Universitat Central de Catalunya, Vic, Spain
| | - Felix Campelo
- Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | - Maria F Garcia-Parajo
- Institute of Photonic Sciences, The Barcelona Institute of Science and Technology, Barcelona, Spain
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7
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Volpe G, Wählby C, Tian L, Hecht M, Yakimovich A, Monakhova K, Waller L, Sbalzarini IF, Metzler CA, Xie M, Zhang K, Lenton ICD, Rubinsztein-Dunlop H, Brunner D, Bai B, Ozcan A, Midtvedt D, Wang H, Sladoje N, Lindblad J, Smith JT, Ochoa M, Barroso M, Intes X, Qiu T, Yu LY, You S, Liu Y, Ziatdinov MA, Kalinin SV, Sheridan A, Manor U, Nehme E, Goldenberg O, Shechtman Y, Moberg HK, Langhammer C, Špačková B, Helgadottir S, Midtvedt B, Argun A, Thalheim T, Cichos F, Bo S, Hubatsch L, Pineda J, Manzo C, Bachimanchi H, Selander E, Homs-Corbera A, Fränzl M, de Haan K, Rivenson Y, Korczak Z, Adiels CB, Mijalkov M, Veréb D, Chang YW, Pereira JB, Matuszewski D, Kylberg G, Sintorn IM, Caicedo JC, Cimini BA, Bell MAL, Saraiva BM, Jacquemet G, Henriques R, Ouyang W, Le T, Gómez-de-Mariscal E, Sage D, Muñoz-Barrutia A, Lindqvist EJ, Bergman J. Roadmap on Deep Learning for Microscopy. ArXiv 2023:2303.03793. [PMID: 36945686 PMCID: PMC10029045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.
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8
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Nune A, Iyengar KP, Botchu R, Barman B, Manzo C. Correction to: "Living with COVID"-implications for immunosuppressed and immunocompromised. Clin Rheumatol 2022; 41:3595. [PMID: 36001246 PMCID: PMC9828856 DOI: 10.1007/s10067-022-06346-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- A. Nune
- Southport and Ormskirk Hospital NHS Trust, Southport, PR8 6PN UK
| | - K. P. Iyengar
- Southport and Ormskirk Hospital NHS Trust, Southport, PR8 6PN UK
| | - R. Botchu
- The Royal Orthopaedic Hospital NHS Trust, Birmingham, UK
| | - Bhupen Barman
- North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya India
| | - C. Manzo
- Azienda Sanitaria Locale Napoli 3 Sud, “Mariano Lauro” Hospital, Rheumatologic Outpatient Clinic, Sant’Agnello, Campania Italy
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9
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Muñoz-Gil G, Volpe G, Garcia-March MA, Aghion E, Argun A, Hong CB, Bland T, Bo S, Conejero JA, Firbas N, Garibo I Orts Ò, Gentili A, Huang Z, Jeon JH, Kabbech H, Kim Y, Kowalek P, Krapf D, Loch-Olszewska H, Lomholt MA, Masson JB, Meyer PG, Park S, Requena B, Smal I, Song T, Szwabiński J, Thapa S, Verdier H, Volpe G, Widera A, Lewenstein M, Metzler R, Manzo C. Objective comparison of methods to decode anomalous diffusion. Nat Commun 2021; 12:6253. [PMID: 34716305 PMCID: PMC8556353 DOI: 10.1038/s41467-021-26320-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022] Open
Abstract
Deviations from Brownian motion leading to anomalous diffusion are found in transport dynamics from quantum physics to life sciences. The characterization of anomalous diffusion from the measurement of an individual trajectory is a challenging task, which traditionally relies on calculating the trajectory mean squared displacement. However, this approach breaks down for cases of practical interest, e.g., short or noisy trajectories, heterogeneous behaviour, or non-ergodic processes. Recently, several new approaches have been proposed, mostly building on the ongoing machine-learning revolution. To perform an objective comparison of methods, we gathered the community and organized an open competition, the Anomalous Diffusion challenge (AnDi). Participating teams applied their algorithms to a commonly-defined dataset including diverse conditions. Although no single method performed best across all scenarios, machine-learning-based approaches achieved superior performance for all tasks. The discussion of the challenge results provides practical advice for users and a benchmark for developers.
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Affiliation(s)
- Gorka Muñoz-Gil
- ICFO - Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss 3, 08860, Castelldefels (Barcelona), Spain
| | - Giovanni Volpe
- Department of Physics, University of Gothenburg, Origovägen 6B, SE-41296, Gothenburg, Sweden.
| | - Miguel Angel Garcia-March
- Instituto Universitario de Matemática Pura y Aplicada, Universitat Politècnica de València, Valencia, Spain
| | - Erez Aghion
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, DE-01187, Dresden, Germany
| | - Aykut Argun
- Department of Physics, University of Gothenburg, Origovägen 6B, SE-41296, Gothenburg, Sweden
| | - Chang Beom Hong
- Department of Physics, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Tom Bland
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stefano Bo
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, DE-01187, Dresden, Germany
| | - J Alberto Conejero
- Instituto Universitario de Matemática Pura y Aplicada, Universitat Politècnica de València, Valencia, Spain
| | - Nicolás Firbas
- Instituto Universitario de Matemática Pura y Aplicada, Universitat Politècnica de València, Valencia, Spain
| | - Òscar Garibo I Orts
- Instituto Universitario de Matemática Pura y Aplicada, Universitat Politècnica de València, Valencia, Spain
| | - Alessia Gentili
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Zihan Huang
- School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Jae-Hyung Jeon
- Department of Physics, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Hélène Kabbech
- Department of Cell Biology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Yeongjin Kim
- Department of Physics, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Patrycja Kowalek
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, Wrocław, Poland
| | - Diego Krapf
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Hanna Loch-Olszewska
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, Wrocław, Poland
| | - Michael A Lomholt
- PhyLife, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230, Odense M, Denmark
| | - Jean-Baptiste Masson
- Institut Pasteur, Université de Paris, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Decision and Bayesian Computation lab, F-75015, Paris, France
| | - Philipp G Meyer
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, DE-01187, Dresden, Germany
| | - Seongyu Park
- Department of Physics, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Borja Requena
- ICFO - Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss 3, 08860, Castelldefels (Barcelona), Spain
| | - Ihor Smal
- Department of Cell Biology, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015, GD, Rotterdam, the Netherlands
| | - Taegeun Song
- Department of Physics, Pohang University of Science and Technology, Pohang, 37673, Korea
- Center for AI and Natural Sciences, Korea Institute for Advanced Study, Seoul, Korea
- Department of Data Information and Physics, Kongju National University, Kongju, 32588, Korea
| | - Janusz Szwabiński
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, Wrocław, Poland
| | - Samudrajit Thapa
- Institute of Physics & Astronomy, University of Potsdam, Karl-Liebknecht-Str 24/25, D-14476, Potsdam-Golm, Germany
- Sackler Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv, 69978, Israel
- School of Mechanical Engineering, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Hippolyte Verdier
- Institut Pasteur, Université de Paris, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Decision and Bayesian Computation lab, F-75015, Paris, France
| | - Giorgio Volpe
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Artur Widera
- Department of Physics and Research Center OPTIMAS, Technische Universität Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Maciej Lewenstein
- ICFO - Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss 3, 08860, Castelldefels (Barcelona), Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, Karl-Liebknecht-Str 24/25, D-14476, Potsdam-Golm, Germany
| | - Carlo Manzo
- ICFO - Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss 3, 08860, Castelldefels (Barcelona), Spain.
- Facultat de Ciències i Tecnologia, Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), C. de la Laura,13, 08500, Vic, Spain.
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Cullell-Dalmau M, Noé S, Otero-Viñas M, Meić I, Manzo C. Convolutional Neural Network for Skin Lesion Classification: Understanding the Fundamentals Through Hands-On Learning. Front Med (Lausanne) 2021; 8:644327. [PMID: 33748163 PMCID: PMC7969634 DOI: 10.3389/fmed.2021.644327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/10/2021] [Indexed: 11/13/2022] Open
Abstract
Deep learning architectures for the classification of images have shown outstanding results in a variety of disciplines, including dermatology. The expectations generated by deep learning for, e.g., image-based diagnosis have created the need for non-experts to become familiar with the working principles of these algorithms. In our opinion, getting hands-on experience with these tools through a simplified but accurate model can facilitate their understanding in an intuitive way. The visualization of the results of the operations performed by deep learning algorithms on dermatological images can help students to grasp concepts like convolution, even without an advanced mathematical background. In addition, the possibility to tune hyperparameters and even to tweak computer code further empower the reach of an intuitive comprehension of these processes, without requiring advanced computational and theoretical skills. This is nowadays possible thanks to recent advances that have helped to lower technical and technological barriers associated with the use of these tools, making them accessible to a broader community. Therefore, we propose a hands-on pedagogical activity that dissects the procedures to train a convolutional neural network on a dataset containing images of skin lesions associated with different skin cancer categories. The activity is available open-source and its execution does not require the installation of software. We further provide a step-by-step description of the algorithm and of its functions, following the development of the building blocks of the computer code, guiding the reader through the execution of a realistic example, including the visualization and the evaluation of the results.
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Affiliation(s)
- Marta Cullell-Dalmau
- The QuBI Lab, Facultat de Ciències i Tecnologia, Universitat de Vic – Universitat Central de Catalunya, Vic, Spain
| | - Sergio Noé
- The QuBI Lab, Facultat de Ciències i Tecnologia, Universitat de Vic – Universitat Central de Catalunya, Vic, Spain
| | - Marta Otero-Viñas
- Tissue Repair and Regeneration Laboratory, Facultat de Ciències i Tecnologia, Universitat de Vic – Universitat Central de Catalunya, Vic, Spain
| | - Ivan Meić
- The QuBI Lab, Facultat de Ciències i Tecnologia, Universitat de Vic – Universitat Central de Catalunya, Vic, Spain
- University of Zagreb, Zagreb, Croatia
| | - Carlo Manzo
- The QuBI Lab, Facultat de Ciències i Tecnologia, Universitat de Vic – Universitat Central de Catalunya, Vic, Spain
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11
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Cullell-Dalmau M, Otero-Viñas M, Ferrer-Solà M, Sureda-Vidal H, Manzo C. A toolkit for the quantitative evaluation of chronic wounds evolution for early detection of non-healing wounds. J Tissue Viability 2021; 30:161-167. [PMID: 33707158 DOI: 10.1016/j.jtv.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/03/2021] [Accepted: 02/24/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND Chronic wounds resulting from a number of conditions do not heal properly and can pose serious health problems. Beyond clinician visual inspection, an objective evaluation of the wound is required to assess wound evolution and the effectiveness of therapies. AIM Our objective is to provide a methodology for the analysis of wound area vs. time for the early prediction of non-healing wounds evolution. METHODS We propose a two-step approach consisting of: i) wound area quantification from planimetries and ii) classification of wound healing through the inference of characteristic parameters. For the first step, we describe a user-friendly software (Woundaries) to automatically calculate the wound area and other geometric parameters from hand-traced planimetries. For the second, we use a procedure for the objective classification of wound time evolution and the early assessment of treatment efficacy. The methodology was tested on simulations and retrospectively applied to data from 85 patients to compare the effect of a biological therapy with respect to general basic therapeutics. RESULTS Woundaries provides measurements of wound surface equivalent to a validated device. The two-step methodology allows to determine if a wound is healing with high sensitivity, even with limited amount of data. Therefore, it allows the early assessment of the efficacy of a therapy. CONCLUSION The performance of this methodology for the quantification and the objective evaluation of wound area evolution suggest it as a useful toolkit to assist clinicians in the early assessment of the efficacy of treatments, leading to a timely change of therapy.
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Affiliation(s)
- Marta Cullell-Dalmau
- The Quantitative BioImaging (QuBI) Lab, University of Vic - Central University of Catalonia (UVic-UCC), C. de La Laura, 13, 08500, Vic, Spain
| | - Marta Otero-Viñas
- Tissue Repair and Regeneration Laboratory (TR2Lab), University of Vic - Central University of Catalonia (UVic-UCC), Fundació Hospital Universitari de la Santa Creu de Vic, and Hospital Universitari de Vic, 08500, Vic, Spain; University of Vic - Central University of Catalonia, C. de La Laura, 13, 08500, Vic, Spain.
| | - Marta Ferrer-Solà
- Tissue Repair and Regeneration Laboratory (TR2Lab), University of Vic - Central University of Catalonia (UVic-UCC), Fundació Hospital Universitari de la Santa Creu de Vic, and Hospital Universitari de Vic, 08500, Vic, Spain; Fundació Hospital Universitari de la Santa Creu de Vic, Rambla de l'Hospital, 52, 08500, Vic, Spain
| | - Helena Sureda-Vidal
- Tissue Repair and Regeneration Laboratory (TR2Lab), University of Vic - Central University of Catalonia (UVic-UCC), Fundació Hospital Universitari de la Santa Creu de Vic, and Hospital Universitari de Vic, 08500, Vic, Spain; Fundació Hospital Universitari de la Santa Creu de Vic, Rambla de l'Hospital, 52, 08500, Vic, Spain
| | - Carlo Manzo
- The Quantitative BioImaging (QuBI) Lab, University of Vic - Central University of Catalonia (UVic-UCC), C. de La Laura, 13, 08500, Vic, Spain
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12
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Manzo C. Clinical practice guidelines for patients with polymyalgia rheumatica: the need for an active involvement of all stakeholder is still unmet. Reumatismo 2020; 72:120-121. [PMID: 32700879 DOI: 10.4081/reumatismo.2020.1290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 11/23/2022] Open
Abstract
Not available.
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Affiliation(s)
- C Manzo
- Azienda Sanitaria Locale Napoli 3 sud, Rheumatologic Outpatient Clinic, Health Distict no. 59, Sant'Agnello (NA).
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13
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Sibilo R, Mannelli I, Reigada R, Manzo C, Noyan MA, Mazumder P, Pruneri V. Direct and Fast Assessment of Antimicrobial Surface Activity Using Molecular Dynamics Simulation and Time-Lapse Imaging. Anal Chem 2020; 92:6795-6800. [PMID: 32295344 DOI: 10.1021/acs.analchem.0c00367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the alarming rise of antimicrobial resistance, studies on bacteria-surface interactions are both relevant and timely. Scanning electron microscopy and colony forming unit counting are commonly used techniques but require sophisticated sample preparation and long incubation time. Here, we present a direct method based on molecular dynamics simulation of nanostructured surfaces providing in silico predictions, complemented with time-lapse fluorescence imaging to study live interactions of bacteria at the membrane-substrate level. We evaluate its effectiveness in predicting and statistically analyzing the temporal evolution and spatial distribution of prototypical bacteria with costained nucleoids and membranes (E. coli) on surfaces with nanopillars. We observed cell reorientation, clustering, membrane damage, growth inhibition, and in the extreme case of hydrocarbon-coated nanopillars, this was followed by cell disappearance, validating the obtained simulation results. Contrary to commonly used experimental methods, microscopy data are fast processed, in less than 1 h. In particular, the bactericidal effects can be straightforwardly detected and correlated with surface morphology and/or wettability.
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Affiliation(s)
- Rafaël Sibilo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Avinguda Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
| | - Ilaria Mannelli
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Avinguda Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
| | - Ramon Reigada
- Departament de Ciència dels Materials i Quı́mica Fı́sica and Institut de Quı́mica Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Carrer Martı́ i Franqués 1, Planta 4, 08028 Barcelona, Spain
| | - Carlo Manzo
- Facultat de Ciències i Tecnologia, Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), Carrer de la Laura, 13, 08500 Vic, Spain
| | - Mehmet A Noyan
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Avinguda Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain.,Ipsumio B.V., High Tech Campus 29, 5656 AE Eindhoven, The Netherlands
| | - Prantik Mazumder
- Corning Research and Development Corporation, Painted Post, New York 14870, United States
| | - Valerio Pruneri
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Avinguda Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain.,ICREA-Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
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14
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Košuta T, Cullell-Dalmau M, Cella Zanacchi F, Manzo C. Bayesian analysis of data from segmented super-resolution images for quantifying protein clustering. Phys Chem Chem Phys 2020; 22:1107-1114. [PMID: 31895350 DOI: 10.1039/c9cp05616e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further permits the quantitation relevant parameters to determine the molecular organization and stoichiometry in cells. However, the inherently stochastic nature of fluorescence emission and labeling strategies imposes the use of dedicated methods to accurately estimate these parameters. Here, we describe a Bayesian approach to precisely quantitate the relative abundance of molecular aggregates of different stoichiometry from segmented images. The distribution of proxies for the number of molecules in a cluster, such as the number of localizations or the fluorescence intensity, is fitted via a nested sampling algorithm to compare mixture models of increasing complexity and thus determine the optimum number of mixture components and their weights. We test the performance of the algorithm on in silico data as a function of the number of data points, threshold, and distribution shape. We compare these results to those obtained with other statistical methods, showing the improved performance of our approach. Our method provides a robust tool for model selection in fitting data extracted from fluorescence imaging, thus improving the precision of parameter determination. Importantly, the largest benefit of this method occurs for small-statistics or incomplete datasets, enabling an accurate analysis at the single image level. We further present the results of its application to experimental data obtained from the super-resolution imaging of dynein in HeLa cells, confirming the presence of a mixed population of cytoplasmic single motors and higher-order structures.
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Affiliation(s)
- Tina Košuta
- The Quantitative BioImaging lab, Facultat de Ciències i Tecnologia, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain. and University of Ljubljana, Ljubljana, Slovenia
| | - Marta Cullell-Dalmau
- The Quantitative BioImaging lab, Facultat de Ciències i Tecnologia, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain.
| | - Francesca Cella Zanacchi
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy and Biophysics Institute (IBF), National Research Council (CNR), Genoa, Italy
| | - Carlo Manzo
- The Quantitative BioImaging lab, Facultat de Ciències i Tecnologia, Universitat de Vic - Universitat Central de Catalunya, Vic, Spain.
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15
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Sil P, Mateos N, Nath S, Buschow S, Manzo C, Suzuki KGN, Fujiwara T, Kusumi A, Garcia-Parajo MF, Mayor S. Dynamic actin-mediated nano-scale clustering of CD44 regulates its meso-scale organization at the plasma membrane. Mol Biol Cell 2019; 31:561-579. [PMID: 31577524 PMCID: PMC7202065 DOI: 10.1091/mbc.e18-11-0715] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transmembrane adhesion receptors at the cell surface, such as CD44, are often equipped with modules to interact with the extracellular matrix (ECM) and the intracellular cytoskeletal machinery. CD44 has been recently shown to compartmentalize the membrane into domains by acting as membrane pickets, facilitating the function of signaling receptors. While spatial organization and diffusion studies of membrane proteins are usually conducted separately, here we combine observations of organization and diffusion by using high spatio-temporal resolution imaging on living cells to reveal a hierarchical organization of CD44. CD44 is present in a meso-scale meshwork pattern where it exhibits enhanced confinement and is enriched in nanoclusters of CD44 along its boundaries. This nanoclustering is orchestrated by the underlying cortical actin dynamics. Interaction with actin is mediated by specific segments of the intracellular domain. This influences the organization of the protein at the nano-scale, generating a selective requirement for formin over Arp2/3-based actin-nucleation machinery. The extracellular domain and its interaction with elements of ECM do not influence the meso-scale organization, but may serve to reposition the meshwork with respect to the ECM. Taken together, our results capture the hierarchical nature of CD44 organization at the cell surface, with active cytoskeleton-templated nanoclusters localized to a meso-scale meshwork pattern.
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Affiliation(s)
- Parijat Sil
- National Centre for Biological Sciences (NCBS)
| | - Nicolas Mateos
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona 08860, Spain
| | - Sangeeta Nath
- Institute of Stem Cell and Regenerative Medicine.,Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education, Bangalore 560065, India
| | - Sonja Buschow
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, Rotterdam 3015 GD Rotterdam, The Netherlands
| | - Carlo Manzo
- Facultat de Ciències i Tecnologia, Universitat de Vic-Universitat Central de Catalunya, Vic 08500, Spain
| | - Kenichi G N Suzuki
- Centre for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan.,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Takahiro Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Akihiro Kusumi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan.,Okinawa Institute of Science and Technology, Graduate University, Okinawa 904-0412, Japan
| | - Maria F Garcia-Parajo
- Institute of Stem Cell and Regenerative Medicine.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Satyajit Mayor
- National Centre for Biological Sciences (NCBS).,Institute of Stem Cell and Regenerative Medicine
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16
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Sosa-Costa A, Piechocka IK, Gardini L, Pavone FS, Capitanio M, Garcia-Parajo MF, Manzo C. PLANT: A Method for Detecting Changes of Slope in Noisy Trajectories. Biophys J 2019; 114:2044-2051. [PMID: 29742398 DOI: 10.1016/j.bpj.2018.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 03/17/2018] [Accepted: 04/02/2018] [Indexed: 01/13/2023] Open
Abstract
Time traces obtained from a variety of biophysical experiments contain valuable information on underlying processes occurring at the molecular level. Accurate quantification of these data can help explain the details of the complex dynamics of biological systems. Here, we describe PLANT (Piecewise Linear Approximation of Noisy Trajectories), a segmentation algorithm that allows the reconstruction of time-trace data with constant noise as consecutive straight lines, from which changes of slopes and their respective durations can be extracted. We present a general description of the algorithm and perform extensive simulations to characterize its strengths and limitations, providing a rationale for the performance of the algorithm in the different conditions tested. We further apply the algorithm to experimental data obtained from tracking the centroid position of lymphocytes migrating under the effect of a laminar flow and from single myosin molecules interacting with actin in a dual-trap force-clamp configuration.
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Affiliation(s)
- Alberto Sosa-Costa
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Izabela K Piechocka
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Lucia Gardini
- LENS - European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy; National Institute of Optics-National Research Council, Florence, Italy
| | - Francesco S Pavone
- LENS - European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy; National Institute of Optics-National Research Council, Florence, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Marco Capitanio
- LENS - European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain; ICREA, Barcelona, Spain
| | - Carlo Manzo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain; Universitat de Vic - Universitat Central de Catalunya, Vic, Spain.
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17
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Martínez-Muñoz L, Rodríguez-Frade JM, Barroso R, Sorzano CÓS, Torreño-Pina JA, Santiago CA, Manzo C, Lucas P, García-Cuesta EM, Gutierrez E, Barrio L, Vargas J, Cascio G, Carrasco YR, Sánchez-Madrid F, García-Parajo MF, Mellado M. Separating Actin-Dependent Chemokine Receptor Nanoclustering from Dimerization Indicates a Role for Clustering in CXCR4 Signaling and Function. Mol Cell 2019; 70:106-119.e10. [PMID: 29625032 DOI: 10.1016/j.molcel.2018.02.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 01/08/2018] [Accepted: 02/27/2018] [Indexed: 01/03/2023]
Abstract
A current challenge in cell motility studies is to understand the molecular and physical mechanisms that govern chemokine receptor nanoscale organization at the cell membrane, and their influence on cell response. Using single-particle tracking and super-resolution microscopy, we found that the chemokine receptor CXCR4 forms basal nanoclusters in resting T cells, whose extent, dynamics, and signaling strength are modulated by the orchestrated action of the actin cytoskeleton, the co-receptor CD4, and its ligand CXCL12. We identified three CXCR4 structural residues that are crucial for nanoclustering and generated an oligomerization-defective mutant that dimerized but did not form nanoclusters in response to CXCL12, which severely impaired signaling. Overall, our data provide new insights to the field of chemokine biology by showing that receptor dimerization in the absence of nanoclustering is unable to fully support CXCL12-mediated responses, including signaling and cell function in vivo.
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Affiliation(s)
- Laura Martínez-Muñoz
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CSIC), 41092 Sevilla, Spain.
| | - José Miguel Rodríguez-Frade
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Rubén Barroso
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Carlos Óscar S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Juan A Torreño-Pina
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - César A Santiago
- X-ray Crystallography Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain; Universitat de Vic, Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
| | - Pilar Lucas
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Eva M García-Cuesta
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Enric Gutierrez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Laura Barrio
- B Cell Dynamics Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Javier Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Graciela Cascio
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Yolanda R Carrasco
- B Cell Dynamics Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | | | - María F García-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Mario Mellado
- Chemokine Signaling Group, Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain.
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18
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Balcerek M, Loch-Olszewska H, Torreno-Pina JA, Garcia-Parajo MF, Weron A, Manzo C, Burnecki K. Inhomogeneous membrane receptor diffusion explained by a fractional heteroscedastic time series model. Phys Chem Chem Phys 2019; 21:3114-3121. [DOI: 10.1039/c8cp06781c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fractional heteroscedastic time series model explains inhomogeneous membrane receptor diffusion and interprets ergodicity when the diffusion parameter fluctuates in time.
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Affiliation(s)
- Michał Balcerek
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Hanna Loch-Olszewska
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Juan A. Torreno-Pina
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology
- 08860 Castelldefels (Barcelona)
- Spain
| | - Maria F. Garcia-Parajo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology
- 08860 Castelldefels (Barcelona)
- Spain
- ICREA
- 08010 Barcelona
| | - Aleksander Weron
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Carlo Manzo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology
- 08860 Castelldefels (Barcelona)
- Spain
- Facultat de Ciències i Tecnologia, Universitat de Vic – Universitat Central de Catalunya
- 08550 Vic
| | - Krzysztof Burnecki
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
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19
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Martínez-Muñoz L, Rodríguez-Frade JM, Barroso R, Sorzano CÓS, Torreño-Pina JA, Santiago CA, Manzo C, Lucas P, García-Cuesta EM, Gutierrez E, Barrio L, Vargas J, Cascio G, Carrasco YR, Sánchez-Madrid F, García-Parajo MF, Mellado M. Separating Actin-Dependent Chemokine Receptor Nanoclustering from Dimerization Indicates a Role for Clustering in CXCR4 Signaling and Function. Mol Cell 2018; 71:873. [PMID: 30193101 DOI: 10.1016/j.molcel.2018.08.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Manzo C, Longo C, Bianchin A. C1q Solid-Phase Enzymatic Microassay for Detection of Circulating Immune Complexes: Its Application in Human Breast Cancer. Tumori 2018; 68:47-52. [PMID: 7041380 DOI: 10.1177/030089168206800108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Circulating immune complexes (CIC) were detected and quantitated in human breast cancer to monitor the efficiency of mastectomy. For this aim a microimmunoenzymatic test was set up, applying a solid-phase C1q. Features of this assay can be summarized as follows: ability to estimate as low as 10 ng of aggregated human IgG (ΔIgG), good reproducibility and simplicity of execution, and small serum sample required. A group of women with breast cancer at different stages (TNM classification) was tested for CIC, and 31.75 % were positive. Almost all patients submitted to surgery showed a reduction of this parameter thereafter. A parallel study was carried out in another group of women with benign breast disease, and a significant incidence of CIC was found.
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Sobrero A, Manzo C, Stimamiglio A. The role of the general practitioner and the out-of-hospital public rheumatologist in the diagnosis and follow-up of patients with polymyalgia rheumatica. Reumatismo 2018; 70:44-50. [PMID: 29589402 DOI: 10.4081/reumatismo.2018.1036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 01/23/2018] [Accepted: 01/27/2018] [Indexed: 11/22/2022] Open
Abstract
Polymyalgia rheumatica (PMR) is a chronic inflammatory disease characterized by shoulder and pelvic girdle pain. Its onset peaks around the age of 75; the prevalence increases until the age of 90 and it is more frequent in females. Diagnosis is mostly performed on the basis of symptoms. An increase of serum inflammatory markers is indicative, but not essential, while therapy is mainly based on glucocorticoids. Since there is no universal agreement about diagnostic criteria for PMR, its detection is still difficult. There are discordant opinions about the fact that PMR can be recognised and managed by general practitioners (GPs), while patients with atypical features need to be referred to the rheumatologist. In the Italian setting, the absence of recent epidemiological studies is associated with the total lack of a research protocol in primary care, from which relevant information could be derived. The out-of-hospital public rheumatologist is a peculiar figure of the Italian National Health System, who takes care of outpatients. Although differences between the different Italian regional health services exist, this professional figure has proved to be effective in reducing delay and increasing accuracy in PMR diagnosis.
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22
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Mazzoccanti G, Ismail OH, D'Acquarica I, Villani C, Manzo C, Wilcox M, Cavazzini A, Gasparrini F. Cannabis through the looking glass: chemo- and enantio-selective separation of phytocannabinoids by enantioselective ultra high performance supercritical fluid chromatography. Chem Commun (Camb) 2018; 53:12262-12265. [PMID: 29072720 DOI: 10.1039/c7cc06999e] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By using the Inverted Chirality Columns Approach (ICCA) we have developed an enantioselective UHPSFC method to determine the enantiomeric excess (ee) of (-)-Δ9-THC in medicinal marijuana (Bedrocan®). The ee was high (99.73%), but the concentration of the (+)-enantiomer (0.135%) was not negligible, and it is worth a systematic evaluation of bioactivity.
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Affiliation(s)
- G Mazzoccanti
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, p.le A. Moro 5, 00185 Roma, Italy.
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23
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Cella Zanacchi F, Magrassi R, Diaspro A, Manzo C, Derr ND, Lakadamyali M. Quantitative Super-Resolution Microscopy using DNA Origami. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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24
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Muñoz-Gil G, Charalambous C, García-March MA, Garcia-Parajo MF, Manzo C, Lewenstein M, Celi A. Transient subdiffusion from an Ising environment. Phys Rev E 2018; 96:052140. [PMID: 29347809 DOI: 10.1103/physreve.96.052140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 11/07/2022]
Abstract
We introduce a model in which a particle performs a continuous-time random walk (CTRW) coupled to an environment with Ising dynamics. The particle shows locally varying diffusivity determined by the geometrical properties of the underlying Ising environment, that is, the diffusivity depends on the size of the connected area of spins pointing in the same direction. The model shows anomalous diffusion when the Ising environment is at critical temperature. We show that any finite scale introduced by a temperature different from the critical one, or a finite size of the environment, cause subdiffusion only during a transient time. The characteristic time, at which the system returns to normal diffusion after the subdiffusive plateau depends on the limiting scale and on how close the temperature is to criticality. The system also displays apparent ergodicity breaking at intermediate time, while ergodicity breaking at longer time occurs only under the idealized infinite environment at the critical temperature.
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Affiliation(s)
- G Muñoz-Gil
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - C Charalambous
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - M A García-March
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - M F Garcia-Parajo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain.,ICREA-Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - C Manzo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain.,Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), C. de la Laura, 13, 08500 Vic, Spain
| | - M Lewenstein
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain.,ICREA-Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - A Celi
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
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25
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Regmi R, Winkler PM, Flauraud V, Borgman KJE, Manzo C, Brugger J, Rigneault H, Wenger J, García-Parajo MF. Planar Optical Nanoantennas Resolve Cholesterol-Dependent Nanoscale Heterogeneities in the Plasma Membrane of Living Cells. Nano Lett 2017; 17:6295-6302. [PMID: 28926278 DOI: 10.1021/acs.nanolett.7b02973] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Optical nanoantennas can efficiently confine light into nanoscopic hotspots, enabling single-molecule detection sensitivity at biological relevant conditions. This innovative approach to breach the diffraction limit offers a versatile platform to investigate the dynamics of individual biomolecules in living cell membranes and their partitioning into cholesterol-dependent lipid nanodomains. Here, we present optical nanoantenna arrays with accessible surface hotspots to study the characteristic diffusion dynamics of phosphoethanolamine (PE) and sphingomyelin (SM) in the plasma membrane of living cells at the nanoscale. Fluorescence burst analysis and fluorescence correlation spectroscopy performed on nanoantennas of different gap sizes show that, unlike PE, SM is transiently trapped in cholesterol-enriched nanodomains of 10 nm diameter with short characteristic times around 100 μs. The removal of cholesterol led to the free diffusion of SM, consistent with the dispersion of nanodomains. Our results are consistent with the existence of highly transient and fluctuating nanoscale assemblies enriched by cholesterol and sphingolipids in living cell membranes, also known as lipid rafts. Quantitative data on sphingolipids partitioning into lipid rafts is crucial to understand the spatiotemporal heterogeneous organization of transient molecular complexes on the membrane of living cells at the nanoscale. The proposed technique is fully biocompatible and thus provides various opportunities for biophysics and live cell research to reveal details that remain hidden in confocal diffraction-limited measurements.
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Affiliation(s)
- Raju Regmi
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- Aix Marseille Univ , CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Pamina M Winkler
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Valentin Flauraud
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Kyra J E Borgman
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Jürgen Brugger
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Hervé Rigneault
- Aix Marseille Univ , CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Jérôme Wenger
- Aix Marseille Univ , CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - María F García-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- ICREA , Pg. Lluı́s Companys 23, 08010 Barcelona, Spain
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26
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Abstract
Single-molecule-based super-resolution microscopy offers a unique opportunity for quantifying protein copy-number with nanoscale resolution. However, while fluorescent proteins have been characterized for quantitative imaging using calibration standards, similar calibration tools for immunofluorescence with small organic fluorophores are lacking. Here, we show that DNA origami in combination with GFP antibodies is a versatile platform for calibrating fluorophore and antibody labeling efficiency to quantify protein copy-number in cellular contexts using super-resolution microscopy.
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Affiliation(s)
- Francesca Cella Zanacchi
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain.,Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain
| | - Angel S Alvarez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Nathan D Derr
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA.,Center for Microscopy and Imaging, Smith College, Northampton, Massachusetts, USA
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain.,ICREA, Barcelona, Spain
| | - Melike Lakadamyali
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
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27
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Manzo C, Mei A, Zampetti E, Bassani C, Paciucci L, Manetti P. Top-down approach from satellite to terrestrial rover application for environmental monitoring of landfills. Sci Total Environ 2017; 584-585:1333-1348. [PMID: 28104331 DOI: 10.1016/j.scitotenv.2017.01.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 06/06/2023]
Abstract
This paper describes a methodology to perform chemical analyses in landfill areas by integrating multisource geomatic data. We used a top-down approach to identify Environmental Point of Interest (EPI) based on very high-resolution satellite data (Pleiades and WorldView 2) and on in situ thermal and photogrammetric surveys. Change detection techniques and geostatistical analysis supported the chemical survey, undertaken using an accumulation chamber and an RIIA, an unmanned ground vehicle developed by CNR IIA, equipped with a multiparameter sensor platform for environmental monitoring. Such an approach improves site characterization, identifying the key environmental points of interest where it is necessary to perform detailed chemical analyses.
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Affiliation(s)
- C Manzo
- Institute of Atmospheric Pollution Research (IIA), CNR (National Research Council of Italy), Research Area of Rome 1 Via Salaria Km 29.300, Monterotondo 00016, Rome, Italy.
| | - A Mei
- Institute of Atmospheric Pollution Research (IIA), CNR (National Research Council of Italy), Research Area of Rome 1 Via Salaria Km 29.300, Monterotondo 00016, Rome, Italy
| | - E Zampetti
- Institute of Atmospheric Pollution Research (IIA), CNR (National Research Council of Italy), Research Area of Rome 1 Via Salaria Km 29.300, Monterotondo 00016, Rome, Italy
| | - C Bassani
- Institute of Atmospheric Pollution Research (IIA), CNR (National Research Council of Italy), Research Area of Rome 1 Via Salaria Km 29.300, Monterotondo 00016, Rome, Italy
| | - L Paciucci
- Institute of Atmospheric Pollution Research (IIA), CNR (National Research Council of Italy), Research Area of Rome 1 Via Salaria Km 29.300, Monterotondo 00016, Rome, Italy
| | - P Manetti
- Department of Earth Sciences, Via La Pira 4, 50121 Florence, Italy
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28
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Charalambous C, Muñoz-Gil G, Celi A, Garcia-Parajo MF, Lewenstein M, Manzo C, García-March MA. Nonergodic subdiffusion from transient interactions with heterogeneous partners. Phys Rev E 2017; 95:032403. [PMID: 28415278 DOI: 10.1103/physreve.95.032403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Indexed: 06/07/2023]
Abstract
Spatiotemporal disorder has been recently associated to the occurrence of anomalous nonergodic diffusion of molecular components in biological systems, but the underlying microscopic mechanism is still unclear. We introduce a model in which a particle performs continuous Brownian motion with changes of diffusion coefficients induced by transient molecular interactions with diffusive binding partners. In spite of the exponential distribution of waiting times, the model shows subdiffusion and nonergodicity similar to the heavy-tailed continuous time random walk. The dependence of these properties on the density of binding partners is analyzed and discussed. Our work provides an experimentally testable microscopic model to investigate the nature of nonergodicity in disordered media.
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Affiliation(s)
- C Charalambous
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - G Muñoz-Gil
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - A Celi
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - M F Garcia-Parajo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
- ICREA - Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - M Lewenstein
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
- ICREA - Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - C Manzo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
- Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), C. de la Laura, 13, 08500 Vic, Spain
| | - M A García-March
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
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29
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Molina-García D, Pham TM, Paradisi P, Manzo C, Pagnini G. Fractional kinetics emerging from ergodicity breaking in random media. Phys Rev E 2016; 94:052147. [PMID: 27967076 DOI: 10.1103/physreve.94.052147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Indexed: 06/06/2023]
Abstract
We present a modeling approach for diffusion in a complex medium characterized by a random length scale. The resulting stochastic process shows subdiffusion with a behavior in qualitative agreement with single-particle tracking experiments in living cells, such as ergodicity breaking, p variation, and aging. In particular, this approach recapitulates characteristic features previously described in part by the fractional Brownian motion and in part by the continuous-time random walk. Moreover, for a proper distribution of the length scale, a single parameter controls the ergodic-to-nonergodic transition and, remarkably, also drives the transition of the diffusion equation of the process from nonfractional to fractional, thus demonstrating that fractional kinetics emerges from ergodicity breaking.
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Affiliation(s)
- Daniel Molina-García
- BCAM - Basque Center for Applied Mathematics, Alameda de Mazarredo 14, E-48009 Bilbao, Basque Country, Spain
| | - Tuan Minh Pham
- BCAM - Basque Center for Applied Mathematics, Alameda de Mazarredo 14, E-48009 Bilbao, Basque Country, Spain
- Department of Theoretical Physics, Belgorod National Research University, 14 Studencheskaya, 308015 Belgorod, Russia
| | - Paolo Paradisi
- BCAM - Basque Center for Applied Mathematics, Alameda de Mazarredo 14, E-48009 Bilbao, Basque Country, Spain
- ISTI-CNR, Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo," Via Moruzzi 1, I-56124 Pisa, Italy
| | - Carlo Manzo
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - Gianni Pagnini
- BCAM - Basque Center for Applied Mathematics, Alameda de Mazarredo 14, E-48009 Bilbao, Basque Country, Spain
- Ikerbasque - Basque Foundation for Science, Calle de Mará Díaz de Haro 3, E-48013 Bilbao, Basque Country, Spain
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30
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Sosa-Costa A, Isern de Val S, Sevilla-Movilla S, Borgman KJE, Manzo C, Teixidó J, Garcia-Parajo MF. Lateral Mobility and Nanoscale Spatial Arrangement of Chemokine-activated α4β1 Integrins on T Cells. J Biol Chem 2016; 291:21053-21062. [PMID: 27481944 PMCID: PMC5076515 DOI: 10.1074/jbc.m116.733709] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Indexed: 01/13/2023] Open
Abstract
Chemokine stimulation of integrin α4β1-dependent T lymphocyte adhesion is a key step during lymphocyte trafficking. A central question regarding α4β1 function is how its lateral mobility and organization influence its affinity and avidity following cell stimulation with chemokines and/or ligands. Using single particle tracking and superresolution imaging approaches, we explored the lateral mobility and spatial arrangement of individual α4β1integrins on T cells exposed to different activating stimuli. We show that CXCL12 stimulation leads to rapid and transient α4β1activation, measured by induction of the activation epitope recognized by the HUTS-21 anti-β1antibody and by increased talin-β1 association. CXCL12-dependent α4β1 activation directly correlated with restricted lateral diffusion and integrin immobilization. Moreover, co-stimulation by CXCL12 together with soluble VCAM-1 potentiated integrin immobilization with a 5-fold increase in immobile integrins compared with unstimulated conditions. Our data indicate that docking by talin of the chemokine-activated α4β1 to the actin cytoskeleton favors integrin immobilization, which likely facilitates ligand interaction and increased adhesiveness. Superresolution imaging showed that the nanoscale organization of high-affinity α4β1 remains unaffected following chemokine and/or ligand addition. Instead, newly activated α4β1 integrins organize on the cell membrane as independent units without joining pre-established integrin sites to contribute to cluster formation. Altogether, our results provide a rationale to understand how the spatiotemporal organization of activated α4β1 integrins regulates T lymphocyte adhesion.
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Affiliation(s)
- Alberto Sosa-Costa
- From the Institut de Ciencies Fotoniques, Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Sol Isern de Val
- the Centro de Investigaciones Biológicas, Department of Cellular and Molecular Medicine, 28040 Madrid, Spain, and
| | - Silvia Sevilla-Movilla
- the Centro de Investigaciones Biológicas, Department of Cellular and Molecular Medicine, 28040 Madrid, Spain, and
| | - Kyra J E Borgman
- From the Institut de Ciencies Fotoniques, Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Carlo Manzo
- From the Institut de Ciencies Fotoniques, Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Joaquin Teixidó
- the Centro de Investigaciones Biológicas, Department of Cellular and Molecular Medicine, 28040 Madrid, Spain, and
| | - Maria F Garcia-Parajo
- From the Institut de Ciencies Fotoniques, Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain, the ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
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31
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Eich C, Manzo C, de Keijzer S, Bakker GJ, Reinieren-Beeren I, García-Parajo MF, Cambi A. Changes in membrane sphingolipid composition modulate dynamics and adhesion of integrin nanoclusters. Sci Rep 2016; 6:20693. [PMID: 26869100 PMCID: PMC4751618 DOI: 10.1038/srep20693] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/11/2016] [Indexed: 12/14/2022] Open
Abstract
Sphingolipids are essential constituents of the plasma membrane (PM) and play an important role in signal transduction by modulating clustering and dynamics of membrane receptors. Changes in lipid composition are therefore likely to influence receptor organisation and function, but how this precisely occurs is difficult to address given the intricacy of the PM lipid-network. Here, we combined biochemical assays and single molecule dynamic approaches to demonstrate that the local lipid environment regulates adhesion of integrin receptors by impacting on their lateral mobility. Induction of sphingomyelinase (SMase) activity reduced sphingomyelin (SM) levels by conversion to ceramide (Cer), resulting in impaired integrin adhesion and reduced integrin mobility. Dual-colour imaging of cortical actin in combination with single molecule tracking of integrins showed that this reduced mobility results from increased coupling to the actin cytoskeleton brought about by Cer formation. As such, our data emphasizes a critical role for the PM local lipid composition in regulating the lateral mobility of integrins and their ability to dynamically increase receptor density for efficient ligand binding in the process of cell adhesion.
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Affiliation(s)
- Christina Eich
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
| | - Sandra de Keijzer
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
| | - Gert-Jan Bakker
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
| | - Inge Reinieren-Beeren
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
| | - Maria F García-Parajo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain.,ICREA-Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Alessandra Cambi
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands
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32
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Torreno-Pina JA, Manzo C, Salio M, Aichinger MC, Oddone A, Lakadamyali M, Shepherd D, Besra GS, Cerundolo V, Garcia-Parajo MF. The actin cytoskeleton modulates the activation of iNKT cells by segregating CD1d nanoclusters on antigen-presenting cells. Proc Natl Acad Sci U S A 2016; 113:E772-81. [PMID: 26798067 PMCID: PMC4760795 DOI: 10.1073/pnas.1514530113] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 12/23/2022] Open
Abstract
Invariant natural killer T (iNKT) cells recognize endogenous and exogenous lipid antigens presented in the context of CD1d molecules. The ability of iNKT cells to recognize endogenous antigens represents a distinct immune recognition strategy, which underscores the constitutive memory phenotype of iNKT cells and their activation during inflammatory conditions. However, the mechanisms regulating such "tonic" activation of iNKT cells remain unclear. Here, we show that the spatiotemporal distribution of CD1d molecules on the surface of antigen-presenting cells (APCs) modulates activation of iNKT cells. By using superresolution microscopy, we show that CD1d molecules form nanoclusters at the cell surface of APCs, and their size and density are constrained by the actin cytoskeleton. Dual-color single-particle tracking revealed that diffusing CD1d nanoclusters are actively arrested by the actin cytoskeleton, preventing their further coalescence. Formation of larger nanoclusters occurs in the absence of interactions between CD1d cytosolic tail and the actin cytoskeleton and correlates with enhanced iNKT cell activation. Importantly and consistently with iNKT cell activation during inflammatory conditions, exposure of APCs to the Toll-like receptor 7/8 agonist R848 increases nanocluster density and iNKT cell activation. Overall, these results define a previously unidentified mechanism that modulates iNKT cell autoreactivity based on the tight control by the APC cytoskeleton of the sizes and densities of endogenous antigen-loaded CD1d nanoclusters.
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Affiliation(s)
- Juan A Torreno-Pina
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Mariolina Salio
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Michael C Aichinger
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Anna Oddone
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Melike Lakadamyali
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - Dawn Shepherd
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Gurdyal S Besra
- School of Biosciences, University of Birmingham, Birmingham B11 2TT, United Kingdom
| | - Vincenzo Cerundolo
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom;
| | - Maria F Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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33
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Abstract
Optical microscopy has for centuries been a key tool to study living cells with minimum invasiveness. The advent of single molecule techniques over the past two decades has revolutionized the field of cell biology by providing a more quantitative picture of the complex and highly dynamic organization of living systems. Amongst these techniques, single particle tracking (SPT) has emerged as a powerful approach to study a variety of dynamic processes in life sciences. SPT provides access to single molecule behavior in the natural context of living cells, thereby allowing a complete statistical characterization of the system under study. In this review we describe the foundations of SPT together with novel optical implementations that nowadays allow the investigation of single molecule dynamic events with increasingly high spatiotemporal resolution using molecular densities closer to physiological expression levels. We outline some of the algorithms for the faithful reconstruction of SPT trajectories as well as data analysis, and highlight biological examples where the technique has provided novel insights into the role of diffusion regulating cellular function. The last part of the review concentrates on different theoretical models that describe anomalous transport behavior and ergodicity breaking observed from SPT studies in living cells.
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Affiliation(s)
- Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
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Flauraud V, van Zanten TS, Mivelle M, Manzo C, Garcia Parajo MF, Brugger J. Large-Scale Arrays of Bowtie Nanoaperture Antennas for Nanoscale Dynamics in Living Cell Membranes. Nano Lett 2015; 15:4176-4182. [PMID: 25926327 DOI: 10.1021/acs.nanolett.5b01335] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a novel blurring-free stencil lithography patterning technique for high-throughput fabrication of large-scale arrays of nanoaperture optical antennas. The approach relies on dry etching through nanostencils to achieve reproducible and uniform control of nanoantenna geometries at the nanoscale, over millimeter-sizes in a thin aluminum film. We demonstrate the fabrication of over 400 000 bowtie nanoaperture (BNA) antennas on biocompatible substrates, having gap sizes ranging from (80 ± 5) nm down to (20 ± 10) nm. To validate their applicability on live cell research, we used the antenna substrates as hotspots of localized illumination to excite fluorescently labeled lipids on living cell membranes. The high signal-to-background afforded by the BNA arrays allowed the recording of single fluorescent bursts corresponding to the passage of freely diffusing individual lipids through hotspot excitation regions as small as 20 nm. Statistical analysis of burst length and intensity together with simulations demonstrate that the measured signals arise from the ultraconfined excitation region of the antennas. Because these inexpensive antenna arrays are fully biocompatible and amenable to their integration in most fluorescence microscopes, we foresee a large number of applications including the investigation of the plasma membrane of living cells with nanoscale resolution at endogenous expression levels.
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Affiliation(s)
- Valentin Flauraud
- †Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Thomas S van Zanten
- ‡ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
| | - Mathieu Mivelle
- ‡ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
| | - Carlo Manzo
- ‡ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
| | - Maria F Garcia Parajo
- ‡ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
- §ICREA-Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Jürgen Brugger
- †Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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Ricci MA, Manzo C, García-Parajo MF, Lakadamyali M, Cosma MP. Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo. Cell 2015; 160:1145-58. [PMID: 25768910 DOI: 10.1016/j.cell.2015.01.054] [Citation(s) in RCA: 416] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 10/10/2014] [Accepted: 01/16/2015] [Indexed: 11/19/2022]
Abstract
Nucleosomes help structure chromosomes by compacting DNA into fibers. To gain insight into how nucleosomes are arranged in vivo, we combined quantitative super-resolution nanoscopy with computer simulations to visualize and count nucleosomes along the chromatin fiber in single nuclei. Nucleosomes assembled in heterogeneous groups of varying sizes, here termed "clutches," and these were interspersed with nucleosome-depleted regions. The median number of nucleosomes inside clutches and their compaction defined as nucleosome density were cell-type-specific. Ground-state pluripotent stem cells had, on average, less dense clutches containing fewer nucleosomes and clutch size strongly correlated with the pluripotency potential of induced pluripotent stem cells. RNA polymerase II preferentially associated with the smallest clutches while linker histone H1 and heterochromatin were enriched in the largest ones. Our results reveal how the chromatin fiber is formed at nanoscale level and link chromatin fiber architecture to stem cell state.
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Affiliation(s)
- Maria Aurelia Ricci
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Carlo Manzo
- ICFO, Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
| | - María Filomena García-Parajo
- ICFO, Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Melike Lakadamyali
- ICFO, Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain.
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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36
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Manzo C, Torreno-Pina JA, Massignan P, Lapeyre GJ, Lewenstein M, Garcia-Parajo MF. Weak Ergodicity Breaking of Membrane Receptor Motion Stemming from Random Diffusivity. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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37
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Torreno-Pina JA, Castro B, Cambi A, Manzo C, Garcia-Parajo M. Glycan-Based Connectivity Regulates the Hierarchical Organization of Membrane Receptors by Coupling their Micro- and Nano-Scale Lateral Mobility. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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38
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Kumar S, Manzo C, Zurla C, Ucuncuoglu S, Finzi L, Dunlap D. Enhanced tethered-particle motion analysis reveals viscous effects. Biophys J 2014; 106:399-409. [PMID: 24461015 DOI: 10.1016/j.bpj.2013.11.4501] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/16/2013] [Accepted: 11/25/2013] [Indexed: 12/29/2022] Open
Abstract
Tethered-particle motion experiments do not require expensive or technically complex hardware, and increasing numbers of researchers are adopting this methodology to investigate the topological effects of agents that act on the tethering polymer or the characteristics of the polymer itself. These investigations depend on accurate measurement and interpretation of changes in the effective length of the tethering polymer (often DNA). However, the bead size, tether length, and buffer affect the confined diffusion of the bead in this experimental system. To evaluate the effects of these factors, improved measurements to calibrate the two-dimensional range of motion (excursion) versus DNA length were carried out. Microspheres of 160 or 240 nm in radius were tethered by DNA molecules ranging from 225 to 3477 basepairs in length in aqueous buffers containing 100 mM potassium glutamate and 8 mM MgCl2 or 10 mM Tris-HCl and 200 mM KCl, with or without 0.5% Tween added to the buffer, and the motion was recorded. Different buffers altered the excursion of beads on identical DNA tethers. Buffer with only 10 mM NaCl and >5 mM magnesium greatly reduced excursion. Glycerol added to increase viscosity slowed confined diffusion of the tethered beads but did not change excursion. The confined-diffusion coefficients for all tethered beads were smaller than those expected for freely diffusing beads and decreased for shorter tethers. Tethered-particle motion is a sensitive framework for diffusion experiments in which small beads on long leashes most closely resemble freely diffusing, untethered beads.
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Affiliation(s)
- Sandip Kumar
- Department of Cell Biology, Emory University, Atlanta, Georgia
| | - Carlo Manzo
- Department of Physics, Emory University, Atlanta, Georgia
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | | | - Laura Finzi
- Department of Physics, Emory University, Atlanta, Georgia
| | - David Dunlap
- Department of Cell Biology, Emory University, Atlanta, Georgia.
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Borgman KJE, van Zanten TS, Manzo C, Cabezón R, Cambi A, Benítez-Ribas D, Garcia-Parajo MF. Priming by chemokines restricts lateral mobility of the adhesion receptor LFA-1 and restores adhesion to ICAM-1 nano-aggregates on human mature dendritic cells. PLoS One 2014; 9:e99589. [PMID: 24945611 PMCID: PMC4063950 DOI: 10.1371/journal.pone.0099589] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 04/18/2014] [Indexed: 01/12/2023] Open
Abstract
LFA-1 is a leukocyte specific β2 integrin that plays a major role in regulating adhesion and migration of different immune cells. Recent data suggest that LFA-1 on mature dendritic cells (mDCs) may function as a chemokine-inducible anchor during homing of DCs through the afferent lymphatics into the lymph nodes, by transiently switching its molecular conformational state. However, the role of LFA-1 mobility in this process is not yet known, despite that the importance of lateral organization and dynamics for LFA-1-mediated adhesion regulation is broadly recognized. Using single particle tracking approaches we here show that LFA-1 exhibits higher mobility on resting mDCs compared to monocytes. Lymphoid chemokine CCL21 stimulation of the LFA-1 high affinity state on mDCs, led to a significant reduction of mobility and an increase on the fraction of stationary receptors, consistent with re-activation of the receptor. Addition of soluble monomeric ICAM-1 in the presence of CCL21 did not alter the diffusion profile of LFA-1 while soluble ICAM-1 nano-aggregates in the presence of CCL21 further reduced LFA-1 mobility and readily bound to the receptor. Overall, our results emphasize the importance of LFA-1 lateral mobility across the membrane on the regulation of integrin activation and its function as adhesion receptor. Importantly, our data show that chemokines alone are not sufficient to trigger the high affinity state of the integrin based on the strict definition that affinity refers to the adhesion capacity of a single receptor to its ligand in solution. Instead our data indicate that nanoclustering of the receptor, induced by multi-ligand binding, is required to maintain stable cell adhesion once LFA-1 high affinity state is transiently triggered by inside-out signals.
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Affiliation(s)
| | | | - Carlo Manzo
- ICFO-Institut de Ciències Fotòniques, Barcelona, Spain
| | - Raquel Cabezón
- Department of Gastroenterology, Hospital Clinic de Barcelona, IDIBAPS, Barcelona, Spain
| | - Alessandra Cambi
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daniel Benítez-Ribas
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Centre Esther Koplowitz, Barcelona, Spain
| | - Maria F. Garcia-Parajo
- ICFO-Institut de Ciències Fotòniques, Barcelona, Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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40
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Massignan P, Manzo C, Torreno-Pina JA, García-Parajo MF, Lewenstein M, Lapeyre GJ. Nonergodic subdiffusion from Brownian motion in an inhomogeneous medium. Phys Rev Lett 2014; 112:150603. [PMID: 24785018 DOI: 10.1103/physrevlett.112.150603] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 06/03/2023]
Abstract
Nonergodicity observed in single-particle tracking experiments is usually modeled by transient trapping rather than spatial disorder. We introduce models of a particle diffusing in a medium consisting of regions with random sizes and random diffusivities. The particle is never trapped but rather performs continuous Brownian motion with the local diffusion constant. Under simple assumptions on the distribution of the sizes and diffusivities, we find that the mean squared displacement displays subdiffusion due to nonergodicity for both annealed and quenched disorder. The model is formulated as a walk continuous in both time and space, similar to the Lévy walk.
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Affiliation(s)
- P Massignan
- ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels, Spain
| | - C Manzo
- ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels, Spain
| | - J A Torreno-Pina
- ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels, Spain
| | - M F García-Parajo
- ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels, Spain and ICREA-Institució Catalana de Recerca i Estudis Avançats, Lluis Companys 23, 08010 Barcelona, Spain
| | - M Lewenstein
- ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels, Spain and ICREA-Institució Catalana de Recerca i Estudis Avançats, Lluis Companys 23, 08010 Barcelona, Spain
| | - G J Lapeyre
- ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Castelldefels, Spain
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41
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Mivelle M, Van Zanten TS, Manzo C, Garcia-Parajo MF. Nanophotonic approaches for nanoscale imaging and single-molecule detection at ultrahigh concentrations. Microsc Res Tech 2014; 77:537-45. [DOI: 10.1002/jemt.22369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/28/2014] [Accepted: 03/27/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Mathieu Mivelle
- ICFO-Institut de Ciencies Fotoniques; Mediterranean Technology Park; Castelldefels 08860 Barcelona Spain
| | - Thomas. S. Van Zanten
- ICFO-Institut de Ciencies Fotoniques; Mediterranean Technology Park; Castelldefels 08860 Barcelona Spain
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques; Mediterranean Technology Park; Castelldefels 08860 Barcelona Spain
| | - Maria F. Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques; Mediterranean Technology Park; Castelldefels 08860 Barcelona Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats; 08010 Barcelona Spain
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Torreno-Pina JA, Aichinger M, Manzo C, Salio M, Cerundolo V, Garcia-Parajo MF. The Actin Cytoskeleton Controls the Activation of Invariant Natural Killer T Cells by Fine-Tuning CD1d Nanoscale Aggregation on Antigen Presenting Cells. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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43
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Mendes MA, Guerra RF, Berns MC, Manzo C, Masiero S, Finzi L, Kater MM, Colombo L. MADS domain transcription factors mediate short-range DNA looping that is essential for target gene expression in Arabidopsis. Plant Cell 2013; 25:2560-72. [PMID: 23847151 PMCID: PMC3753383 DOI: 10.1105/tpc.112.108688] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
MADS domain transcription factors are key regulators of eukaryotic development. In plants, the homeotic MIKC MADS factors that regulate floral organ identity have been studied in great detail. Based on genetic and protein-protein interaction studies, a floral quartet model was proposed that describes how these MADS domain proteins assemble into higher order complexes to regulate their target genes. However, despite the attractiveness of this model and its general acceptance in the literature, solid in vivo proof has never been provided. To gain deeper insight into the mechanisms of transcriptional regulation by MADS domain factors, we studied how SEEDSTICK (STK) and SEPALLATA3 (SEP3) directly regulate the expression of the reproductive meristem gene family transcription factor-encoding gene VERDANDI (VDD). Our data show that STK-SEP3 dimers can induce loop formation in the VDD promoter by binding to two nearby CC(A/T)6GG (CArG) boxes and that this is essential for promoter activity. Our in vivo data show that the size and position of this loop, determined by the choice of CArG element usage, is essential for correct expression. Our studies provide solid in vivo evidence for the floral quartet model.
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Affiliation(s)
- Marta Adelina Mendes
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | | | | | - Carlo Manzo
- Department of Physics, Emory University, Atlanta, Georgia 30322
| | - Simona Masiero
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Laura Finzi
- Department of Physics, Emory University, Atlanta, Georgia 30322
| | - Martin M. Kater
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Lucia Colombo
- Dipartimento di BioScienze, Università degli Studi di Milano, 20133 Milan, Italy
- Consiglio Nazionale delle Richerche, Istituto di Biofisica, Università di Milano, 20133 Milan, Italy
- Address correspondence to
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Manzo C, Torreno-Pina JA, van Zanten TS, Garcia-Parajo MF. Automated Algorithm for Quantitative Analysis of Fluorescence Nanoscopy Images. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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45
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Ding Y, Manzo C, Dunlap D, Finzi L. DNA supercoiling affects Stability of Genetic Switch. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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46
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Torreno-Pina JA, Manzo C, Figdor CG, Cambi A, Garcia-Parajo MF. The Neck Region Regulates Spatiotemporal Organization and Virus-Binding Capability of the Pathogen Recognition Receptor DC-Sign. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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47
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Manzo C, Zurla C, Dunlap DD, Finzi L. The effect of nonspecific binding of lambda repressor on DNA looping dynamics. Biophys J 2012; 103:1753-61. [PMID: 23083719 DOI: 10.1016/j.bpj.2012.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 08/31/2012] [Accepted: 09/05/2012] [Indexed: 12/11/2022] Open
Abstract
The λ repressor (CI) protein-induced DNA loop maintains stable lysogeny, yet allows efficient switching to lysis. Herein, the kinetics of loop formation and breakdown has been characterized at various concentrations of protein using tethered particle microscopy and a novel, to our knowledge, method of analysis. Our results show that a broad distribution of rate constants and complex kinetics underlie loop formation and breakdown. In addition, comparison of the kinetics of looping in wild-type DNA and DNA with mutated o3 operators showed that these sites may trigger nucleation of nonspecific binding at the closure of the loop. The average activation energy calculated from the rate constant distribution is consistent with a model in which nonspecific binding of CI between the operators shortens their effective separation, thereby lowering the energy barrier for loop formation and broadening the rate constant distribution for looping. Similarly, nonspecific binding affects the kinetics of loop breakdown by increasing the number of loop-securing protein interactions, and broadens the rate constant distribution for this reaction. Therefore, simultaneous increase of the rate constant for loop formation and reduction of that for loop breakdown stabilizes lysogeny. Given these simultaneous changes, the frequency of transitions between the looped and the unlooped state remains nearly constant. Although the loop becomes more stable thermodynamically with increasing CI concentration, it still opens periodically, conferring sensitivity to environmental changes, which may require switching to lytic conditions.
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Affiliation(s)
- Carlo Manzo
- Physics Department, Emory University, Atlanta, Georgia, USA
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Manzo C, Torreno-Pina JA, Joosten B, Reinieren-Beeren I, Gualda EJ, Loza-Alvarez P, Figdor CG, Garcia-Parajo MF, Cambi A. The neck region of the C-type lectin DC-SIGN regulates its surface spatiotemporal organization and virus-binding capacity on antigen-presenting cells. J Biol Chem 2012; 287:38946-55. [PMID: 23019323 DOI: 10.1074/jbc.m112.380121] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The C-type lectin DC-SIGN expressed on dendritic cells (DCs) facilitates capture and internalization of a plethora of different pathogens. Although it is known that DC-SIGN organizes in nanoclusters at the surface of DCs, the molecular mechanisms responsible for this well defined nanopatterning and role in viral binding remain enigmatic. By combining biochemical and advanced biophysical techniques, including optical superresolution and single particle tracking, we demonstrate that DC-SIGN intrinsic nanoclustering strictly depends on its molecular structure. DC-SIGN nanoclusters exhibited free, Brownian diffusion on the cell membrane. Truncation of the extracellular neck region, known to abrogate tetramerization, significantly reduced nanoclustering and concomitantly increased lateral diffusion. Importantly, DC-SIGN nanocluster dissolution exclusively compromised binding to nanoscale size pathogens. Monte Carlo simulations revealed that heterogeneity on nanocluster density and spatial distribution confers broader binding capabilities to DC-SIGN. As such, our results underscore a direct relationship between spatial nanopatterning, driven by intermolecular interactions between the neck regions, and receptor diffusion to provide DC-SIGN with the exquisite ability to dock pathogens at the virus length scale. Insight into how virus receptors are organized prior to virus binding and how they assemble into functional platforms for virus docking is helpful to develop novel strategies to prevent virus entry and infection.
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Affiliation(s)
- Carlo Manzo
- Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
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van den Dries K, van Helden SFG, te Riet J, Diez-Ahedo R, Manzo C, Oud MM, van Leeuwen FN, Brock R, Garcia-Parajo MF, Cambi A, Figdor CG. Geometry sensing by dendritic cells dictates spatial organization and PGE(2)-induced dissolution of podosomes. Cell Mol Life Sci 2011; 69:1889-901. [PMID: 22204022 PMCID: PMC3350765 DOI: 10.1007/s00018-011-0908-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 11/28/2011] [Accepted: 12/13/2011] [Indexed: 01/01/2023]
Abstract
Assembly and disassembly of adhesion structures such as focal adhesions (FAs) and podosomes regulate cell adhesion and differentiation. On antigen-presenting dendritic cells (DCs), acquisition of a migratory and immunostimulatory phenotype depends on podosome dissolution by prostaglandin E2 (PGE2). Whereas the effects of physico-chemical and topographical cues have been extensively studied on FAs, little is known about how podosomes respond to these signals. Here, we show that, unlike for FAs, podosome formation is not controlled by substrate physico-chemical properties. We demonstrate that cell adhesion is the only prerequisite for podosome formation and that substrate availability dictates podosome density. Interestingly, we show that DCs sense 3-dimensional (3-D) geometry by aligning podosomes along the edges of 3-D micropatterned surfaces. Finally, whereas on a 2-dimensional (2-D) surface PGE2 causes a rapid increase in activated RhoA levels leading to fast podosome dissolution, 3-D geometric cues prevent PGE2-mediated RhoA activation resulting in impaired podosome dissolution even after prolonged stimulation. Our findings indicate that 2-D and 3-D geometric cues control the spatial organization of podosomes. More importantly, our studies demonstrate the importance of substrate dimensionality in regulating podosome dissolution and suggest that substrate dimensionality plays an important role in controlling DC activation, a key process in initiating immune responses.
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Affiliation(s)
- Koen van den Dries
- Department of Tumor Immunology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
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Manzo C, van Zanten TS, Garcia-Parajo MF. Nanoscale fluorescence correlation spectroscopy on intact living cell membranes with NSOM probes. Biophys J 2011; 100:L8-10. [PMID: 21244822 DOI: 10.1016/j.bpj.2010.12.3690] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 11/30/2010] [Accepted: 12/03/2010] [Indexed: 12/13/2022] Open
Abstract
Characterization of molecular dynamics on living cell membranes at the nanoscale is fundamental to unravel the mechanisms of membrane organization and compartmentalization. Here we demonstrate the feasibility of fluorescence correlation spectroscopy (FCS) based on the nanometric illumination of near-field scanning optical microscopy (NSOM) probes on intact living cells. NSOM-FCS applied to fluorescent lipid analogs allowed us to reveal details of the diffusion hidden by larger illumination areas. Moreover, the technique offers the unique advantages of evanescent axial illumination and straightforward implementation of multiple color excitation. As such, NSOM-FCS represents a powerful tool to study a variety of dynamic processes occurring at the nanometer scale on cell membranes.
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