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Laine RF, Heil HS, Coelho S, Nixon-Abell J, Jimenez A, Wiesner T, Martínez D, Galgani T, Régnier L, Stubb A, Follain G, Webster S, Goyette J, Dauphin A, Salles A, Culley S, Jacquemet G, Hajj B, Leterrier C, Henriques R. High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation. Nat Methods 2023; 20:1949-1956. [PMID: 37957430 PMCID: PMC10703683 DOI: 10.1038/s41592-023-02057-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/29/2023] [Indexed: 11/15/2023]
Abstract
Live-cell super-resolution microscopy enables the imaging of biological structure dynamics below the diffraction limit. Here we present enhanced super-resolution radial fluctuations (eSRRF), substantially improving image fidelity and resolution compared to the original SRRF method. eSRRF incorporates automated parameter optimization based on the data itself, giving insight into the trade-off between resolution and fidelity. We demonstrate eSRRF across a range of imaging modalities and biological systems. Notably, we extend eSRRF to three dimensions by combining it with multifocus microscopy. This realizes live-cell volumetric super-resolution imaging with an acquisition speed of ~1 volume per second. eSRRF provides an accessible super-resolution approach, maximizing information extraction across varied experimental conditions while minimizing artifacts. Its optimal parameter prediction strategy is generalizable, moving toward unbiased and optimized analyses in super-resolution microscopy.
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Affiliation(s)
- Romain F Laine
- Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
- Micrographia Bio, Translation and Innovation Hub, London, UK
| | - Hannah S Heil
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Simao Coelho
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Jonathon Nixon-Abell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Cambridge Institute for Medical Research, Cambridge Univeristy, Cambridge, UK
| | - Angélique Jimenez
- Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Theresa Wiesner
- Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
| | - Damián Martínez
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Tommaso Galgani
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Paris, France
- Revvity Signals, Tres Cantos, Madrid, Spain
| | - Louise Régnier
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Paris, France
| | - Aki Stubb
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Munster, Germany
| | - Gautier Follain
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Samantha Webster
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Aurelien Dauphin
- Unite Genetique et Biologie du Développement U934, PICT-IBiSA, Institut Curie, INSERM, CNRS, PSL Research University, Paris, France
| | - Audrey Salles
- Institut Pasteur, Université Paris Cité, Unit of Technology and Service Photonic BioImaging (UTechS PBI), C2RT, Paris, France
| | - Siân Culley
- Laboratory for Molecular Cell Biology, University College London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, UK
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, Turku, Finland
| | - Bassam Hajj
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Paris, France.
| | | | - Ricardo Henriques
- Laboratory for Molecular Cell Biology, University College London, London, UK.
- The Francis Crick Institute, London, UK.
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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2
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Delille F, Balloul E, Hajj B, Hanafi M, Morand C, Xu XZ, Dumas S, Coulon A, Lequeux N, Pons T. Sulfobetaine-Phosphonate Block Copolymer Coated Iron Oxide Nanoparticles for Genomic Locus Targeting and Magnetic Micromanipulation in the Nucleus of Living Cells. Nano Lett 2023. [PMID: 37390368 DOI: 10.1021/acs.nanolett.3c00688] [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] [Indexed: 07/02/2023]
Abstract
Exerting forces on biomolecules inside living cells would allow us to probe their dynamic interactions in their native environment. Magnetic iron oxide nanoparticles represent a unique tool capable of pulling on biomolecules with the application of an external magnetic field gradient; however, their use has been restricted to biomolecules accessible from the extracellular medium. Targeting intracellular biomolecules represents an additional challenge due to potential nonspecific interactions with cytoplasmic or nuclear components. We present the synthesis of sulfobetaine-phosphonate block copolymer ligands, which provide magnetic nanoparticles that are stealthy and targetable in living cells. We demonstrate, for the first time, their efficient targeting in the nucleus and their use for magnetic micromanipulation of a specific genomic locus in living cells. We believe that these stable and sensitive magnetic nanoprobes represent a promising tool to manipulate specific biomolecules in living cells and probe the mechanical properties of living matter at the molecular scale.
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Affiliation(s)
- Fanny Delille
- Laboratoire Physique et Etude des Matériaux, ESPCI-Paris, PSL Research University, CNRS, Sorbonne Université, UMR 8213, 10, rue Vauquelin, 75005 Paris, France
| | - Elie Balloul
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005 Paris, France
| | - Bassam Hajj
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005 Paris, France
| | - Mohamed Hanafi
- Sciences et Ingénierie de la Matière Molle, UMR 7615, ESPCI Paris PSL-CNRS-Sorbonne Université, 10 Rue Vauquelin, 75005 Paris, France
| | - Colin Morand
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005 Paris, France
- Laboratoire Dynamique du Noyau, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, 75005 Paris, France
| | - Xiang Zhen Xu
- Laboratoire Physique et Etude des Matériaux, ESPCI-Paris, PSL Research University, CNRS, Sorbonne Université, UMR 8213, 10, rue Vauquelin, 75005 Paris, France
| | - Simon Dumas
- Institut Pierre-Gilles de Gennes, Institut Curie, Sorbonne Université, PSL Research University, 6 rue Jean Calvin, 75005 Paris, France
| | - Antoine Coulon
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005 Paris, France
- Laboratoire Dynamique du Noyau, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, 75005 Paris, France
| | - Nicolas Lequeux
- Laboratoire Physique et Etude des Matériaux, ESPCI-Paris, PSL Research University, CNRS, Sorbonne Université, UMR 8213, 10, rue Vauquelin, 75005 Paris, France
| | - Thomas Pons
- Laboratoire Physique et Etude des Matériaux, ESPCI-Paris, PSL Research University, CNRS, Sorbonne Université, UMR 8213, 10, rue Vauquelin, 75005 Paris, France
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3
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Nakazawa K, Kumar G, Chauvin B, Di Cicco A, Pellegrino L, Trichet M, Hajj B, Cabral J, Sain A, Mangenot S, Bertin A. A human septin octamer complex sensitive to membrane curvature drives membrane deformation with a specific mesh-like organization. J Cell Sci 2023; 136:316658. [PMID: 37305997 DOI: 10.1242/jcs.260813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/04/2023] [Indexed: 06/13/2023] Open
Abstract
Septins are cytoskeletal proteins interacting with the inner plasma membrane and other cytoskeletal partners. Being key in membrane remodeling processes, they often localize at specific micrometric curvatures. To analyze the behavior of human septins at the membrane and decouple their role from other partners, we used a combination of bottom-up in vitro methods. We assayed their ultrastructural organization, their curvature sensitivity, as well as their role in membrane reshaping. On membranes, human septins organize into a two-layered mesh of orthogonal filaments, instead of generating parallel sheets of filaments observed for budding yeast septins. This peculiar mesh organization is sensitive to micrometric curvature and drives membrane reshaping as well. The observed membrane deformations together with the filamentous organization are recapitulated in a coarse-grained computed simulation to understand their mechanisms. Our results highlight the specific organization and behavior of animal septins at the membrane as opposed to those of fungal proteins.
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Affiliation(s)
- Koyomi Nakazawa
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - Gaurav Kumar
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, Bangalore, Karnataka 560012, India
| | - Brieuc Chauvin
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - Aurélie Di Cicco
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - Luca Pellegrino
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Michael Trichet
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Service de microscopie électronique (IBPS-SME), F-75005, Paris, France
| | - Bassam Hajj
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - João Cabral
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Anirban Sain
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Stéphanie Mangenot
- Laboratoire Matière et Systèmes Complexes (MSC), Université Paris Cité, CNRS UMR 7057, 75006 Paris, France
| | - Aurélie Bertin
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 75005, Paris, France
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4
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Prigent S, Nguyen HN, Leconte L, Valades-Cruz CA, Hajj B, Salamero J, Kervrann C. SPITFIR(e): a supermaneuverable algorithm for fast denoising and deconvolution of 3D fluorescence microscopy images and videos. Sci Rep 2023; 13:1489. [PMID: 36707688 PMCID: PMC9883505 DOI: 10.1038/s41598-022-26178-y] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/12/2022] [Indexed: 01/28/2023] Open
Abstract
Modern fluorescent microscopy imaging is still limited by the optical aberrations and the photon budget available in the specimen. A direct consequence is the necessity to develop flexible and "off-road" algorithms in order to recover structural details and improve spatial resolution, which is critical when restraining the illumination to low levels in order to limit photo-damages. Here, we report SPITFIR(e) a flexible method designed to accurately and quickly restore 2D-3D fluorescence microscopy images and videos (4D images). We designed a generic sparse-promoting regularizer to subtract undesirable out-of-focus background and we developed a primal-dual algorithm for fast optimization. SPITFIR(e) is a "swiss-knife" method for practitioners as it adapts to any microscopy techniques, to various sources of signal degradation (noise, blur), to variable image contents, as well as to low signal-to-noise ratios. Our method outperforms existing state-of-the-art algorithms, and is more flexible than supervised deep-learning methods requiring ground truth datasets. The performance, the flexibility, and the ability to push the spatiotemporal resolution limit of sub-diffracted fluorescence microscopy techniques are demonstrated on experimental datasets acquired with various microscopy techniques from 3D spinning-disk confocal up to lattice light sheet microscopy.
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Affiliation(s)
- Sylvain Prigent
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Hoai-Nam Nguyen
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Ludovic Leconte
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Cesar Augusto Valades-Cruz
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Bassam Hajj
- grid.465542.40000 0004 1759 735XLaboratoire Physico-Chimie, Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR168, 75005 Paris, France
| | - Jean Salamero
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
| | - Charles Kervrann
- SERPICO Project-Team, Inria Centre Rennes-Bretagne Atlantique, 35042 Rennes Cedex, France ,grid.462844.80000 0001 2308 1657SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universités, 75005 Paris, France
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5
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Valades-Cruz CA, Leconte L, Fouche G, Blanc T, Van Hille N, Fournier K, Laurent T, Gallean B, Deslandes F, Hajj B, Faure E, Argelaguet F, Trubuil A, Isenberg T, Masson JB, Salamero J, Kervrann C. Challenges of intracellular visualization using virtual and augmented reality. Front Bioinform 2022; 2:997082. [PMID: 36304296 PMCID: PMC9580941 DOI: 10.3389/fbinf.2022.997082] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022] Open
Abstract
Microscopy image observation is commonly performed on 2D screens, which limits human capacities to grasp volumetric, complex, and discrete biological dynamics. With the massive production of multidimensional images (3D + time, multi-channels) and derived images (e.g., restored images, segmentation maps, and object tracks), scientists need appropriate visualization and navigation methods to better apprehend the amount of information in their content. New modes of visualization have emerged, including virtual reality (VR)/augmented reality (AR) approaches which should allow more accurate analysis and exploration of large time series of volumetric images, such as those produced by the latest 3D + time fluorescence microscopy. They include integrated algorithms that allow researchers to interactively explore complex spatiotemporal objects at the scale of single cells or multicellular systems, almost in a real time manner. In practice, however, immersion of the user within 3D + time microscopy data represents both a paradigm shift in human-image interaction and an acculturation challenge, for the concerned community. To promote a broader adoption of these approaches by biologists, further dialogue is needed between the bioimaging community and the VR&AR developers.
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Affiliation(s)
- Cesar Augusto Valades-Cruz
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
| | - Ludovic Leconte
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
| | - Gwendal Fouche
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
- Inria, CNRS, IRISA, University Rennes, Rennes, France
| | - Thomas Blanc
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, Sorbonne Universites, CNRS UMR168, Paris, France
| | | | - Kevin Fournier
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
- Inria, CNRS, IRISA, University Rennes, Rennes, France
| | - Tao Laurent
- LIRMM, Université Montpellier, CNRS, Montpellier, France
| | | | | | - Bassam Hajj
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, Sorbonne Universites, CNRS UMR168, Paris, France
| | - Emmanuel Faure
- LIRMM, Université Montpellier, CNRS, Montpellier, France
| | | | - Alain Trubuil
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Jean-Baptiste Masson
- Decision and Bayesian Computation, Neuroscience and Computational Biology Departments, CNRS UMR 3571, Institut Pasteur, Université Paris Cité, Paris, France
| | - Jean Salamero
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
| | - Charles Kervrann
- SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Rennes, France
- SERPICO/STED Team, UMR144 CNRS Institut Curie, PSL Research University, Sorbonne Universites, Paris, France
- *Correspondence: Charles Kervrann,
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Chauvin B, Nakazawa K, Beber A, Di Cicco A, Hajj B, Iv F, Mavrakis M, Koenderink GH, Cabral JT, Trichet M, Mangenot S, Bertin A. Bottom-Up <em>In Vitro</em> Methods to Assay the Ultrastructural Organization, Membrane Reshaping, and Curvature Sensitivity Behavior of Septins. J Vis Exp 2022. [DOI: 10.3791/63889] [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: 10/31/2022] Open
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7
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Guérinot C, Marcon V, Godard C, Blanc T, Verdier H, Planchon G, Raimondi F, Boddaert N, Alonso M, Sailor K, Lledo PM, Hajj B, El Beheiry M, Masson JB. New Approach to Accelerated Image Annotation by Leveraging Virtual Reality and Cloud Computing. Front Bioinform 2022; 1:777101. [PMID: 36303792 PMCID: PMC9580868 DOI: 10.3389/fbinf.2021.777101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/14/2021] [Accepted: 12/15/2021] [Indexed: 01/02/2023] Open
Abstract
Three-dimensional imaging is at the core of medical imaging and is becoming a standard in biological research. As a result, there is an increasing need to visualize, analyze and interact with data in a natural three-dimensional context. By combining stereoscopy and motion tracking, commercial virtual reality (VR) headsets provide a solution to this critical visualization challenge by allowing users to view volumetric image stacks in a highly intuitive fashion. While optimizing the visualization and interaction process in VR remains an active topic, one of the most pressing issue is how to utilize VR for annotation and analysis of data. Annotating data is often a required step for training machine learning algorithms. For example, enhancing the ability to annotate complex three-dimensional data in biological research as newly acquired data may come in limited quantities. Similarly, medical data annotation is often time-consuming and requires expert knowledge to identify structures of interest correctly. Moreover, simultaneous data analysis and visualization in VR is computationally demanding. Here, we introduce a new procedure to visualize, interact, annotate and analyze data by combining VR with cloud computing. VR is leveraged to provide natural interactions with volumetric representations of experimental imaging data. In parallel, cloud computing performs costly computations to accelerate the data annotation with minimal input required from the user. We demonstrate multiple proof-of-concept applications of our approach on volumetric fluorescent microscopy images of mouse neurons and tumor or organ annotations in medical images.
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Affiliation(s)
- Corentin Guérinot
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience Department CNRS UMR 3751, Université de Paris, Institut Pasteur, Paris, France
- Perception and Memory Unit, CNRS UMR3571, Institut Pasteur, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Valentin Marcon
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience Department CNRS UMR 3751, Université de Paris, Institut Pasteur, Paris, France
| | - Charlotte Godard
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience Department CNRS UMR 3751, Université de Paris, Institut Pasteur, Paris, France
- École Doctorale Physique en Île-de-France, PSL University, Paris, France
| | - Thomas Blanc
- Sorbonne Université, Collège Doctoral, Paris, France
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - Hippolyte Verdier
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience Department CNRS UMR 3751, Université de Paris, Institut Pasteur, Paris, France
- Histopathology and Bio-Imaging Group, Sanofi R&D, Vitry-Sur-Seine, France
- Université de Paris, UFR de Physique, Paris, France
| | - Guillaume Planchon
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience Department CNRS UMR 3751, Université de Paris, Institut Pasteur, Paris, France
| | - Francesca Raimondi
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience Department CNRS UMR 3751, Université de Paris, Institut Pasteur, Paris, France
- Unité Médicochirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de Référence des Malformations Cardiaques Congénitales Complexes M3C, Hôpital Universitaire Necker-Enfants Malades, Université de Paris, Paris, France
- Pediatric Radiology Unit, Hôpital Universitaire Necker-Enfants Malades, Université de Paris, Paris, France
- UMR-1163 Institut Imagine, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Nathalie Boddaert
- Pediatric Radiology Unit, Hôpital Universitaire Necker-Enfants Malades, Université de Paris, Paris, France
- UMR-1163 Institut Imagine, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Paris, France
| | - Mariana Alonso
- Perception and Memory Unit, CNRS UMR3571, Institut Pasteur, Paris, France
| | - Kurt Sailor
- Perception and Memory Unit, CNRS UMR3571, Institut Pasteur, Paris, France
| | - Pierre-Marie Lledo
- Perception and Memory Unit, CNRS UMR3571, Institut Pasteur, Paris, France
| | - Bassam Hajj
- Sorbonne Université, Collège Doctoral, Paris, France
- École Doctorale Physique en Île-de-France, PSL University, Paris, France
| | - Mohamed El Beheiry
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience Department CNRS UMR 3751, Université de Paris, Institut Pasteur, Paris, France
| | - Jean-Baptiste Masson
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience Department CNRS UMR 3751, Université de Paris, Institut Pasteur, Paris, France
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8
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Blanc T, Verdier H, Regnier L, Planchon G, Guérinot C, El Beheiry M, Masson JB, Hajj B. Towards Human in the Loop Analysis of Complex Point Clouds: Advanced Visualizations, Quantifications, and Communication Features in Virtual Reality. Front Bioinform 2022; 1:775379. [PMID: 36303735 PMCID: PMC9580855 DOI: 10.3389/fbinf.2021.775379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple fields in biological and medical research produce large amounts of point cloud data with high dimensionality and complexity. In addition, a large set of experiments generate point clouds, including segmented medical data or single-molecule localization microscopy. In the latter, individual molecules are observed within their natural cellular environment. Analyzing this type of experimental data is a complex task and presents unique challenges, where providing extra physical dimensions for visualization and analysis could be beneficial. Furthermore, whether highly noisy data comes from single-molecule recordings or segmented medical data, the necessity to guide analysis with user intervention creates both an ergonomic challenge to facilitate this interaction and a computational challenge to provide fluid interactions as information is being processed. Several applications, including our software DIVA for image stack and our platform Genuage for point clouds, have leveraged Virtual Reality (VR) to visualize and interact with data in 3D. While the visualization aspects can be made compatible with different types of data, quantifications, on the other hand, are far from being standard. In addition, complex analysis can require significant computational resources, making the real-time VR experience uncomfortable. Moreover, visualization software is mainly designed to represent a set of data points but lacks flexibility in manipulating and analyzing the data. This paper introduces new libraries to enhance the interaction and human-in-the-loop analysis of point cloud data in virtual reality and integrate them into the open-source platform Genuage. We first detail a new toolbox of communication tools that enhance user experience and improve flexibility. Then, we introduce a mapping toolbox allowing the representation of physical properties in space overlaid on a 3D mesh while maintaining a point cloud dedicated shader. We introduce later a new and programmable video capture tool in VR and desktop modes for intuitive data dissemination. Finally, we highlight the protocols that allow simultaneous analysis and fluid manipulation of data with a high refresh rate. We illustrate this principle by performing real-time inference of random walk properties of recorded trajectories with a pre-trained Graph Neural Network running in Python.
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Affiliation(s)
- Thomas Blanc
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Hippolyte Verdier
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
| | - Louise Regnier
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Guillaume Planchon
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
| | - Corentin Guérinot
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
- Sorbonne Universités, Collège Doctoral, Paris, France
| | - Mohamed El Beheiry
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
| | - Jean-Baptiste Masson
- Decision and Bayesian Computation, CNRS USR 3756, Department of Computational Biology and Neuroscience, CNRS UMR 3571, Université de Paris, Institut Pasteur, Université de Paris, Paris, France
- *Correspondence: Jean-Baptiste Masson, ; Bassam Hajj,
| | - Bassam Hajj
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
- *Correspondence: Jean-Baptiste Masson, ; Bassam Hajj,
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9
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Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Saux AL, Coulon A, Mirny LA, Pollard KS, Dahan M, Bruneau BG. Molecular basis of CTCF binding polarity in genome folding. Nat Commun 2020; 11:5612. [PMID: 33154377 PMCID: PMC7645679 DOI: 10.1038/s41467-020-19283-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin. While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize loops, the molecular basis of this polarity remains unclear. By combining ChIP-seq and single molecule live imaging we report that CTCF positions cohesin, but does not control its overall binding dynamics on chromatin. Using an inducible complementation system, we find that CTCF mutants lacking the N-terminus cannot insulate TADs properly. Cohesin remains at CTCF sites in this mutant, albeit with reduced enrichment. Given the orientation of CTCF motifs presents the N-terminus towards cohesin as it translocates from the interior of TADs, these observations explain how the orientation of CTCF binding sites translates into genome folding patterns.
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Affiliation(s)
- Elphège P Nora
- Gladstone Institutes, San Francisco, CA, 94158, USA.
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA.
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Laura Caccianini
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 26 Rue D'Ulm, Paris, 75005, France
| | | | - Kevin So
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Vasumathi Kameswaran
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA
| | - Abigail Nagle
- Gladstone Institutes, San Francisco, CA, 94158, USA
- University of Washington, Seattle, WA, USA
| | - Alec Uebersohn
- Gladstone Institutes, San Francisco, CA, 94158, USA
- University of California Berkeley, Berkeley, CA, USA
| | - Bassam Hajj
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 26 Rue D'Ulm, Paris, 75005, France
| | - Agnès Le Saux
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Mammalian Developmental Epigenetics group, F-75005, Paris, France
- Sorbonne Université, F-75005, Paris, France
| | - Antoine Coulon
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 26 Rue D'Ulm, Paris, 75005, France
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR3664, Nuclear Dynamics unit, F-75005, Paris, France
| | - Leonid A Mirny
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Maxime Dahan
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, 26 Rue D'Ulm, Paris, 75005, France
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, 94158, USA.
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, 94158, USA.
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, 94143, USA.
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10
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El Beheiry M, Godard C, Caporal C, Marcon V, Ostertag C, Sliti O, Doutreligne S, Fournier S, Hajj B, Dahan M, Masson JB. DIVA: Natural Navigation Inside 3D Images Using Virtual Reality. J Mol Biol 2020; 432:4745-4749. [DOI: 10.1016/j.jmb.2020.05.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
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11
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Clément C, Orsi GA, Gatto A, Boyarchuk E, Forest A, Hajj B, Miné-Hattab J, Garnier M, Gurard-Levin ZA, Quivy JP, Almouzni G. High-resolution visualization of H3 variants during replication reveals their controlled recycling. Nat Commun 2018; 9:3181. [PMID: 30093638 PMCID: PMC6085313 DOI: 10.1038/s41467-018-05697-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [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: 12/21/2017] [Accepted: 07/05/2018] [Indexed: 12/11/2022] Open
Abstract
DNA replication is a challenge for the faithful transmission of parental information to daughter cells, as both DNA and chromatin organization must be duplicated. Replication stress further complicates the safeguard of epigenome integrity. Here, we investigate the transmission of the histone variants H3.3 and H3.1 during replication. We follow their distribution relative to replication timing, first in the genome and, second, in 3D using super-resolution microscopy. We find that H3.3 and H3.1 mark early- and late-replicating chromatin, respectively. In the nucleus, H3.3 forms domains, which decrease in density throughout replication, while H3.1 domains increase in density. Hydroxyurea impairs local recycling of parental histones at replication sites. Similarly, depleting the histone chaperone ASF1 affects recycling, leading to an impaired histone variant landscape. We discuss how faithful transmission of histone variants involves ASF1 and can be impacted by replication stress, with ensuing consequences for cell fate and tumorigenesis. Epigenetic modifications are a key contributor to cell identity, and their propagation is crucial for proper development. Here the authors use a super-resolution microscopy approach to reveal how histone variants are faithfully transmitted during genome duplication, and reveal an important role for the histone chaperone ASF1 in the redistribution of parental histones.
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Affiliation(s)
- Camille Clément
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Guillermo A Orsi
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Alberto Gatto
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Ekaterina Boyarchuk
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Audrey Forest
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Bassam Hajj
- Institut Curie, PSL Research University, CNRS, UMR168, Laboratoire Physico-Chimie, F-75005, Paris, France
| | - Judith Miné-Hattab
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.,Institut Curie, PSL Research University, CNRS, UMR3664, F-75005, Paris, France
| | - Mickaël Garnier
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.,Institut Curie, PSL Research University, CNRS, UMR3664, F-75005, Paris, France
| | - Zachary A Gurard-Levin
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.,SAMDI Tech, Inc., Chicago, IL, 60657, USA
| | - Jean-Pierre Quivy
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, UMR3664, Equipe Labellisée Ligue contre le Cancer, F-75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, F-75005, Paris, France.
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12
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Hajj B, El Beheiry M, Dahan M. PSF engineering in multifocus microscopy for increased depth volumetric imaging. Biomed Opt Express 2016; 7:726-31. [PMID: 27231584 PMCID: PMC4866451 DOI: 10.1364/boe.7.000726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 01/27/2016] [Accepted: 01/27/2016] [Indexed: 05/15/2023]
Abstract
Imaging and localizing single molecules with high accuracy in a 3D volume is a challenging task. Here we combine multifocal microscopy, a recently developed volumetric imaging technique, with point spread function engineering to achieve an increased depth for single molecule imaging. Applications in 3D single molecule localization-based super-resolution imaging is shown over an axial depth of 4 µm as well as for the tracking of diffusing beads in a fluid environment over 8 µm.
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Affiliation(s)
- Bassam Hajj
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France; Transcription Imaging Consortium, Janelia Research Campus, 19700 Helix Drive, Ashburn VA, 20147, USA;
| | - Mohamed El Beheiry
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France; Transcription Imaging Consortium, Janelia Research Campus, 19700 Helix Drive, Ashburn VA, 20147, USA
| | - Maxime Dahan
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France; Transcription Imaging Consortium, Janelia Research Campus, 19700 Helix Drive, Ashburn VA, 20147, USA;
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13
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Abrahamsson S, Ilic R, Wisniewski J, Mehl B, Yu L, Chen L, Davanco M, Oudjedi L, Fiche JB, Hajj B, Jin X, Pulupa J, Cho C, Mir M, El Beheiry M, Darzacq X, Nollmann M, Dahan M, Wu C, Lionnet T, Liddle JA, Bargmann CI. Multifocus microscopy with precise color multi-phase diffractive optics applied in functional neuronal imaging. Biomed Opt Express 2016; 7:855-69. [PMID: 27231594 PMCID: PMC4866461 DOI: 10.1364/boe.7.000855] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/10/2016] [Accepted: 02/03/2016] [Indexed: 05/05/2023]
Abstract
Multifocus microscopy (MFM) allows high-resolution instantaneous three-dimensional (3D) imaging and has been applied to study biological specimens ranging from single molecules inside cells nuclei to entire embryos. We here describe pattern designs and nanofabrication methods for diffractive optics that optimize the light-efficiency of the central optical component of MFM: the diffractive multifocus grating (MFG). We also implement a "precise color" MFM layout with MFGs tailored to individual fluorophores in separate optical arms. The reported advancements enable faster and brighter volumetric time-lapse imaging of biological samples. In live microscopy applications, photon budget is a critical parameter and light-efficiency must be optimized to obtain the fastest possible frame rate while minimizing photodamage. We provide comprehensive descriptions and code for designing diffractive optical devices, and a detailed methods description for nanofabrication of devices. Theoretical efficiencies of reported designs is ≈90% and we have obtained efficiencies of > 80% in MFGs of our own manufacture. We demonstrate the performance of a multi-phase MFG in 3D functional neuronal imaging in living C. elegans.
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Affiliation(s)
- Sara Abrahamsson
- HHMI and Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Rob Ilic
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jan Wisniewski
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Brian Mehl
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Liya Yu
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Lei Chen
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Marcelo Davanco
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Laura Oudjedi
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Jean-Bernard Fiche
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Bassam Hajj
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- Laboratoire Physico Chimie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris France
| | - Xin Jin
- HHMI and Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Joan Pulupa
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Christine Cho
- HHMI and Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Mustafa Mir
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- University of California, Berkeley, CA 94720, USA
| | - Mohamed El Beheiry
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- Laboratoire Physico Chimie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris France
| | - Xavier Darzacq
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- University of California, Berkeley, CA 94720, USA
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Maxime Dahan
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
- Laboratoire Physico Chimie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris France
| | - Carl Wu
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - Timothée Lionnet
- Transcription Imaging Consortium, HHMI Janelia Research Campus, Ashburn, VA 20147, USA
| | - J. Alexander Liddle
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Cornelia I. Bargmann
- HHMI and Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
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Hajj B, El Beheiry M, Izeddin I, Darzacq X, Dahan M. Accessing the third dimension in localization-based super-resolution microscopy. Phys Chem Chem Phys 2015; 16:16340-8. [PMID: 24901106 DOI: 10.1039/c4cp01380h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Only a few years after its inception, localization-based super-resolution microscopy has become widely employed in biological studies. Yet, it is primarily used in two-dimensional imaging and accessing the organization of cellular structures at the nanoscale in three dimensions (3D) still poses important challenges. Here, we review optical and computational techniques that enable the 3D localization of individual emitters and the reconstruction of 3D super-resolution images. These techniques are grouped into three main categories: PSF engineering, multiple plane imaging and interferometric approaches. We provide an overview of their technical implementation as well as commentary on their applicability. Finally, we discuss future trends in 3D localization-based super-resolution microscopy.
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Affiliation(s)
- Bassam Hajj
- Laboratoire Physico-Chimie Curie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris, France.
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15
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Trinh DT, Mayer L, Hajj B, Lautru J, Zyss J, Shynkar V. Full determination of single ferroelectric nanocrystal orientation by Pockels electro-optic microscopy. Appl Opt 2015; 54:3412-3421. [PMID: 25967332 DOI: 10.1364/ao.54.003412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a nanoscale electro-optic imaging method allowing access to the phase response, which is not amenable to classical second-harmonic generation microscopy. This approach is used to infer the vectorial orientation of single domain ferroelectric nanocrystals, based on polarization-resolved Pockels microscopy. The electro-optic phase response of KTP nanoparticles yields the full orientation in the laboratory frame of randomly dispersed single nanoparticles, together with their electric polarization dipole. The complete vector determination of the dipole orientation is a prerequisite to important applications including ferroelectric nanodomain orientation, membrane potential imaging, and rotational dynamics of single biomolecules.
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16
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Wisniewski J, Hajj B, Chen J, Mizuguchi G, Xiao H, Wei D, Dahan M, Wu C. Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres. eLife 2014; 3:e02203. [PMID: 24844245 PMCID: PMC4067749 DOI: 10.7554/elife.02203] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [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] [Indexed: 12/20/2022] Open
Abstract
The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3.DOI: http://dx.doi.org/10.7554/eLife.02203.001.
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Affiliation(s)
- Jan Wisniewski
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Bassam Hajj
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jiji Chen
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Gaku Mizuguchi
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Debbie Wei
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Maxime Dahan
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Carl Wu
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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17
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Cisse II, Izeddin I, Causse SZ, Boudarene L, Senecal A, Muresan L, Dugast-Darzacq C, Hajj B, Dahan M, Darzacq X. Real-time dynamics of RNA polymerase II clustering in live human cells. Science 2013; 341:664-7. [PMID: 23828889 DOI: 10.1126/science.1239053] [Citation(s) in RCA: 326] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells. We observed that Pol II clusters form transiently, with an average lifetime of 5.1 (± 0.4) seconds, which refutes the notion that they are statically assembled substructures. Stimuli affecting transcription yielded orders-of-magnitude changes in the dynamics of Pol II clusters, which implies that clustering is regulated and plays a role in the cell's ability to effect rapid response to external signals. Our results suggest that transient crowding of enzymes may aid in rate-limiting steps of gene regulation.
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Affiliation(s)
- Ibrahim I Cisse
- Functional Imaging of Transcription, CNRS UMR8197, Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, 75005 France
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18
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Abrahamsson S, Chen J, Hajj B, Stallinga S, Katsov AY, Wisniewski J, Mizuguchi G, Soule P, Mueller F, Dugast Darzacq C, Darzacq X, Wu C, Bargmann CI, Agard DA, Dahan M, Gustafsson MGL. Fast multicolor 3D imaging using aberration-corrected multifocus microscopy. Nat Methods 2012; 10:60-3. [PMID: 23223154 PMCID: PMC4161287 DOI: 10.1038/nmeth.2277] [Citation(s) in RCA: 246] [Impact Index Per Article: 20.5] [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: 05/14/2012] [Accepted: 10/22/2012] [Indexed: 12/25/2022]
Abstract
Conventional acquisition of three-dimensional (3D) microscopy data
requires sequential z-scanning and is often too slow to capture biological
events. We report a new aberration-corrected multi-focus microscopy method
capable of producing an instant focal stack of nine 2D images. Appended to an
epifluorescence microscope, the multi-focus system enables high-resolution 3D
imaging in multiple colors with single molecule sensitivity, at speeds limited
by the camera readout time of a single image.
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Affiliation(s)
- Sara Abrahamsson
- Joint Graduate Group in Bioengineering, University of California, San Francisco/University of California, Berkeley, San Francisco, California, USA.
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19
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Chen J, Hajj B, Abrahamsson S, Grunwald D, Gustaffson M, Dahan M. Fast Three-Dimensional Imaging and Tracking of Single Molecules in the Nucleus of Live Cells using a Multifocal Microscope. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3264] [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: 11/27/2022] Open
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20
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Wu TW, Tang J, Hajj B, Cui M. Phase resolved interferometric spectral modulation (PRISM) for ultrafast pulse measurement and compression. Opt Express 2011; 19:12961-12968. [PMID: 21747447 DOI: 10.1364/oe.19.012961] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We show through experiments and simulations that parallel phase modulation, a technique developed in the field of adaptive optics, can be employed to quickly determine the spectral phase profile of ultrafast laser pulses and to perform phase compensation as well as pulse shaping. Different from many existing ultrafast pulse measurement methods, the technique reported here requires no spectrum measurements of nonlinear signals. Instead, the power of nonlinear signals is used directly to quickly measure the spectral phase, a convenient feature for applications such as two-photon fluorescence microscopy. The method is found to work with both smooth and even completely random distortions. The experimental results are verified with MIIPS measurements.
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Affiliation(s)
- Tsai-wei Wu
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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21
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Hajj B, Perruchas S, Lautru J, Dantelle G, Gacoin T, Zyss J, Chauvat D. Electro-optical Pockels scattering from a single nanocrystal. Opt Express 2011; 19:9000-9007. [PMID: 21643153 DOI: 10.1364/oe.19.009000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The electro-optical Pockels response from a single non-centrosymmetric nanocrystal is reported. High sensitivity to the weak electric-field dependent nonlinear scattering is achieved through a dedicated imaging interferometric microscope and the linear dependence of electro-optical signal upon the applied field is checked. Using different incident light polarization states, a priori random spatial orientation of the crystal can be inferred. The electro-optical response from a nanocrystal provides local subwavelength sensor of quasi-static electric fields with potential applications in physics and biology. It also leads to a new sub-wavelength microscopy towards the nanoscale investigation of interesting phenomena such as nanoferroelectricity.
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Affiliation(s)
- Bassam Hajj
- Laboratoire de photonique quantique et moléculaire, D’Alembert Institute, Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94230 Cachan, France.
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22
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Chauvat D, Hajj B, Mojzisova H, Oron D, Sung H, Winter S, Zielinski M, Zyss J. Advances in polarization sensitive multiphoton nano-bio-imaging. EPJ Web of Conferences 2010. [DOI: 10.1051/epjconf/20100506010] [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: 11/14/2022] Open
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23
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Hira PR, Hajj B, al-Ali F, Hall MJ. Ophthalmomyiasis in Kuwait: first report of infections due to the larvae of Oestrus ovis before and after the Gulf conflict. J Trop Med Hyg 1993; 96:241-244. [PMID: 8345545] [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] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We report for the first time four cases of ophthalmomyiasis due to the larvae of Oestrus ovis in Kuwait, before and after Operations Desert Shield and Desert Storm. The larvae were easily removed under local anaesthetic. The symptom complex of acute foreign body sensation, irritation, redness, lacrimation and photophobia resolved rapidly. Ophthalmic antibiotic and corticosteroid drops were also instilled and recovery was uneventful. The ophthalmomyiasis may not always be associated with contact with sheep-rearing per se. Medical personnel should therefore be aware that in cases of what might appear initially as acute, non-specific catarrhal conjunctivitis, patients with the persistent symptom complex should be re-examined to exclude ophthalmomyiasis due to the larvae of O. ovis in endemic areas.
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Affiliation(s)
- P R Hira
- Department of Microbiology, Faculty of Medicine, Kuwait University
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24
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Abstract
Extracts from the seeds of 15 species of legume inhibited the infection of plants by viruses. Extracts could be divided into those with marked inhibitory activity reducible on heating and those with less marked inhibitory activity which increased on heating. Evidence is given is given to suggest that seed extracts contain both virus inhibitors and augmenters and that the inhibitors are high molecular weight proteins possibly related to lectins.
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