1
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Renaud O, Aulner N, Salles A, Halidi N, Brunstein M, Mallet A, Aumayr K, Terjung S, Levy D, Lippens S, Verbavatz JM, Heuser T, Santarella-Mellwig R, Tinevez JY, Woller T, Botzki A, Cawthorne C, Munck S. Staying on track - Keeping things running in a high-end scientific imaging core facility. J Microsc 2024. [PMID: 38656474 DOI: 10.1111/jmi.13304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Modern life science research is a collaborative effort. Few research groups can single-handedly support the necessary equipment, expertise and personnel needed for the ever-expanding portfolio of technologies that are required across multiple disciplines in today's life science endeavours. Thus, research institutes are increasingly setting up scientific core facilities to provide access and specialised support for cutting-edge technologies. Maintaining the momentum needed to carry out leading research while ensuring high-quality daily operations is an ongoing challenge, regardless of the resources allocated to establish such facilities. Here, we outline and discuss the range of activities required to keep things running once a scientific imaging core facility has been established. These include managing a wide range of equipment and users, handling repairs and service contracts, planning for equipment upgrades, renewals, or decommissioning, and continuously upskilling while balancing innovation and consolidation.
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Affiliation(s)
- Oliver Renaud
- Cell and Tissue Imaging Platform (PICT-IBiSA, France-BioImaging), Institut Curie, Université PSL, Sorbonne Université, CNRS, Inserm, Paris, France
| | - Nathalie Aulner
- Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Paris, France
| | - Audrey Salles
- Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Paris, France
| | - Nadia Halidi
- Advanced Light Microscopy Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maia Brunstein
- Bioimaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, Paris, France
| | - Adeline Mallet
- Centre de Ressources et Recherches Technologiques (UBI, C2RT), Institut Pasteur, Université Paris Cité, Ultrastructural BioImaging, Paris, France
| | - Karin Aumayr
- BioOptics Facility, Research Institute of Molecular Pathology (IMP) Campus-Vienna-Biocenter 1, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences (GMI), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Stefan Terjung
- Advanced Light Microscopy Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Daniel Levy
- Cell and Tissue Imaging Platform (PICT-IBiSA, France-BioImaging), Institut Curie, Université PSL, Sorbonne Université, CNRS, Inserm, Paris, France
| | | | - Jean-Marc Verbavatz
- Institut Jacques Monod (Imagoseine), Université Paris Cité, CNRS, Paris, France
| | - Thomas Heuser
- Vienna Biocenter Core Facilities GmbH (VBCF), Wien, Austria
| | | | - Jean-Yves Tinevez
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Tatiana Woller
- VIB Technology Training, Data Core, VIB BioImaging Core, VIB, Ghent, Belgium
- Neuroscience Department, KU Leuven, Leuven, Belgium
| | | | - Christopher Cawthorne
- Department of Imaging and Pathology, Nuclear Medicine and Molecular Imaging, KU Leuven, Leuven, Belgium
| | - Sebastian Munck
- Neuroscience Department, KU Leuven, Leuven, Belgium
- VIB BioImaging Core, VIB, Leuven, Belgium
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2
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Girolamo DD, Benavente-Diaz M, Murolo M, Grimaldi A, Lopes PT, Evano B, Kuriki M, Gioftsidi S, Laville V, Tinevez JY, Letort G, Mella S, Tajbakhsh S, Comai G. Extraocular muscle stem cells exhibit distinct cellular properties associated with non-muscle molecular signatures. Development 2024; 151:dev202144. [PMID: 38240380 DOI: 10.1242/dev.202144] [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: 06/29/2023] [Accepted: 12/27/2023] [Indexed: 02/22/2024]
Abstract
Skeletal muscle stem cells (MuSCs) are recognised as functionally heterogeneous. Cranial MuSCs are reported to have greater proliferative and regenerative capacity when compared with those in the limb. A comprehensive understanding of the mechanisms underlying this functional heterogeneity is lacking. Here, we have used clonal analysis, live imaging and single cell transcriptomic analysis to identify crucial features that distinguish extraocular muscle (EOM) from limb muscle stem cell populations. A MyogeninntdTom reporter showed that the increased proliferation capacity of EOM MuSCs correlates with deferred differentiation and lower expression of the myogenic commitment gene Myod. Unexpectedly, EOM MuSCs activated in vitro expressed a large array of extracellular matrix components typical of mesenchymal non-muscle cells. Computational analysis underscored a distinct co-regulatory module, which is absent in limb MuSCs, as driver of these features. The EOM transcription factor network, with Foxc1 as key player, appears to be hardwired to EOM identity as it persists during growth, disease and in vitro after several passages. Our findings shed light on how high-performing MuSCs regulate myogenic commitment by remodelling their local environment and adopting properties not generally associated with myogenic cells.
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Affiliation(s)
- Daniela Di Girolamo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Maria Benavente-Diaz
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Melania Murolo
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Alexandre Grimaldi
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Sorbonne Universités, Complexité du Vivant, F-75005 Paris, France
| | - Priscilla Thomas Lopes
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Brendan Evano
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Mao Kuriki
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Stamatia Gioftsidi
- Université Paris-Est, 77420 Champs-sur- Marne, France
- Freie Universität Berlin, 14195 Berlin, Germany
- Inserm, IMRB U955-E10, 94000 Créteil, France
| | - Vincent Laville
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, 75015 Paris, France
| | - Gaëlle Letort
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 rue du Dr Roux, 75015 Paris, France
| | - Sebastian Mella
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
| | - Glenda Comai
- Stem Cells and Development Unit, 25 rue du Dr Roux, Institut Pasteur, 75015 Paris, France
- UMR CNRS 3738, Institut Pasteur, Paris, France
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3
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García López de Haro C, Dallongeville S, Musset T, Gómez-de-Mariscal E, Sage D, Ouyang W, Muñoz-Barrutia A, Tinevez JY, Olivo-Marin JC. JDLL: a library to run deep learning models on Java bioimage informatics platforms. Nat Methods 2024; 21:7-8. [PMID: 38191929 DOI: 10.1038/s41592-023-02129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Affiliation(s)
| | - Stéphane Dallongeville
- Bioimage Analysis Unit, Institut Pasteur, Université Paris Cité, Paris, France
- CNRS UMR 3691, Institut Pasteur, Paris, France
| | - Thomas Musset
- Bioimage Analysis Unit, Institut Pasteur, Université Paris Cité, Paris, France
- CNRS UMR 3691, Institut Pasteur, Paris, France
| | | | - Daniel Sage
- Biomedical Imaging Group and Center for Imaging, Ecole Polytechnique de Lausanne (EPFL), Lausanne, Switzerland
| | - Wei Ouyang
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Arrate Muñoz-Barrutia
- Biomedical Sciences and Engineering Laboratory, Universidad Carlos III de Madrid, Leganés, Spain
| | - Jean-Yves Tinevez
- Image Analysis Hub, Institut Pasteur, Université Paris Cité, Paris, France.
| | - Jean-Christophe Olivo-Marin
- Bioimage Analysis Unit, Institut Pasteur, Université Paris Cité, Paris, France.
- CNRS UMR 3691, Institut Pasteur, Paris, France.
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4
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Serres MP, Shaughnessy R, Escot S, Hammich H, Cuvelier F, Salles A, Rocancourt M, Verdon Q, Gaffuri AL, Sourigues Y, Malherbe G, Velikovsky L, Chardon F, Sassoon N, Tinevez JY, Callebaut I, Formstecher E, Houdusse A, David NB, Pylypenko O, Echard A. MiniBAR/GARRE1 is a dual Rac and Rab effector required for ciliogenesis. Dev Cell 2023; 58:2477-2494.e8. [PMID: 37875118 DOI: 10.1016/j.devcel.2023.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/07/2023] [Accepted: 09/29/2023] [Indexed: 10/26/2023]
Abstract
Cilia protrude from the cell surface and play critical roles in intracellular signaling, environmental sensing, and development. Reduced actin-dependent contractility and intracellular trafficking are both required for ciliogenesis, but little is known about how these processes are coordinated. Here, we identified a Rac1- and Rab35-binding protein with a truncated BAR (Bin/amphiphysin/Rvs) domain that we named MiniBAR (also known as KIAA0355/GARRE1), which plays a key role in ciliogenesis. MiniBAR colocalizes with Rac1 and Rab35 at the plasma membrane and on intracellular vesicles trafficking to the ciliary base and exhibits fast pulses at the ciliary membrane. MiniBAR depletion leads to short cilia, resulting from abnormal Rac-GTP/Rho-GTP levels and increased acto-myosin-II-dependent contractility together with defective trafficking of IFT88 and ARL13B into cilia. MiniBAR-depleted zebrafish embryos display dysfunctional short cilia and hallmarks of ciliopathies, including left-right asymmetry defects. Thus, MiniBAR is a dual Rac and Rab effector that controls both actin cytoskeleton and membrane trafficking for ciliogenesis.
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Affiliation(s)
- Murielle P Serres
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Ronan Shaughnessy
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Sophie Escot
- Laboratoire d'Optique et Biosciences (LOB), CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Hussein Hammich
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Frédérique Cuvelier
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Audrey Salles
- Institut Pasteur, Université de Paris, UTechS Photonic BioImaging (UTechS PBI), Centre de Recherche et de Ressources Technologiques C2RT, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Murielle Rocancourt
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Quentin Verdon
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Anne-Lise Gaffuri
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Yannick Sourigues
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Gilles Malherbe
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Leonid Velikovsky
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Florian Chardon
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Nathalie Sassoon
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université de Paris, Image Analysis Hub, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Etienne Formstecher
- Hybrigenics Services SAS, 1 rue Pierre Fontaine 91000 Evry, Courcouronnes, France
| | - Anne Houdusse
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Nicolas B David
- Laboratoire d'Optique et Biosciences (LOB), CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Olena Pylypenko
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Arnaud Echard
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France.
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5
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Mancini L, Guirao B, Ortica S, Labusch M, Cheysson F, Bonnet V, Phan MS, Herbert S, Mahou P, Menant E, Bedu S, Tinevez JY, Baroud C, Beaurepaire E, Bellaiche Y, Bally-Cuif L, Dray N. Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression. Sci Adv 2023; 9:eadg7519. [PMID: 37656795 PMCID: PMC10854430 DOI: 10.1126/sciadv.adg7519] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
The maintenance of neural stem cells (NSCs) in the adult brain depends on their activation frequency and division mode. Using long-term intravital imaging of NSCs in the zebrafish adult telencephalon, we reveal that apical surface area and expression of the Notch ligand DeltaA predict these NSC decisions. deltaA-negative NSCs constitute a bona fide self-renewing NSC pool and systematically engage in asymmetric divisions generating a self-renewing deltaAneg daughter, which regains the size and behavior of its mother, and a neurogenic deltaApos daughter, eventually engaged in neuronal production following further quiescence-division phases. Pharmacological and genetic manipulations of Notch, DeltaA, and apical size further show that the prediction of activation frequency by apical size and the asymmetric divisions of deltaAneg NSCs are functionally independent of Notch. These results provide dynamic qualitative and quantitative readouts of NSC lineage progression in vivo and support a hierarchical organization of NSCs in differently fated subpopulations.
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Affiliation(s)
- Laure Mancini
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris F-75005, France
| | - Boris Guirao
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, Paris 75005, France
| | - Sara Ortica
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
| | - Miriam Labusch
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
- Sorbonne Université, Collège Doctoral, Paris F-75005, France
| | - Felix Cheysson
- LPSM, Sorbonne Université, UMR CNRS 8001, Paris 75005, France
| | - Valentin Bonnet
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris F-75015, France
- LadHyX, CNRS, Ecole Polytechnique, IP Paris, Palaiseau 91120, France
| | - Minh Son Phan
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, Paris, France
| | - Sébastien Herbert
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, Paris, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, CNRS, INSERM, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Emilie Menant
- Laboratory for Optics and Biosciences, CNRS, INSERM, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Sébastien Bedu
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, Paris, France
| | - Charles Baroud
- Institut Pasteur, Université Paris Cité, Physical Microfluidics and Bioengineering, Paris F-75015, France
- LadHyX, CNRS, Ecole Polytechnique, IP Paris, Palaiseau 91120, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, CNRS, INSERM, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Yohanns Bellaiche
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 3215, Inserm U934, Genetics and Developmental Biology, Paris 75005, France
| | - Laure Bally-Cuif
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
| | - Nicolas Dray
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Zebrafish Neurogenetics Unit, Team supported by the Ligue Nationale Contre le Cancer, Paris 75015, France
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6
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Xingi E, Koutsoudaki PN, Thanou I, Phan MS, Margariti M, Scheller A, Tinevez JY, Kirchhoff F, Thomaidou D. LPS-Induced Systemic Inflammation Affects the Dynamic Interactions of Astrocytes and Microglia with the Vasculature of the Mouse Brain Cortex. Cells 2023; 12:1418. [PMID: 37408252 DOI: 10.3390/cells12101418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/05/2023] [Accepted: 05/13/2023] [Indexed: 07/07/2023] Open
Abstract
The Neurovascular Unit (NVU), composed of glia (astrocytes, oligodendrocytes, microglia), neurons, pericytes and endothelial cells, is a dynamic interface ensuring the physiological functioning of the central nervous system (CNS), which gets affected and contributes to the pathology of several neurodegenerative diseases. Neuroinflammation is a common feature of neurodegenerative diseases and is primarily related to the activation state of perivascular microglia and astrocytes, which constitute two of its major cellular components. Our studies focus on monitoring in real time the morphological changes of perivascular astrocytes and microglia, as well as their dynamic interactions with the brain vasculature, under physiological conditions and following systemic neuroinflammation triggering both microgliosis and astrogliosis. To this end, we performed 2-photon laser scanning microscopy (2P-LSM) for intravital imaging of the cortex of transgenic mice visualizing the dynamics of microglia and astroglia following neuroinflammation induced by systemic administration of the endotoxin lipopolysaccharide (LPS). Our results indicate that following neuroinflammation the endfeet of activated perivascular astrocytes lose their close proximity and physiological cross-talk with vasculature, an event that most possibly contributes to a loss of blood-brain barrier (BBB) integrity. At the same time, microglial cells become activated and exhibit a higher extent of physical contact with the blood vessels. These dynamic responses of perivascular astrocytes and microglia are peaking at 4 days following LPS administration; however, they still persist at a lower level at 8 days after LPS injection, revealing incomplete reversal of inflammation affecting the glial properties and interactions within the NVU.
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Affiliation(s)
- Evangelia Xingi
- Light Microscopy Unit, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Paraskevi N Koutsoudaki
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Irini Thanou
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Minh-Son Phan
- Institut Pasteur, Université de Paris, Image Analysis Hub, F-75015 Paris, France
| | - Maria Margariti
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, 11521 Athens, Greece
| | - Anja Scheller
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), University of Saarland, 66421 Homburg, Germany
| | - Jean-Yves Tinevez
- Institut Pasteur, Université de Paris, Image Analysis Hub, F-75015 Paris, France
| | - Frank Kirchhoff
- Molecular Physiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), University of Saarland, 66421 Homburg, Germany
| | - Dimitra Thomaidou
- Light Microscopy Unit, Hellenic Pasteur Institute, 11521 Athens, Greece
- Neural Stem Cells and Neuroimaging Group, Department of Neurobiology, Hellenic Pasteur Institute, 11521 Athens, Greece
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7
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Simon F, Tinevez JY, van Teeffelen S. ExTrack characterizes transition kinetics and diffusion in noisy single-particle tracks. J Cell Biol 2023; 222:e202208059. [PMID: 36880553 PMCID: PMC9997658 DOI: 10.1083/jcb.202208059] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 12/01/2022] [Accepted: 01/27/2023] [Indexed: 03/08/2023] Open
Abstract
Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis of tracks is confounded by noisy molecule localization, short tracks, and rapid transitions between different motion states, notably between immobile and diffusive states. Here, we propose a probabilistic method termed ExTrack that uses the full spatio-temporal information of tracks to extract global model parameters, to calculate state probabilities at every time point, to reveal distributions of state durations, and to refine the positions of bound molecules. ExTrack works for a wide range of diffusion coefficients and transition rates, even if experimental data deviate from model assumptions. We demonstrate its capacity by applying it to slowly diffusing and rapidly transitioning bacterial envelope proteins. ExTrack greatly increases the regime of computationally analyzable noisy single-particle tracks. The ExTrack package is available in ImageJ and Python.
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Affiliation(s)
- François Simon
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Sven van Teeffelen
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Université de Paris Cité, Paris, France
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8
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Simon F, Tinevez JY, van Teeffelen S. ExTrack characterizes transition kinetics and diffusion in noisy single-particle tracks. J Cell Biol 2023; 222:e202208059. [PMID: 36880553 PMCID: PMC9997658 DOI: 10.1083/jcb.202208059 10.1101/2022.07.13.499913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 12/01/2022] [Accepted: 01/27/2023] [Indexed: 03/23/2024] Open
Abstract
Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis of tracks is confounded by noisy molecule localization, short tracks, and rapid transitions between different motion states, notably between immobile and diffusive states. Here, we propose a probabilistic method termed ExTrack that uses the full spatio-temporal information of tracks to extract global model parameters, to calculate state probabilities at every time point, to reveal distributions of state durations, and to refine the positions of bound molecules. ExTrack works for a wide range of diffusion coefficients and transition rates, even if experimental data deviate from model assumptions. We demonstrate its capacity by applying it to slowly diffusing and rapidly transitioning bacterial envelope proteins. ExTrack greatly increases the regime of computationally analyzable noisy single-particle tracks. The ExTrack package is available in ImageJ and Python.
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Affiliation(s)
- François Simon
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Sven van Teeffelen
- Département de Microbiologie, Infectiologie, et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
- Microbial Morphogenesis and Growth Lab, Institut Pasteur, Université de Paris Cité, Paris, France
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9
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Scoca V, Morin R, Collard M, Tinevez JY, Di Nunzio F. HIV-induced membraneless organelles orchestrate post-nuclear entry steps. J Mol Cell Biol 2022; 14:6781009. [PMID: 36314049 PMCID: PMC10117160 DOI: 10.1093/jmcb/mjac060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Abstract
HIV integration occurs in chromatin sites that favor the release of high levels of viral progeny, alternatively the virus is also able to discreetly coexist with the host. The viral infection perturbs the cellular environment inducing the remodeling of the nuclear landscape. Indeed, HIV-1 triggers the nuclear clustering of the host factor CPSF6, but the underlying mechanism is poorly understood. Our data indicate that HIV usurps a recently discovered biological phenomenon, called liquid–liquid phase separation (LLPS), to hijack the host cell. We observed CPSF6 clusters as part of HIV-induced membraneless organelles (HIV-1 MLOs) in macrophages, which are one of the main HIV target cells. We describe that HIV-1 MLOs follow phase separation rules and represent functional biomolecular condensates. We highlight HIV-1 MLOs as hubs of nuclear reverse transcription, while the double stranded viral DNA, once formed, rapidly migrates outside these structures. Transcription-competent proviruses localize outside, but near HIV-1 MLOs, in LEDGF-abundant regions, known to be active chromatin sites. Therefore, HIV-1 MLOs orchestrate viral events prior to the integration step and create a favorable environment for the viral replication. This study uncovers single functional host–viral complexes in their nuclear landscape, which is markedly restructured by HIV-1.
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Affiliation(s)
- Viviana Scoca
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur , Université Paris Cité, 75015 Paris , France
| | - Renaud Morin
- Imactiv-3D, 1 Place Pierre Potier , 31106 Toulouse
| | - Maxence Collard
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur , Université Paris Cité, 75015 Paris , France
| | - Jean-Yves Tinevez
- Image Analysis Hub/C2RT, Institut Pasteur , Université Paris Cité, 75015 Paris , France
| | - Francesca Di Nunzio
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur , Université Paris Cité, 75015 Paris , France
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10
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Trébeau C, de Monvel JB, Altay G, Tinevez JY, Etournay R. Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. BMC Biol 2022; 20:183. [PMID: 35999534 PMCID: PMC9397159 DOI: 10.1186/s12915-022-01378-0] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/22/2022] [Indexed: 11/27/2022] Open
Abstract
Background Efficient tools allowing the extraction of 2D surfaces from 3D-microscopy data are essential for studies aiming to decipher the complex cellular choreography through which epithelium morphogenesis takes place during development. Most existing methods allow for the extraction of a single and smooth manifold of sufficiently high signal intensity and contrast, and usually fail when the surface of interest has a rough topography or when its localization is hampered by other surrounding structures of higher contrast. Multiple surface segmentation entails laborious manual annotations of the various surfaces separately. Results As automating this task is critical in studies involving tissue-tissue or tissue-matrix interaction, we developed the Zellige software, which allows the extraction of a non-prescribed number of surfaces of varying inclination, contrast, and texture from a 3D image. The tool requires the adjustment of a small set of control parameters, for which we provide an intuitive interface implemented as a Fiji plugin. Conclusions As a proof of principle of the versatility of Zellige, we demonstrate its performance and robustness on synthetic images and on four different types of biological samples, covering a wide range of biological contexts. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01378-0.
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Affiliation(s)
- Céline Trébeau
- Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, F-75012, Paris, France
| | | | - Gizem Altay
- Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, F-75012, Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, F-75015, Paris, France.
| | - Raphaël Etournay
- Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, F-75012, Paris, France.
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11
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Ershov D, Phan MS, Pylvänäinen JW, Rigaud SU, Le Blanc L, Charles-Orszag A, Conway JRW, Laine RF, Roy NH, Bonazzi D, Duménil G, Jacquemet G, Tinevez JY. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat Methods 2022; 19:829-832. [PMID: 35654950 DOI: 10.1038/s41592-022-01507-1] [Citation(s) in RCA: 159] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/25/2022] [Indexed: 11/09/2022]
Abstract
TrackMate is an automated tracking software used to analyze bioimages and is distributed as a Fiji plugin. Here, we introduce a new version of TrackMate. TrackMate 7 is built to address the broad spectrum of modern challenges researchers face by integrating state-of-the-art segmentation algorithms into tracking pipelines. We illustrate qualitatively and quantitatively that these new capabilities function effectively across a wide range of bio-imaging experiments.
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Affiliation(s)
- Dmitry Ershov
- Institut Pasteur, Université de Paris Cité, Image Analysis Hub, Paris, France.,Institut Pasteur, Université de Paris Cité, Biostatistics and Bioinformatic Hub, Paris, France
| | - Minh-Son Phan
- Institut Pasteur, Université de Paris Cité, Image Analysis Hub, Paris, France
| | - Joanna W Pylvänäinen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku, Finland.,Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland
| | - Stéphane U Rigaud
- Institut Pasteur, Université de Paris Cité, Image Analysis Hub, Paris, France
| | - Laure Le Blanc
- Institut Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis of Vascular Infections unit, Paris, France
| | - Arthur Charles-Orszag
- Institut Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis of Vascular Infections unit, Paris, France
| | - James R W Conway
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Romain F Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.,The Francis Crick Institute, London, UK.,Micrographia Bio, Translation and Innovation Hub, London, UK
| | - Nathan H Roy
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Daria Bonazzi
- Institut Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis of Vascular Infections unit, Paris, France
| | - Guillaume Duménil
- Institut Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis of Vascular Infections unit, Paris, France
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland. .,Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku, Finland. .,Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland.
| | - Jean-Yves Tinevez
- Institut Pasteur, Université de Paris Cité, Image Analysis Hub, Paris, France.
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12
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Nunes Vicente F, Lelek M, Tinevez JY, Tran QD, Pehau-Arnaudet G, Zimmer C, Etienne-Manneville S, Giannone G, Leduc C. Molecular organization and mechanics of single vimentin filaments revealed by super-resolution imaging. Sci Adv 2022; 8:eabm2696. [PMID: 35213220 PMCID: PMC8880768 DOI: 10.1126/sciadv.abm2696] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/11/2022] [Indexed: 05/30/2023]
Abstract
Intermediate filaments (IFs) are involved in key cellular functions including polarization, migration, and protection against large deformations. These functions are related to their remarkable ability to extend without breaking, a capacity that should be determined by the molecular organization of subunits within filaments. However, this structure-mechanics relationship remains poorly understood at the molecular level. Here, using super-resolution microscopy (SRM), we show that vimentin filaments exhibit a ~49-nanometer axial repeat both in cells and in vitro. As unit-length filaments (ULFs) were measured at ~59 nanometers, this demonstrates a partial overlap of ULFs during filament assembly. Using an SRM-compatible stretching device, we also provide evidence that the extensibility of vimentin is due to the unfolding of its subunits and not to their sliding, thus establishing a direct link between the structural organization and its mechanical properties. Overall, our results pave the way for future studies of IF assembly, mechanical, and structural properties in cells.
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Affiliation(s)
- Filipe Nunes Vicente
- Institut Interdisciplinaire des Neurosciences, CNRS UMR 5297, Université de Bordeaux, Bordeaux F-33000, France
| | - Mickael Lelek
- Imaging and Modeling Unit, Institut Pasteur, CNRS UMR 3691, Paris F-75015, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, 2RT / DTPS, Institut Pasteur, Paris F-75015 , France
| | - Quang D. Tran
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, CNRS UMR 3691, équipe labellisée Ligue contre le cancer, Paris F-75015, France
- CNRS UMR 7592, Institut Jacques Monod, Université de Paris, Paris F-75013, France
| | - Gerard Pehau-Arnaudet
- CNRS UMR 3528, Institut Pasteur, Paris F-75015, France
- Ultrastructural BioImaging Platform, Institut Pasteur, Paris F-75015, France
| | - Christophe Zimmer
- Imaging and Modeling Unit, Institut Pasteur, CNRS UMR 3691, Paris F-75015, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, CNRS UMR 3691, équipe labellisée Ligue contre le cancer, Paris F-75015, France
| | - Gregory Giannone
- Institut Interdisciplinaire des Neurosciences, CNRS UMR 5297, Université de Bordeaux, Bordeaux F-33000, France
| | - Cécile Leduc
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, CNRS UMR 3691, équipe labellisée Ligue contre le cancer, Paris F-75015, France
- CNRS UMR 7592, Institut Jacques Monod, Université de Paris, Paris F-75013, France
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13
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Herbert S, Valon L, Mancini L, Dray N, Caldarelli P, Gros J, Esposito E, Shorte SL, Bally-Cuif L, Aulner N, Levayer R, Tinevez JY. LocalZProjector and DeProj: a toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images. BMC Biol 2021; 19:136. [PMID: 34215263 PMCID: PMC8254216 DOI: 10.1186/s12915-021-01037-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 01/20/2021] [Accepted: 04/23/2021] [Indexed: 12/02/2022] Open
Abstract
Background Quantitative imaging of epithelial tissues requires bioimage analysis tools that are widely applicable and accurate. In the case of imaging 3D tissues, a common preprocessing step consists of projecting the acquired 3D volume on a 2D plane mapping the tissue surface. While segmenting the tissue cells is amenable on 2D projections, it is still very difficult and cumbersome in 3D. However, for many specimen and models used in developmental and cell biology, the complex content of the image volume surrounding the epithelium in a tissue often reduces the visibility of the biological object in the projection, compromising its subsequent analysis. In addition, the projection may distort the geometry of the tissue and can lead to strong artifacts in the morphology measurement. Results Here we introduce a user-friendly toolbox built to robustly project epithelia on their 2D surface from 3D volumes and to produce accurate morphology measurement corrected for the projection distortion, even for very curved tissues. Our toolbox is built upon two components. LocalZProjector is a configurable Fiji plugin that generates 2D projections and height-maps from potentially large 3D stacks (larger than 40 GB per time-point) by only incorporating signal of the planes with local highest variance/mean intensity, despite a possibly complex image content. DeProj is a MATLAB tool that generates correct morphology measurements by combining the height-map output (such as the one offered by LocalZProjector) and the results of a cell segmentation on the 2D projection, hence effectively deprojecting the 2D segmentation in 3D. In this paper, we demonstrate their effectiveness over a wide range of different biological samples. We then compare its performance and accuracy against similar existing tools. Conclusions We find that LocalZProjector performs well even in situations where the volume to project also contains unwanted signal in other layers. We show that it can process large images without a pre-processing step. We study the impact of geometrical distortions on morphological measurements induced by the projection. We measured very large distortions which are then corrected by DeProj, providing accurate outputs. Supplementary Information The online version contains supplementary material available at (10.1186/s12915-021-01037-w).
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Affiliation(s)
- Sébastien Herbert
- Image Analysis Hub, C2RT / DTPS, Institut Pasteur, Paris, France.,Present Address: Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Léo Valon
- Cell death and epithelial homeostasis unit, Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France
| | - Laure Mancini
- Zebrafish Neurogenetics unit (Team supported by the Ligue Nationale Contre le Cancer), Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France.,Collège doctoral, Sorbonne Université, Paris, France
| | - Nicolas Dray
- Zebrafish Neurogenetics unit (Team supported by the Ligue Nationale Contre le Cancer), Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France
| | - Paolo Caldarelli
- Dynamic Regulation of Morphogenesis, Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France
| | - Jérôme Gros
- Dynamic Regulation of Morphogenesis, Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France
| | - Elric Esposito
- UTechS PBI, C2RT / DTPS, Institut Pasteur, Paris, France
| | | | - Laure Bally-Cuif
- Zebrafish Neurogenetics unit (Team supported by the Ligue Nationale Contre le Cancer), Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France
| | | | - Romain Levayer
- Cell death and epithelial homeostasis unit, Developmental and Stem Cell Biology Department, UMR3738 CNRS, Institut Pasteur, Paris, France
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14
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Martins GG, Cordelières FP, Colombelli J, D'Antuono R, Golani O, Guiet R, Haase R, Klemm AH, Louveaux M, Paul-Gilloteaux P, Tinevez JY, Miura K. Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists. F1000Res 2021; 10:334. [PMID: 34164115 PMCID: PMC8215561 DOI: 10.12688/f1000research.25485.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 11/20/2022] Open
Abstract
NEUBIAS, the European Network of Bioimage Analysts, was created in 2016 with the goal of improving the communication and the knowledge transfer among the various stakeholders involved in the acquisition, processing and analysis of biological image data, and to promote the establishment and recognition of the profession of Bioimage Analyst. One of the most successful initiatives of the NEUBIAS programme was its series of 15 training schools, which trained over 400 new Bioimage Analysts, coming from over 40 countries. Here we outline the rationale behind the innovative three-level program of the schools, the curriculum, the trainer recruitment and turnover strategy, the outcomes for the community and the career path of analysts, including some success stories. We discuss the future of the materials created during this programme and some of the new initiatives emanating from the community of NEUBIAS-trained analysts, such as the NEUBIAS Academy. Overall, we elaborate on how this training programme played a key role in collectively leveraging Bioimaging and Life Science research by bringing the latest innovations into structured, frequent and intensive training activities, and on why we believe this should become a model to further develop in Life Sciences.
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Affiliation(s)
| | - Fabrice P Cordelières
- Bordeaux Imaging Center (BIC), Université de Bordeaux - US4 INSERM, Bordeaux, France
| | - Julien Colombelli
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy STP (CALM), The Francis Crick Institute, London, UK
| | - Ofra Golani
- The department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Romain Guiet
- BioImaging and Optics Platform (BIOP), Faculty of Life Sciences (SV), École Polytechnique Fédérale (EPFL), Lausanne, Switzerland
| | - Robert Haase
- DFG Cluster of Excellence "Physics of Life", University of Technology TU, Dresden, Germany
| | - Anna H Klemm
- Science for Life Laboratory BioImage Informatics Facility and Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Marion Louveaux
- BioImage Analysis Unit, Institut Pasteur, Paris, France.,Image Analysis Hub, C2RT Institut Pasteur, Paris, France
| | - Perrine Paul-Gilloteaux
- Université de Nantes, CNRS, INSERM, Nantes, France.,Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Sante, Inserm UMS 016, CNRS UMS3556, Nantes, France
| | | | - Kota Miura
- Nikon Imaging Center, University of Heidelberg, Heidelberg, Germany.,Bioimage Analysis & Research, Heidelberg, Germany
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15
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Dray N, Mancini L, Binshtok U, Cheysson F, Supatto W, Mahou P, Bedu S, Ortica S, Than-Trong E, Krecsmarik M, Herbert S, Masson JB, Tinevez JY, Lang G, Beaurepaire E, Sprinzak D, Bally-Cuif L. Dynamic spatiotemporal coordination of neural stem cell fate decisions occurs through local feedback in the adult vertebrate brain. Cell Stem Cell 2021; 28:1457-1472.e12. [PMID: 33823144 PMCID: PMC8363814 DOI: 10.1016/j.stem.2021.03.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 07/23/2020] [Revised: 12/21/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022]
Abstract
Neural stem cell (NSC) populations persist in the adult vertebrate brain over a lifetime, and their homeostasis is controlled at the population level through unknown mechanisms. Here, we combine dynamic imaging of entire NSC populations in their in vivo niche over several weeks with pharmacological manipulations, mathematical modeling, and spatial statistics and demonstrate that NSCs use spatiotemporally resolved local feedback signals to coordinate their decision to divide in adult zebrafish brains. These involve Notch-mediated short-range inhibition from transient neural progenitors and a dispersion effect from the dividing NSCs themselves exerted with a delay of 9–12 days. Simulations from a stochastic NSC lattice model capturing these interactions demonstrate that these signals are linked by lineage progression and control the spatiotemporal distribution of output neurons. These results highlight how local and temporally delayed interactions occurring between brain germinal cells generate self-propagating dynamics that maintain NSC population homeostasis and coordinate specific spatiotemporal correlations. NSC activation events are spatiotemporally coordinated within adult NSC populations This involves inhibition by neural progenitors (relying on Notch) and by dividing NSCs A dynamic lattice model shows that these interactions are linked by lineage progression NSCs dynamics generate an intrinsic niche that maintains the NSC population long-term
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Affiliation(s)
- Nicolas Dray
- Zebrafish Neurogenetics Unit, Institut Pasteur, UMR3738, CNRS, team supported by La Ligue Nationale Contre le Cancer, 75015 Paris, France.
| | - Laure Mancini
- Zebrafish Neurogenetics Unit, Institut Pasteur, UMR3738, CNRS, team supported by La Ligue Nationale Contre le Cancer, 75015 Paris, France; Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Udi Binshtok
- School of Neurobiology, Biochemistry, and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Felix Cheysson
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005 Paris, France; Epidemiology and Modeling of Bacterial Evasion to Antibacterials Unit (EMEA), Institut Pasteur, 75015 Paris, France; Anti-infective Evasion and Pharmacoepidemiology Team, Centre for Epidemiology and Public Health (CESP), INSERM/UVSQ, Villejuif Cedex, France
| | - Willy Supatto
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Sébastien Bedu
- Zebrafish Neurogenetics Unit, Institut Pasteur, UMR3738, CNRS, team supported by La Ligue Nationale Contre le Cancer, 75015 Paris, France
| | - Sara Ortica
- Zebrafish Neurogenetics Unit, Institut Pasteur, UMR3738, CNRS, team supported by La Ligue Nationale Contre le Cancer, 75015 Paris, France
| | - Emmanuel Than-Trong
- Zebrafish Neurogenetics Unit, Institut Pasteur, UMR3738, CNRS, team supported by La Ligue Nationale Contre le Cancer, 75015 Paris, France
| | - Monika Krecsmarik
- Zebrafish Neurogenetics Unit, Institut Pasteur, UMR3738, CNRS, team supported by La Ligue Nationale Contre le Cancer, 75015 Paris, France
| | - Sébastien Herbert
- Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France; Image Analysis Hub, Institut Pasteur, 75015 Paris, France
| | - Jean-Baptiste Masson
- Department of Neuroscience and Department of Computational Biology, Institut Pasteur, 75015 Paris, France
| | | | - Gabriel Lang
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005 Paris, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - David Sprinzak
- School of Neurobiology, Biochemistry, and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel.
| | - Laure Bally-Cuif
- Zebrafish Neurogenetics Unit, Institut Pasteur, UMR3738, CNRS, team supported by La Ligue Nationale Contre le Cancer, 75015 Paris, France.
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16
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Fazeli E, Roy NH, Follain G, Laine RF, von Chamier L, Hänninen PE, Eriksson JE, Tinevez JY, Jacquemet G. Automated cell tracking using StarDist and TrackMate. F1000Res 2020. [DOI: 10.12688/f1000research.27019.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance, and wound healing. Therefore, the mechanisms governing cellular locomotion have been under intense scrutiny over the last 50 years. One of the main tools of this scrutiny is live-cell quantitative imaging, where researchers image cells over time to study their migration and quantitatively analyze their dynamics by tracking them using the recorded images. Despite the availability of computational tools, manual tracking remains widely used among researchers due to the difficulty setting up robust automated cell tracking and large-scale analysis. Here we provide a detailed analysis pipeline illustrating how the deep learning network StarDist can be combined with the popular tracking software TrackMate to perform 2D automated cell tracking and provide fully quantitative readouts. Our proposed protocol is compatible with both fluorescent and widefield images. It only requires freely available and open-source software (ZeroCostDL4Mic and Fiji), and does not require any coding knowledge from the users, making it a versatile and powerful tool for the field. We demonstrate this pipeline's usability by automatically tracking cancer cells and T cells using fluorescent and brightfield images. Importantly, we provide, as supplementary information, a detailed step-by-step protocol to allow researchers to implement it with their images.
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17
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Abstract
The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance, and wound healing. Therefore, the mechanisms governing cellular locomotion have been under intense scrutiny over the last 50 years. One of the main tools of this scrutiny is live-cell quantitative imaging, where researchers image cells over time to study their migration and quantitatively analyze their dynamics by tracking them using the recorded images. Despite the availability of computational tools, manual tracking remains widely used among researchers due to the difficulty setting up robust automated cell tracking and large-scale analysis. Here we provide a detailed analysis pipeline illustrating how the deep learning network StarDist can be combined with the popular tracking software TrackMate to perform 2D automated cell tracking and provide fully quantitative readouts. Our proposed protocol is compatible with both fluorescent and widefield images. It only requires freely available and open-source software (ZeroCostDL4Mic and Fiji), and does not require any coding knowledge from the users, making it a versatile and powerful tool for the field. We demonstrate this pipeline's usability by automatically tracking cancer cells and T cells using fluorescent and brightfield images. Importantly, we provide, as supplementary information, a detailed step-by-step protocol to allow researchers to implement it with their images.
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Affiliation(s)
- Elnaz Fazeli
- Laboratory of Biophysics, Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Nathan H. Roy
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Gautier Follain
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Romain F. Laine
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Lucas von Chamier
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Pekka E. Hänninen
- Laboratory of Biophysics, Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - John E. Eriksson
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | | | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
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18
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Samassa F, Ferrari ML, Husson J, Mikhailova A, Porat Z, Sidaner F, Brunner K, Teo TH, Frigimelica E, Tinevez JY, Sansonetti PJ, Thoulouze MI, Phalipon A. Shigella impairs human T lymphocyte responsiveness by hijacking actin cytoskeleton dynamics and T cell receptor vesicular trafficking. Cell Microbiol 2020; 22:e13166. [PMID: 31957253 PMCID: PMC7187243 DOI: 10.1111/cmi.13166] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Strategies employed by pathogenic enteric bacteria, such as Shigella, to subvert the host adaptive immunity are not well defined. Impairment of T lymphocyte chemotaxis by blockage of polarised edge formation has been reported upon Shigella infection. However, the functional impact of Shigella on T lymphocytes remains to be determined. Here, we show that Shigella modulates CD4+ T cell F‐actin dynamics and increases cell cortical stiffness. The scanning ability of T lymphocytes when encountering antigen‐presenting cells (APC) is subsequently impaired resulting in decreased cell–cell contacts (or conjugates) between the two cell types, as compared with non‐infected T cells. In addition, the few conjugates established between the invaded T cells and APCs display no polarised delivery and accumulation of the T cell receptor to the contact zone characterising canonical immunological synapses. This is most likely due to the targeting of intracellular vesicular trafficking by the bacterial type III secretion system (T3SS) effectors IpaJ and VirA. The collective impact of these cellular reshapings by Shigella eventually results in T cell activation dampening. Altogether, these results highlight the combined action of T3SS effectors leading to T cell defects upon Shigella infection.
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Affiliation(s)
- Fatoumata Samassa
- Molecular Microbial Pathogenesis Unit, Institut Pasteur, INSERM U1202, Paris, France
| | - Mariana L Ferrari
- Molecular Microbial Pathogenesis Unit, Institut Pasteur, INSERM U1202, Paris, France
| | - Julien Husson
- Laboratoire d'Hydrodynamique (LadHyX), Ecole polytechnique, CNRS, Institut Polytechnique de Paris, Palaiseau, France
| | | | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facility, Weizmann Institute of Sciences, Rehovot, Israel
| | | | - Katja Brunner
- Molecular Microbial Pathogenesis Unit, Institut Pasteur, INSERM U1202, Paris, France
| | - Teck-Hui Teo
- Molecular Microbial Pathogenesis Unit, Institut Pasteur, INSERM U1202, Paris, France
| | | | | | - Philippe J Sansonetti
- Molecular Microbial Pathogenesis Unit, Institut Pasteur, INSERM U1202, Paris, France.,Chaire de Microbiologie et Maladies Infectieuses, Collège de France, Paris, France
| | | | - Armelle Phalipon
- Molecular Microbial Pathogenesis Unit, Institut Pasteur, INSERM U1202, Paris, France
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19
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Sônego F, Bouccara S, Pons T, Lequeux N, Danckaert A, Tinevez JY, Alam IS, Shorte SL, Tournebize R. Imaging of Red-Shifted Light From Bioluminescent Tumors Using Fluorescence by Unbound Excitation From Luminescence. Front Bioeng Biotechnol 2019; 7:73. [PMID: 31024905 PMCID: PMC6460942 DOI: 10.3389/fbioe.2019.00073] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/15/2019] [Indexed: 12/02/2022] Open
Abstract
Early detection of tumors is today a major challenge and requires sensitive imaging methodologies coupled with new efficient probes. In vivo optical bioluminescence imaging has been widely used in the field of preclinical oncology to visualize tumors and several cancer cell lines have been genetically modified to provide bioluminescence signals. However, the light emitted by the majority of commonly used luciferases is usually in the blue part of the visible spectrum, where tissue absorption is still very high, making deep tissue imaging non-optimal, and calling for optimized optical imaging methodologies. We have previously shown that red-shifting of bioluminescence signal by Fluorescence Unbound Excitation from Luminescence (FUEL) is a mean to increase bioluminescence signal sensitivity detection in vivo. Here, we applied FUEL to tumor detection in two different subcutaneous tumor models: the auto-luminescent human embryonic kidney (HEK293) cell line and the murine B16-F10 melanoma cell line previously transfected with a plasmid encoding the Luc2 firefly luciferase. Tumor size and bioluminescence were measured over time and tumor vascularization characterized. We then locally injected near infrared emitting Quantum Dots (NIR QDs) in the tumor site and observed a red-shifting of bioluminescence signal by (FUEL) indicating that FUEL could be used to allow deeper tumor detection in mice.
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Affiliation(s)
- Fabiane Sônego
- UTechS Photonic BioImaging, C2RT, Institut Pasteur, Paris, France
| | - Sophie Bouccara
- UTechS Photonic BioImaging, C2RT, Institut Pasteur, Paris, France
| | - Thomas Pons
- Laboratoire de Physique et d'Etude des Matériaux, ESPCI Paris, CNRS UMR8213, PSL Research University, Université Pierre et Marie Curie, Sorbonne-Universités, Paris, France
| | - Nicolas Lequeux
- Laboratoire de Physique et d'Etude des Matériaux, ESPCI Paris, CNRS UMR8213, PSL Research University, Université Pierre et Marie Curie, Sorbonne-Universités, Paris, France
| | - Anne Danckaert
- UTechS Photonic BioImaging, C2RT, Institut Pasteur, Paris, France
| | | | - Israt S. Alam
- UTechS Photonic BioImaging, C2RT, Institut Pasteur, Paris, France
| | | | - Régis Tournebize
- UTechS Photonic BioImaging, C2RT, Unité Pathogénie Microbienne Moléculaire, Institut Pasteur, INSERM U1202, Paris, France
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20
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Gouder L, Vitrac A, Goubran-Botros H, Danckaert A, Tinevez JY, André-Leroux G, Atanasova E, Lemière N, Biton A, Leblond CS, Poulet A, Boland A, Deleuze JF, Benchoua A, Delorme R, Bourgeron T, Cloëz-Tayarani I. Altered spinogenesis in iPSC-derived cortical neurons from patients with autism carrying de novo SHANK3 mutations. Sci Rep 2019; 9:94. [PMID: 30643170 PMCID: PMC6331634 DOI: 10.1038/s41598-018-36993-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 11/28/2018] [Indexed: 01/19/2023] Open
Abstract
The synaptic protein SHANK3 encodes a multidomain scaffold protein expressed at the postsynaptic density of neuronal excitatory synapses. We previously identified de novo SHANK3 mutations in patients with autism spectrum disorders (ASD) and showed that SHANK3 represents one of the major genes for ASD. Here, we analyzed the pyramidal cortical neurons derived from induced pluripotent stem cells from four patients with ASD carrying SHANK3 de novo truncating mutations. At 40-45 days after the differentiation of neural stem cells, dendritic spines from pyramidal neurons presented variable morphologies: filopodia, thin, stubby and muschroom, as measured in 3D using GFP labeling and immunofluorescence. As compared to three controls, we observed a significant decrease in SHANK3 mRNA levels (less than 50% of controls) in correlation with a significant reduction in dendritic spine densities and whole spine and spine head volumes. These results, obtained through the analysis of de novo SHANK3 mutations in the patients' genomic background, provide further support for the presence of synaptic abnormalities in a subset of patients with ASD.
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Affiliation(s)
- Laura Gouder
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France.,CNRS UMR 3571 « Genes, Synapses and Cognition », Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - Aline Vitrac
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France.,CNRS UMR 3571 « Genes, Synapses and Cognition », Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - Hany Goubran-Botros
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France.,CNRS UMR 3571 « Genes, Synapses and Cognition », Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | | | | | | | - Ekaterina Atanasova
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France.,CNRS UMR 3571 « Genes, Synapses and Cognition », Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - Nathalie Lemière
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France.,CNRS UMR 3571 « Genes, Synapses and Cognition », Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - Anne Biton
- Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Institut Pasteur, Paris, France
| | - Claire S Leblond
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France.,CNRS UMR 3571 « Genes, Synapses and Cognition », Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | | | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, F-91057, Evry, France
| | | | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France.,Assistance Publique-Hôpitaux de Paris, Robert Debré Hospital, Department of Child and Adolescent Psychiatry, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France.,CNRS UMR 3571 « Genes, Synapses and Cognition », Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France
| | - Isabelle Cloëz-Tayarani
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France. .,CNRS UMR 3571 « Genes, Synapses and Cognition », Institut Pasteur, Paris, France. .,Université Paris Diderot, Sorbonne Paris Cité, Human Genetics and Cognitive Functions, Paris, France.
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21
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Bertiaux E, Mallet A, Fort C, Blisnick T, Bonnefoy S, Jung J, Lemos M, Marco S, Vaughan S, Trépout S, Tinevez JY, Bastin P. Bidirectional intraflagellar transport is restricted to two sets of microtubule doublets in the trypanosome flagellum. J Cell Biol 2018; 217:4284-4297. [PMID: 30275108 PMCID: PMC6279389 DOI: 10.1083/jcb.201805030] [Citation(s) in RCA: 31] [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] [Received: 05/09/2018] [Revised: 08/06/2018] [Accepted: 09/21/2018] [Indexed: 12/22/2022] Open
Abstract
Intraflagellar transport (IFT) is the movement of large protein complexes responsible for the construction of cilia and flagella. Using a combination of three-dimensional electron microscopy and high-resolution live imaging, Bertiaux et al. show that IFT takes place on only four microtubule doublets out of the nine available in the trypanosome flagellum. Intraflagellar transport (IFT) is the rapid bidirectional movement of large protein complexes driven by kinesin and dynein motors along microtubule doublets of cilia and flagella. In this study, we used a combination of high-resolution electron and light microscopy to investigate how and where these IFT trains move within the flagellum of the protist Trypanosoma brucei. Focused ion beam scanning electron microscopy (FIB-SEM) analysis of trypanosomes showed that trains are found almost exclusively along two sets of doublets (3–4 and 7–8) and distribute in two categories according to their length. High-resolution live imaging of cells expressing mNeonGreen::IFT81 or GFP::IFT52 revealed for the first time IFT trafficking on two parallel lines within the flagellum. Anterograde and retrograde IFT occurs on each of these lines. At the distal end, a large individual anterograde IFT train is converted in several smaller retrograde trains in the space of 3–4 s while remaining on the same side of the axoneme.
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Affiliation(s)
- Eloïse Bertiaux
- Trypanosome Cell Biology Unit, INSERM U1201, Institut Pasteur, Paris, France.,Université Pierre et Marie Curie Paris 6, Cellule Pasteur, Paris, France
| | - Adeline Mallet
- Trypanosome Cell Biology Unit, INSERM U1201, Institut Pasteur, Paris, France.,Université Pierre et Marie Curie Paris 6, Cellule Pasteur, Paris, France.,UtechS Ultrastructural Bioimaging (Ultrapole), Institut Pasteur, Paris, France
| | - Cécile Fort
- Trypanosome Cell Biology Unit, INSERM U1201, Institut Pasteur, Paris, France.,Université Pierre et Marie Curie Paris 6, Cellule Pasteur, Paris, France
| | - Thierry Blisnick
- Trypanosome Cell Biology Unit, INSERM U1201, Institut Pasteur, Paris, France
| | - Serge Bonnefoy
- Trypanosome Cell Biology Unit, INSERM U1201, Institut Pasteur, Paris, France
| | - Jamin Jung
- Trypanosome Cell Biology Unit, INSERM U1201, Institut Pasteur, Paris, France
| | - Moara Lemos
- Trypanosome Cell Biology Unit, INSERM U1201, Institut Pasteur, Paris, France
| | - Sergio Marco
- Université Paris Sud, Université Paris-Saclay, Centre National de la Recherche Scientifique, UMR 9187, Orsay, France.,Institut Curie, Paris Sciences et Lettres Research University, INSERM U1196, Orsay, France
| | - Sue Vaughan
- Department of Biological and Medical Sciences, Faculty of Health and Life Science, Oxford Brookes University, Oxford, UK
| | - Sylvain Trépout
- Université Paris Sud, Université Paris-Saclay, Centre National de la Recherche Scientifique, UMR 9187, Orsay, France.,Institut Curie, Paris Sciences et Lettres Research University, INSERM U1196, Orsay, France
| | - Jean-Yves Tinevez
- UtechS Photonic Bioimaging (Imagopole), Institut Pasteur, Paris, France.,Image Analysis Hub, Institut Pasteur, Paris, France
| | - Philippe Bastin
- Trypanosome Cell Biology Unit, INSERM U1201, Institut Pasteur, Paris, France
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22
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Lancino M, Majello S, Herbert S, De Chaumont F, Tinevez JY, Olivo-Marin JC, Herbomel P, Schmidt A. Anisotropic organization of circumferential actomyosin characterizes hematopoietic stem cells emergence in the zebrafish. eLife 2018; 7:37355. [PMID: 30132756 PMCID: PMC6105311 DOI: 10.7554/elife.37355] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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: 04/07/2018] [Accepted: 07/28/2018] [Indexed: 12/15/2022] Open
Abstract
Hematopoiesis leads to the formation of blood and immune cells. Hematopoietic stem cells emerge during development, from vascular components, via a process called the endothelial-to-hematopoietic transition (EHT). Here, we reveal essential biomechanical features of the EHT, using the zebrafish embryo imaged at unprecedented spatio-temporal resolution and an algorithm to unwrap the aorta into 2D-cartography. We show that the transition involves anisotropic contraction along the antero-posterior axis, with heterogenous organization of contractile circumferential actomyosin. The biomechanics of the contraction is oscillatory, with unusually long periods in comparison to other apical constriction mechanisms described so far in morphogenesis, and is supported by the anisotropic reinforcement of junctional contacts. Finally, we show that abrogation of blood flow impairs the actin cytoskeleton, the morphodynamics of EHT cells, and the orientation of the emergence. Overall, our results underline the peculiarities of the EHT biomechanics and the influence of the mechanical forces exerted by blood flow. As humans, we have two major types of blood cell: our red blood cells transport oxygen around the body, while our white blood cells fight disease. Both types of cell come from the same stem cells, which first appear early in embryonic development. These stem cells emerge from the walls of major blood vessels, including the aorta – which carries blood from the heart. Stem cells have not yet decided which adult cell to become. Given the right signals, blood stem cells can form red blood cells or any of the different types of white blood cell. Understanding this process could allow scientists to recreate it in the laboratory, making blood stem cells that can give rise to all blood cells found in the body. But, this is not yet possible because we do not know all the conditions needed to make the cells and ensure they survive. One crucial gap in our understanding concerns the importance of blood flow. As the main blood vessel leaving the heart, the aorta experiences mechanical stress every time the heart beats. Lancino et al. wanted to find out whether this influences the development of the blood stem cells. Zebrafish embryos are transparent, making it easy to see their bodies developing under a microscope. Like humans, they also produce both red blood cells and white blood cells meaning Lancino et al. could watch the birth of blood stem cells in these embryos from a part of the aorta called the aortic floor. A new software tool unwrapped pictures of the tube-shaped blood vessel into flat, two-dimensional maps, making it possible to see how the aorta changed over time. This revealed that, as blood stem cells leave the aortic floor, they bend and contract with the direction of the blood flow. Rings of actin and myosin proteins that formed around the stem cells as they are born helped the process along, while stopping the heartbeat changed the way the blood cells emerged. Without any blood flow, the actin proteins did not assemble properly; the stem cells also emerged in the wrong direction and some of them even died. These findings show that physical forces play a role in the formation of blood stem cells. Understanding this process brings scientists a step closer to recreating the conditions for making different kinds of blood cells outside of the body.
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Affiliation(s)
- Mylene Lancino
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.,CNRS, UMR 3738, Paris, France.,Sorbonne Université, UPMC Paris 06, Complexité du Vivant, Paris, France
| | - Sara Majello
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.,CNRS, UMR 3738, Paris, France
| | - Sebastien Herbert
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.,CNRS, UMR 3738, Paris, France.,Image Analysis Hub, UTechSPhotonic BioImaging (Imagopole), Citech, Institut Pasteur, Paris, France
| | - Fabrice De Chaumont
- Department of Cell Biology and Infection, Institut Pasteur, Paris, France.,CNRS, UMR3691, Paris, France
| | - Jean-Yves Tinevez
- Image Analysis Hub, UTechSPhotonic BioImaging (Imagopole), Citech, Institut Pasteur, Paris, France
| | | | - Philippe Herbomel
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.,CNRS, UMR 3738, Paris, France
| | - Anne Schmidt
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.,CNRS, UMR 3738, Paris, France
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23
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Wolff C, Tinevez JY, Pietzsch T, Stamataki E, Harich B, Guignard L, Preibisch S, Shorte S, Keller PJ, Tomancak P, Pavlopoulos A. Multi-view light-sheet imaging and tracking with the MaMuT software reveals the cell lineage of a direct developing arthropod limb. eLife 2018; 7:34410. [PMID: 29595475 PMCID: PMC5929908 DOI: 10.7554/elife.34410] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [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: 12/15/2017] [Accepted: 03/26/2018] [Indexed: 12/11/2022] Open
Abstract
During development, coordinated cell behaviors orchestrate tissue and organ morphogenesis. Detailed descriptions of cell lineages and behaviors provide a powerful framework to elucidate the mechanisms of morphogenesis. To study the cellular basis of limb development, we imaged transgenic fluorescently-labeled embryos from the crustacean Parhyale hawaiensis with multi-view light-sheet microscopy at high spatiotemporal resolution over several days of embryogenesis. The cell lineage of outgrowing thoracic limbs was reconstructed at single-cell resolution with new software called Massive Multi-view Tracker (MaMuT). In silico clonal analyses suggested that the early limb primordium becomes subdivided into anterior-posterior and dorsal-ventral compartments whose boundaries intersect at the distal tip of the growing limb. Limb-bud formation is associated with spatial modulation of cell proliferation, while limb elongation is also driven by preferential orientation of cell divisions along the proximal-distal growth axis. Cellular reconstructions were predictive of the expression patterns of limb development genes including the BMP morphogen Decapentaplegic. During early life, animals develop from a single fertilized egg cell to hundreds, millions or even trillions of cells. These cells specialize to do different tasks; forming different tissues and organs like muscle, skin, lungs and liver. For more than a century, scientists have strived to understand the details of how animal cells become different and specialize, and have created many new techniques and technologies to help them achieve this goal. Limbs – such as arms, legs and wings – form from small lumps of cells called limb buds. Scientists use the shrimp-like crustacean, Parhyale hawaiensis, to study development, including limb growth. This species is useful because it is easy to grow, manipulate and observe its developing young in the laboratory. Understanding how its limbs develop offers important new insights into how limbs develop in other animals too. Wolff, Tinevez, Pietzsch et al. have now combined advanced microscopy with custom computer software, called Massive Multi-view Tracker (MaMuT) to investigate this. As limbs develop in Parhyale, the MaMuT software tracks how cells behave, and how they are organized. This analysis revealed that for cells to produce a limb bud, they need to split at an early stage into separate groups. These groups are organized along two body axes, one that goes from head to tail, and one that runs from back to belly. The limb grows perpendicular to these main body axes, along a new ‘proximal-distal’ axis that goes from nearest to furthest from the body. Wolff et al. found that the cells that contribute to the extremities of the limb divide faster than the ones that stay closer to the body. Finally, the results show that when cells in a limb divide, they mostly divide along the proximal-distal axis, producing one cell that is further from the body than the other. These cell activities may help limbs to get longer as they grow. Notably, the groups of cells seen by Wolff et al. were expressing genes that had previously been identified in developing limbs. This helps to validate the new results and to identify which active genes control the behaviors of the analyzed cells. These findings reveal new ways to study animal development. This approach could have many research uses and may help to link the mechanisms of cell biology to their effects. It could also contribute to new understanding of developmental and genetic conditions that affect human health.
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Affiliation(s)
- Carsten Wolff
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Tobias Pietzsch
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Evangelia Stamataki
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Benjamin Harich
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Léo Guignard
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Stephan Preibisch
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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24
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Aulner N, Danckaert A, Fernandes J, Nicola MA, Roux P, Salles A, Tinevez JY, Shorte SL. Fluorescence imaging host pathogen interactions: fifteen years benefit of hindsight…. Curr Opin Microbiol 2018; 43:193-198. [PMID: 29567588 DOI: 10.1016/j.mib.2018.03.001] [Citation(s) in RCA: 3] [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] [Received: 11/21/2017] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 01/24/2023]
Abstract
We consider in review current state-of-the-art fluorescence microscopy for investigating the host-pathogen interface. Our perspective is honed from years with literally thousands of microbiologists using the variety of imaging technologies available within our dedicated BSL2/BSL3 optical imaging research service facilities at the Institut Pasteur Paris founded from scratch in 2001. During fifteen years learning from the success and failures of introducing different fluorescence imaging technologies, methods, and technical development strategies we provide here a synopsis review of our experience to date and a synthesis of how we see the future in perspective for fluorescence imaging at the host-pathogen interface.
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Affiliation(s)
- Nathalie Aulner
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Anne Danckaert
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Julien Fernandes
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Marie-Anne Nicola
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Pascal Roux
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Audrey Salles
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Spencer L Shorte
- Institut Pasteur, Citech, Imagopole-UTechS-PBI Photonic BioImaging, 25-28 rue du Dr Roux, 75015 Paris, France
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25
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Anderson MC, Chaze T, Coïc YM, Injarabian L, Jonsson F, Lombion N, Selimoglu-Buet D, Souphron J, Ridley C, Vonaesch P, Baron B, Arena ET, Tinevez JY, Nigro G, Nothelfer K, Solary E, Lapierre V, Lazure T, Matondo M, Thornton D, Sansonetti PJ, Baleux F, Marteyn BS. MUB 40 Binds to Lactoferrin and Stands as a Specific Neutrophil Marker. Cell Chem Biol 2018; 25:483-493.e9. [PMID: 29478905 DOI: 10.1016/j.chembiol.2018.01.014] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 02/07/2023]
Abstract
Neutrophils represent the most abundant immune cells recruited to inflamed tissues. A lack of dedicated tools has hampered their detection and study. We show that a synthesized peptide, MUB40, binds to lactoferrin, the most abundant protein stored in neutrophil-specific and tertiary granules. Lactoferrin is specifically produced by neutrophils among other leukocytes, making MUB40 a specific neutrophil marker. Naive mammalian neutrophils (human, guinea pig, mouse, rabbit) were labeled by fluorescent MUB40 conjugates (-Cy5, Dylight405). A peptidase-resistant retro-inverso MUB40 (RI-MUB40) was synthesized and its lactoferrin-binding property validated. Neutrophil lactoferrin secretion during in vitro Shigella infection was assessed with RI-MUB40-Cy5 using live cell microscopy. Systemically administered RI-MUB40-Cy5 accumulated at sites of inflammation in a mouse arthritis inflammation model in vivo and showed usefulness as a potential tool for inflammation detection using non-invasive imaging. Improving neutrophil detection with the universal and specific MUB40 marker will aid the study of broad ranges of inflammatory diseases.
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Affiliation(s)
- Mark C Anderson
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Thibault Chaze
- Institut Pasteur / CNRS USR 2000 Mass Spectrometry for Biology, Proteomics Platform, CITECH, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Yves-Marie Coïc
- Institut Pasteur, Unité de Chimie des Biomolécules, CNRS UMR 3523, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Louise Injarabian
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; CNRS, IBGC, Cell Energetic Metabolism, 1 rue Camille Saint Saëns CS 61390, 33077 Bordeaux Cedex, France
| | - Friederike Jonsson
- Institut Pasteur, Département d'Immunologie, 25 rue du Docteur Roux, 75024 Paris Cedex 15, France; INSERM Unité 1222, 25 rue du Dr Roux, 75015 Paris Cedex 15, France
| | - Naelle Lombion
- Institut Gustave Roussy, Laboratoire de Thérapie Cellulaire, 114 rue Edouard Vaillant, 94800 Villejuif, France
| | | | - Judith Souphron
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Caroline Ridley
- University of Manchester, Wellcome Trust Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, A.V. Hill Building, Manchester M13 9PT, UK
| | - Pascale Vonaesch
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Bruno Baron
- Institut Pasteur, Plate-Forme de Biophysique Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Ellen T Arena
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Jean-Yves Tinevez
- Institut Pasteur, CITECH, Imagopole, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Giulia Nigro
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Katharina Nothelfer
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Eric Solary
- Institut Gustave Roussy Inserm U1009, 114 rue Edouard Vaillant, 94800 Villejuif, France
| | - Valérie Lapierre
- Institut Gustave Roussy, Laboratoire de Thérapie Cellulaire, 114 rue Edouard Vaillant, 94800 Villejuif, France
| | - Thierry Lazure
- APHP Hôpital du Kremlin-Bicêtre, 78 rue du Général Leclerc, 94270 Le Kremlin-Bicêtre, France
| | - Mariette Matondo
- Institut Pasteur / CNRS USR 2000 Mass Spectrometry for Biology, Proteomics Platform, CITECH, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - David Thornton
- Institut Pasteur, Département d'Immunologie, 25 rue du Docteur Roux, 75024 Paris Cedex 15, France
| | - Philippe J Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Collège de France, Paris, France
| | - Françoise Baleux
- Institut Pasteur, Unité de Chimie des Biomolécules, CNRS UMR 3523, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Benoit S Marteyn
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Institut Gustave Roussy, Laboratoire de Thérapie Cellulaire, 114 rue Edouard Vaillant, 94800 Villejuif, France.
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Arena ET, Tinevez JY, Nigro G, Sansonetti PJ, Marteyn BS. The infectious hypoxia: occurrence and causes during Shigella infection. Microbes Infect 2016; 19:157-165. [PMID: 27884799 DOI: 10.1016/j.micinf.2016.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 07/18/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 12/19/2022]
Abstract
Hypoxia is defined as a tissue oxygenation status below physiological needs. During Shigella infection, an infectious hypoxia is induced within foci of infection. In this review, we discuss how Shigella physiology and virulence are modulated and how the main recruited immune cells, the neutrophils, adapt to this environment.
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Affiliation(s)
- Ellen T Arena
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Citech, Imagopole, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Giulia Nigro
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Philippe J Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Collège de France, 11 Place Marcellin Berthelot, F-75231, Paris Cedex 05, France
| | - Benoit S Marteyn
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; INSERM Unité 1202, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Gustave Roussy Cancer Campus, Laboratoire de Thérapie Cellulaire, 114 Rue Edouard Vaillant, 94800 Villejuif, France.
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27
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Tinevez JY, Perry N, Schindelin J, Hoopes GM, Reynolds GD, Laplantine E, Bednarek SY, Shorte SL, Eliceiri KW. TrackMate: An open and extensible platform for single-particle tracking. Methods 2016; 115:80-90. [PMID: 27713081 DOI: 10.1016/j.ymeth.2016.09.016] [Citation(s) in RCA: 1605] [Impact Index Per Article: 200.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 01/12/2023] Open
Abstract
We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over time, 3D over time, or other single and multi-channel image variants. TrackMate provides several visualization and analysis tools that aid in assessing the relevance of results. The utility of TrackMate is further enhanced through its ability to be readily customized to meet specific tracking problems. TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment. This evolving framework provides researchers with the opportunity to quickly develop and optimize new algorithms based on existing TrackMate modules without the need of having to write de novo user interfaces, including visualization, analysis and exporting tools. The current capabilities of TrackMate are presented in the context of three different biological problems. First, we perform Caenorhabditis-elegans lineage analysis to assess how light-induced damage during imaging impairs its early development. Our TrackMate-based lineage analysis indicates the lack of a cell-specific light-sensitive mechanism. Second, we investigate the recruitment of NEMO (NF-κB essential modulator) clusters in fibroblasts after stimulation by the cytokine IL-1 and show that photodamage can generate artifacts in the shape of TrackMate characterized movements that confuse motility analysis. Finally, we validate the use of TrackMate for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells.
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Affiliation(s)
| | - Nick Perry
- Imagopole, Citech, Institut Pasteur, 75724 Paris, France
| | - Johannes Schindelin
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Genevieve M Hoopes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gregory D Reynolds
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Emmanuel Laplantine
- Laboratory of Signaling and Pathogenesis, Centre National de la Recherche Scientifique, UMR 3691, Institut Pasteur, 75724 Paris, France
| | - Sebastian Y Bednarek
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53719, USA
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Abstract
Many questions in developmental biology depend on measuring the position and movement of individual cells within developing embryos. Yet, tools that provide this data are often challenged by high cell density and their accuracy is difficult to measure. Here, we present a three-step procedure to address this problem. Step one is a novel segmentation algorithm based on image derivatives that, in combination with selective post-processing, reliably and automatically segments cell nuclei from images of densely packed tissue. Step two is a quantitative validation using synthetic images to ascertain the efficiency of the algorithm with respect to signal-to-noise ratio and object density. Finally, we propose an original method to generate reliable and experimentally faithful ground truth datasets: Sparse-dense dual-labeled embryo chimeras are used to unambiguously measure segmentation errors within experimental data. Together, the three steps outlined here establish a robust, iterative procedure to fine-tune image analysis algorithms and microscopy settings associated with embryonic 3D image data sets.
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Affiliation(s)
- Bhavna Rajasekaran
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Koichiro Uriu
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Theoretical Biology Laboratory, RIKEN, Saitama, Japan
| | - Guillaume Valentin
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- MRC-National Institute for Medical Research, London, United Kingdom
| | - Jean-Yves Tinevez
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrew C. Oates
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- MRC-National Institute for Medical Research, London, United Kingdom
- Department of Cell and Developmental Biology, University College, London, United Kingdom
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Gouder L, Tinevez JY, Goubran-Botros H, Benchoua A, Bourgeron T, Cloëz-Tayarani I. Three-dimensional Quantification of Dendritic Spines from Pyramidal Neurons Derived from Human Induced Pluripotent Stem Cells. J Vis Exp 2015. [PMID: 26484791 DOI: 10.3791/53197] [Citation(s) in RCA: 4] [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] [Indexed: 10/31/2022] Open
Abstract
Dendritic spines are small protrusions that correspond to the post-synaptic compartments of excitatory synapses in the central nervous system. They are distributed along the dendrites. Their morphology is largely dependent on neuronal activity, and they are dynamic. Dendritic spines express glutamatergic receptors (AMPA and NMDA receptors) on their surface and at the levels of postsynaptic densities. Each spine allows the neuron to control its state and local activity independently. Spine morphologies have been extensively studied in glutamatergic pyramidal cells of the brain cortex, using both in vivo approaches and neuronal cultures obtained from rodent tissues. Neuropathological conditions can be associated to altered spine induction and maturation, as shown in rodent cultured neurons and one-dimensional quantitative analysis (1). The present study describes a protocol for the 3D quantitative analysis of spine morphologies using human cortical neurons derived from neural stem cells (late cortical progenitors). These cells were initially obtained from induced pluripotent stem cells. This protocol allows the analysis of spine morphologies at different culture periods, and with possible comparison between induced pluripotent stem cells obtained from control individuals with those obtained from patients with psychiatric diseases.
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Affiliation(s)
- Laura Gouder
- Human Genetics and Cognitive Functions, Institut Pasteur; CNRS URA 2182 'Genes, synapses and cognition', Institut Pasteur; Human Genetics and Cognitive Functions, Université Paris Diderot, Sorbonne Paris Cité
| | - Jean-Yves Tinevez
- Plateforme d' Imagerie Dynamique, Imagopole, CiTech, Institut Pasteur
| | - Hany Goubran-Botros
- Human Genetics and Cognitive Functions, Institut Pasteur; CNRS URA 2182 'Genes, synapses and cognition', Institut Pasteur; Human Genetics and Cognitive Functions, Université Paris Diderot, Sorbonne Paris Cité
| | | | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur; CNRS URA 2182 'Genes, synapses and cognition', Institut Pasteur; Human Genetics and Cognitive Functions, Université Paris Diderot, Sorbonne Paris Cité
| | - Isabelle Cloëz-Tayarani
- Human Genetics and Cognitive Functions, Institut Pasteur; CNRS URA 2182 'Genes, synapses and cognition', Institut Pasteur; Human Genetics and Cognitive Functions, Université Paris Diderot, Sorbonne Paris Cité;
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Caron J, Fallet C, Tinevez JY, Moisan L, Braitbart LPO, Sirat GY, Shorte SL. Conical diffraction illumination opens the way for low phototoxicity super-resolution imaging. Cell Adh Migr 2015; 8:430-9. [PMID: 25482642 PMCID: PMC4594584 DOI: 10.4161/cam.29358] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 01/15/2023] Open
Abstract
We present a new technology for super-resolution fluorescence imaging, based on conical diffraction. Conical diffraction is a linear, singular phenomenon, taking place when a laser beam is diffracted through a biaxial crystal. We use conical diffraction in a thin biaxial crystal to generate illumination patterns that are more compact than the classical Gaussian beam, and use them to generate a super-resolution imaging modality. While there already exist several super-resolution modalities, our technology (biaxial super-resolution: BSR) is distinguished by the unique combination of several performance features. Using BSR super-resolution data are achieved using low light illumination significantly less than required for classical confocal imaging, which makes BSR ideal for live-cell, long-term time-lapse super-resolution imaging. Furthermore, no specific sample preparation is required, and any fluorophore can be used. Perhaps most exciting, improved resolution BSR-imaging resolution enhancement can be achieved with any type of objective no matter the magnification, numerical aperture, working distance, or the absence or presence of immersion medium. In this article, we present the first implementation of BSR modality on a commercial confocal microscope. We acquire and analyze validation data, showing high quality super-resolved images of biological objects, and demonstrate the wide applicability of the technology. We report live-cell super-resolution imaging over a long period, and show that the light dose required for super-resolution imaging is far below the threshold likely to generate phototoxicity.
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Duval N, Daubas P, Bourcier de Carbon C, St Cloment C, Tinevez JY, Lopes M, Ribes V, Robert B. Msx1 and Msx2 act as essential activators of Atoh1 expression in the murine spinal cord. Development 2014; 141:1726-36. [PMID: 24715462 DOI: 10.1242/dev.099002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dorsal spinal neurogenesis is orchestrated by the combined action of signals secreted from the roof plate organizer and a downstream transcriptional cascade. Within this cascade, Msx1 and Msx2, two homeodomain transcription factors (TFs), are induced earlier than bHLH neuralizing TFs. Whereas bHLH TFs have been shown to specify neuronal cell fate, the function of Msx genes remains poorly defined. We describe dramatic alterations of neuronal patterning in Msx1/Msx2 double-mutant mouse embryos. The most dorsal spinal progenitor pool fails to express the bHLH neuralizing TF Atoh1, which results in a lack of Lhx2-positive and Barhl2-positive dI1 interneurons. Neurog1 and Ascl1 expression territories are dorsalized, leading to ectopic dorsal differentiation of dI2 and dI3 interneurons. In proportion, the amount of Neurog1-expressing progenitors appears unaffected, whereas the number of Ascl1-positive cells is increased. These defects occur while BMP signaling is still active in the Msx1/Msx2 mutant embryos. Cell lineage analysis and co-immunolabeling demonstrate that Atoh1-positive cells derive from progenitors expressing both Msx1 and Msx2. In vitro, Msx1 and Msx2 proteins activate Atoh1 transcription by specifically interacting with several homeodomain binding sites in the Atoh1 3' enhancer. In vivo, Msx1 and Msx2 are required for Atoh1 3' enhancer activity and ChIP experiments confirm Msx1 binding to this regulatory sequence. These data support a novel function of Msx1 and Msx2 as transcriptional activators. Our study provides new insights into the transcriptional control of spinal cord patterning by BMP signaling, with Msx1 and Msx2 acting upstream of Atoh1.
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Affiliation(s)
- Nathalie Duval
- Institut Pasteur, Morphogenesis Molecular Genetics, CNRS URA 2578, 75015 Paris, France
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Tarantino N, Tinevez JY, Crowell EF, Boisson B, Henriques R, Mhlanga M, Agou F, Israël A, Laplantine E. TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO-IKK supramolecular structures. J Cell Biol 2014; 204:231-45. [PMID: 24446482 PMCID: PMC3897181 DOI: 10.1083/jcb.201307172] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [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: 07/26/2013] [Accepted: 12/09/2013] [Indexed: 11/22/2022] Open
Abstract
Nuclear factor κB (NF-κB) essential modulator (NEMO), a regulatory component of the IκB kinase (IKK) complex, controls NF-κB activation through its interaction with ubiquitin chains. We show here that stimulation with interleukin-1 (IL-1) and TNF induces a rapid and transient recruitment of NEMO into punctate structures that are anchored at the cell periphery. These structures are enriched in activated IKK kinases and ubiquitinated NEMO molecules, which suggests that they serve as organizing centers for the activation of NF-κB. These NEMO-containing structures colocalize with activated TNF receptors but not with activated IL-1 receptors. We investigated the involvement of nondegradative ubiquitination in the formation of these structures, using cells deficient in K63 ubiquitin chains or linear ubiquitin chain assembly complex (LUBAC)-mediated linear ubiquitination. Our results indicate that, unlike TNF, IL-1 requires K63-linked and linear ubiquitin chains to recruit NEMO into higher-order complexes. Thus, different mechanisms are involved in the recruitment of NEMO into supramolecular complexes, which appear to be essential for NF-κB activation.
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Affiliation(s)
- Nadine Tarantino
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
| | - Jean-Yves Tinevez
- Plateforme d’Imagerie Dynamique and Computational Imaging and Modeling Group, Institut Pasteur, Paris 75015, France
| | - Elizabeth Faris Crowell
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Ricardo Henriques
- Plateforme d’Imagerie Dynamique and Computational Imaging and Modeling Group, Institut Pasteur, Paris 75015, France
- Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisboa, 1649-028 Portugal
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, England, UK
| | - Musa Mhlanga
- Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisboa, 1649-028 Portugal
- Gene Expression and Biophysics Group, Synthetic Biology Emerging Research Area, Biosciences Unit, Council for Scientific and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Fabrice Agou
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
| | - Alain Israël
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
| | - Emmanuel Laplantine
- Unité de Signalisation Moléculaire et Activation Cellulaire and Laboratoire Trafic Membranaire et Division Cellulaire, Institut Pasteur, Centre National de la Recherche Scientifique URA 2582, Paris 75015, France
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Holland AD, Rückerl F, Dragavon JM, Rekiki A, Tinevez JY, Tournebize R, Shorte SL. In vitro characterization of Fluorescence by Unbound Excitation from Luminescence: broadening the scope of energy transfer. Methods 2013; 66:353-61. [PMID: 24045025 DOI: 10.1016/j.ymeth.2013.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 07/19/2013] [Revised: 08/20/2013] [Accepted: 09/02/2013] [Indexed: 01/10/2023] Open
Abstract
Energy transfer mechanisms represent the basis for an array of valuable tools to infer interactions in vitro and in vivo, enhance detection or resolve interspecies distances such as with resonance. Based upon our own previously published studies and new results shown here we present a novel framework describing for the first time a model giving a view of the biophysical relationship between Fluorescence by Unbound Excitation from Luminescence (FUEL), a conventional radiative excitation-emission process, and bioluminescence resonance energy transfer. We show here that in homogeneous solutions and in fluorophore-targeted bacteria, FUEL is the dominant mechanism responsible for the production of red-shifted photons. The minor resonance contribution was ascertained by comparing the intensity of the experimental signal to its theoretical resonance counterpart. Distinctive features of the in vitro FUEL signal include a macroscopic depth dependency, a lack of enhancement upon targeting at a constant fluorophore concentration cf and a non-square dependency on cf. Significantly, FUEL is an important, so far overlooked, component of all resonance phenomena which should guide the design of appropriate controls when elucidating interactions. Last, our results highlight the potential for FUEL as a means to enhance in vivo and in vitro detection through complex media while alleviating the need for targeting.
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Affiliation(s)
- Alexandra D Holland
- Plate-Forme d'Imagerie Dynamique, Imagopole, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Florian Rückerl
- Plate-Forme d'Imagerie Dynamique, Imagopole, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Joseph M Dragavon
- Plate-Forme d'Imagerie Dynamique, Imagopole, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Abdessalem Rekiki
- Plate-Forme d'Imagerie Dynamique, Imagopole, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Jean-Yves Tinevez
- Plate-Forme d'Imagerie Dynamique, Imagopole, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Régis Tournebize
- Plate-Forme d'Imagerie Dynamique, Imagopole, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris cedex 15, France; Unité INSERM U786, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France.
| | - Spencer L Shorte
- Plate-Forme d'Imagerie Dynamique, Imagopole, Institut Pasteur, 25-28 Rue du Dr. Roux, 75724 Paris cedex 15, France.
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Crowell EF, Tinevez JY, Echard A. A simple model for the fate of the cytokinesis midbody remnant: implications for remnant degradation by autophagy. Bioessays 2013; 35:472-81. [PMID: 23450621 DOI: 10.1002/bies.201200132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
When a cell divides, it produces two daughter cells initially connected by a cytokinesis bridge, which is eventually cut through abscission. One of the two daughter cells inherits a bridge "remnant", which has been proposed to be degraded by autophagy. The fate and function of remnants is attracting increasing attention, as their accumulation appears to influence proliferation versus differentiation of the daughter cells. Here, we present a simple model for bridge and remnant turnover in a dynamic cell population. We demonstrate that remnant proportions depend on the ratio of remnant and bridge lifetimes to the cell population doubling time. Our results yield new alternative interpretations for published experimental data, leading us to believe that autophagy-independent pathways for remnant degradation may exist. In addition, using the model, we determined experimentally inaccessible parameters such as remnant lifetime. Our model proves to be a useful tool for studying bridge and remnant populations.
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Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012. [PMID: 22743772 DOI: 10.1038/nmeth.2019.fiji] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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Affiliation(s)
- Johannes Schindelin
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012. [PMID: 22743772 DOI: 10.1038/nmeth.2019.pmid:22743772;pmcid:pmc3855844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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Affiliation(s)
- Johannes Schindelin
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nat Methods 2012; 9:676-82. [PMID: 22743772 DOI: 10.1038/nmeth.2019] [Citation(s) in RCA: 33648] [Impact Index Per Article: 2804.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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Affiliation(s)
- Johannes Schindelin
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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Tinevez JY, Salbreux G, Paluch E. [The mechanics of the cellular division or how to split a sphere into two?]. Med Sci (Paris) 2012; 28:144-6. [PMID: 22377299 DOI: 10.1051/medsci/2012282009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Tinevez JY, Dragavon J, Baba-Aissa L, Roux P, Perret E, Canivet A, Galy V, Shorte S. A quantitative method for measuring phototoxicity of a live cell imaging microscope. Methods Enzymol 2012; 506:291-309. [PMID: 22341230 DOI: 10.1016/b978-0-12-391856-7.00039-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescence-based imaging regimes require exposure of living samples under study to high intensities of focused incident illumination. An often underestimated, overlooked, or simply ignored fact in the design of any experimental imaging protocol is that exposure of the specimen to these excitation light sources must itself always be considered a potential source of phototoxicity. This can be problematic, not just in terms of cell viability, but much more worrisome in its more subtle manifestation where phototoxicity causes anomalous behaviors that risk to be interpreted as significant, whereas they are mere artifacts. This is especially true in the case of microbial pathogenesis, where host-pathogen interactions can prove especially fragile to light exposure in a manner that can obscure the very processes we are trying to observe. For these reasons, it is important to be able to bring the parameter of phototoxicity into the equation that brings us to choose one fluorescent imaging modality, or setup, over another. Further, we need to be able to assess the risk that phototoxicity may occur during any specific imaging experiment. To achieve this, we describe here a methodological approach that allows meaningful measurement, and therefore relative comparison of phototoxicity, in most any variety of different imaging microscopes. In short, we propose a quantitative approach that uses microorganisms themselves to reveal the range over which any given fluorescent imaging microscope will yield valid results, providing a metrology of phototoxic damage, distinct from photobleaching, where a clear threshold for phototoxicity is identified. Our method is widely applicable and we show that it can be adapted to other paradigms, including mammalian cell models.
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Affiliation(s)
- Jean-Yves Tinevez
- Institut Pasteur, Imagopole, Plateforme d'imagerie dynamique, Paris, France
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Colucci-Guyon E, Tinevez JY, Renshaw SA, Herbomel P. Strategies of professional phagocytes in vivo: unlike macrophages, neutrophils engulf only surface-associated microbes. J Cell Sci 2011; 124:3053-9. [PMID: 21868367 DOI: 10.1242/jcs.082792] [Citation(s) in RCA: 93] [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: 11/20/2022] Open
Abstract
The early control of potentially invading microbes by our immune system primarily depends on its main professional phagocytes - macrophages and neutrophils. Although the different functions of these two cell types have been extensively studied, little is known about their respective contributions to the initial control of invading microorganisms before the onset of adaptive immune responses. The naturally translucent zebrafish larva has recently emerged as a powerful model vertebrate in which to visualise the dynamic interactions between leukocytes and microbes in vivo. Using high-resolution live imaging, we found that whereas macrophages efficiently engulf bacteria from blood or fluid-filled body cavities, neutrophils barely do so. By contrast, neutrophils very efficiently sweep up surface-associated, but not fluid-borne, bacteria. Thus the physical presentation of unopsonised microbes is a crucial determinant of neutrophil phagocytic ability. Neutrophils engulf microbes only as they move over them, in a 'vacuum-cleaner' type of behaviour. This context-dependent nature of phagocytosis by neutrophils should be of particular relevance to human infectious diseases, especially for the early phase of encounter with microbes new to the host.
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Affiliation(s)
- Emma Colucci-Guyon
- Institut Pasteur, Unité Macrophages et Développement de l'Immunité, Département de Biologie du Développement, Paris, France.
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Sedzinski J, Biro M, Oswald A, Tinevez JY, Salbreux G, Paluch E. Polar actomyosin contractility destabilizes the position of the cytokinetic furrow. Nature 2011; 476:462-6. [PMID: 21822289 DOI: 10.1038/nature10286] [Citation(s) in RCA: 236] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 06/13/2011] [Indexed: 12/21/2022]
Abstract
Cytokinesis, the physical separation of daughter cells at the end of mitosis, requires precise regulation of the mechanical properties of the cell periphery. Although studies of cytokinetic mechanics mostly focus on the equatorial constriction ring, a contractile actomyosin cortex is also present at the poles of dividing cells. Whether polar forces influence cytokinetic cell shape and furrow positioning remains an open question. Here we demonstrate that the polar cortex makes cytokinesis inherently unstable. We show that limited asymmetric polar contractions occur during cytokinesis, and that perturbing the polar cortex leads to cell shape oscillations, resulting in furrow displacement and aneuploidy. A theoretical model based on a competition between cortex turnover and contraction dynamics accurately accounts for the oscillations. We further propose that membrane blebs, which commonly form at the poles of dividing cells and whose role in cytokinesis has long been enigmatic, stabilize cell shape by acting as valves releasing cortical contractility. Our findings reveal an inherent instability in the shape of the dividing cell and unveil a novel, spindle-independent mechanism ensuring the stability of cleavage furrow positioning.
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Affiliation(s)
- Jakub Sedzinski
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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Abstract
The dazzling sensitivity and frequency selectivity of the vertebrate ear rely on mechanical amplification of the hair cells' responsiveness to small stimuli. As revealed by spontaneous oscillations and forms of mechanical excitability in response to force steps, the hair bundle that adorns each hair cell is both a mechanosensory antenna and a force generator that might participate in the amplificatory process. To study the various incarnations of active hair-bundle motility, we combined Ca(2+) iontophoresis with mechanical stimulation of single hair bundles from the bullfrog's sacculus. We identified three classes of active hair-bundle movements: a hair bundle could be quiescent but display nonmonotonic twitches in response to either excitatory or inhibitory force steps, or oscillate spontaneously. Extracellular Ca(2+) changes could affect the kinetics of motion and, when large enough, evoke transitions between the three classes of motility. We found that the Ca(2+)-dependent location of a bundle's operating point within its force-displacement relation controlled the type of movement observed. In response to an iontophoretic pulse of Ca(2+) or of a Ca(2+) chelator, a hair bundle displayed a movement whose polarity could be reversed by applying a static bias to the bundle's position at rest. Moreover, such polarity reversal was accompanied by a 10-fold change in the kinetics of the Ca(2+)-evoked hair-bundle movement. A unified theoretical description, in which mechanical activity stems solely from myosin-based adaptation, could account for the fast and slow manifestations of active hair-bundle motility observed in frog, as well as in auditory organs of the turtle and the rat.
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Affiliation(s)
- Jean-Yves Tinevez
- Laboratoire Physico-Chimie Curie, CNRS, Institut Curie, Paris, France
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