College de France View Institution's Website 8 articles published in JoVE Biology Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C Antonia Hauth1, Rafael Galupa1, Nicolas Servant2, Laura Villacorta1, Kai Hauschulz3, Joke Gerarda van Bemmel4, Agnese Loda1, Edith Heard1,5 1EMBL: European Molecular Biology Laboratory, 2Institut Curie, 3Agilent Technologies, 4Genmab BV, 5Collège de France This protocol describes the Capture Hi-C method used to characterize the 3D organization of megabased-sized targeted genomic regions at high-resolution, including boundaries of topologically associating domains (TADs) and long-range chromatin interactions between regulatory and other DNA sequence elements. Biology Analyzing Oxidative Stress in Murine Intestinal Organoids using Reactive Oxygen Species-Sensitive Fluorogenic Probe Aline Stedman1,3, Antonin Levy1,4, Philippe J. Sansonetti1,2,5, Giulia Nigro1,6 1Molecular Microbial Pathogenesis Unit, Institut Pasteur, 2Chaire de Microbiologie et Maladies Infectieuses, Collège de France, 3Institut de Biologie Paris Seine (IBPS) - Developmental Biology Unit, Sorbonne Université, CNRS UMR7622, INSERM U1156, 4Molecular Radiotherapy, INSERM U1030, Gustave Roussy, Université Paris-Saclay, 5The Center for Microbes, Development and Health, Institut Pasteur Shanghai and Chinese Academy of Sciences, 6Microenvironment and Immunity Unit, Institut Pasteur The present protocol describes a method to detect reactive oxygen species (ROS) in the intestinal murine organoids using qualitative imaging and quantitative cytometry assays. This work can be potentially extended to other fluorescent probes to test the effect of selected compounds on ROS. Immunology and Infection Imaging Ca2+ Responses During Shigella Infection of Epithelial Cells Yasmine Smail1,2,3,4, Chunhui Sun1,2,3,4, Laurent Combettes5, Guy Tran Van Nhieu1,2,3,4 1Equipe Communication Intercellulaire et Infections Microbiennes, Centre de Recherche Interdisciplinaire en Biologie (CIRB), Collège de France, 2Institut National de la Santé et de la Recherche Médicale (Inserm), U1050, 3Centre Nationale de la Recherche Scientifique (CNRS), UMR7241, 4MEMOLIFE Laboratory of Excellence and Paris Sciences et Lettres, 5Inserm, UMRS1174, Université Paris Sud Here, we present protocols to visualize calcium (Ca2+) responses elicited by HeLa cells infected by Shigella. By optimizing the parameters of bacterial infection and imaging with Ca2+ fluorescent probes, atypical global and local Ca2+ signals induced by bacteria over a large range of infection kinetics are characterized. Immunology and Infection Immunofluorescence Analysis of Stress Granule Formation After Bacterial Challenge of Mammalian Cells Pascale Vonaesch1, Philippe J. Sansonetti1,2, Pamela Schnupf3 1Unité de Pathogénie Microbienne Moléculaire, INSERM U786, Institut Pasteur, 2Microbiologie et Maladies Infectieuses, Collège de France, 3Laboratory of Intestinal Immunity, Institut Imagine-INSERM UMR 1163, Université Paris Descartes-Sorbonne Paris Cité We describe a method for the qualitative and quantitative analysis of stress granule formation in mammalian cells after the cells are challenged with bacteria and a number of different stresses. This protocol can be applied to investigate the cellular stress granule response in a wide range of host-bacterial interactions. Medicine Multi-electrode Array Recordings of Human Epileptic Postoperative Cortical Tissue Elena Dossi1, Thomas Blauwblomme2,3, Rima Nabbout2,4, Gilles Huberfeld2,5, Nathalie Rouach1 1Neuroglial Interactions in Cerebral Physiopathology, Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France, 2Infantile Epilepsies & Brain Plasticity, INSERM U1129, PRES, Paris Descartes University, Sorbonne Paris Cité, CEA, 3Neurosurgery Department, Necker Hospital, AP-HP, Paris Descartes University, 4Rare Epilepsies Reference Center, Necker Hospital, AP-HP, Paris Descartes University, 5Neurophysiology Department, La Pitié-Salpêtrière Hospital, AP-HP, Sorbonne and Pierre and Marie Curie University We here describe how to perform multi-electrode array recordings of human epileptic cortical tissue. Epileptic tissue resection, slice preparation and multi-electrode array recordings of interictal and ictal events are demonstrated in detail. Neuroscience Dual Electrophysiological Recordings of Synaptically-evoked Astroglial and Neuronal Responses in Acute Hippocampal Slices Ulrike Pannasch*1, Jérémie Sibille*1,2, Nathalie Rouach1 1Neuroglial Interactions in Cerebral Physiopathology, Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France, 2Paris Diderot University The preparation of acute brain slices from isolated hippocampi, as well as the simultaneous electrophysiological recordings of astrocytes and neurons in stratum radiatum during stimulation of schaffer collaterals is described. The pharmacological isolation of astroglial potassium and glutamate transporter currents is demonstrated. Neuroscience MPI CyberMotion Simulator: Implementation of a Novel Motion Simulator to Investigate Multisensory Path Integration in Three Dimensions Michael Barnett-Cowan1, Tobias Meilinger1, Manuel Vidal2, Harald Teufel1, Heinrich H. Bülthoff1,3 1Department of Human Perception, Cognition and Action, Max Planck Institute for Biological Cybernetics, 2Laboratoire de Physiologie de la Perception et de l'Action, Collège de France - CNRS, 3Department of Brain and Cognitive Engineering, Korea University An efficient way to gain insight into how humans navigate themselves in three dimensions is described. The method takes advantage of a motion simulator capable of moving observers in ways unattainable by traditional simulators. Results confirm that movement in the horizontal plane is underestimated, while vertical movement is overestimated. Neuroscience Large-scale Recording of Neurons by Movable Silicon Probes in Behaving Rodents Marie Vandecasteele1,2, S. M.1, Sébastien Royer1,3, Mariano Belluscio1, Antal Berényi1, Kamran Diba1,4, Shigeyoshi Fujisawa1, Andres Grosmark1, Dun Mao1, Kenji Mizuseki1, Jagdish Patel1, Eran Stark1, David Sullivan1, Brendon Watson1, György Buzsáki1 1Center for Molecular and Behavioral Neuroscience, University of New Jersey, 2Center for Interdisciplinary Research in Biology, Collège de France, 3Janelia Farm Research Campus, Howards Hughes Medical Institute, 4Deptartment of Psychology, University of Wisconsin at Milwaukee We describe methods for large-scale recording of multiple single units and local field potential in behaving rodents with silicon probes. Drive fabrication, probe attachment to the drive and probe implantation processes are illustrated in sufficient details for easy replication.
