Universite Paris-Saclay 7 articles published in JoVE Biology Visualization and Quantification of Endogenous Intra-Organelle Protein Interactions at ER-Mitochondria Contact Sites by Proximity Ligation Assays Vera Filipa Monteiro-Cardoso1,2, Romain Le Bars1,3, Francesca Giordano1,2 1Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 2Inserm U1280, 3Imagerie-Gif, Light Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay The need for new approaches to study membrane contact sites (MCSs) has grown due to increasing interest in studying these cellular structures and their components. Here, we present a protocol that integrates previously available microscopy technologies to identify and quantify intra-organelle and inter-organelle protein complexes that reside at MCSs. Developmental Biology Generating Retinal Injury Models in Xenopus Tadpoles Karine Parain*1, Alicia Donval*1, Albert Chesneau*1, Jing Xian Lun1, Caroline Borday1, Muriel Perron1 1Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay We have developed several protocols to induce retinal damage or retinal degeneration in Xenopus laevis tadpoles. These models offer the possibility of studying retinal regeneration mechanisms. Biology Multimodal Analytical Platform on a Multiplexed Surface Plasmon Resonance Imaging Chip for the Analysis of Extracellular Vesicle Subsets Geetika Raizada1, Balasubramaniam Namasivayam2, Sameh Obeid3, Benjamin Brunel1, Wilfrid Boireau1, Eric Lesniewska4, Celine Elie-Caille1 1Université de Franche-Comté, CNRS UMR-6174, FEMTO-ST Institute, 2Lille Neuroscience & Cognition research centre, 3Institut Galien Paris-Saclay, CNRS UMR-8612 , Université Paris-Saclay, 4Interdisciplinary Lab Carnot Bourgogne LICB, CNRS UMR-6303, Université de Bourgogne Franche-Comté This paper proposes a new generation of multiparametric analytical platforms with increased throughput for the characterization of extracellular vesicle subsets. The method is based on a combination of multiplexed biosensing methods with metrological and morphomechanical analyses by atomic force microscopy, coupled with Raman spectroscopy, to qualify vesicular targets trapped on a microarray biochip. Bioengineering Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates Mahnaz Sabeti Azad*1, Angelo Cardoso Batista*1, Jean-Loup Faulon1, Chase L. Beisel2,3, Jerome Bonnet4, Manish Kushwaha1 1INRAe, AgroParisTech, Micalis Institute, Université Paris-Saclay, 2Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 3Medical Faculty, University of Würzburg, 4Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, University of Montpellier Presented here is a protocol for the preparation and buffer calibration of cell extracts from exonuclease V knockout strains of Escherichia coli BL21 Rosetta2 (ΔrecBCD and ΔrecB). This is a fast, easy, and direct approach for expression in cell-free protein synthesis systems using linear DNA templates. Engineering Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress Kevin Baudry1,2,3, Christine Paysant-Le Roux1,2, Stefano Colella4, Benoît Castandet1,2, Marie-Laure Martin1,2,5 1Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France, 2Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France, 3Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France, 4LSTM, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France, 5Universitté Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, Paris, France DiCoExpress is a script-based tool implemented in R to perform an RNA-Seq analysis from quality control to co-expression. DiCoExpress handles complete and unbalanced design up to 2 biological factors. This video tutorial guides the user through the different features of DiCoExpress. Neuroscience Characterization of Neuromuscular Junctions in Mice by Combined Confocal and Super-Resolution Microscopy Martina Marinello*1,2, Jérémie Cosette*1, Caroline Bogni1,2, Jérôme Denard1,2, Daniel Stockholm*1,3, Ana Buj-Bello*1,2 1Genethon, 91000, Evry, France, 2Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France, 3Ecole Pratique des Hautes Etudes, PSL Research University, 75014, Paris, France This protocol describes a method for morphometric analysis of neuromuscular junctions by combined confocal and STED microscopy that is used to quantify pathological changes in mouse models of SMA and ColQ-related CMS. 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.
