University of Lausanne View Institution's Website 20 articles published in JoVE Biology Monitoring On-Target Signaling Responses in Larval Zebrafish - Z-REX Unmasks Precise Mechanisms of Electrophilic Drugs and Metabolites Kuan-Ting Huang1, Phillippe Ly1, Jesse R. Poganik2, Saba Parvez3, Marcus J. C. Long4, Yimon Aye1 1Swiss Federal Institute of Technology Lausanne (EPFL), 2Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, 3Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, 4University of Lausanne (UNIL) Zebrafish targeting reactive electrophiles and oxidants (Z-REX) is a chemical biology-based method for the investigation of reactive small-molecule signaling. This technique can be applied to live fish of different developmental stages. Here, we couple standard assays in zebrafish with Z-REX for signaling pathway analysis. Biology Two-Step Tag-Free Isolation of Mitochondria for Improved Protein Discovery and Quantification Joan Blanco-Fernandez1, Alexis A. Jourdain1 1Department of Immunobiology, University of Lausanne We present a two-step protocol for high-quality mitochondria isolation that is compatible with protein discovery and quantification at a proteome scale. Our protocol does not require genetic engineering and is thus suitable for studying mitochondria from any primary cells and tissues. Biology Array Tomography Workflow for the Targeted Acquisition of Volume Information using Scanning Electron Microscopy Tilman Franke1, Irina Kolotuev2 1Thermo Fisher, 2Universite de Lausanne We describe the preparation of ribbons of serial sections and their collection on large transfer support for use as Array Tomography samples, along with automated imaging procedures in a scanning electron microscope. The protocol allows screening, retrieval, and targeted imaging of local, rare events, and the acquisition of large data volumes. Environment Combining Fluidic Devices with Microscopy and Flow Cytometry to Study Microbial Transport in Porous Media Across Spatial Scales David Scheidweiler1,2, Pietro De Anna2, Tom J. Battin1, Hannes Peter1 1Stream Biofilm and Ecosystem Research Laboratory, École Polytechnique Fédérale de Lausanne, 2Institute of Earth Sciences, University of Lausanne, CH-1015 Breakthrough curves (BTCs) are efficient tools to study the transport of bacteria in porous media. Here we introduce tools based on fluidic devices in combination with microscopy and flow cytometric counting to obtain BTCs. Neuroscience Morphological and Functional Evaluation of Axons and their Synapses during Axon Death in Drosophila melanogaster Maria Paglione*1, Arnau Llobet Rosell*1, Jean-Yves Chatton1, Lukas J. Neukomm1 1Department of Fundamental Neurosciences, University of Lausanne Here, we provide protocols to perform three simple injury-induced axon degeneration (axon death) assays in Drosophila melanogaster to evaluate the morphological and functional preservation of severed axons and their synapses. Biology Measurement of Mitochondrial Mass and Membrane Potential in Hematopoietic Stem Cells and T-cells by Flow Cytometry Mukul Girotra*1,2, Anne-Christine Thierry3, Alexandre Harari1,3, George Coukos1, Olaia Naveiras2,4, Nicola Vannini*1 1Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, 2Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), 3Center of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois, 4Hematology Service, Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV) Here we describe a reliable method to measure mitochondrial mass and membrane potential in ex vivo cultured hematopoietic stem cells and T cells. Genetics Detection of Human Immunodeficiency Virus Type 1 (HIV-1) Antisense Protein (ASP) RNA Transcripts in Patients by Strand-Specific RT-PCR Antonio Mancarella1, Francesco A. Procopio1, Tilmann Achsel2, Elisa De Crignis3, Brian T. Foley4, Giampietro Corradin5, Claudia Bagni2, Giuseppe Pantaleo1, Cecilia Graziosi1 1Division of Immunology and Allergy, Lausanne University Hospital, 2Department of Fundamental Neuroscience, University of Lausanne, 3Department of Biochemistry, Erasmus Medical Center, 4Theoretical Biology and Biophysics Group, Los Alamos National Laboratories, 5Department of Biochemistry, University of Lausanne RNA hairpins and loops can function as primers for reverse transcription (RT) in absence of sequence-specific primers, interfering with the study of overlapping antisense transcripts. We have developed a technique able to identify strand-specific RNA, and we have used it to study HIV-1 antisense protein ASP. Medicine Murine Myocardial Infarction Model using Permanent Ligation of Left Anterior Descending Coronary Artery Jérôme Lugrin1,2, Roumen Parapanov1,2, Thorsten Krueger2, Lucas Liaudet1 1Service of Adult Intensive Care Medicine, Department of Interdisciplinary Centers and Logistics, Lausanne University Hospital and Faculty of Biology and Medicine, Lausanne University, 2Service of Thoracic Surgery, Department of Surgery and Anesthesiology Services, Lausanne University Hospital and Faculty of Biology and Medicine, Lausanne University Herein we describe a surgical procedure showing how to achieve permanent ligation of the left-anterior descending coronary artery in mice. This model is of high relevance to investigate the pathophysiology of myocardial infarction and the concomitant biological processes. Behavior Supramaximal Intensity Hypoxic Exercise and Vascular Function Assessment in Mice Jessica Lavier1,2, Manon Beaumann3, Steeve Ménetrey3, Lucia Mazzolai1, Anne-Christine Peyter3, Maxime Pellegrin1, Grégoire P. Millet2 1Division of Angiology, Heart and Vessel Department, Lausanne University Hospital (CHUV), 2Institute of Sport Sciences, Faculty of Biology and Medicine, University of Lausanne, 3Neonatal Research Laboratory, Clinic of Neonatology, Department Woman-Mother-Child, Lausanne University Hospital High-intensity training in hypoxia is a protocol that has been proven to induce vascular adaptations potentially beneficial in some patients and to improve athletes' repeated sprint ability. Here, we test the feasibility of training mice using that protocol and identify those vascular adaptations using ex vivo vascular function assessment. Environment Combined Size and Density Fractionation of Soils for Investigations of Organo-Mineral Interactions Fanny Viret1, Stephanie Grand1 1Faculty of Geosciences and Environment, University of Lausanne Combined size and density fractionation (CSDF) is a method to physically separate soil into fractions differing in texture (particle size) and mineralogy (density). The purpose is to isolate fractions with different reactivities towards soil organic matter (SOM), in order to better understand organo-mineral interactions and SOM dynamics. Biochemistry In Vitro Polymerization of F-actin on Early Endosomes Olivia Muriel1,2, Cameron Christopher Scott1, Jorge Larios1, Vicent Mercier1, Jean Gruenberg1 1Department of Biochemistry, University of Geneva, 2Department of Fundamental Microbiology, University of Lausanne Early endosome functions depend on F-actin polymerization. Here, we describe a microscopy-based in vitro assay that reconstitutes the nucleation and polymerization of F-actin on early endosomal membranes in test tubes, thus rendering this complex series of reactions amenable to biochemical and genetic manipulations. Neuroscience Quantifying Infra-slow Dynamics of Spectral Power and Heart Rate in Sleeping Mice Laura M. J. Fernandez1, Sandro Lecci1, Romain Cardis1, Gil Vantomme1, Elidie Béard1, Anita Lüthi1 1Department of Fundamental Neurosciences, University of Lausanne Here, we present experimental and analytical procedures to describe the temporal dynamics of the neural and cardiac variables of non-REM sleep in mice, which modulate sleep responsiveness to acoustic stimuli. Immunology and Infection Using X-ray Crystallography, Biophysics, and Functional Assays to Determine the Mechanisms Governing T-cell Receptor Recognition of Cancer Antigens Bruce J. MacLachlan*1, Alexander Greenshields-Watson*1, Georgina H Mason*1, Andrea J Schauenburg1, Valentina Bianchi1,2,3, Pierre J Rizkallah1, Andrew K Sewell1, Anna Fuller1, David K Cole1 1Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University, 2Department of Oncology, University Hospital of Lausanne (CHUV), 3Ludwig Insitutue for Cancer Research, Lausanne Branch, University of Lausanne Here, we describe methods that we commonly employ in the laboratory to determine how the nature of the interaction between the T-cell receptor and tumor antigens, presented by human leukocyte antigens, governs T-cell functionality; these methods include protein production, X-ray crystallography, biophysics, and functional T-cell experiments. Engineering A System to Create Stable Nanoparticle Aerosols from Nanopowders Yaobo Ding1, Michael Riediker1,2 1Institute for Work and Health (IST), Universities of Lausanne and Geneva, 2IOM Singapore We designed and developed an effective nanopowder aerosolization setup and operating protocol. The system generated nanoparticle aerosols with stable number concentrations and size distributions for long durations, requiring only small quantities of test material (min. 200 mg). Biology Microscopy of Fission Yeast Sexual Lifecycle Aleksandar Vjestica*1, Laura Merlini*1, Omaya Dudin*1, Felipe O. Bendezu1, Sophie G. Martin1 1Department of Fundamental Microbiology, University of Lausanne We provide a reproducible basic method for the long-term microscopy of the fission yeast sexual lifecycle. With minor adjustments described, the presented protocol allows research focus on different steps of the reproductive process. Immunology and Infection Preparation of a Blood Culture Pellet for Rapid Bacterial Identification and Antibiotic Susceptibility Testing Antony Croxatto1, Guy Prod'hom1, Christian Durussel1, Gilbert Greub1 1Institute of Microbiology, University Hospital Center and University of Lausanne A rapid bacterial pellet preparation from a positive blood culture can be used as a sample for applications such as identification by MALDI-TOF, Gram staining, antibiotic susceptibility testing and PCR-based test. The results can be rapidly communicated to clinicians to improve the outcome of patients suffering from bloodstream infections. Biology Temporal Quantification of MAPK Induced Expression in Single Yeast Cells Serge Pelet1, Delphine Aymoz1, Eric Durandau1 1Department of Fundamental Microbiology, University of Lausanne Two complementary methods based on flow cytometry and microscopy are presented which enable the quantification, at the single cell level, of the dynamics of gene expression induced by the activation of a MAPK pathway in yeast. Neuroscience Calcium Imaging of Odor-evoked Responses in the Drosophila Antennal Lobe Ana F. Silbering1, Rati Bell1, C. Giovanni Galizia2, Richard Benton1 1Center for Integrative Genomics, University of Lausanne, 2Department of Biology, University of Konstanz We describe an established technique to measure and analyze odor-evoked calcium responses in the antennal lobe of living Drosophila melanogaster. Medicine How to Measure Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute Local Gyrification Index Marie Schaer1, Meritxell Bach Cuadra2,3, Nick Schmansky4, Bruce Fischl4, Jean-Philippe Thiran2, Stephan Eliez1 1Department of Psychiatry, University of Geneva School of Medicine, 2Signal Processing Laboratory, École Polytechnique Fédérale de Lausanne, 3Department of Radiology, University Hospital Center and University of Lausanne, 4Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital Measuring gyrification (cortical folding) at any age represents a window into early brain development. Hence, we previously developed an algorithm to measure local gyrification at thousands of points over the hemisphere1. In this paper, we detail the computation of this local gyrification index. Neuroscience Imaging Pheromone Sensing in a Mouse Vomeronasal Acute Tissue Slice Preparation Julien Brechbühl1, Gaëlle Luyet1, Fabian Moine1, Ivan Rodriguez2, Marie-Christine Broillet1 1Department of Pharmacology and Toxicology, University of Lausanne, 2Department of Genetics and Evolution, University of Geneva In mice, the ability to detect pheromones is principally mediated by the vomeronasal organ (VNO). Here, an acute tissue slice preparation of VNO for performing calcium imaging is described. This physiological approach allows observations of subpopulations and/or individual neurons in a living tissue and is convenient for receptor-ligand identification.