Ecole Polytechnique Federale de Lausanne (EPFL) 16 articles published in JoVE Bioengineering A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression Ardjan J. van der Linden1, Maaruthy Yelleswarapu2, Pascal A. Pieters1, Zoe Swank3, Wilhelm T. S. Huck2, Sebastian J. Maerkl3, Tom F. A. de Greef1,2 1Institute for Complex Molecular Systems, Department of Biomedical Engineering, Computational Biology Group, Eindhoven University of Technology, 2Institute for Molecules and Materials, Radboud University, 3Institute of Bioengineering, School of Engineering École Polytechnique Fédérale de Lausanne (EPFL) The fabrication process of a PDMS-based, multilayer, microfluidic device that allows in vitro transcription and translation (IVTT) reactions to be performed over prolonged periods is described. Furthermore, a comprehensive overview of the hardware and software required to automate and maintain these reactions for prolonged durations is provided. Environment Automated 3D Optical Coherence Tomography to Elucidate Biofilm Morphogenesis Over Large Spatial Scales Anna Depetris1, Antoine Wiedmer2, Michael Wagner3, Sebastian Schäfer4, Tom J. Battin1, Hannes Peter1 1Stream Biofilm and Ecosystem Research Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, 2Plateforme technique, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, 3Water Chemistry and Water Technology, Engler-Bunte-Institut, Karlsruhe Institute of Technology, 4Thorlabs GmbH Microbial biofilms form complex architectures at interphases and develop into highly scale-dependent spatial patterns. Here, we introduce an experimental system (hard- and software) for the automated acquisition of 3D optical coherence tomography (OCT) datasets. This toolset allows the non-invasive and multi-scale characterization of biofilm morphogenesis in space and time. Chemistry Synthesis and Characterization of Amphiphilic Gold Nanoparticles Zekiye P. Guven*1, Paulo H. Jacob Silva*1, Zhi Luo1, Urszula B. Cendrowska1, Matteo Gasbarri1, Samuel T. Jones1,2, Francesco Stellacci1,3 1Institute of Materials, École Polytechnique Fédérale de Lausanne, 2School of Materials, University of Manchester, 3Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne Amphiphilic gold nanoparticles can be used in many biological applications. A protocol to synthesize gold nanoparticles coated by a binary mixture of ligands and a detailed characterization of these particles is presented. Chemistry A Continuous-flow Photocatalytic Reactor for the Precisely Controlled Deposition of Metallic Nanoparticles Sina Abdolhosseinzadeh1,2, Mirsajjad Mousavi3, Navid Haghmoradi3, Selmiye Alkan Gürsel3,4 1Institut des matériaux, École Polytechnique Fédérale de Lausanne (EPFL), 2Laboratory for Functional Polymers, Swiss Federal Laboratories for Materials Science and Technology (Empa), 3Faculty of Engineering and Natural Sciences, Sabanci University, 4SUNUM Nanotechnology Research Centre, Sabanci University For a continuous and scalable synthesis of noble-metal-based nanocomposites, a novel photocatalytic reactor is developed and its structure, operation principles, and product quality optimization strategies are described. Neuroscience Dynamic Inter-subject Functional Connectivity Reveals Moment-to-Moment Brain Network Configurations Driven by Continuous or Communication Paradigms Thomas A.W. Bolton1,2, Delphine Jochaut3, Anne-Lise Giraud3, Dimitri Van De Ville1,2 1Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 2Department of Radiology and Medical Informatics, University of Geneva, 3Department of Neuroscience, University of Geneva The goal of the described approach is to determine at what moments of the paradigm (temporal perspective), and between which regions (spatial perspective), significant reconfigurations in functional connectivity occur on functional magnetic resonance imaging recordings during which a time-locked stimulus is played. Chemistry Electrophoretic Crystallization of Ultrathin High-performance Metal-organic Framework Membranes Guangwei He1, Deepu J. Babu1, Kumar Varoon Agrawal1 1Laboratory of Advanced Separations (LAS), École Polytechnique Fédérale de Lausanne (EPFL) A simple, reproducible, and versatile approach for the synthesis of intergrown, polycrystalline metal-organic framework membranes on a wide range of unmodified porous and non-porous supports is presented. Biochemistry Generation of Native, Untagged Huntingtin Exon1 Monomer and Fibrils Using a SUMO Fusion Strategy Andreas Reif1, Anass Chiki1, Jonathan Ricci1, Hilal A. Lashuel1 1Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne (EPFL) Here, we present a robust and optimized protocol for the production of milligram quantities of native, tag-free monomers and fibrils of the exon1 of the Huntingtin protein (Httex1) based on the transient fusion of small ubiquitin related modifier (SUMO). Medicine Improvement of a Closed Chest Porcine Myocardial Infarction Model by Standardization of Tissue and Blood Sampling Procedures Mai M. Abdelhafez1,2, Jane Shaw1, Jonas Wilbs3, Alain Despont1, Robert Rieben1 1Department for Biomedical Research, University of Bern, 2Graduate School for Cellular and Biomedical Sciences, University of Bern, 3Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) Here we demonstrate a protocol to standardize sampling procedures of an established porcine model of acute myocardial infarction in order to increase its translational value in the understanding of the pathophysiology of myocardial ischemia/reperfusion injury and to test novel drug candidates. Developmental Biology Single-Cell Quantification of Protein Degradation Rates by Time-Lapse Fluorescence Microscopy in Adherent Cell Culture Andrea Brigitta Alber1, David Michael Suter1 1UPSUTER, Institute of Bioengineering (IBI), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) This protocol describes a method to determine protein half-lives in single living adherent cells, using pulse labeling and fluorescence time-lapse imaging of SNAP-tag fusion proteins. Chemistry A Practical Guide on Coupling a Scanning Mobility Sizer and Inductively Coupled Plasma Mass Spectrometer (SMPS-ICPMS) Mohamed Tarik1, Debora Foppiano1,2, Adrian Hess1,3, Christian Ludwig1,2 1Bioenergy and Catalysis Laboratory (LBK), Energy and Environment Research Division (ENE), Paul Scherrer Institute, 2Environmental Engineering Institute (IIE), School of Architecture, Civil and Environmental Engineering (ENAC), École; Polytechnique Fédérale de Lausanne (EPFL), 3Institute for Atmospheric and Climate Science ETH Zurich In this work a practical guide is provided, describing the different steps to establish the coupling of SMPS and ICPMS systems, and how to use them. Three descriptive examples are presented. Chemistry Preparation of Carbon Nanosheets at Room Temperature Stephen Schrettl1, Bjoern Schulte1, Cristina Stefaniu2, Joana Oliveira2, Gerald Brezesinski2, Holger Frauenrath1 1Institute of Materials, Ecole Polytechnique Fédérale de Lausanne (EPFL), 2Colloid Chemistry Department, Max Planck Institute of Colloids and Interfaces We present the synthesis of an amphiphilic hexayne and its use in the preparation of carbon nanosheets at the air-water interface from a self-assembled monolayer of these reactive, carbon-rich molecular precursors. Chemistry Dissolution Dynamic Nuclear Polarization Instrumentation for Real-time Enzymatic Reaction Rate Measurements by NMR Riccardo Balzan1, Laetitia Fernandes1, Arnaud Comment2, Laetitia Pidial3, Bertrand Tavitian3, Paul R. Vasos1 1LCBPT - UMR8601, Institut de Chimie, Université Paris Descartes, 2Institute of Physics of Biological Systems, EPFL, 3PARCC - INSERM U970, Université Paris Descartes The sensitivity enhancement provided by dissolution dynamic nuclear polarization (DNP) enables following metabolic processes in real time by NMR and MRI. The characteristics and performances of a dedicated dissolution DNP setup designed for study enzymatic reactions are discussed. Engineering Fabrication Process of Silicone-based Dielectric Elastomer Actuators Samuel Rosset1, Oluwaseun A. Araromi1, Samuel Schlatter1, Herbert R. Shea1 1Microsystems for Space Technologies Laboratory, Ecole Polytechnique Fédérale de Lausanne This manuscript shows the fabrication process for the manufacture of dielectric elastomer soft actuators based on silicone membranes. The three key stages of production are presented in detail: blade casting of thin silicone membranes; pad printing of compliant electrodes; and the assembly of all the components. Neuroscience Dorsal Root Ganglia Neurons and Differentiated Adipose-derived Stem Cells: An In Vitro Co-culture Model to Study Peripheral Nerve Regeneration Alba C. de Luca1, Alessandro Faroni2, Adam J. Reid2,3 1Centre for Neuroprosthesis, EPFL | STI | IMT/IBI | LSBI, 2Blond McIndoe Research Laboratories, Institute of Inflammation & Repair, The University of Manchester, 3University Hospital of South Manchester Dorsal root ganglia (DRG) are structures containing the sensory neurons of the peripheral nervous system. When dissociated, they can be co-cultured with SC-like adipose-derived stem cells (ASC), providing a valuable model to study in vitro nerve regeneration and myelination, mimicking the in vivo environment at the injury site. Medicine An Ex vivo Model to Study Hormone Action in the Human Breast George Sflomos1, Marie Shamseddin1, Cathrin Brisken1 1Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole polytechnique fédérale de Lausanne We have developed a novel ex vivo model to study hormone action in the human breast. It is based on tissue microstructures isolated from surgical breast tissue specimens which preserve tissue architecture, intercellular interactions, and paracrine signaling. Neuroscience A Computer-assisted Multi-electrode Patch-clamp System Rodrigo Perin1, Henry Markram1 1Laboratory of Neural Microcircuitry - Brain Mind Institute, Ecole Polytechnique Federale de Lausanne Multi-electrode patch-clamp recordings constitute a complex task. Here we show how, by automating of many of the experimental steps, it is possible to accelerate the process leading to qualitative improvement in performance and number of recordings.
