ETH Zurich 36 articles published in JoVE Bioengineering Engineering Tendon Assembloids to Probe Cellular Crosstalk in Disease and Repair Tino Stauber1,2, Maja Wolleb1,2, Jess G. Snedeker1,2 1Department of Orthopedics, Balgrist, University Hospital Zurich, University of Zurich, 2Department of Health Sciences and Technology, Institute for Biomechanics, ETH Zurich Here, we present an assembloid model system to mimic tendon cellular crosstalk between the load-bearing tendon core tissue and an extrinsic compartment containing cell populations activated by disease and injury. As an important use case, we demonstrate how the system can be deployed to probe disease-relevant activation of extrinsic endothelial cells. Environment A Microfluidic Platform to Study Bioclogging in Porous Media Dorothee L. Kurz1,2, Eleonora Secchi1, Roman Stocker1, Joaquin Jimenez-Martinez1,2 1Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, 2Department Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology The present protocol describes a microfluidic platform to study biofilm development in quasi-2D porous media by combining high-resolution microscopy imaging with simultaneous pressure difference measurements. The platform quantifies the influence of pore size and fluid flow rates in porous media on bioclogging. Bioengineering Experimental and Data Analysis Workflow for Soft Matter Nanoindentation Giuseppe Ciccone1, Mariana Azevedo Gonzalez Oliva1, Nelda Antonovaite2, Ines Lüchtefeld3, Manuel Salmeron-Sanchez1, Massimo Vassalli1 1Centre for the Cellular Microenvironment, James Watt School of Engineering, University of Glasgow, 2Optics 11 life, 3Laboratory of Biosensors and Bioelectronics, ETH Zürich The protocol presents a complete workflow for soft material nanoindentation experiments, including hydrogels and cells. First, the experimental steps to acquire force spectroscopy data are detailed; then, the analysis of such data is detailed through a newly developed open-source Python software, which is free to download from GitHub. Engineering Patterning of Microorganisms and Microparticles through Sequential Capillarity-assisted Assembly Roberto Pioli1, Roman Stocker1, Lucio Isa2, Eleonora Secchi1 1Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 2Department of Materials, ETH Zurich We present a technology that uses capillarity-assisted assembly in a microfluidic platform to pattern micro-sized objects suspended in a liquid, such as bacteria and colloids, into prescribed arrays on a polydimethylsiloxane substrate. Biochemistry Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports Hamed Khakzad1,2, Swen Vermeul3, Lars Malmström4,5,6 1Equipe Signalisation Calcique et Infections Microbiennes, Ecole Normale Supérieure Paris-Saclay, 2Institut National de la Santé et de la Recherche Médicale, 3Scientific IT Services, ETH Zurich, 4Institute for Computational Science, University of Zurich, 5S3IT, University of Zurich, 6Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University Targeted cross-linking mass spectrometry creates quaternary protein structure models using mass spectrometry data acquired using up to three different acquisition protocols. When executed as a simplified workflow on the Cheetah-MS web server, the results are reported in a Jupyter Notebook. Here, we demonstrate the technical aspects of how the Jupyter Notebook can be extended for a more in-depth analysis. Developmental Biology Application of Mouse Parthenogenetic Haploid Embryonic Stem Cells as a Substitute of Sperm Eishi Aizawa1, Charles-Etienne Dumeau1, Anton Wutz1 1Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich This article aims to demonstrate the use of parthenogenetic haploid embryonic stem cells as a substitute for sperm for the construction of semi-cloned embryos. Environment In Situ Chemotaxis Assay to Examine Microbial Behavior in Aquatic Ecosystems Estelle E. Clerc1, Jean-Baptiste Raina2, Bennett S. Lambert3, Justin Seymour2, Roman Stocker1 1Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 2Climate Change Cluster, University of Technology Sydney, 3School of Oceanography, University of Washington Presented here is the protocol for an in situ chemotaxis assay, a recently developed microfluidic device that enables studies of microbial behavior directly in the environment. Biochemistry Strategic Screening and Characterization of the Visual GPCR-mini-G Protein Signaling Complex for Successful Crystallization Filip Pamula1,2, Jonas Mühle1, Alain Blanc3, Rony Nehmé4, Patricia C. Edwards4, Christopher G. Tate4, Ching-Ju Tsai1 1Laboratory of Biomolecular Research, Paul Scherrer Institute, 2Department of Biology, ETH Zürich, 3Center for Radiopharmaceutical Sciences, Paul Scherrer Institute, 4Laboratory of Molecular Biology, Medical Research Council This report describes screening of different detergents for preparing the visual GPCR, rhodopsin, and its complex with mini-Go. Biochemical methods characterizing the quality of the complex at different stages during purification are demonstrated. This protocol can be generalized to other membrane protein complexes for their future structural studies. Engineering Fabrication and Design of Wood-Based High-Performance Composites Marion Frey1,2, Meri Zirkelbach3, Clemens Dransfeld4, Eric Faude1, Etienne Trachsel1, Mikael Hannus5, Ingo Burgert1,2, Tobias Keplinger1,2 1Wood Materials Science, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 2Cellulose & Wood Materials, Functional Materials, EMPA, 3Design and Arts, Lucerne University of Applied Sciences and Arts, 4Aerospace Manufacturing Technologies, Aerospace Engineering, Delft University of Technology, 5Stora Enso Oyj Delignified densified wood represents a new promising lightweight, high-performance and bio-based material with great potential to partially substitute natural fiber reinforced- or glass fiber reinforced composites in the future. We here present two versatile fabrication routes and demonstrate the possibility to create complex composite parts. Chemistry Improving High Viscosity Extrusion of Microcrystals for Time-resolved Serial Femtosecond Crystallography at X-ray Lasers Daniel James1, Tobias Weinert1, Petr Skopintsev1, Antonia Furrer1, Dardan Gashi1,2, Tomoyuki Tanaka3,4, Eriko Nango3,4, Przemyslaw Nogly1,5, Joerg Standfuss1 1Division of Biology and Chemistry - Laboratory for Biomolecular Research, Paul Scherrer Institut, 2Photon Science Division - SwissFEL, Paul Scherrer Institut, 3RIKEN SPring-8 Center, 4Department of Cell Biology, Graduate School of Medicine, Kyoto University, 5Department of Biology, ETH Zürich The success of a time-resolved serial femtosecond crystallography experiment is dependent on efficient sample delivery. Here, we describe protocols to optimize the extrusion of bacteriorhodopsin microcrystals from a high viscosity micro-extrusion injector. The methodology relies on sample homogenization with a novel three-way coupler and visualization with a high-speed camera. Behavior Virtual Reality Experiments with Physiological Measures Raphael P. Weibel1, Jascha Grübel1, Hantao Zhao1, Tyler Thrash1,2,3, Dario Meloni1, Christoph Hölscher1, Victor R. Schinazi1 1Chair of Cognitive Science, ETH Zürich, 2Geographic Information Visualization and Analysis, University of Zürich, 3Digital Society Initiative, University of Zürich Virtual reality (VR) experiments can be difficult to implement and require meticulous planning. This protocol describes a method for the design and implementation of VR experiments that collect physiological data from human participants. The Experiments in Virtual Environments (EVE) framework is employed to accelerate this process. Behavior A Networked Desktop Virtual Reality Setup for Decision Science and Navigation Experiments with Multiple Participants Hantao Zhao1, Tyler Thrash1,2,3, Stefan Wehrli4, Christoph Hölscher1, Mubbasir Kapadia5, Jascha Grübel1, Raphael P. Weibel1, Victor R. Schinazi1 1Chair of Cognitive Science, ETH Zürich, 2Digital Society Initiative, University of Zürich, 3Department of Geography, University of Zürich, 4Decision Science Laboratory, ETH Zürich, 5Computer Science Department, Rutgers University This paper describes a method for conducting multi-user experiments on decision-making and navigation using a networked computer laboratory. Neuroscience Adeno-associated Virus-mediated Transgene Expression in Genetically Defined Neurons of the Spinal Cord Karen Haenraets*1,2, Gioele W. Albisetti*1, Edmund Foster1, Hendrik Wildner1 1Institute of Pharmacology and Toxicology, University of Zurich, 2Institute of Pharmaceutical Sciences, Swiss Federal Institute (ETH) Zurich Intraspinal injection of recombinase dependent recombinant adeno-associated virus (rAAV) can be used to manipulate any genetically labelled cell type in the spinal cord. Here we describe how to transduce neurons in the dorsal horn of the lumbar spinal cord. This technique enables functional interrogation of the manipulated neuron subtype. Biology Cystometric and External Urethral Sphincter Measurements in Awake Rats with Implanted Catheter and Electrodes Allowing for Repeated Measurements Elena E. Foditsch1,2, Karin Roider1,2, Andrea M. Sartori3,4,5, Thomas M. Kessler5, Sabik Raj Kayastha6, Ludwig Aigner2, Marc P. Schneider7 1Department of Urology, Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, 2Institute of Molecular Regenerative Medicine, Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, 3Brain Research Institute, University of Zürich, 4Department of Health Sciences and Technology, Swiss Federal Institute of Technology Zürich, 5Neuro-Urology, Spinal Cord Injury Center & Research, University of Zürich, Balgrist University Hospital, 6Department of Orthopaedics and Traumatology, Dhulikhel Hospital, Kathmandu University Hospital, 7Department of Urology, Inselspital, Bern University Hospital This protocol first describes the surgical procedure of the permanent implantation of a urinary bladder catheter combined with external urethral sphincter electrodes, and second, the measurement of the function of the urinary bladder and external urethral sphincter in implanted awake animals. Engineering Fabrication Procedures and Birefringence Measurements for Designing Magnetically Responsive Lanthanide Ion Chelating Phospholipid Assemblies Stéphane Isabettini1, Mirjam E. Baumgartner1, Peter Fischer1, Erich J. Windhab1, Marianne Liebi2, Simon Kuster1 1Laboratory of Food Process Engineering, ETH Zurich, 2MAX IV Laboratory, Lund University Fabrication procedures for highly magnetically responsive lanthanide ion chelating polymolecular assemblies are presented. The magnetic response is dictated by the assembly size, which is tailored by extrusion through nanopore membranes. The assemblies' magnetic alignability and temperature-induced structural changes are monitored by birefringence measurements, a complimentary technique to nuclear magnetic resonance and small angle neutron scattering. Neuroscience Live Imaging Followed by Single Cell Tracking to Monitor Cell Biology and the Lineage Progression of Multiple Neural Populations Rosa Gómez-Villafuertes*1,2,3, Lucía Paniagua-Herranz*1,2,3, Sergio Gascon*4,5, David de Agustín-Durán1,2,3, María de la O Ferreras1,2,3, Juan Carlos Gil-Redondo1,2,3, María José Queipo1,2,3, Aida Menendez-Mendez1,2,3, Ráquel Pérez-Sen1,2,3, Esmerilda G. Delicado1,2,3, Javier Gualix1,2,3, Marcos R. Costa6, Timm Schroeder7, María Teresa Miras-Portugal1,2,3, Felipe Ortega1,2,3 1Biochemistry and Molecular Biology Department, Faculty of Veterinary medicine, Complutense University, 2University Institute for Neurochemistry Research (IUIN), 3Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 4Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg/Munich, Germany Physiological Genomics, Biomedical Center, Ludwig-Maximilians University Munich, 5Toxicology and Pharmacology Department, Faculty of Veterinary medicine, Complutense University, 6Brain Institute, Federal University of Rio Grande do Norte, 7Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich A robust protocol to monitor neural populations by time-lapse video-microscopy followed by software-based post-processing is described. This method represents a powerful tool to identify biological events in a selected population during live imaging experiments. Medicine An Optimized Hemagglutination Inhibition (HI) Assay to Quantify Influenza-specific Antibody Titers Lukas Kaufmann*1, Mohammedyaseen Syedbasha*1, Dominik Vogt1, Yvonne Hollenstein1, Julia Hartmann1, Janina E. Linnik1,2,3, Adrian Egli1,4 1Applied Microbiology Research, Department of Biomedicine, University of Basel, 2Department of Biosystems Science and Engineering, ETH Zurich, 3Swiss Institute of Bioinformatics, 4Clinical Microbiology, University Hospital Basel The presented protocols describe how to perform a hemagglutination inhibition assay to quantify influenza-specific antibody titers from serum samples of influenza vaccine recipients. The first assay determines optimal viral antigen concentrations by hemagglutination. The second assay quantifies influenza-specific antibody titers by hemagglutination inhibition. Medicine Echocardiographic and Histological Examination of Cardiac Morphology in the Mouse Delphine Baudouy1, Jean-François Michiels1,2, Ana Vukolic3, Kay-Dietrich Wagner1, Nicole Wagner1 1Université Côte d’Azur, CNRS, INSERM, iBV, 2Department of Pathology, CHU Nice, 3Institute for Molecular Health Sciences, ETH Zurich Echocardiographic examination is frequently used in mice. Expensive high-resolution ultrasound devices have been developed for this purpose. This protocol describes an affordable echocardiographic procedure combined with histological morphometric analyses to determine cardiac morphology. Bioengineering Dry Film Photoresist-based Electrochemical Microfluidic Biosensor Platform: Device Fabrication, On-chip Assay Preparation, and System Operation Richard Bruch*1, André Kling*1,3, Gerald A. Urban1,2, Can Dincer1,2 1Department of Microsystems Engineering, University of Freiburg, 2Freiburg Materials Research Center, University of Freiburg, 3Department of Biosystems Science and Engineering, ETH Zurich A microfluidic biosensor platform was designed and fabricated using low-cost dry film photoresist technology for the rapid and sensitive quantification of various analytes. This single-use system allows for the electrochemical readout of on-chip-immobilized enzyme-linked assays by means of the stop-flow technique. Engineering Experimental Protocol to Determine the Chloride Threshold Value for Corrosion in Samples Taken from Reinforced Concrete Structures Ueli M. Angst1, Carolina Boschmann1, Matthias Wagner2, Bernhard Elsener1,3 1Institute for Building Materials, ETH Zurich, 2Tecnotest AG, 3Department of Chemical and Geological Science, University of Cagliari We propose a method to measure a parameter that is highly relevant for corrosion assessments or predictions of reinforced concrete structures, with the main advantage of permitting testing of samples from engineering structures. This ensures real conditions at the steel-concrete interface, which are crucial to avoid artifacts of laboratory-made samples. Neuroscience Live Imaging of Primary Cerebral Cortex Cells Using a 2D Culture System Bruna Soares Landeira1, Jéssica Alves de Medeiros Araújo1, Timm Schroeder2, Ulrich Müller3, Marcos R. Costa1 1Brain Institute, Federal University of Rio Grande do Norte, 2Department of Biosystems Science and Engineering, ETH Zurich, 3The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University Live imaging is a powerful tool to study cellular behaviors in real time. Here, we describe a protocol for time-lapse video-microscopy of primary cerebral cortex cells that allows a detailed examination of the phases enacted during the lineage progression from primary neural stem cells to differentiated neurons and glia. Chemistry Microfluidic-based Synthesis of Covalent Organic Frameworks (COFs): A Tool for Continuous Production of COF Fibers and Direct Printing on a Surface Afshin Abrishamkar1, David Rodríguez-San-Miguel2, Jorge Andrés Rodríguez Navarro3, Romen Rodriguez-Trujillo4, David B. Amabilino5, Ruben Mas-Ballesté2, Félix Zamora2,6,7, Andrew J. deMello1, Josep Puigmarti-Luis1 1Institute of Chemical and Bioengineering, Department of Chemistry and Applied Bioscience, ETH Zurich, 2Departamento de Química Inorgánica, Universidad Autónoma de Madrid, 3Departamento de Química Inorgánica, Universidad de Granada, 4Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), 5School of Chemistry, University of Nottingham, 6Condensed Matter Physics Center (IFMAC), Universidad Autónoma de Madrid, 7Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) We present a novel microfluidic-based method for synthesis of covalent organic frameworks (COFs). We demonstrate how this approach can be used to produce continuous COF fibers, and also 2D or 3D COF structures on surfaces. Behavior Investigating Motor Skill Learning Processes with a Robotic Manipulandum Susan Leemburg1, Maiko Iijima1, Olivier Lambercy2, Lauriane Nallet-Khosrofian1, Roger Gassert2, Andreas Luft1 1Division of Vascular Neurology and Rehabilitation, Department of Neurology, University Hospital Zurich, 2Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich A paradigm is presented for training and analysis of an automated skilled reaching task in rats. Analysis of pulling attempts reveals distinct subprocesses of motor learning. Chemistry Microfluidic Pneumatic Cages: A Novel Approach for In-chip Crystal Trapping, Manipulation and Controlled Chemical Treatment Afshin Abrishamkar1,2, Markos Paradinas3, Elena Bailo4, Romen Rodriguez-Trujillo5, Raphael Pfattner5, René M. Rossi1, Carmen Ocal5, Andrew J. deMello2, David B. Amabilino6, Josep Puigmartí-Luis1 1Empa - Swiss Federal Laboratories for Materials Science and Technology, 2Institute of Chemical and Bioengineering, Department of Chemistry and Applied Bioscience, ETH Zurich, 3ICN2-Institut Catala de Nanociencia i Nanotecnologia, 4WITec GmbH, 5Institut de Ciència de Materials de Barcelona, 6School of Chemistry, The University of Nottingham Herein, we describe the fabrication and operation of a double-layer microfluidic system made of polydimethylsiloxane (PDMS). We demonstrate the potential of this device for trapping, directing the coordination pathway of a crystalline molecular material and controlling chemical reactions onto on-chip trapped structures. Chemistry Characterization, Quantification and Compound-specific Isotopic Analysis of Pyrogenic Carbon Using Benzene Polycarboxylic Acids (BPCA) Daniel B. Wiedemeier1, Susan Q. Lang2, Merle Gierga3, Samuel Abiven1, Stefano M. Bernasconi3, Gretchen L. Früh-Green3, Irka Hajdas4, Ulrich M. Hanke1, Michael D. Hilf1, Cameron P. McIntyre4, Maximilian P. W. Scheider1, Rienk H. Smittenberg5, Lukas Wacker4, Guido L. B. Wiesenberg1, Michael W. I. Schmidt1 1Department of Geography, University of Zurich, 2Department of Earth and Ocean Sciences, University of South Carolina, 3Department of Earth Sciences, ETH Zurich, 4Laboratory of Ion Beam Physics, ETH Zurich, 5Department of Geological Sciences, Stockholm University We present the benzene polycarboxylic acid (BPCA) method for assessing pyrogenic carbon (PyC) in the environment. The compound-specific approach uniquely provides simultaneous information about the characteristics, quantity and isotopic composition (13C and 14C) of PyC. Immunology and Infection In Vitro Disassembly of Influenza A Virus Capsids by Gradient Centrifugation Sarah Stauffer1,2, Firat Nebioglu3, Ari Helenius1 1Institute of Biochemistry, ETH Zurich, 2Department of Biochemistry, University of Zurich, 3Institute for Molecular Health Sciences, ETH Zurich Disassembly of influenza A virus cores during virus entry into host cells is a multistep process. We describe an in vitro method to analyze the early stages of viral uncoating. In this approach, velocity gradient centrifugation is used to biochemically dissect the steps that initiate uncoating under defined conditions. Environment A Simple Method for Automated Solid Phase Extraction of Water Samples for Immunological Analysis of Small Pollutants Sarah Heub1,2, Noe Tscharner1, Florian Kehl1,3, Petra S. Dittrich2, Stéphane Follonier1, Laurent Barbe1 1 A protocol for the extraction and pre-concentration of estradiol from water samples by using an automated and miniaturized system is presented. Bioengineering Easy and Accurate Mechano-profiling on Micropost Arrays Nils Goedecke1, Maja Bollhalder1, Remo Bernet1, Unai Silvan1, Jess Snedeker1,2 1University of Zurich, Balgrist University Hospital, 2Institute for Biomechanics, ETH Zurich Described are protocols for quantifying mechanical interactions between adherent cells and microstructured substrates. These interactions are closely linked to essential cell behaviors including migration, proliferation, differentiation, and apoptosis. The protocols present an open-source image analysis software called MechProfiler, which enables determination of involved forces for each micropost. Engineering Speciation and Bioavailability Measurements of Environmental Plutonium Using Diffusion in Thin Films Ruslan Cusnir1, Philipp Steinmann2, Marcus Christl3, François Bochud1, Pascal Froidevaux1 1Institute of Radiation Physics, Lausanne University Hospital, 2Federal Office of Public Health, Bern, Switzerland, 3Laboratory of Ion Beam Physics, ETH Zurich The technique of diffusive gradients in thin films (DGT) is proposed for speciation studies of plutonium. This protocol describes diffusion experiments probing the behavior of Pu(IV) and Pu(V) in presence of organic matter. DGTs deployed in a karstic spring allow assessment of the bioavailability of Pu. Behavior Acquisition of a High-precision Skilled Forelimb Reaching Task in Rats Ajmal Zemmar*1,2, Brigitte Kast*1,2, Karin Lussi1,2, Andreas R. Luft*3, Martin E. Schwab*1,2 1Brain Research Institute, University of Zurich, 2Department of Biology and Department of Health Sciences and Technology, ETH Zurich, 3Clinical Neurorehabilitation, Department of Neurology, University of Zurich & University Hospital Zurich A paradigm is presented to analyze the acquisition of a high-precision skilled forelimb reaching task in rats. Bioengineering A Microfluidic Chip for ICPMS Sample Introduction Pascal E. Verboket1, Olga Borovinskaya1, Nicole Meyer1, Detlef Günther1, Petra S. Dittrich1 1Department of Chemistry and Applied Biosciences, ETH Zurich We present a discrete droplet sample introduction system for inductively coupled plasma mass spectrometry (ICPMS). It is based on a cheap and disposable microfluidic chip that generates highly monodisperse droplets in a size range of 40−60 µm at frequencies from 90 to 7,000 Hz. Environment Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry Colin Ruprecht1, Takayuki Tohge1, Alisdair Fernie1, Cara L. Mortimer2, Amanda Kozlo2, Paul D. Fraser2, Norma Funke1, Igor Cesarino3,4, Ruben Vanholme3,4, Wout Boerjan3,4, Kris Morreel3,4, Ingo Burgert5,6, Notburga Gierlinger5,6, Vincent Bulone7, Vera Schneider8, Andrea Stockero8, Juan Navarro-Aviñó9, Frank Pudel10, Bart Tambuyser11, James Hygate12, Jon Bumstead13, Louis Notley13, Staffan Persson1,14 1Max Planck Institute for Molecular Plant Physiology, 2School of Biological Sciences, Plant Molecular Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, 3Department of Plant Systems Biology, VIB, 4Department of Plant Biotechnology and Bioinformatics, UGhent, 5Institute for Building Materials, ETH Zurich, 6Applied Wood Materials, EMPA, 7Division of Glycoscience, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), 8European Research and Project Office GmbH, 9ABBA Gaia S.L., 10Pflanzenöltechnologie, 11Capax Environmental Services, 12Green Fuels, 13Neutral Consulting Ltd, 14Plant Cell Biology Research Centre, School of Botany, University of Melbourne Plant biomass offers a renewable resource for multiple products, including fuel, feed, food, and a variety of materials. In this paper we investigate the properties of tobacco tree (Nicotiana glauca) and poplar as suitable sources for a biorefinery pipeline. Behavior Two-photon Calcium Imaging in Mice Navigating a Virtual Reality Environment Marcus Leinweber*1,2, Pawel Zmarz*1,2, Peter Buchmann3, Paul Argast1, Mark Hübener2, Tobias Bonhoeffer2, Georg B. Keller1,2 1Friedrich Miescher Institute for Biomedical Research, 2Max Planck Institute of Neurobiology, 3Department of Biosystems Science and Engineering, ETH Zurich Here we describe the experimental procedures involved in two-photon imaging of mouse cortex during behavior in a virtual reality environment. Bioengineering A Microfluidic Chip for the Versatile Chemical Analysis of Single Cells Klaus Eyer1, Phillip Kuhn1, Simone Stratz1, Petra S Dittrich1 1Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland In this article we present a microfluidic chip for single cell analysis. It allows the quantification of intracellular proteins, enzymes, cofactors, and second messengers by means of fluorescent assays or immunoassays. Immunology and Infection Imaging InlC Secretion to Investigate Cellular Infection by the Bacterial Pathogen Listeria monocytogenes Andreas Kühbacher1,2,3, Edith Gouin1,2,3, Jason Mercer4, Mario Emmenlauer5, Christoph Dehio5, Pascale Cossart1,2,3, Javier Pizarro-Cerdá1,2,3 1Unité des Interactions Bactéries Cellules, Pasteur Institute, 2INSERM U604, 3Institut National de la Recherche Agronomique (INRA), USC2020, 4Institute of Biochemistry, ETH Zürich, 5Focal Area Infection Biology, Biozentrum, University of Basel Listeria monocytogenes is a Gram positive bacterial pathogen frequently used as a major model for the study of intracellular parasitism. Imaging late L. monocytogenes infection stages within the context of small-interfering RNA screens allows for the global study of cellular pathways required for bacterial infection of target host cells. Bioengineering Continuous High-resolution Microscopic Observation of Replicative Aging in Budding Yeast Daphne H. E. W. Huberts1, Georges E. Janssens2, Sung Sik Lee3, Ima Avalos Vizcarra4, Matthias Heinemann1,5 1Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 2Department for the Biology of Ageing, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, 3Institute of Biochemistry, ETH Zurich, 4Department of Health Sciences and Technology, ETH Zurich, 5Institute of Molecular Systems Biology, ETH Zurich We describe here the operation of a microfluidic device that allows continuous and high-resolution microscopic imaging of single budding yeast cells during their complete replicative and/or chronological lifespan.
