University of Zurich View Institution's Website 46 articles published in JoVE Biology A Versatile Glass Jar System for Semihydroponic Root Exudate Profiling Sarah McLaughlin1, Charlotte Joller1,2, Alexandra Siffert1, Eva Marina Stirnemann1, Joelle Sasse1 1Institute of Plant and Microbial Biology, University of Zürich, 2Department of Environmental Sciences, University of Basel We present a protocol for a glass-based, semihydroponic experimental system supporting the growth of a variety of phylogenetically distinct plants with or without microbes. The system is compatible with different growth media and permits nondestructive root exudate sampling for downstream analysis. Biochemistry Measuring Caspase Activity Using a Fluorometric Assay or Flow Cytometry Jing Tong1, Stefanie Rufli1, Wendy Wei-Lynn Wong1 1Institute of Experimental Immunology, University of Zürich The present protocol describes two methods to measure caspase activity through a fluorogenic substrate using flow cytometry or a spectrofluorometer. Biology Live Imaging of Arabidopsis Pollen Tube Reception and Double Fertilization Using the Semi-In Vitro Cum Septum Method Nicholas J. Desnoyer1, Ueli Grossniklaus1 1Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich Here, we describe an improvement of the semi-in vitro (SIV) method for observing pollen tube guidance and reception in Arabidopsis thaliana, which increases the receptivity of ovules. The high-throughput SIV cum septum method may be coupled with gametophyte marker lines and genetically encoded biosensors to monitor the dynamic process of fertilization. Neuroscience Intracerebral Transplantation and In Vivo Bioluminescence Tracking of Human Neural Progenitor Cells in the Mouse Brain Rebecca Z. Weber1,2, Chantal Bodenmann1, Daniela Uhr1, Kathrin J. Zürcher1, Debora Wanner1, Melanie Generali1, Roger M. Nitsch1, Ruslan Rust*1,2, Christian Tackenberg*1,2 1Institute for Regenerative Medicine, University of Zurich, 2Neuroscience Center Zurich, University of Zurich and ETH Zurich We describe the intraparenchymal transplantation of human neural progenitor cells transduced with a dual reporter vector expressing luciferase-green fluorescent protein (GFP) in the mouse brain. After transplantation, the luciferase signal is repeatedly measured using in vivo bioluminescence and GFP-expressing grafted cells identified in brain sections using fluorescence microscopy. 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. Medicine A Reproducible Intensive Care Unit-Oriented Endotoxin Model in Rats Jan Heil1, Martin Schläpfer1,2 1Institute of Physiology, University of Zurich, 2Institute of Anesthesiology, University Hospital of Zurich Here, we present a reproducible intensive care unit-oriented endotoxin model in rats. Developmental Biology Translating Ribosome Affinity Purification (TRAP) to Investigate Arabidopsis thaliana Root Development at a Cell Type-Specific Scale Martha Thellmann1, Tonni Grube Andersen2, Joop EM Vermeer1,3 1Department of Plant and Microbial Biology, University of Zurich, 2Biophore - UNIL, 3Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel Translating ribosome affinity purification (TRAP) offers the possibility to dissect developmental programs with minimal processing of organs and tissues. The protocol yields high-quality RNA from cells targeted with a green fluorescent protein (GFP)-labeled ribosomal subunit. Downstream analysis tools, such as qRT-PCR or RNA-seq, reveal tissue and cell type-specific expression profiles. Immunology and Infection Infecting Mice with Malassezia spp. to Study the Fungus-Host Interaction Florian Sparber1, Salomé LeibundGut-Landmann1 1Section of Immunology, Vetsuisse Faculty, University of Zürich This protocol outlines the establishment of a mouse model for studying Malassezia-host interactions in the skin. It describes the cultivation of Malassezia in vitro, the infection of the murine skin with Malassezia, and the subsequent analysis of the inflammation and the fungal burden in the skin tissue. Neuroscience Delivery of Antibodies into the Murine Brain via Convection-enhanced Delivery Michal Beffinger1, Linda Schellhammer1, Stanislav Pantelyushin1, Johannes vom Berg1 1Institute of Laboratory Animal Science, University of Zurich Convection-enhanced delivery (CED) is a method enabling effective delivery of therapeutics into the brain by direct perfusion of large tissue volumes. The procedure requires the use of catheters and an optimized injection procedure. This protocol describes a methodology for CED of an antibody into a mouse brain. Biology Flow Cytometric Analysis of Extracellular Vesicles from Cell-conditioned Media Carolina Balbi*1, Sara Bolis*1, Giuseppe Vassalli1,2,3, Lucio Barile1 1Cellular and Molecular Cardiology Laboratory, Cardiocentro Ticino Foundation, Switzerland, 2Molecular Cardiology Institute, Dept. of Cardiology, University of Zürich, 3Faculty of Biomedical Science, Università Svizzera Italiana, Switzerland The protocol describes a reproducible method designed for use with cell culture supernatants to detect surface epitopes on small extracellular vesicles (EV). It utilizes specific EV immunoprecipitation using beads coupled with antibodies that recognize surface antigen CD9, CD63, and CD81. The method is optimized for downstream flow cytometry analysis. 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. Developmental Biology Whole-mount Clearing and Staining of Arabidopsis Flower Organs and Siliques Afif Hedhly1, Hannes Vogler1, Christof Eichenberger1, Ueli Grossniklaus1 1Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich In this protocol, we describe techniques for the proper dissection of Arabidopsis flowers and siliques, some basic clearing techniques, and selected staining procedures for whole-mount observations of reproductive structures. Medicine Technique and Patient Selection Criteria of Right Anterior Mini-Thoracotomy for Minimal Access Aortic Valve Replacement Reza Tavakoli1,2, Pascal Leprince1, Max Gassmann2, Peiman Jamshidi3, Nassrin Yamani4, Julien Amour5, Guillaume Lebreton1 1Department of Cardiovascular and Thoracic Surgery, Pitié Salpêtrière University Hospital, Assistance Publique, Hôpitaux de Paris (APHP), Institut de Cardiologie, 2Institute of Veterinary Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, 3Herzzentrum Hirslanden, Klinik St Anna, 4Department of Radiology, Canton Hospital Lucerne, 5Department of Anesthesiology and Intensive Care Unit, Pitié Salpêtrière University Hospital, Assistance Publique, Hôpitaux de Paris (APHP), Institut de Cardiologie The goal of this protocol is to describe in detail the technique of minimally invasive aortic valve replacement through a right anterior mini-thoracotomy and central aortic cannulation. This technique can potentially enhance patients' comfort and, by reducing post-operative morbidity, promote lowering the length of stay and global costs. 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. Medicine Standardized Technique of Aortic Valve Re-implantation for Valve-sparing Aortic Root Replacement Reza Tavakoli1,2, Guillaume Lebreton1, Max Gassmann2, Peiman Jamshidi3, Pascal Leprince1 1Department of Cardiovascular and Thoracic Surgery, Pitie Salpetriere University Hospital, Assistance Publique, Hopitaux de Paris (APHP), Institut de Cardiologie, 2Institute of Veterinary Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, 3Herzzentrum Hirslanden, Klinik St Anna Valve-sparing aortic root replacement has the advantage of preserving the patient's own aortic valve. The complexity of the reported techniques to date restricts their use to a limited number of cardiac surgeons. This protocol describes step-by-step a standardized technique reproducible by a greater number of cardiac surgeons. Developmental Biology Reprogramming Primary Amniotic Fluid and Membrane Cells to Pluripotency in Xeno-free Conditions Jaroslav Slamecka1, Javier Laurini2, Troy Shirley1, Simon Philipp Hoerstrup3, Benedikt Weber3,4,5, Laurie Owen1, Steven McClellan1 1Mitchell Cancer Institute, University of South Alabama, 2College of Medicine, University of South Alabama, 3Institute for Regenerative Medicine, University of Zurich, 4Department of Dermatology, University Hospital Zurich, 5Center for Applied Biotechnology and Molecular Medicine (CABMM), University of Zurich - Irchel Campus This protocol describes the reprogramming of primary amniotic fluid and membrane mesenchymal stem cells into induced pluripotent stem cells using a non-integrating episomal approach in fully chemically defined conditions. Procedures of extraction, culture, reprogramming, and characterization of the resulting induced pluripotent stem cells by stringent methods are detailed. Developmental Biology Correlative Super-resolution and Electron Microscopy to Resolve Protein Localization in Zebrafish Retina José M. Mateos1, Gery Barmettler1, Jana Doehner1, Irene Ojeda Naharros2, Bruno Guhl1, Stephan C.F. Neuhauss2, Andres Kaech1, Ruxandra Bachmann-Gagescu2,3, Urs Ziegler1 1Center for Microscopy and Image Analysis, University of Zurich, 2Institute for Molecular Life Sciences, University of Zurich, 3Institute for Medical Genetics, University of Zurich This protocol describes the necessary steps to obtain subcellular protein localization results on zebrafish retina by correlating super-resolution light microscopy and scanning electron microscopy images. Medicine Technique of Minimally Invasive Transverse Aortic Constriction in Mice for Induction of Left Ventricular Hypertrophy Reza Tavakoli1, Simona Nemska1,2, Peiman Jamshidi3, Max Gassmann1, Nelly Frossard2 1Institute of Veterinary Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 2Laboratoire d'Innovation Thérapeutique, UMR7200, Université de Strasbourg - CNRS, 3Department of Cardiology, Canton Hospital Lucerne The aim of this protocol is to describe step-by-step the technique of minimally invasive transverse aortic constriction (TAC) in mice. By elimination of intubation and ventilation which are mandatory for the commonly used standard procedure, minimally invasive TAC simplifies the operative procedure and reduces the strain put on the animal. Medicine Rat Model of the Associating Liver Partition and Portal Vein Ligation for Staged Hepatectomy (ALPPS) Procedure Erik Schadde1,2,3, Martin Hertl2, Stefan Breitenstein3, Beatrice Beck-Schimmer1,4, Martin Schläpfer1,4 1Institute of Physiology - Center for Integrative Human Physiology, University of Zurich, 2Department of Surgery, Rush University Medical Center, 3Department of Surgery, Cantonal Hospital Winterthur, 4Institute of Anesthesiology, University and University Hospital Zurich Inducing rapid liver hypertrophy using Associating Liver Partition and Portal vein ligation for a Staged hepatectomy (ALPPS) has been proposed for resection of borderline resectable liver tumors. This model may elucidate mechanisms involved in rapid hypertrophy and allows testing of drugs that promote or block the acceleration of regeneration. Genetics Studying Cell Cycle-regulated Gene Expression by Two Complementary Cell Synchronization Protocols Aintzane Apraiz*1, Jone Mitxelena*2,3, Ana Zubiaga2 1Department of Cell Biology and Histology, University of the Basque Country, UPV/EHU, 2Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, 3Department of Molecular Mechanisms of Disease, University of Zurich We report two cell synchronization protocols that provide a context for studying events related to specific phases of the cell cycle. We show that this approach is useful for analyzing the regulation of specific genes in an unperturbed cell cycle or upon exposure to agents affecting the cell cycle. Medicine Full-root Aortic Valve Replacement by Stentless Aortic Xenografts in Patients with Small Aortic Roots Reza Tavakoli1,2, Peiman Jamshidi3, Max Gassmann1,2 1Institute of Veterinary Physiology, University of Zurich, 2Zurich Center of Integrative Human Physiology, University of Zurich, 3Department of Cardiology, Canton Hospital Lucerne Full-root aortic valve replacement by stentless aortic xenograft is a viable option in patients with small aortic roots. We describe, a technique for the full-root implantation of stentless aortic xenografts, with emphasis on the management of the proximal suture line and coronary anastomoses, and discuss its limitations and alternative options. Medicine Direct Re-implantation of Left Coronary Artery into the Aorta in Adults with Anomalous Origin of Left Coronary Artery from the Pulmonary Artery (ALCAPA) Reza Tavakoli1, Peiman Jamshidi2, Nassrin Yamani3, Max Gassmann1 1Institute of Veterinary Physiology and Zurich Center of Integrative Human Physiology (ZIHP), University of Zurich, 2Department of Cardiology, Canton Hospital Lucerne, 3Department of Radiology, Canton Hospital Lucerne Surgical correction of ALCAPA is highly recommended, regardless of age or the degree of intercoronary collateralization. This protocol presents a technique for the direct re-implantation of adult-type ALCAPA into the aorta to re-establish the dual-coronary perfusion. Whenever feasible, direct re-implantation is preferred to other surgical correction techniques. Genetics Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing Joanna M. Feehan*1,2, Katherine E. Scheibel*1, Salim Bourras3, William Underwood4, Beat Keller3, Shauna C. Somerville1 1Department of Plant and Microbial Biology, University of California Berkeley, 2John Innes Centre, Norwich Research Park, 3Department of Plant and Microbial Biology, University of Zürich, 4USDA-ARS Sunflower and Plant Biology Research Unit Described here is a method for the extraction, purification, and quality control of genomic DNA from the obligate biotrophic fungal pathogen, powdery mildew, for use in long-read genome sequencing. Biology The Mouse Isolated Perfused Kidney Technique Jan Czogalla1, Frank Schweda2, Johannes Loffing1 1Institute of Anatomy, Swiss National Centre of Competence in Research Kidney, University of Zürich, 2Department of Physiology, University of Regensburg The mouse isolated perfused kidney (MIPK) is a technique for keeping a mouse kidney under ex vivo conditions perfused and functional for 1 hr. The buffers and surgical technique are described in detail. Biochemistry Characterization of Multi-subunit Protein Complexes of Human MxA Using Non-denaturing Polyacrylamide Gel-electrophoresis Patricia E. Nigg1,2, Jovan Pavlovic1 1Institute for Medical Virology, University of Zurich, 2Friedrich Miescher Institute for Biomedical Research This article describes a simple and rapid protocol to evaluate the oligomeric state of the dynamin-like GTPase MxA protein from lysates of human cells using a combination of non-denaturing PAGE with western blot analysis. 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. Immunology and Infection Measuring Attachment and Internalization of Influenza A Virus in A549 Cells by Flow Cytometry Marie O. Pohl1, Silke Stertz1 1Institute of Medical Virology, University of Zurich We present a protocol describing a semi-quantitative method for measuring both, the attachment of influenza A virus to A549 cells, as well as the internalization of virus particles into the target cells by flow cytometry. Neuroscience Analysis of Developing Tooth Germ Innervation Using Microfluidic Co-culture Devices Pierfrancesco Pagella1, Shayee Miran1, Tim Mitsiadis1 1Institute of Oral Biology, Unit of Orofacial Development and Regeneration, University of Zurich Co-cultures represent a valuable method to study the interactions between nerves and target tissues and organs. Microfluidic systems allow co-culturing ganglia and whole developing organs or tissues in different culture media, thus representing a valuable tool for the in vitro study of the crosstalk between neurons and their targets. 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. Developmental Biology An Enzymatic Method to Rescue Mesenchymal Stem Cells from Clotted Bone Marrow Samples Philipp Schlaefli*1, Alessandro Bertolo*1, Cherry Malonzo1, Tobias Poetzel2, Martin Baur3, Frank Steffen4, Jivko Stoyanov1 1Swiss Paraplegic Research, 2Orthopaedics and Spinal Surgery, Swiss Paraplegic Centre, 3Department of Neurosurgery, Lucerne Cantonal Hospital (LUKS), 4Section of Small Animal Surgery/Neurology, Vetsuisse Faculty, University of Zurich Mesenchymal stem cells are usually obtained from bone marrow and require expansion culture. When samples clot before processing, a protocol using the (enzymatic) thrombolytic drug urokinase can be applied to degrade the clot. Thus, cells are released and available for expansion culture. This protocol provides a rapid and inexpensive alternative to resampling. Neuroscience Real-Time Impedance-based Cell Analyzer as a Tool to Delineate Molecular Pathways Involved in Neurotoxicity and Neuroprotection in a Neuronal Cell Line Zoya Marinova1, Susanne Walitza1, Edna Grünblatt1 1University Clinics for Child and Adolescent Psychiatry, University of Zürich Improved in vitro neurotoxicity assays would aid the identification of new neuroprotective compounds. The utility of a real-time impedance-based cell analyzer to determine cytotoxicity and cytoprotection in neuronal cell lines and to delineate the involvement of second messenger pathways, thus gaining insight in the mechanism of neuroprotection is presented. Biology An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis Wenjing She1, Daniel Grimanelli2, Célia Baroux1 1Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 2Institut de Recherche pour le Développement (UMR 232), Centre National de la Recherche Scientifique (ERL 5300), Université de Montpellier II We provide here an efficient and reliable protocol for immunostaining, Fluorescence in situ Hybridization, DNA staining followed by quantitative, high-resolution imaging in whole-mount Arabidopsis thaliana ovules. This method was successfully used to analyze chromatin modifications and nuclear architecture. Medicine Accuracy in Dental Medicine, A New Way to Measure Trueness and Precision Andreas Ender1, Albert Mehl1 1Division of Computer-assisted Restorative Dentistry, Center of Dental Medicine, University of Zürich Accuracy is a major demand in dental medicine. To verify accuracy, reference scanners are needed. This article presents a new reference scanner with an adjusted scanning method to acquire a broad variety of dental morphologies with high trueness and precision. Biology Mouse Genome Engineering Using Designer Nucleases Mario Hermann1, Tomas Cermak2, Daniel F. Voytas2, Pawel Pelczar1 1Institute of Laboratory Animal Science, University of Zurich, 2Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota Designer nucleases such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) can be used to modify the genome of mouse preimplantation embryos by triggering both the nonhomologous end joining (NHEJ) and homologous recombination (HR) pathways. These advances enable the rapid generation of mice with precise genetic modifications. Chemistry Mizoroki-Heck Cross-coupling Reactions Catalyzed by Dichloro{bis[1,1',1''-(phosphinetriyl)tripiperidine]}palladium Under Mild Reaction Conditions Miriam Oberholzer1, Christian M. Frech2 1Institute of Inorganic Chemistry, University of Zürich, 2Institute of Chemistry & Biological Chemistry, Zürich University of Applied Sciences Dichloro{bis[1,1',1''-(phosphinetriyl)tripiperidine]}palladium [(P(NC5H10)3)2Pd(Cl)2] (1) is an easy accessible, cheap, and air stable, but highly active Heck catalyst with an excellent functional group tolerance that efficiently operates under mild reaction conditions to give the coupling products in very high yields. Biology Efficient and Rapid Isolation of Early-stage Embryos from Arabidopsis thaliana Seeds Michael T. Raissig1, Valeria Gagliardini1, Johan Jaenisch1, Ueli Grossniklaus1, Célia Baroux1 1Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich We report an efficient and simple method to isolate embryos at early stages of development from Arabidopsis thaliana seeds. Up to 40 embryos can be isolated in 1 hr to 4 hr, depending on the downstream application. The procedure is suitable for transcriptome, DNA methylation, reporter gene expression, immunostaining and fluorescence in situ hybridization analyses. Behavior Perceptual and Category Processing of the Uncanny Valley Hypothesis' Dimension of Human Likeness: Some Methodological Issues Marcus Cheetham1, Lutz Jancke1 1Department of Neuropsychology, University of Zurich Investigation of the Uncanny Valley Hypothesis and affective experience requires an understanding of the hypothesis' dimension of human likeness (DHL). This protocol allows representation of the DHL and examination of categorical perception. Use of the same stimuli and fMRI to distinguish brain regions responsive to physical and category change is illustrated. Neuroscience In ovo Electroporation of miRNA-based Plasmids in the Developing Neural Tube and Assessment of Phenotypes by DiI Injection in Open-book Preparations Nicole H. Wilson1, Esther T. Stoeckli1 1Institute of Molecular Life Sciences, University of Zurich A method by which gene expression in the neural tube can be downregulated in a cell type-specific, traceable manner is described. We demonstrate how in ovo electroporation of microRNA-based plasmids that elicit spatiotemporally controlled RNA interference can be used to investigate commissural axon guidance in the developing neural tube. Medicine Roux-en-Y Gastric Bypass Operation in Rats Marco Bueter1,2, Kathrin Abegg2,3, Florian Seyfried4, Thomas A. Lutz2,3, Carel W. le Roux4 1Department of Surgery, University Hospital Zürich, 2Zürich Centre for Integrative Human Physiology, University of Zürich, 3Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zürich, 4Imperial Weight Centre, Department of Investigative Medicine, Imperial College London Numerous studies using gastric bypass rat models have been recently conducted to uncover the underlying physiological mechanisms of Roux-en-Y gastric bypass operations. This article aims to demonstrate and discuss the technical and experimental details of our published gastric bypass rat model to understand advantages and limitations of this experimental tool. Medicine Implantation of Radiotelemetry Transmitters Yielding Data on ECG, Heart Rate, Core Body Temperature and Activity in Free-moving Laboratory Mice Nikola Cesarovic1, Paulin Jirkof2, Andreas Rettich2, Margarete Arras1 1Division of Surgical Research, University Hospital Zurich, 2Institute of Laboratory Animal Science, University of Zurich A surgical technique for implantation of commercially available telemetry transmitters used for continuous measurement of biopotential (one-lead ECG), heart rate, core body temperature and locomotor activity in freely moving mice is shown. Recommendations and protocols for post-operative care and pain relief, improving recovery, well being and survival rate are also presented. Neuroscience VisioTracker, an Innovative Automated Approach to Oculomotor Analysis Kaspar P. Mueller1, Oliver D. R. Schnaedelbach2, Holger D. Russig2, Stephan C. F. Neuhauss1 1Institute of Molecular Life Sciences, University of Zurich, 2TSE Systems GmbH The VisioTracker is an automated system for the quantitative analysis of visual performance of larval and small adult fish based on the recording of eye movements. It features full control over visual stimulus properties and real-time analysis, enabling high-throughput research in fields such as visual system development and function, pharmacology, neural circuit studies and sensorimotor integration. Neuroscience Combining Behavioral Endocrinology and Experimental Economics: Testosterone and Social Decision Making Christoph Eisenegger*1, Michael Naef*2 1Institute for Empirical Research in Economics, Laboratory for Social and Neural Systems Research, University of Zurich, 2Department of Economics, Royal Holloway, University of London The procedure described in this protocol shows that testosterone administration and folk beliefs about testosterone may be associated with directly opposed social behaviors. Biology Making MR Imaging Child's Play - Pediatric Neuroimaging Protocol, Guidelines and Procedure Nora M. Raschle1,2, Michelle Lee1, Roman Buechler1, Joanna A. Christodoulou3, Maria Chang1, Monica Vakil1, Patrice L. Stering1, Nadine Gaab1,3,4 1Department of Developmental Medicine, Children’s Hospital Boston, 2Department of Neuropsychology, University of Zurich, 3Graduate School of Education, Harvard, 4Harvard Medical School Despite an increase in the use of structural and functional magnetic resonance imaging (fMRI) in humans, the study of young pediatric populations remains a challenge. We present a hands-on, step-by-step video protocol including guidelines for clinicians and researchers intending to perform (f)MRI in young children.
