University Hospital Basel 17 articles published in JoVE Neuroscience Whole Neonatal Cochlear Explants as an In vitro Model Soledad Levano1, Yu Lu1, Maurizio Cortada1, Daniel Bodmer1,2 1Department of Biomedicine, University of Basel Hospital, 2Department of Otorhinolaryngology, Head and Neck Surgery, University of Basel Hospital The current protocol updates previous protocols and incorporates relatively straightforward approaches for culturing high-quality cochlear explants. This provides reliable data acquisition and high-resolution imaging in live and fixed cells. This protocol supports the ongoing trend of studying inner ear cells. Medicine Functional Characterization of Endogenously Expressed Human RYR1 Variants Susan Treves1,2, Thierry Girard3, Francesco Zorzato1,2 1Department of Biomedicine, Basel University Hospital, 2Department of Life Sciences, University of Ferrara, 3Department of Anesthesia, Basel University Hospital Here methods used to study the functional effect of RYR1 mutations endogenously expressed in Epstein Barr Virus immortalized human B-lymphocytes and muscle biopsy derived satellite cells differentiated into myotubes are described. Cancer Research Two Flow Cytometric Approaches of NKG2D Ligand Surface Detection to Distinguish Stem Cells from Bulk Subpopulations in Acute Myeloid Leukemia Henrik Landerer*1, Marlon Arnone*1, Ronja Wieboldt2, Elsa Goersch1, Anna M. Paczulla Stanger3, Martina Konantz1, Claudia Lengerke1,2,3 1Department of Biomedicine, University Hospital Basel and University of Basel, 2Division for Hematology, University Hospital Basel and University of Basel, 3Department of Internal Medicine, Hematology and Oncology, University Hospital Tübingen We present two different staining protocols for NKG2D ligand (NKG2DL) detection in human primary acute myeloid leukemia (AML) samples. The first approach is based on a fusion protein, able to recognize all known and potentially yet unknown ligands, while the second protocol relies on the addition of multiple anti-NKG2DL antibodies. Cancer Research Micromanipulation of Circulating Tumor Cells for Downstream Molecular Analysis and Metastatic Potential Assessment Cinzia Donato*1, Barbara M. Szczerba*1, Manuel C. Scheidmann*1, Francesc Castro-Giner1,2, Nicola Aceto1 1Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, 2SIB Swiss Institute of Bioinformatics Here, we present an integrated workflow to identify phenotypic and molecular features that characterize circulating tumor cells (CTCs). We combine live immunostaining and robotic micromanipulation of single and clustered CTCs with single cell-based techniques for downstream analysis and assessment of metastasis-seeding ability. Medicine Measurements of Motor Function and Other Clinical Outcome Parameters in Ambulant Children with Duchenne Muscular Dystrophy Sara Nagy1,2, Simone Schmidt1,2, Patricia Hafner1,3, Andrea Klein1,4,5, Daniela Rubino-Nacht1, Vanya Gocheva1, Oliver Bieri6, Carole Vuillerot7, Ulrike Bonati1,2, Dirk Fischer1,2,3 1Division of Pediatric Neurology, University Children's Hospital Basel (UKBB), University of Basel, 2Department of Neurology, University Hospital Basel, University of Basel, 3Division of Neurology, University Clinic of Medicine, Cantonal Hospital Baselland, Bruderholz, 4Division of Pediatric Neurology, CHUV, 5Division of Neuropaediatrics, Inselspital, University Children's Hospital Bern, 6Department of Radiology, Division of Radiological Physics, University Hospital Basel, University of Basel, 7Hospices Civils de Lyon, Hôpital Femme-Mère-Enfant, L'Escale, Service de Médecine Physique et de Réadaptation Pédiatrique The aim of this study is to present the most reliable clinical outcome measures and their correlations with quantitative muscle MRI in ambulant patients with Duchenne muscular dystrophy. Developmental Biology Induction of Endothelial Differentiation in Cardiac Progenitor Cells Under Low Serum Conditions Michika Mochizuki*1, Giacomo Della Verde*1, Habiba Soliman1, Otmar Pfister1,2, Gabriela M. Kuster1,2 1Department of Biomedicine, University Hospital and University of Basel, 2Division of Cardiology, University Hospital Basel This protocol describes an endothelial differentiation technique for cardiac progenitor cells. It particularly focuses on how serum concentration and cell-seeding density affect the endothelial differentiation potential. Immunology and Infection Injections of Lipopolysaccharide into Mice to Mimic Entrance of Microbial-derived Products After Intestinal Barrier Breach Katarina Radulovic1, Rachel Mak’Anyengo1, Berna Kaya1, Anna Steinert1, Jan Hendrik Niess1,2 1Department of Biomedicine, University of Basel, 2Division of Gastroenterology and Hepatology, University Hospital of Basel Here a protocol to mimic the entrance of bacterial-derived compounds after intestinal barrier breach is presented. A low sublethal dose of lipopolysaccharide was injected systemically into mice, which were monitored for 24 h post-injection. The expression of pro-inflammatory cytokines was determined at several time points in spleen, liver, and colon. Behavior An Objective and Child-friendly Assessment of Arm Function by Using a 3-D Sensor Xing Chen1, Detlef Wolf1, Juliane Siebourg-Polster2, Christian Czech3, Ulrike Bonati4,5, Dirk Fischer4,5, Omar Khwaja6, Martin Strahm1 1Data Science, Roche Pharmaceutical Research and Early Development Informatics, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., 2Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., 3Biomarker Experimental Medicine, Neuroscience, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., 4 An objective measure of muscle functions is challenging especially in children. Based on a commercially available digital 3-D sensor, a child-friendly gaming test was developed to assess upper limb function for clinical trials. 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. Immunology and Infection Development of an Antigen-driven Colitis Model to Study Presentation of Antigens by Antigen Presenting Cells to T Cells Valerio Rossini1, Katarina Radulovic2, Christian U. Riedel3, Jan Hendrik Niess2 1APC Microbiome Institute, University College Cork, 2Division of Gastroenterology and Hepatology, University Hospital Basel, 3Institute of Microbiology and Biotechnology, University of Ulm In this antigen-driven colitis model, OT-II CD4+ T cells expressing a red fluorescent protein were adoptively transferred into RAG-/- mice that express a green fluorescent protein in mononuclear phagocytes (MPs). The hosts were challenged with Escherichia coli (E.coli) expressing the ovalbumin protein (OVA) fused to a cyan fluorescent protein (CFP). Developmental Biology An Enzyme- and Serum-free Neural Stem Cell Culture Model for EMT Investigation Suited for Drug Discovery Martin H. M. Sailer1, Durga Sarvepalli2, Catherine Brégère3, Urs Fisch3, Marin Guentchev4, Michael Weller6, Raphael Guzman3, Bernhard Bettler1, Arkasubhra Ghosh*2, Gregor Hutter*5 1Dept. of Biomedicine, Pharmacenter, University of Basel, 2Molecular Signalling and Gene Therapy, Narayana Nethralaya Foundation, Narayana Health City, 3Brain Ischemia and Regeneration, Department of Biomedicine, University Hospital Basel, 4Department of Neurosurgery, Klinikum Idar-Oberstein, 5Department of Neurosurgery and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, 6Department of Neurology, Laboratory of Molecular Neuro Oncology, University Hospital of Zurich Epithelial to mesenchymal transition (EMT) allows cancers to become invasive. To investigate EMT, a neural stem cell (NSC)-based in vitro model devoid of serum and enzymes is described. This standardized system allows quantitative and qualitative assessment of cell migration, gene and protein expression. The model is suited for drug discovery. Chemistry An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions Mohameedyaseen Syedbasha1, Janina Linnik1,2,3, Deanna Santer4, Daire O'Shea5, Khaled Barakat4,6, Michael Joyce4, Nina Khanna7, D. Lorne Tyrrell4, Michael Houghton4, Adrian Egli1,8 1Applied Microbiology Research, Department of Biomedicine, University of Basel, 2Department of Biosystems Science and Engineering, ETH Zurich, and Swiss Institute of Bioinformatics, 3Swiss Institute of Bioinformatics, 4Li Ka Shing Institute for Virology, University of Alberta, 5Regional Infectious Diseases Unit, University of Edinburgh, 6Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, 7Infection Biology, Department of Biomedicine, University of Basel, 8Clinical Microbiology, University Hospital Basel The presented protocols describe two enzyme-linked immunosorbent assay (ELISA) based techniques for the rapid investigation of ligand-receptor interactions: The first assay allows the determination of dissociation constant between ligand and receptor. The second assay enables a rapid screening of blocking peptides for ligand-receptor interactions. Medicine Evaluation of Stem Cell Properties in Human Ovarian Carcinoma Cells Using Multi and Single Cell-based Spheres Assays Hui Wang1,2, Anna Paczulla1, Claudia Lengerke1,2 1Department of Biomedicine, University Hospital Basel, 2Department of Internal Medicine II, University Hospital Tübingen In vitro spheres assays are commonly used to identify cancer stem cells. Here we compare single with multi cell-based spheres assays. The more laborious single cell-based assays or methylcellulose supplementation give more accurate results while multi cell-based assays performed in liquid medium can be highly influenced by cell density. Medicine Ischemic Tissue Injury in the Dorsal Skinfold Chamber of the Mouse: A Skin Flap Model to Investigate Acute Persistent Ischemia Yves Harder1, Daniel Schmauss1, Reto Wettstein2, José T. Egaña1, Fabian Weiss1, Andrea Weinzierl1, Anna Schuldt1, Hans-Günther Machens1, Michael D. Menger3, Farid Rezaeian4 1Department of Plastic Surgery and Hand Surgery, Klinikum rechts der Isar, Technische Universität München, 2Department of Plastic, Reconstructive, Aesthetic and Hand Surgery, University Hospital of Basel, 3Institute for Clinical and Experimental Surgery, University of Saarland, 4Division of Plastic and Hand Surgery, University Hospital Zurich The window of the murine dorsal skinfold chamber presented visualizes a zone of acute persistent ischemia of a musculocutaneous flap. Intravital epi-fluorescence microscopy permits for direct and repetitive assessment of the microvasculature and quantification of hemodynamics. Morphologic and hemodynamic results can further be correlated with histological and molecular analyses. Biology Methylnitrosourea (MNU)-induced Retinal Degeneration and Regeneration in the Zebrafish: Histological and Functional Characteristics Ellinor Maurer1, Markus Tschopp1,2, Christoph Tappeiner1, Pauline Sallin3, Anna Jazwinska3, Volker Enzmann1 1Department of Ophthalmology, Inselspital, University of Bern, 2Department of Ophthalmology, University Hospital of Basel, 3Department of Biology, University of Fribourg Herein we demonstrate quantification of retinal de- and regeneration and its impact on visual function using N-methyl-N-nitrosourea in the adult zebrafish. Loss of visual acuity and decreased photoreceptor numbers were followed by proliferation in the inner nuclear layer. Complete morphological and functional regeneration occurred 30 days after the initial treatment. Immunology and Infection Isolation of Murine Lymph Node Stromal Cells Maria A. S. Broggi*1, Mathias Schmaler*1, Nadège Lagarde1, Simona W. Rossi1 1Department of Biomedicine, Immunoregulation, University of Basel and University Hospital Basel Isolation of lymph node stromal cells is a multistep procedure including enzymatic digestion and mechanical disaggregation to obtain fibroblastic reticular cells, lymphatic and blood endothelial cells. In the described procedure, a short digestion is combined with automated mechanical disaggregation to minimize surface marker degradation of viable lymph node stromal cells. Immunology and Infection Transplantation of Tail Skin to Study Allogeneic CD4 T Cell Responses in Mice Mathias Schmaler*1, Maria A. S. Broggi*1, Simona W. Rossi1 1Department of Biomedicine, Immunoregulation, University of Basel and University Hospital Basel Tail-skin transplantation is a powerful model for studying T cell-dependent rejection and tolerance induction during allogeneic immune responses in mice. The advantages of this protocol are minor invasive surgery, and ease of monitoring with no need to sacrifice the recipient mouse.