DZNE, German Center for Neurodegenerative Diseases 14 articles published in JoVE Biology Cost-Efficient Transcriptomic-Based Drug Screening Jacqueline Leidner1,2, Heidi Theis3, Michael Kraut3, Alice Ragogna1, Marc Beyer1,3,4, Joachim Schultze1,2,3, Jonas Schulte-Schrepping1,2, Caterina Carraro1,2, Lorenzo Bonaguro1,2 1Systems Medicine, German Center for Neurodegenerative Diseases (DZNE) eV., 2Genomics & Immunoregulation, LIMES Institute, University of Bonn, 3PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE and University of Bonn, 4Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE) eV. This protocol describes a workflow from ex vivo or in vitro cell cultures to transcriptomic data pre-processing for cost-effective transcriptome-based drug screening. Neuroscience Manual Segmentation of the Human Choroid Plexus Using Brain MRI Deepthi Bannai*1,2, Yuan Cao*3,4, Matcheri Keshavan1,2, Martin Reuter5,6,7, Paulo Lizano1,2,8 1Department of Psychiatry, Beth Israel Deaconess Medical Center, 2Division of Translational Neuroscience, Beth Israel Deaconess Medical Center, 3Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, 4Department of Psychiatry and Psychotherapy, Jena University Hospital, 5AI in Medical Imaging, German Center for Neurodegenerative Diseases (DZNE), 6A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, 7Department of Radiology, Harvard Medical School, 8Department of Psychiatry, Harvard Medical School Despite the crucial role of the choroid plexus in the brain, neuroimaging studies of this structure are scarce due to the lack of reliable automated segmentation tools. The present protocol aims to ensure gold-standard manual segmentation of the choroid plexus that can inform future neuroimaging studies. Bioengineering Fibroblast Derived Human Engineered Connective Tissue for Screening Applications Gabriela L. Santos1,2, Tim Meyer1,2, Malte Tiburcy1,2, Alisa DeGrave1,2, Wolfram-Hubertus Zimmermann1,2,3,4,5, Susanne Lutz1,2 1Institute of Pharmacology and Toxicology, University Medical Center Goettingen, 2DZHK (German Center for Cardiovascular Research) partner site, Goettingen, 3Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Goettingen, 4Center for Neurodegenerative Diseases (DZNE), 5Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) Presented here is a protocol to generate engineered connective tissues for a parallel culture of 48 tissues in a multi-well plate with double poles, suitable for mechanistic studies, disease modeling, and screening applications. The protocol is compatible with fibroblasts from different organs and species and is exemplified here with human primary cardiac fibroblasts. Biology Automated Production of Human Induced Pluripotent Stem Cell-Derived Cortical and Dopaminergic Neurons with Integrated Live-Cell Monitoring Ashutosh Dhingra*1, Joachim Täger*1, Elisangela Bressan*1, Salvador Rodriguez-Nieto1, Manmeet-Sakshi Bedi1, Stefanie Bröer1, Eldem Sadikoglou1, Noémia Fernandes2, Melissa Castillo-Lizardo1, Patrizia Rizzu2, Peter Heutink1,3 1Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 2Applied Genomics for Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 3Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen We show the automation of human induced pluripotent stem cell (hiPSC) cultures and neuronal differentiations compatible with automated imaging and analysis. Cancer Research Generation of Orthotopic Pancreatic Tumors and Ex vivo Characterization of Tumor-Infiltrating T Cell Cytotoxicity Sarah Spear1,2, Iain A McNeish1, Melania Capasso2,3 1Division of Cancer, Department of Surgery and Cancer, Imperial College London, 2Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, 3German Center for Neurodegenerative Diseases (DZNE) This protocol describes the surgical generation of orthotopic pancreatic tumors and the rapid digestion of freshly isolated murine pancreatic tumors. Following digestion, viable immune cell populations can be used for further downstream analysis, including ex vivo stimulation of T cells for intracellular cytokine detection by flow cytometry. Neuroscience Data Acquisition and Analysis In Brainstem Evoked Response Audiometry In Mice Andreas Lundt1,2, Julien Soos1, Christina Henseler1, Muhammad Imran Arshaad1, Ralf Müller3, Dan Ehninger4, Jürgen Hescheler5, Agapios Sachinidis5, Karl Broich6, Carola Wormuth1,7, Anna Papazoglou1, Marco Weiergräber1 1Experimental Neuropsychopharmacology, Federal Institute for Drugs and Medical Devices, 2KBRwyle GmbH, 3Cognitive Neurophysiology, Department of Psychiatry and Psychotherapy, Faculty of Medicine, University of Cologne, 4Molecular and Cellular Cognition, German Center for Neurodegenerative Diseases (DZNE), 5Institute of Neurophysiology, Faculty of Medicine, University of Cologne, 6Federal Institute for Drugs and Medical Devices (BfArM), 7Thescon GmbH Brainstem evoked response audiometry is an important tool in clinical neurophysiology. Nowadays, brainstem evoked response audiometry is also applied in the basic science and preclinical studies involving both pharmacological and genetic animal models. Here we provide a detailed description of how auditory brainstem responses can be successfully recorded and analyzed in mice. Neuroscience Visualization of Cortical Modules in Flattened Mammalian Cortices Simon M. Lauer*1, Undine Schneeweiß1, Michael Brecht1,2,3, Saikat Ray*1 1Bernstein Center for Computational Neuroscience, Humboldt University of Berlin, 2NeuroCure Cluster of Excellence, 3German Center for Neurodegenerative Diseases This article describes a detailed methodology to obtain flattened tangential sections from mammalian cortices and visualize cortical modules using histochemical and immunohistochemical methods. Biology Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans Nicole Groh1,2, Ivan Gallotta1, Marie C. Lechler1,2, Chaolie Huang1, Raimund Jung1, Della C. David1 1Protein Aggregation and Aging, German Center for Neurodegenerative Diseases (DZNE), 2Graduate School of Cellular and Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE) The goal of the method presented here is to explore protein aggregation during normal aging in the model organism C. elegans. The protocol represents a powerful tool to study the highly insoluble large aggregates that form with age and to determine how changes in proteostasis impact protein aggregation. Neuroscience Bioluminescence Imaging of Neuroinflammation in Transgenic Mice After Peripheral Inoculation of Alpha-Synuclein Fibrils Sara Breid1, Maria E. Bernis1, Julius B. Tachu1, Maria C. Garza2, Holger Wille2, Gültekin Tamgüney1 1German Center for Neurodegenerative Diseases (DZNE), 2Centre for Prions and Protein Folding Diseases & Department of Biochemistry, University of Alberta Peripheral injection of alpha-synuclein fibrils into the peritoneum or tongue of Tg(M83+/-:Gfap-luc+/-) mice, which express human alpha-synuclein with the familial A53T mutation and firefly luciferase, can induce neuropathology, including neuroinflammation, in their central nervous system. Behavior Automatic Detection of Highly Organized Theta Oscillations in the Murine EEG Ralf Müller1, Anna Papazoglou2, Julien Soos2, Andreas Lundt2, Carola Wormuth2, Christina Henseler2, Dan Ehninger3, Karl Broich4, Marco Weiergräber2 1Department of Psychiatry and Psychotherapy, University of Cologne, 2Department of Neuropsychopharmacology, Federal Institute for Drugs and Medical Devices, 3Molecular and Cellular Cognition Lab, German Center for Neurodegenerative Diseases, 4Federal Institute for Drugs and Medical Devices Theta activity in the hippocampus is related to specific cognitive and behavioral stages. Here, we describe an analytical method to detect highly-organized theta oscillations within the hippocampus using a time-frequency (i.e., wavelet analysis)-based approach. Neuroscience Analyzing Synaptic Modulation of Drosophila melanogaster Photoreceptors after Exposure to Prolonged Light Atsushi Sugie1,2,5, Christoph Möhl3, Satoko Hakeda-Suzuki4, Hideaki Matsui1,2, Takashi Suzuki*4, Gaia Tavosanis*5 1Department of Neuroscience of Disease, Center for Transdisciplinary Research, Niigata University, 2Brain Research Institute, Niigata University, 3Image and Data Analysis Facility, German Center for Neurodegenerative Diseases (DZNE), 4Graduate School of Life Science and Technology, Tokyo Institute of Technology (Titech), 5Dendrite Differentiation, German Center for Neurodegenerative Diseases (DZNE) Here we show how to quantify the number and spatial distribution of synaptic active zones in Drosophila melanogaster photoreceptors, highlighted with a genetically encoded molecular marker, and their modulation after prolonged exposure to light. Neuroscience Non-restraining EEG Radiotelemetry: Epidural and Deep Intracerebral Stereotaxic EEG Electrode Placement Anna Papazoglou1, Andreas Lundt1, Carola Wormuth1, Dan Ehninger2, Christina Henseler1, Julien Soós1, Karl Broich1, Marco Weiergräber1 1Department of Neuropsychopharmacology, Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte, BfArM), 2Molecular and Cellular Cognition Lab, German Center for Neurodegenerative Diseases (Deutsches Zentrum für Neurodegenerative Erkrankungen, DZNE) Non-restraining EEG radiotelemetry is a valuable methodological approach to record in vivo long-term electroencephalograms from freely moving rodents. This detailed protocol describes stereotaxic epidural and deep intracerebral electrode placement in different brain regions in order to obtain reliable recordings of CNS rhythmicity and CNS related behavioral stages. Developmental Biology Imaging Subcellular Structures in the Living Zebrafish Embryo Peter Engerer1, Gabriela Plucinska1,2, Rachel Thong1,3, Laura Trovò1, Dominik Paquet4,5,6, Leanne Godinho1 1Institute of Neuronal Cell Biology, Technische Universität München, 2Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3Faculty of Biology, Ludwig-Maximilians-Universität-München, 4Adolf-Butenandt-Institute, Biochemistry, Ludwig-Maximilians-Universität-München, 5German Center for Neurodegenerative Diseases, 6Laboratory of Brain Development and Repair, The Rockefeller University Imaging the dynamic behavior of organelles and other subcellular structures in vivo can shed light on their function in physiological and disease conditions. Here, we present methods for genetically tagging two organelles, centrosomes and mitochondria, and imaging their dynamics in living zebrafish embryos using wide-field and confocal microscopy. Medicine In vivo 19F MRI for Cell Tracking Mangala Srinivas1, Philipp Boehm-Sturm2, Markus Aswendt2, Eberhard D. Pracht2,3, Carl G. Figdor1, I. Jolanda de Vries1, Mathias Hoehn2 1Department of Tumor Immunology, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Center, 2In-Vivo-NMR Laboratory, Max Planck Institute for Neurological Research, 3German Center for Neurodegenerative Diseases (DZNE) We describe a general protocol for in vivo cell tracking using MRI in a mouse model with ex vivo labeled cells. A typical protocol for cell labeling, image acquisition processing and quantification is included.
