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University of Basel

33 ARTICLES PUBLISHED IN JoVE

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Biology

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
Markus Hafner 1, Markus Landthaler 2, Lukas Burger 3, Mohsen Khorshid 3, Jean Hausser 4, Philipp Berninger 4, Andrea Rothballer 1, Manuel Ascano 1, Anna-Carina Jungkamp 2, Mathias Munschauer 2, Alexander Ulrich 1, Greg S. Wardle 1, Scott Dewell 5, Mihaela Zavolan 3, Thomas Tuschl 1
1Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, 2Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 3Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), 4Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), 5Genomics Resource Center, Rockefeller University

RNA transcripts are subject to extensive posttranscriptional regulation that is mediated by a multitude of trans-acting RNA-binding proteins (RBPs). Here we present a generalizable method to identify precisely and on a transcriptome-wide scale the RNA binding sites of RBPs.

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Neuroscience

A Functional Motor Unit in the Culture Dish: Co-culture of Spinal Cord Explants and Muscle Cells
Anne-Sophie Arnold 1, Martine Christe 1, Christoph Handschin 1
1Biozentrum, University of Basel

Cultured muscle cells are an inadequate model to recapitulate innervated muscle in vivo. A functional motor unit can be reproduced in vitro by innervation of differentiated human primary muscle cells using rat embryo spinal cord explants. This article describes how co-cultures of spinal cord explants and muscle cells are established.

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Neuroscience

The Analysis of Purkinje Cell Dendritic Morphology in Organotypic Slice Cultures
Josef P. Kapfhammer 1, Olivia S. Gugger 1
1Anatomical Institute, Department of Biomedicine, University of Basel

We present a protocol that permits to view and to quantitatively asses the morphology of the dendritic tree of individual Purkinje cells grown in organotypic cerebellar slice cultures. This protocol is intended to promote studies on the mechanisms of Purkinje cell dendritic development.

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Immunology and Infection

Determining Soil-transmitted Helminth Infection Status and Physical Fitness of School-aged Children
Peiling Yap 1,2, Thomas Fürst 1,2, Ivan Müller 1,2, Susi Kriemler 1,2, Jürg Utzinger 1,2, Peter Steinmann 1,2
1Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland, 2University of Basel, Basel, Switzerland

Chronic infection with soil-transmitted helminths (STHs) causes malabsorption, stunting, and wasting in the growing child. Hence, it is plausible that these infections also reduce the physical fitness of children. Here, we visualize two techniques for the diagnosis of STHs and the 20-meter shuttle run test for assessing children's physical fitness.

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Immunology and Infection

Imaging InlC Secretion to Investigate Cellular Infection by the Bacterial Pathogen Listeria monocytogenes
Andreas Kühbacher 1,2,3, Edith Gouin 1,2,3, Jason Mercer 4, Mario Emmenlauer 5, Christoph Dehio 5, Pascale Cossart 1,2,3, Javier Pizarro-Cerdá 1,2,3
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.

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Neuroscience

The Analysis of Neurovascular Remodeling in Entorhino-hippocampal Organotypic Slice Cultures
Sophorn Chip 1, Xinzhou Zhu 2, Josef P. Kapfhammer 1
1Anatomical Institute, Department of Biomedicine Basel, University of Basel, 2Department of Neonatology, University Children's Hospital (UKBB), University of Basel

A protocol for entorhino-hippocampal organotypic slice cultures, which allows reproducing many aspects of ischemic brain injury, is presented. By studying changes of the neurovasculature in addition to changes in the neurons, this protocol is a versatile tool to study plastic changes in neural tissue after injury.

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Biology

Comet Assay as an Indirect Measure of Systemic Oxidative Stress
Lei Fang 1,2, Albert Neutzner 1,2, Stephanie Turtschi 1, Josef Flammer 1, Maneli Mozaffarieh 1
1Department of Ophthalmology, University of Basel, 2Department of Biomedicine, University of Basel

Comet assay measures DNA breaks, induced by different factors. If all factors (except oxidative stress) causing DNA damage are kept constant, the amount of DNA damage is a good indirect parameter of oxidative stress. The goal of this protocol is to use comet assay for indirect measurement of oxidative stress.

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Immunology and Infection

Quantification of Cytosolic vs. Vacuolar Salmonella in Primary Macrophages by Differential Permeabilization
Etienne Meunier 1, Petr Broz 1
1Focal Area Infection Biology, Biozentrum, University of Basel

We describe the quantification of cytosolic and vacuolar Salmonella typhimurium in bone-marrow derived macrophages using differential digitonin permeabilization.

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Chemistry

An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions
Mohameedyaseen Syedbasha 1, Janina Linnik 1,2,3, Deanna Santer 4, Daire O'Shea 5, Khaled Barakat 4,6, Michael Joyce 4, Nina Khanna 7, D. Lorne Tyrrell 4, Michael Houghton 4, Adrian Egli 1,8
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.

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Biology

Investigating the Function of Coronin A in the Early Starvation Response of Dictyostelium discoideum by Aggregation Assays
Stefan K. Drexler 1, Francesco Brogna 1, Adrien Vinet 1, Jean Pieters 1
1Biozentrum, University of Basel

The social amoeba Dictyostelium discoideum undergoes a developmental transition into a multicellular organism when starved. The evolutionary conserved protein coronin A plays a crucial role in the initiation of development. Using aggregation assays as our main method, we aim to elucidate the role of coronin A in early development.

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Developmental Biology

An Enzyme- and Serum-free Neural Stem Cell Culture Model for EMT Investigation Suited for Drug Discovery
Martin H. M. Sailer 1, Durga Sarvepalli 2, Catherine Brégère 3, Urs Fisch 3, Marin Guentchev 4, Michael Weller 6, Raphael Guzman 3, Bernhard Bettler 1, 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.

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Immunology and Infection

Microscopy-based Assays for High-throughput Screening of Host Factors Involved in Brucella Infection of Hela Cells
Alain Casanova *1, Shyan H. Low *1, Mario Emmenlauer *1,4, Raquel Conde-Alvarez *1,3, Suzana P. Salcedo 2, Jean-Pierre Gorvel 2, Christoph Dehio 1
1Focal Area Infection Biology, Biozentrum, University of Basel, 2Centre d’Immunologie de Marseille-Luminy, Université de la Méditérannée UM2, INSERM U1104 CNRS UM7280, 3Departmento de Microbiologìa and Instituto de Salud Tropical, Universidad de Navarra, 4BioDataAnalysis GmbH

Two assays for microscopy-based high-throughput screening of host factors involved in Brucella infection are described. The entry assay detects host factors required for Brucella entry and the endpoint assay those required for intracellular replication. While applicable for alternative approaches, siRNA screening in HeLa cells is used to illustrate the protocols.

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Immunology and Infection

Development of an Antigen-driven Colitis Model to Study Presentation of Antigens by Antigen Presenting Cells to T Cells
Valerio Rossini 1, Katarina Radulovic 2, Christian U. Riedel 3, Jan Hendrik Niess 2
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).

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Biochemistry

Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay
Xinzhou Zhu 1, Andrea Zelmer 1, Sven Wellmann 1,2
1University Children's Hospital Basel (UKBB), University of Basel, 2Department of Clinical Research, University of Basel

Protein-protein interactions can occur in both the nucleus and the cytoplasm of a cell. To investigate these interactions, traditional co-immunoprecipitation and modern proximity ligation assay are applied. In this study, we compare these two methods to visualize the distribution of NF90-RBM3 interactions in the nucleus and the cytoplasm.

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Medicine

An Optimized Hemagglutination Inhibition (HI) Assay to Quantify Influenza-specific Antibody Titers
Lukas Kaufmann *1, Mohammedyaseen Syedbasha *1, Dominik Vogt 1, Yvonne Hollenstein 1, Julia Hartmann 1, Janina E. Linnik 1,2,3, Adrian Egli 1,4
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.

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Biology

3' End Sequencing Library Preparation with A-seq2
Georges Martin 1, Ralf Schmidt 1, Andreas J. Gruber 1, Souvik Ghosh 1, Walter Keller 1, Mihaela Zavolan 1,2
1Computational and Systems Biology, Biozentrum, University of Basel, 2Swiss Institute of Bioinformatics, Biozentrum, University of Basel

This protocol describes a method for mapping pre-mRNA 3' end processing sites.

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Medicine

Electrophysiological Measurement of Noxious-evoked Brain Activity in Neonates Using a Flat-tip Probe Coupled to Electroencephalography
Noemi Klarer *1, Hanna Rickenbacher *1, Severin Kasser 1, Antoinette Depoorter 2, Sven Wellmann 1
1Division of Neonatology, University of Basel Children's Hospital, 2Divison of Neuropediatrics and Developmental Medicine, University of Basel Children's Hospital

Measuring pain in non-verbal patients is a challenge. In this study we combine EEG recording with stimulation using a flat-tip probe to detect noxious-evoked brain activity in an objective manner.

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Behavior

An Objective and Child-friendly Assessment of Arm Function by Using a 3-D Sensor
Xing Chen 1, Detlef Wolf 1, Juliane Siebourg-Polster 2, Christian Czech 3, Ulrike Bonati 4,5, Dirk Fischer 4,5, Omar Khwaja 6, Martin Strahm 1
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., 4Division of Neuropediatrics, University of Basel Children's Hospital, 5Department of Neurology, University of Basel Hospital, 6Translational Medicine, Neuroscience and Rare Diseases, Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd.

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.

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Biology

Miniaturized Sample Preparation for Transmission Electron Microscopy
Claudio Schmidli *1,2, Luca Rima *1, Stefan A. Arnold *1,2, Thomas Stohler 1, Anastasia Syntychaki 1, Andrej Bieri 1, Stefan Albiez 1, Kenneth N. Goldie 1, Mohamed Chami 3, Henning Stahlberg 1, Thomas Braun 1
1Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, 2Swiss Nanoscience Institute, University of Basel, 3BioEM lab, Biozentrum, University of Basel

An instrument and methods for the preparation of nanoliter-sized sample volumes for transmission electron microscopy is presented. No paper-blotting steps are required, thus avoiding the detrimental consequences this can have for proteins, significantly reducing sample loss and enabling the analysis of single cell lysate for visual proteomics.

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JoVE Journal

Injections of Lipopolysaccharide into Mice to Mimic Entrance of Microbial-derived Products After Intestinal Barrier Breach
Katarina Radulovic 1, Rachel Mak’Anyengo 1, Berna Kaya 1, Anna Steinert 1, Jan Hendrik Niess 1,2
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.

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Environment

A Loop-mediated Isothermal Amplification (LAMP) Assay for Rapid Identification of Bemisia tabaci
Simon Blaser 1,2,3, Hanspeter Diem 4, Andreas von Felten 4, Morgan Gueuning 1, Michael Andreou 5, Neil Boonham 6,7, Jennifer Tomlinson 6, Pie Müller 2,3, Jürg Utzinger 2,3, Beatrice Frey 1, Jürg E. Frey 1, Andreas Bühlmann 8
1Department of Method Development and Analytics, Agroscope, 2Swiss Tropical and Public Health Institute, 3University of Basel, 4Swiss Federal Plant Protection Service, Federal Office for Agriculture, 5OptiGene Limited, 6Fera Science Limited, 7School of Natural and Environmental Sciences, Newcastle University, 8Department of Plants and Plant Products, Agroscope

This paper reports the protocol for a rapid identification assay for Bemisia tabaci based on loop-mediated isothermal amplification (LAMP) technology. The protocol requires minimal laboratory training and can, therefore, be implemented on-site at points of entry for plant imports such as seaports and airports.

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Medicine

Measurements of Motor Function and Other Clinical Outcome Parameters in Ambulant Children with Duchenne Muscular Dystrophy
Sara Nagy 1,2, Simone Schmidt 1,2, Patricia Hafner 1,3, Andrea Klein 1,4,5, Daniela Rubino-Nacht 1, Vanya Gocheva 1, Oliver Bieri 6, Carole Vuillerot 7, Ulrike Bonati 1,2, Dirk Fischer 1,2,3
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.

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Biochemistry

Identification of Functional Protein Regions Through Chimeric Protein Construction
Juan M. Adrian-Segarra 1, Holger Lörchner 1,2, Thomas Braun 1,2, Jochen Pöling 1,2
1Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, 2Partner site Rhein-Main, German Centre for Cardiovascular Research (DZHK)

Structurally related proteins frequently exert distinct biological functions. The exchange of equivalent regions of these proteins in order to create chimeric proteins constitutes an innovative approach to identify critical protein regions that are responsible for their functional divergence.

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JoVE Journal

Analysis of Endocytic Uptake and Retrograde Transport to the Trans-Golgi Network Using Functionalized Nanobodies in Cultured Cells
Dominik P. Buser 1, Martin Spiess 1
1Biozentrum, University of Basel

Retrograde transport of proteins from the cell surface to the Golgi is essential to maintain membrane homeostasis. Here, we describe a method to biochemically analyze cell surface-to-Golgi transport of recombinant proteins using functionalized nanobodies in HeLa cells.

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Immunology and Infection

Field Postmortem Rabies Rapid Immunochromatographic Diagnostic Test for Resource-Limited Settings with Further Molecular Applications
Stephanie Mauti 1, Monique Léchenne 2, Service Naïssengar 3, Abdallah Traoré 4, Vessaly Kallo 5,6, Casimir Kouakou 7, Emmanuel Couacy-Hymann 7, Morgane Gourlaouen 8, Céline Mbilo 9,10, Pati Patient Pyana 11, Enos Madaye 3, Ibrahima Dicko 4, Pascal Cozette 1, Paola De Benedictis 8, Hervé Bourhy 1, Jakob Zinsstag 9,10, Laurent Dacheux 1
1Unit Lyssavirus Epidemiology and Neuropathology, National Reference Center for Rabies and WHO Collaborating Center for Reference and Research on Rabies, Institut Pasteur, 2Environment and Sustainability Institute, University of Exeter, Penryn Campus, 3Institut de Recherche en Elevage pour le Développement, 4Laboratoire Central Vétérinaire, 5Direction des Services Vétérinaires, 6Ecole Inter Etats de Sciences et de Médecine Vétérinaires de Dakar, 7Laboratoire Central Vétérinaire de Bingerville, Laboratoire National d'Appui au Développement Agricole Bingerville, 8FAO Reference Centre for Rabies, Istituto Zooprofilattico Sperimentale delle Venezie, 9Swiss Tropical and Public Health Institute, 10University of Basel, 11Institut National de Recherche Biomédicale

We present a complete protocol for postmortem diagnosis of animal rabies under field conditions using a rapid immunochromatographic diagnostic test (RIDT), from brain biopsy sampling to final interpretation. We also describe further applications using the device for molecular analysis and viral genotyping.

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JoVE Core

Mass Spectrometry Analysis to Identify Ubiquitylation of EYFP-tagged CENP-A (EYFP-CENP-A)
Yohei Niikura *1, Lei Fang *2, Risa Kitagawa *3, Peizhao Li 1, Yao Xi 1, Ju You 1, Yan Guo 2, Katsumi Kitagawa 3
1MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 2Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 3Greehey Children's Cancer Institute, Department of Molecular Medicine, UT Health Science Center San Antonio

CENP-A ubiquitylation is an important requirement for CENP-A deposition at the centromere, inherited through dimerization between cell division, and indispensable to cell viability. Here we describe mass spectrometry analysis to identify ubiquitylation of EYFP-tagged CENP-A (EYFP-CENP-A) protein.

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Medicine

Detection and Removal of Tooth-Colored Composite Resin Using the Fluorescence-Aided Identification Technique
Eva Magni *1, Wadim Leontiev *1, Christian Meller 2, Roland Weiger 1, Thomas Connert 1
1Department of Periodontology, Endodontology and Cariology, University Center for Dental Medicine Basel UZB, University of Basel, 2Department of Restorative Dentistry, Periodontology, Endodontology and Pediatric Dentistry, School of Dental Medicine, Eberhard-Karls University

The Fluorescence-aided Identification Technique is a practicable, fast, and reliable approach for the differentiation of composite resin restorations from tooth substance, and facilitates the minimally invasive and complete removal of composite resin restorations and composite bonded trauma splints.

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Medicine

Dynamic Navigation in Endodontics: Guided Access Cavity Preparation by Means of a Miniaturized Navigation System
Wadim Leontiev 1, Thomas Connert 1, Roland Weiger 1, Gabriel Krastl 2, Eva Magni 1
1Department of Periodontology, Endodontology and Cariology, University Center for Dental Medicine Basel UZB, University of Basel, 2Department of Conservative Dentistry and Periodontology, University Hospital of Würzburg

Dynamic navigation systems (DNS) provide real-time visualization and guidance to the operator during endodontic access cavities preparation. The planning of the procedure requires three-dimensional imaging utilizing cone beam computed tomography and surface scans. After the export of the planning data to the DNS, access cavities can be prepared with minimal invasion.

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Medicine

Guided Endodontics: Three-Dimensional Planning and Template-Aided Preparation of Endodontic Access Cavities
Wadim Leontiev 1, Thomas Connert 1, Roland Weiger 1, Dorothea Dagassan-Berndt 2, Gabriel Krastl 3, Eva Magni 1
1Department of Periodontology, Endodontology and Cariology, University Center for Dental Medicine Basel UZB, University of Basel, 2Center for Dental Imaging, University Center for Dental Medicine, University of Basel, 3Department of Conservative Dentistry and Periodontology, University Hospital of Würzburg

Guided endodontics describes a template-aided approach for access cavity preparation. The procedure requires cone-beam computed tomography and a surface scan to produce a template. An incorporated sleeve guides the drill to the target point. This allows the preparation of minimally invasive endodontic access cavities in calcified teeth.

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Biology

A Versatile Glass Jar System for Semihydroponic Root Exudate Profiling
Sarah McLaughlin 1, Charlotte Joller 1,2, Alexandra Siffert 1, Eva Marina Stirnemann 1, Joelle Sasse 1
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.

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Cancer Research

A Hepatocellular Cancer Patient-Derived Organoid Xenograft Model to Investigate Impact of Liver Regeneration on Tumor Growth
Fabian Haak *1, Gabriel Fridolin Hess *1, Philipp Sedlaczek 1, Savas Deniz Soysal 2, Jürg Vosbeck 3, Salvatore Piscuoglio 4,5, Mairene Coto-Llerena *4, Otto Kollmar *1
1Clarunis, Department of Visceral Surgery, University Center for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, 2Faculty of Medicine, University of Basel, 3Institute of Medical Genetics and Pathology, University Hospital Basel, 4Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, 5IRCCS Humanitas Research Hospital

Organoids generated from patient tumors are orthotopically injected into the mouse liver. The resection of non-tumorous liver tissue leads to a regenerative environment in the liver tissue where the tumor is located.

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Immunology and Infection

High-Resolution Three-Dimensional Whole-Organ Tomography of Microbial Infections
Jiagui Li 1, Alaa Alhayek 1, Heng Wang 1, Dirk Bumann 1
1Biozentrum, University of Basel

Here, we describe a procedure that enables organ-wide detection of pathogenic bacteria during infection and quantification of fluorescent reporter activities.

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Immunology and Infection

Three-Dimensional Cell Culture Models to Investigate the Epithelial Barrier in Eosinophilic Esophagitis
Tanay Kaymak 1, Jan Hendrik Niess 1,2
1Department of Biomedicine, University of Basel, 2Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis

Here, a protocol for the culture of human esophageal organoids and air-liquid interface culture is provided. Esophageal organoids' air-liquid interface culture can be used to study the impact of cytokines on the esophageal epithelial barrier.

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