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University of Zürich

16 ARTICLES PUBLISHED IN JoVE

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Medicine

Roux-en-Y Gastric Bypass Operation in Rats
Marco Bueter 1,2, Kathrin Abegg 2,3, Florian Seyfried 4, Thomas A. Lutz 2,3, Carel W. le Roux 4
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.

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Biology

Efficient and Rapid Isolation of Early-stage Embryos from Arabidopsis thaliana Seeds
Michael T. Raissig 1, Valeria Gagliardini 1, Johan Jaenisch 1, Ueli Grossniklaus 1, Célia Baroux 1
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.

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Medicine

Accuracy in Dental Medicine, A New Way to Measure Trueness and Precision
Andreas Ender 1, Albert Mehl 1
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.

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JoVE Journal

Mizoroki-Heck Cross-coupling Reactions Catalyzed by Dichloro{bis[1,1',1''-(phosphinetriyl)tripiperidine]}palladium Under Mild Reaction Conditions
Miriam Oberholzer 1, Christian M. Frech 2
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.

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Biology

An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis
Wenjing She 1, Daniel Grimanelli 2, Célia Baroux 1
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.

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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 Marinova 1, Susanne Walitza 1, Edna Grünblatt 1
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.

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Biology

Laser-assisted Microdissection (LAM) as a Tool for Transcriptional Profiling of Individual Cell Types
Ana Marcela Florez Rueda 1, Ueli Grossniklaus 1, Anja Schmidt 1
1University of Zürich & Zürich-Basel Plant Science Center

Here we present a protocol for laser-assisted microdissection of specific plant cell types for transcriptional profiling. While the protocol is suitable for different species and cell types, the focus is on highly inaccessible cells of the female germline important for sexual and apomictic reproduction in the crucifer genus Boechera.

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Biology

The Mouse Isolated Perfused Kidney Technique
Jan Czogalla 1, Frank Schweda 2, Johannes Loffing 1
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.

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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 Bourras 3, William Underwood 4, Beat Keller 3, Shauna C. Somerville 1
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.

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Developmental Biology

Whole-mount Clearing and Staining of Arabidopsis Flower Organs and Siliques
Afif Hedhly 1, Hannes Vogler 1, Christof Eichenberger 1, Ueli Grossniklaus 1
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.

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Biology

Cystometric and External Urethral Sphincter Measurements in Awake Rats with Implanted Catheter and Electrodes Allowing for Repeated Measurements
Elena E. Foditsch 1,2, Karin Roider 1,2, Andrea M. Sartori 3,4,5, Thomas M. Kessler 5, Sabik Raj Kayastha 6, Ludwig Aigner 2, Marc P. Schneider 7
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.

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Behavior

A Networked Desktop Virtual Reality Setup for Decision Science and Navigation Experiments with Multiple Participants
Hantao Zhao 1, Tyler Thrash 1,2,3, Stefan Wehrli 4, Christoph Hölscher 1, Mubbasir Kapadia 5, Jascha Grübel 1, Raphael P. Weibel 1, Victor R. Schinazi 1
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.

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Behavior

Virtual Reality Experiments with Physiological Measures
Raphael P. Weibel 1, Jascha Grübel 1, Hantao Zhao 1, Tyler Thrash 1,2,3, Dario Meloni 1, Christoph Hölscher 1, Victor R. Schinazi 1
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.

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Biology

Flow Cytometric Analysis of Extracellular Vesicles from Cell-conditioned Media
Carolina Balbi *1, Sara Bolis *1, Giuseppe Vassalli 1,2,3, Lucio Barile 1
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.

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Immunology and Infection

Infecting Mice with Malassezia spp. to Study the Fungus-Host Interaction
Florian Sparber 1, Salomé LeibundGut-Landmann 1
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.

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Biochemistry

Measuring Caspase Activity Using a Fluorometric Assay or Flow Cytometry
Jing Tong 1, Stefanie Rufli 1, Wendy Wei-Lynn Wong 1
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.

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