Masaryk University 7 articles published in JoVE Biology Measurement of Liver Stiffness Using Atomic Force Microscopy Coupled with Polarization Microscopy Srikant Ojha1, Jan Pribyl2, Simon Klimovic2,3, Daniel Hadraba4, Marketa Jirouskova1, Martin Gregor1 1Laboratory of Integrative Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 2CEITEC MU, Masaryk University, 3Department of Biochemistry, Faculty of Science, Masaryk University, 4Laboratory of Biomathematics, Czech-BioImaging IPHYS, Institute of Physiology of the Czech Academy of Sciences We present a protocol to measure the elastic moduli of collagen-rich areas in normal and diseased liver using atomic force microscopy. The simultaneous use of polarization microscopy provides high spatial precision for localizing collagen-rich areas in the liver sections. Biochemistry Preparation and Cryo-FIB micromachining of Saccharomyces cerevisiae for Cryo-Electron Tomography Jana Moravcová1, Matyáš Pinkas1, Radka Holbová1, Jiří Nováček1 1Central European Institute of Technology, Masaryk University We present a protocol for lamella preparation of plunge frozen biological specimens by cryo-focused ion beam micromachining for high-resolution structural studies of macromolecules in situ with cryo-electron tomography. The presented protocol provides guidelines for the preparation of high-quality lamellae with high reproducibility for structural characterization of macromolecules inside the Saccharomyces cerevisiae. Developmental Biology Rapid Isolation of Single Cells from Mouse and Human Teeth Jan Krivanek1, Josef Lavicky1, Thibault Bouderlique2, Igor Adameyko2,3 1Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 2Department of Molecular Neuroimmunology, Centre for Brain Research, Medical University of Vienna, 3Department of Physiology and Pharmacology, Karolinska Institute The current protocol presents a fast, efficient, and gentle method for isolating single cells suitable for single-cell RNA-seq analysis from a continuously growing mouse incisor, mouse molar, and human teeth. Biochemistry Cryo-EM and Single-Particle Analysis with Scipion A. Jiménez-Moreno1, L. del Caño1, M. Martínez1, E. Ramírez-Aportela1, A. Cuervo1, R. Melero1, R. Sánchez-García1, D. Strelak1,2,3, E. Fernández-Giménez1, F.P. de Isidro-Gómez1, D. Herreros1, P. Conesa1, Y. Fonseca1, D. Maluenda1, J. Jiménez de la Morena1, J.R. Macías1, P. Losana1, R. Marabini1, J.M. Carazo1, C.O.S. Sorzano1,4 1Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid, 2Faculty of Informatics, Masaryk University, 3Institute of Computer Science, Masaryk University, 4Campus Urbanización Montepríncipe, Universidad San Pablo CEU Single-particle analysis in cryo-electron microscopy is one of the main techniques used to determine the structure of biological ensembles at high resolution. Scipion provides the tools to create the whole pipeline to process the information acquired by the microscope and achieve a 3D reconstruction of the biological specimen. Developmental Biology Human Egg Maturity Assessment and Its Clinical Application Zuzana Holubcová1,2, Drahomíra Kyjovská1, Martina Martonová1, Darja Páralová1, Tereza Klenková1, Soňa Kloudová1 1Reprofit International, Clinic of Reproductive Medicine, 2Department of Histology and Embryology, Faculty of Medicine, Masaryk University We provide an outline of the clinical protocol for non-invasive assessment of human egg maturity using polarized light microscopy. Biochemistry Spectrophotometric Determination of Phycobiliprotein Content in Cyanobacterium Synechocystis Tomáš Zavřel1, Dominik Chmelík1,2, Maria A. Sinetova3, Jan Červený1 1Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences, 2Department of Plant Physiology, Faculty of Science, Masaryk University, 3Laboratory of Intracellular Regulation, Institute of Plant Physiology, Russian Academy of Sciences Here, we present a protocol to quantitatively determine phycobiliprotein content in the cyanobacterium Synechocystis using a spectrophotometric method. The extraction procedure was also successfully applied to other cyanobacteria and algae strains; however, due to variations in pigment absorption spectra, it is necessary to test the spectrophotometric equations for each strain individually. Biology Gap Junctional Intercellular Communication: A Functional Biomarker to Assess Adverse Effects of Toxicants and Toxins, and Health Benefits of Natural Products Brad L. Upham1, Iva Sovadinová2, Pavel Babica2 1Department of Pediatrics & Human Development, Institute for Integrative Toxicology, Michigan State University, 2RECETOX — Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University This protocol describes a scalpel loading-fluorescent dye transfer technique that measures intercellular communication through gap junction channels. Gap junctional intercellular communication is a major cellular process by which tissue homeostasis is maintained and disruption of this cell signaling has adverse health effects.