Lomonosov Moscow State University 5 articles published in JoVE Biology Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches Dmitry K. Nilov1, Alexey V. Zamaraev2, Boris Zhivotovsky2,3, Gelina S. Kopeina2 1Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 2Faculty of Medicine, Lomonosov Moscow State University, 3Division of Toxicology, Institute of Environmental Medicine, Karolinska Institute The present protocol uses a biomolecular simulation package and describes the molecular dynamics (MD) approach for modeling the wild-type caspase and its mutant forms. The MD method allows for assessing the dynamic evolution of the caspase structure and the potential effect of mutations or post-translational modifications. Biology Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography Sophie Sosnovskaya*1,2, Amir N. Zakirov*1,2, Ekaterina D. Ryumina*1,3, Ekaterina Kharybina1,2, Sergei A. Golyshev1, Olga S. Strelkova1, Oxana A. Zhironkina1, Andrei Moiseenko2, Anton Orekhov4, Igor I. Kireev1,2,5 1Belozersky Institute of Physico-chemical Biology, Lomonosov Moscow State University, 2Faculty of Biology, Lomonosov Moscow State University, 3Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 4National Research Center, Kurchatov Institute, 5V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology, and Perinatology This protocol presents a technique for high-resolution mapping of replication sites in structurally preserved chromatin in situ that employs a combination of pre-embedding EdU-streptavidin-Nanogold labeling and ChromEMT. Biochemistry Analyzing the Interaction of Fluorescent-Labeled Proteins with Artificial Phospholipid Microvesicles using Quantitative Flow Cytometry Nadezhda Podoplelova1,2, Polina Soloveva1,4, Andrei Garzon Dasgupta1,2,3, Aleksandra Filkova1,2, Mikhail Panteleev1,2,3,4 1Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 2National Medical Research Center of Pediatric Hematology, Oncology and Immunology named after Dmitry Rogachev, 3Faculty of Physics, Lomonosov Moscow State University, 4Faculty of Biological and Medical Physics, Moscow Institute of Physics and Technology Here, we describe a set of methods for characterizing the interaction of proteins with membranes of cells or microvesicles. Bioengineering Microtubule Plus-End Dynamics Visualization in Huntington's Disease Model based on Human Primary Skin Fibroblasts Aleksandra Taran*1,2, Lilia Belikova (Shuvalova)*2,3, Svetlana Lavrushkina1,2, Alexandra Bogomazova3,4, Maria Lagarkova3,4, Irina Alieva1,3 1A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 2Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 3Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 4Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency This protocol is dedicated to the microtubule plus-end visualization by EB3 protein transfection to study their dynamic properties in primary cell culture. The protocol was implemented on human primary skin fibroblasts obtained from Huntington's disease patients. Developmental Biology Brain Organoid Generation from Induced Pluripotent Stem Cells in Home-Made Mini Bioreactors Artem Eremeev1,3, Lilia Belikova1,2, Evgeny Ruchko1, Egor Volovikov1,5, Olga Zubkova1, Alexy Emelin4, Roman Deev4, Olga Lebedeva1,3, Alexandra Bogomazova1,3, Maria Lagarkova1,3 1Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, 2Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 3Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, 4Department of Pathological Anatomy, North-Western State Medical University, 5Department of Biology, Lomonosov State University Here we describe a protocol for generating brain organoids from human induced pluripotent stem cells (iPSCs). To obtain brain organoids in large quantities and of high quality, we use home-made mini bioreactors.