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Russian Academy of Sciences

10 ARTICLES PUBLISHED IN JoVE

Biology

Tracking Morphogenetic Tissue Deformations in the Early Chick Embryo

Benjamen A. Filas¹, Victor D. Varner¹, Dmitry A. Voronov^1,2, Larry A. Taber^1,3

¹Department of Biomedical Engineering, Washington University, ²Institute for Information Transmission Problems, Russian Academy of Sciences, ³Department of Mechanical Engineering and Materials Science, Washington University

This article describes surface labeling and ex ovo tissue culture in the early chick embryo. Techniques amenable to time-lapse bright field, fluorescence, and optical coherence tomography imaging are presented. Tracking surface labels with high spatiotemporal resolution enables kinematic quantities such as morphogenetic strains (deformations) to be calculated in both two and three dimensions.

Biology

Preparation of Segmented Microtubules to Study Motions Driven by the Disassembling Microtubule Ends

Vladimir A. Volkov^1,2, Anatoly V. Zaytsev³, Ekaterina L. Grishchuk³

¹Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, ²Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia, ³Physiology Department, Perelman School of Medicine, University of Pennsylvania

Microtubules are inherently unstable polymers, and their switching between growth and shortening is stochastic and difficult to control. Here we describe protocols using segmented microtubules with photoablatable stabilizing caps. Depolymerization of segmented microtubules can be triggered with high temporal and spatial resolution, thereby assisting analysis of motions with the disassembling microtubule ends.

Neuroscience

Loading a Calcium Dye into Frog Nerve Endings Through the Nerve Stump: Calcium Transient Registration in the Frog Neuromuscular Junction

Dmitry V. Samigullin^1,2,3, Eduard F. Khaziev^1,2,3, Nikita V. Zhilyakov^1,2, Ellya A. Bukharaeva^1,2, Eugeny E. Nikolsky^1,2,4

¹Laboratory of Biophysics of Synaptic Processes, Kazan Scientific Centre, Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, ²Open Laboratory of Neuropharmacology, Kazan Federal University, ³Department of Radiophotonics and Microwave Technologies, A.N. Tupolev Kazan National Research Technical University, ⁴Department of Medical and Biological Physics, Kazan State Medical University

Here, we describe a method for loading a calcium-sensitive dye through the frog nerve stump into the nerve endings. We also present a protocol for the recording and analysis of fast calcium transients in the peripheral nerve endings.

Immunology and Infection

Printed Glycan Array: A Sensitive Technique for the Analysis of the Repertoire of Circulating Anti-carbohydrate Antibodies in Small Animals

Sara Olivera-Ardid^*1, Nailya Khasbiullina^*2,3, Alexey Nokel³, Andrey Formanovsky², Inna Popova², Tatiana Tyrtysh², Roman Kunetskiy², Nadezhda Shilova², Nicolai Bovin^2,4, Daniel Bello-Gil¹, Rafael Mañez^1,5

¹Infectious Pathology and Transplantation Division, Bellvitge Biomedical Research Institute (IDIBELL), ²Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, ³Semiotik LLC, ⁴Auckland University of Technology, ⁵Intensive Care Department, Bellvitge University Hospital

This work shows the potential of printed glycan array (PGA) technology for the analysis of circulating anti-carbohydrate antibodies in small animals.

Biochemistry

Spectrophotometric Determination of Phycobiliprotein Content in Cyanobacterium Synechocystis

Tomáš Zavřel¹, Dominik Chmelík^1,2, 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.

Neuroscience

Geir Ogrim^1,2,3, Juri D. Kropotov^4,5

¹Neuropsychiatric Team, Åsebråten Outpatient Clinic, Østfold Hospital Trust, ²Institute of Psychology, Norwegian University of Science and Technology, ³Gillberg Neuropsychiatry Centre, University of Gothenburg, ⁴P. Bechtereva Institute of the Human Brain, Russian Academy of Sciences, ⁵Department of Neuropsychology, Andrzej Frycz-Modrzewski Krakow University

EEG-methods are applied for extracting biomarkers of brain dysfunctions. The focus is on multi-channel event-related potentials (ERPs) recorded in a cued GO/NOGO task. Non-brain artifacts are corrected and ERPs are compared with the normative data. Examples relate to biomarkers for ADHD diagnosis and prediction of medication response.

Immunology and Infection

Confocal Laser Scanning Microscopy-Based Quantitative Analysis of Aspergillus fumigatus Conidia Distribution in Whole-Mount Optically Cleared Mouse Lung

Ivan V. Maslov¹, Andrey O. Bogorodskiy¹, Mariia V. Pavelchenko¹, Ilia O. Zykov¹, Natalya I. Troyanova², Valentin I. Borshchevskiy^1,3, Marina A. Shevchenko²

¹Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, ²Department of Immunology, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ³Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich

We describe the method for quantitative analysis of the distribution of Aspergillus fumigatus conidia (3 µm in size) in the airways of mice. The method also can be used for the analysis of microparticles and nanoparticle agglomerate distribution in the airways in various pathological condition models.

Biochemistry

Simple In-House Ultra-High Performance Capillary Column Manufacturing with the FlashPack Approach

Sergey I. Kovalchuk¹, Rustam Ziganshin¹, Irina Shelukhina²

¹Laboratory of Bioinformatics Methods in Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ²Department of Molecular Neuroimmune Signalling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences

Here we present a protocol for the optimized FlashPack capillary column packing procedure. Application of an optimized protocol to a common 100-bar pressure bomb setup allows 10-times faster packing and manufacturing of long ultra-high performance capillary columns.

Biochemistry

Analyzing the Interaction of Fluorescent-Labeled Proteins with Artificial Phospholipid Microvesicles using Quantitative Flow Cytometry

Nadezhda Podoplelova^1,2, Polina Soloveva^1,4, Andrei Garzon Dasgupta^1,2,3, Aleksandra Filkova^1,2, Mikhail Panteleev^1,2,3,4

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.

Biochemistry

Pulldown Assay Coupled with Co-Expression in Bacteria Cells as a Time-Efficient Tool for Testing Challenging Protein-Protein Interactions

Artem Bonchuk^1,2, Nikolay Zolotarev¹, Konstantin Balagurov^1,2, Olga Arkova², Pavel Georgiev¹

¹Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, ²Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences

Here, we describe a method for the bacterial co-expression of differentially tagged proteins using a set of compatible vectors, followed by the conventional pulldown techniques to study protein complexes that cannot assemble in vitro.