Seoul National University 25 articles published in JoVE Chemistry Synthesis of Triazole and Tetrazole-Functionalized Zr-Based Metal-Organic Frameworks Through Post-Synthetic Ligand Exchange Sangho Lee*1, Daeyeon Lee*1, Jin Yeong Kim2, Min Kim1 1Department of Chemistry, Chungbuk National University, 2Department of Chemistry Education, Seoul National University Post-synthetic ligand exchange (PSE) is a versatile and powerful tool for installing functional groups into metal-organic frameworks (MOFs). Exposing MOFs to solutions containing triazole- and tetrazole-functionalized ligands can incorporate these heterocyclic moieties into Zr-MOFs through PSE processes. Biochemistry High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements Celine Park*1, Taehyun Yang*1, Sang-Hyun Rah1, Hyun Gyu Kim2,3, Tae-Young Yoon2,3, Min Ju Shon1,4 1Department of Physics, Pohang University of Science and Technology (POSTECH), 2School of Biological Sciences, Seoul National University, 3Institute for Molecular Biology and Genetics, Seoul National University, 4School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH) Here, we describe a high-speed magnetic tweezer setup that performs nanomechanical measurements on force-sensitive biomolecules at the maximum rate of 1.2 kHz. We introduce its application to DNA hairpins and SNARE complexes as model systems, but it will be also applicable to other molecules involved in mechanobiological events. Neuroscience Optrode Array for Simultaneous Optogenetic Modulation and Electrical Neural Recording Youjin Lee*1,2, Daeho Ryu*3, Saeyeong Jeon3, Yena Lee1, Yoon Kyung Cho1, Chang-Hyeon Ji1,2, Yong-Kweon Kim3,4, Sang Beom Jun1,2,5 1Department of Electronic and Electrical Engineering, Ewha Womans University, 2Graduate Program in Smart Factory, Ewha Womans University, 3Department of Electrical and Computer Engineering, Seoul National University, 4Graduate School of Engineering Practice, Seoul National University, 5Department of Brain and Cognitive Sciences, Ewha Womans University Here, we present the fabrication method of an optrode system with optical fibers for light delivery and an electrode array for neural recording. In vivo experiments with transgenic mice expressing channelrhodopsin-2 show the feasibility of the system for simultaneous optogenetic stimulation and electrophysiological recording. Engineering Fabrication of Micro-Patterned Chip with Controlled Thickness for High-Throughput Cryogenic Electron Microscopy Min-Ho Kang1,2, Minyoung Lee3,4, Sungsu Kang3,4, Jungwon Park3,4,5,6 1Department of Biomedical-Chemical Engineering, The Catholic University of Korea, 2Department of Biotechnology, The Catholic University of Korea, 3School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, 4Center for Nanoparticle Research, Institute of Basic Science (IBS), 5Institute of Engineering Research, College of Engineering, Seoul National University, 6Advanced Institutes of Convergence Technology, Seoul National University A newly developed micro-patterned chip with graphene oxide windows is fabricated by applying microelectromechanical system techniques, enabling efficient and high-throughput cryogenic electron microscopy imaging of various biomolecules and nanomaterials. Neuroscience µTongue: A Microfluidics-Based Functional Imaging Platform for the Tongue In Vivo Jisoo Han1,2, Pyonggang Choi3, Myunghwan Choi3 1Department of Biomedical Engineering, Sungkyunkwan University, 2Center for Neuroscience Imaging Research, Institute for Basic Science, 3School of Biological Sciences, Seoul National University The article introduces the µTongue (microfluidics-on-a-tongue) device for functional taste cell imaging in vivo by integrating microfluidics into an intravital imaging window on the tongue. Behavior Using a Virtual Reality Walking Simulator to Investigate Pedestrian Behavior Hyun Chae Chung1, Soon Ho Kim2, Gyoojae Choi3, Jong Won Kim4, Moo Young Choi2, Hui Li1 1Department of Sport and Exercise Sciences, Kunsan National University, 2Department of Physics and Astronomy, Seoul National University, 3School of Mechanical and Automotive Engineering, Kunsan National University, 4Department of Healthcare Information Technology, Inje University This protocol describes use of a walking simulator that serves as a safe and ecologically valid method to study pedestrian behavior in the presence of moving traffic. Bioengineering Lab-on-a-CD Platform for Generating Multicellular Three-dimensional Spheroids Daehan Kim1, Gi-Hun Lee1, Jiheum Park2, Jung Chan Lee2, Joong Yull Park1 1Department of Mechanical Engineering, Graduate School, Chung-Ang University, 2Department of Biomedical Engineering, College of Medicine, Seoul National University We present a motor-powered centrifugal microfluidic device that can cultivate cell spheroids. Using this device, spheroids of single or multiple cell types could be easily cocultured under high gravity conditions. Bioengineering Isokinetic Robotic Device to Improve Test-Retest and Inter-Rater Reliability for Stretch Reflex Measurements in Stroke Patients with Spasticity Minki Sin*1, Won-Seok Kim*2, Kyujin Cho3, Nam-Jong Paik2 1Department of Medical Assistant Robot, Daegu Research Center, Korea Institute of Machinery & Materials, 2Department of Rehabilitation Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 3School of Mechanical and Aerospace Engineering, Seoul National University/IAMD Using a robotic isokinetic device with electromyography (EMG) measurements, this protocol illustrates that isokinetic motion itself can improve inter-rater reliability for the angle of catch measurements in stroke patients with mild elbow flexor spasticity. Bioengineering Design and Synthesis of a Reconfigurable DNA Accordion Rack Yeongjae Choi*1, Hansol Choi*1, Amos C. Lee*2, Sunghoon Kwon1,2,3,4 1Department of Electrical and Computer Engineering, Seoul National University, 2Interdisciplinary Program for Bioengineering, Seoul National University, 3Institute of Entrepreneurial Bio Convergence, Seoul National University, 4Seoul National University Hospital Biomedical Research Institute, Seoul National University Hospital We describe the detailed protocol for design, simulation, wet-lab experiments, and analysis for a reconfigurable DNA accordion rack of 6 by 6 meshes. Cancer Research Preclinical Assessment of the Bioactivity of the Anticancer Coumarin OT48 by Spheroids, Colony Formation Assays, and Zebrafish Xenografts Jin-Young Lee*1, Aloran Mazumder*1, Marc Diederich1 1Department of Pharmacy, College of Pharmacy, Seoul National University Here, we present the preclinical screening of anticancer coumarins using 3D culture and zebrafish. Biology Split Green Fluorescent Protein System to Visualize Effectors Delivered from Bacteria During Infection Hye-Young Lee1, So Eui Lee1, Jongchan Woo2, Doil Choi1, Eunsook Park1 1Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, 2Department of Bioindustry and Bioresource Engineering, Sejong University Fluorescent protein-based approaches to monitor effectors secreted by bacteria into host cells are challenging. This is due to the incompatibility between fluorescent proteins and the type-III secretion system. Here, an optimized split superfolder GFP system is used for visualization of effectors secreted by bacteria into the host plant cell. Engineering Design and Evaluation of Smart Glasses for Food Intake and Physical Activity Classification Jungman Chung1, Wonjoon Oh2, Dongyoub Baek3, Sunwoong Ryu2, Won Gu Lee4, Hyunwoo Bang2 1School of Mechanical and Aerospace Engineering, Seoul National University, 2Envisible, Inc., 3Curiosis, Inc., 4Department of Mechanical Engineering, Kyung Hee University This study presents a protocol of designing and manufacturing a glasses-type wearable device that detects the patterns of food intake and other featured physical activities using load cells inserted in both hinges of the glasses. Chemistry Liquid-cell Transmission Electron Microscopy for Tracking Self-assembly of Nanoparticles Byung Hyo Kim1,2, Junyoung Heo1,2, Won Chul Lee3, Jungwon Park1,2 1Center for Nanoparticle Research, Institute for Basic Science (IBS), 2School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 3Department of Mechanical Engineering, Hanyang University Here we introduce experimental protocols for the real-time observation of a self-assembly process using liquid-cell transmission electron microscopy. Engineering Experimental Methods for Trapping Ions Using Microfabricated Surface Ion Traps Seokjun Hong1, Minjae Lee1, Yeong-Dae Kwon2, Dong-il "Dan" Cho1, Taehyun Kim2 1ISRC/ASRI, Department of Electrical and Computer Engineering, Seoul National University, 2Quantum Tech. Lab, SK Telecom This paper presents a microfabrication methodology for surface ion traps, as well as a detailed experimental procedure for trapping ytterbium ions in a room-temperature environment. Biochemistry Oligopeptide Competition Assay for Phosphorylation Site Determination Min Sung Joo1, Ja Hyun Koo1, Sol-Bi Shin2, Hyungshin Yim2, Sang Geon Kim1 1College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 2College of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University Peptide competition assays are widely used in a variety of molecular and immunological experiments. This paper describes a detailed method for an in vitro oligopeptide-competing kinase assay and the associated validation procedures, which may be useful to find specific phosphorylation sites. Bioengineering Merging Ion Concentration Polarization between Juxtaposed Ion Exchange Membranes to Block the Propagation of the Polarization Zone Minyoung Kim1,2, Hyunjoon Rhee1,3, Ji Yoon Kang1, Tae Song Kim1, Rhokyun Kwak1 1Center for BioMicrosystems, Korea Institute of Science and Technology, 2Department of Mechanical Engineering, Seoul National University, 3Department of Industrial Engineering, University of Illinois Urbana-Champaign The protocol for a novel ion concentration polarization (ICP) platform that can stop the propagation of the ICP zone, regardless of the operating conditions is described. This unique ability of the platform lies in the use of merging ion depletion and enrichment, which are two polarities of the ICP phenomenon. Behavior Repetitive Transcranial Magnetic Stimulation to the Unilateral Hemisphere of Rat Brain Jaewon Beom1,2, Jung Chan Lee2,3,4, Jin Chul Paeng5, Tai Ryoon Han6, Moon Suk Bang7, Byung-Mo Oh7 1Department of Rehabilitation Medicine, Chungnam National University Hospital, Daejeon, 2Department of Biomedical Engineering, Seoul National University College of Medicine, 3Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University, 4Department of Biomedical Engineering, Seoul National University Hospital, 5Department of Nuclear Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 6Department of Rehabilitation Medicine, Gangwon Do Rehabilitation Hospital, 7Department of Rehabilitation Medicine, Seoul National University Hospital, Seoul National University College of Medicine We applied repetitive transcranial magnetic stimulation (rTMS) to the unilateral hemisphere of rat brain, by placing a 25-mm figure-8 coil 1 cm lateral to the vertex on the biauricular line and angulating the coil by 45°. An in-house water cooling system was used for rTMS for more than 20 min. Medicine Combined Near-infrared Fluorescent Imaging and Micro-computed Tomography for Directly Visualizing Cerebral Thromboemboli Dong-Eog Kim1, Jeong-Yeon Kim1, Su-Kyoung Lee1, Ju Hee Ryu2, Ick Chan kwon2, Cheol-Hee Ahn3, Kwangmeyung Kim2, Dawid Schellingerhout4 1Molecular Imaging and Neurovascular Research Laboratory, Dongguk University College of Medicine, 2Biomedical Research Center, Korea Institute of Science and Technology, 3Research Institute of Advanced Materials, Department of Materials Science and Engineering, Seoul National University, 4Departments of Radiology and Cancer Systems Imaging, University of Texas M.D. Anderson Cancer Center This protocol describes the application of combined near-infrared fluorescent (NIRF) imaging and micro-computed tomography (microCT) for visualizing cerebral thromboemboli. This technique allows the quantification of thrombus burden and evolution. The NIRF imaging technique visualizes fluorescently labeled thrombus in excised brain, while the microCT technique visualizes thrombus inside living animals using gold-nanoparticles. Bioengineering Robotic Mirror Therapy System for Functional Recovery of Hemiplegic Arms Jaewon Beom*1,2, Sukgyu Koh*3, Hyung Seok Nam1, Wonshik Kim3, Yoonjae Kim3, Han Gil Seo4, Byung-Mo Oh4,5, Sun Gun Chung4,5, Sungwan Kim1,6 1Department of Biomedical Engineering, Seoul National University College of Medicine, 2Department of Rehabilitation Medicine, Chungnam National University Hospital, 3Interdisciplinary Program for Bioengineering, Seoul National University Graduate School, 4Department of Rehabilitation Medicine, Seoul National University Hospital, 5Seoul National University College of Medicine, 6Institute of Medical and Biological Engineering, Seoul National University We developed a real-time mirror robot system for functional recovery of hemiplegic arms using automatic control technology, conducted a clinical study on healthy subjects, and determined tasks through feedback from rehabilitation doctors. This simple mirror robot can be applied effectively to occupational therapy in stroke patients with a hemiplegic arm. Biology Observation and Quantification of Telomere and Repetitive Sequences Using Fluorescence In Situ Hybridization (FISH) with PNA Probes in Caenorhabditis elegans Beomseok Seo1, Junho Lee1,2,3 1Institute of Molecular Biology and Genetics (IMBG), Seoul National University, 2Department of Biological Sciences, Seoul National University, 3Department of Biophysics and Chemical Biology, Seoul National University We report a concise procedure of fluorescence in situ hybridization (FISH) in the gonad and embryos of Caenorhabditis elegans for observing and quantifying repetitive sequences. We successfully observed and quantified two different repetitive sequences, telomere repeats and template of alternative lengthening of telomeres (TALT). Neuroscience Imaging Membrane Potential with Two Types of Genetically Encoded Fluorescent Voltage Sensors Sungmoo Lee1,2, Hong Hua Piao2, Masoud Sepheri-Rad2, Arong Jung2,3, Uhna Sung2, Yoon-Kyu Song1,4, Bradley J. Baker2 1Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, 2Center for Functional Connectomics, Korea Institute of Science and Technology, 3College of Life Sciences and Biotechnology, Korea University, 4Advanced Institutes of Convergence Technology A method for imaging changes in membrane potential using genetically encoded voltage indicators is described. Bioengineering Fabrication of Mechanically Tunable and Bioactive Metal Scaffolds for Biomedical Applications Hyun-Do Jung1, Hyun Lee2, Hyoun-Ee Kim2,3, Young-Hag Koh4, Juha Song3 1Liquid Processing & Casting Technology R&D Group, Korea Institute of Industrial Technology, 2Department of Materials Science and Engineering, Seoul National University, 3Advanced Institutes of Convergence Technology, Seoul National University, 4School of Biomedical Engineering, Korea University Bioactive and mechanically reliable metal scaffolds have been fabricated through a method which consists of two processes, dynamic freeze casting for the fabrication of porous Ti, and coating and densification of the Ti scaffolds. The densification process is simple, effective and applicable to the fabrication of functionally graded scaffolds. Biology Employing Digital Droplet PCR to Detect BRAF V600E Mutations in Formalin-fixed Paraffin-embedded Reference Standard Cell Lines Nirmal Rajasekaran1, Myung Ryurl Oh3, Sung-Su Kim1, Si Eun Kim3, Young Deug Kim4, Hyun-Jeung Choi2, Bohyun Byun2, Young Kee Shin1,2 1Research Institute of Pharmaceutical Science, Department of Pharmacy, College of Pharmacy, Seoul National University, 2The Center for Anti-Cancer CDx, N-Bio, Seoul National University, 3ABION CRO, 4ABION Inc., R&D Center The goal of this video is to demonstrate how to perform automated DNA extraction from formalin-fixed paraffin-embedded (FFPE) reference standard cell lines and digital droplet PCR (ddPCR) analysis to detect rare mutations in a clinical setting. Detecting mutations in FFPE samples demonstrates the clinical utility of ddPCR in FFPE samples. Immunology and Infection In Situ Detection of Bacteria within Paraffin-embedded Tissues Using a Digoxin-labeled DNA Probe Targeting 16S rRNA Yun Sik Choi1, Yong Cheol Kim1, Keum Jin Baek1, Youngnim Choi1 1Department of Oral Microbiology and Immunology, School of Dentistry and Dental Research Institute, Seoul National University Here a method to localize bacteria within paraffin-embedded tissues using DIG-labeled 16S rRNA-targeting DNA probes has been described. This protocol can be applied to study the role of bacteria in various diseases such as periodontitis, cancers, and inflammatory immune diseases. Chemistry Surface Passivation for Single-molecule Protein Studies Stanley D. Chandradoss1, Anna C. Haagsma1, Young Kwang Lee2, Jae-Ho Hwang2, Jwa-Min Nam2, Chirlmin Joo1 1Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2Department of Chemistry, Seoul National University We describe a method for passivating a glass surface using polyethylene glycol (PEG). This protocol covers surface cleaning, surface functionalization, and PEG coating. We introduce a new strategy for treating the surface with PEG molecules over two rounds, which yields superior quality of passivation compared to existing methods.