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26 ARTICLES PUBLISHED IN JoVE

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Chemistry

Surface Passivation for Single-molecule Protein Studies
Stanley D. Chandradoss 1, Anna C. Haagsma 1, Young Kwang Lee 2, Jae-Ho Hwang 2, Jwa-Min Nam 2, Chirlmin Joo 1
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.

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Biology

Employing Digital Droplet PCR to Detect BRAF V600E Mutations in Formalin-fixed Paraffin-embedded Reference Standard Cell Lines
Nirmal Rajasekaran 1, Myung Ryurl Oh 3, Sung-Su Kim 1, Si Eun Kim 3, Young Deug Kim 4, Hyun-Jeung Choi 2, Bohyun Byun 2, Young Kee Shin 1,2
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.

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JoVE Core

Fabrication of Mechanically Tunable and Bioactive Metal Scaffolds for Biomedical Applications
Hyun-Do Jung 1, Hyun Lee 2, Hyoun-Ee Kim 2,3, Young-Hag Koh 4, Juha Song 3
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.

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Neuroscience

Imaging Membrane Potential with Two Types of Genetically Encoded Fluorescent Voltage Sensors
Sungmoo Lee 1,2, Hong Hua Piao 2, Masoud Sepheri-Rad 2, Arong Jung 2,3, Uhna Sung 2, Yoon-Kyu Song 1,4, Bradley J. Baker 2
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.

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Medicine

Use of Rabbit Eyes in Pharmacokinetic Studies of Intraocular Drugs
Seong Joon Ahn 1,2,3, Hye Kyoung Hong 1, Young Mi Na 1, Sang Jun Park 1,2, Jeeyun Ahn 1,2,4, Jaeseong Oh 5, Jae Yong Chung 6, Kyu Hyung Park 1,2, Se Joon Woo 1,2
1Department of Ophthalmology, Seoul National University Bundang Hospital, 2Department of Ophthalmology, College of Medicine, Seoul National University, 3Department of Ophthalmology, Hanyang University Hospital, 4Department of Ophthalmology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, 5Department of Clinical Pharmacology, Seoul National University Hospital, 6Department of Clinical Pharmacology, Seoul National University Bundang Hospital

Rabbits are widely used to study the pharmacokinetics of intraocular drugs. We describe a method for conducting pharmacokinetic studies of intraocular drugs using rabbit eyes.

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Behavior

Repetitive Transcranial Magnetic Stimulation to the Unilateral Hemisphere of Rat Brain
Jaewon Beom 1,2, Jung Chan Lee 2,3,4, Jin Chul Paeng 5, Tai Ryoon Han 6, Moon Suk Bang 7, Byung-Mo Oh 7
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.

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Biology

Observation and Quantification of Telomere and Repetitive Sequences Using Fluorescence In Situ Hybridization (FISH) with PNA Probes in Caenorhabditis elegans
Beomseok Seo 1, Junho Lee 1,2,3
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).

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Medicine

Combined Near-infrared Fluorescent Imaging and Micro-computed Tomography for Directly Visualizing Cerebral Thromboemboli
Dong-Eog Kim 1, Jeong-Yeon Kim 1, Su-Kyoung Lee 1, Ju Hee Ryu 2, Ick Chan kwon 2, Cheol-Hee Ahn 3, Kwangmeyung Kim 2, Dawid Schellingerhout 4
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.

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Bioengineering

Robotic Mirror Therapy System for Functional Recovery of Hemiplegic Arms
Jaewon Beom *1,2, Sukgyu Koh *3, Hyung Seok Nam 1, Wonshik Kim 3, Yoonjae Kim 3, Han Gil Seo 4, Byung-Mo Oh 4,5, Sun Gun Chung 4,5, Sungwan Kim 1,6
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.

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Bioengineering

Merging Ion Concentration Polarization between Juxtaposed Ion Exchange Membranes to Block the Propagation of the Polarization Zone
Minyoung Kim 1,2, Hyunjoon Rhee 1,3, Ji Yoon Kang 1, Tae Song Kim 1, Rhokyun Kwak 1
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.

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Biochemistry

Oligopeptide Competition Assay for Phosphorylation Site Determination
Min Sung Joo 1, Ja Hyun Koo 1, Sol-Bi Shin 2, Hyungshin Yim 2, Sang Geon Kim 1
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.

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Engineering

Experimental Methods for Trapping Ions Using Microfabricated Surface Ion Traps
Seokjun Hong 1, Minjae Lee 1, Yeong-Dae Kwon 2, Dong-il "Dan" Cho 1, Taehyun Kim 2
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.

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Chemistry

Liquid-cell Transmission Electron Microscopy for Tracking Self-assembly of Nanoparticles
Byung Hyo Kim 1,2, Junyoung Heo 1,2, Won Chul Lee 3, Jungwon Park 1,2
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.

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Engineering

Design and Evaluation of Smart Glasses for Food Intake and Physical Activity Classification
Jungman Chung 1, Wonjoon Oh 2, Dongyoub Baek 3, Sunwoong Ryu 2, Won Gu Lee 4, Hyunwoo Bang 2
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.

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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 Diederich 1
1Department of Pharmacy, College of Pharmacy, Seoul National University

Here, we present the preclinical screening of anticancer coumarins using 3D culture and zebrafish.

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Biology

Split Green Fluorescent Protein System to Visualize Effectors Delivered from Bacteria During Infection
Hye-Young Lee 1, So Eui Lee 1, Jongchan Woo 2, Doil Choi 1, Eunsook Park 1
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.

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Neuroscience

Spectral Reflectometric Microscopy on Myelinated Axons In Situ
Junhwan Kwon 1,2, Myunghwan Choi 1,2
1Department of Biomedical Engineering, Sungkyunkwan University, 2Center for Neuroscience Imaging Research, Institute for Basic Science (IBS)

Here, we present a step-by-step protocol for imaging myelinated axons in a fixed brain slice using a label-free nanoscale imaging technique based on spectral reflectometry.

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Bioengineering

Design and Synthesis of a Reconfigurable DNA Accordion Rack
Yeongjae Choi *1, Hansol Choi *1, Amos C. Lee *2, Sunghoon Kwon 1,2,3,4
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.

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Biochemistry

Studying Protein Import into Chloroplasts Using Protoplasts
Junho Lee 1, Hyangju Kang 1, Inhwan Hwang 1,2
1Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, 2Department of Life Sciences, Pohang University of Science and Technology

Here we describe a protocol to express proteins into protoplasts by using PEG-mediated transformation method. The method provides easy expression of proteins of interest, and efficient investigation of protein localization and the import process for various experimental conditions in vivo.

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Bioengineering

Lab-on-a-CD Platform for Generating Multicellular Three-dimensional Spheroids
Daehan Kim 1, Gi-Hun Lee 1, Jiheum Park 2, Jung Chan Lee 2, Joong Yull Park 1
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.

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Behavior

Using a Virtual Reality Walking Simulator to Investigate Pedestrian Behavior
Hyun Chae Chung 1, Soon Ho Kim 2, Gyoojae Choi 3, Jong Won Kim 4, Moo Young Choi 2, Hui Li 1
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.

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Neuroscience

µTongue: A Microfluidics-Based Functional Imaging Platform for the Tongue In Vivo
Jisoo Han 1,2, Pyonggang Choi 3, Myunghwan Choi 3
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.

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Neuroscience

Optrode Array for Simultaneous Optogenetic Modulation and Electrical Neural Recording
Youjin Lee *1,2, Daeho Ryu *3, Saeyeong Jeon 3, Yena Lee 1, Yoon Kyung Cho 1, Chang-Hyeon Ji 1,2, Yong-Kweon Kim 3,4, Sang Beom Jun 1,2,5
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.

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Engineering

Fabrication of Micro-Patterned Chip with Controlled Thickness for High-Throughput Cryogenic Electron Microscopy
Min-Ho Kang 1,2, Minyoung Lee 3,4, Sungsu Kang 3,4, Jungwon Park 3,4,5,6
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.

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Biochemistry

High-Speed Magnetic Tweezers for Nanomechanical Measurements on Force-Sensitive Elements
Celine Park *1, Taehyun Yang *1, Sang-Hyun Rah 1, Hyun Gyu Kim 2,3, Tae-Young Yoon 2,3, Min Ju Shon 1,4
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.

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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 Kim 2, Min Kim 1
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.

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