Korea Advanced Institute of Science and Technology (KAIST) 8 articles published in JoVE Neuroscience Successful In vivo Calcium Imaging with a Head-Mount Miniaturized Microscope in the Amygdala of Freely Behaving Mouse Han-Sol Lee1,2, Jin-Hee Han1,2 1Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 2KAIST Institute for BioCentury (KIB), Korea Advanced Institute of Science and Technology (KAIST) In vivo microendoscopic calcium imaging is an invaluable tool that enables real-time monitoring of neuronal activities in freely behaving animals. However, applying this technique to the amygdala has been difficult. This protocol aims to provide a useful guideline for successfully targeting amygdala cells with a miniaturized microscope in mice. Neuroscience Three-Dimensional Shape Modeling and Analysis of Brain Structures Jaeil Kim1, Maria del Carmen Valdés Hernández2, Jinah Park3 1School of Computer Science and Engineering, Kyungpook National University, 2Centre for Clinical Brain Sciences, University of Edinburgh, 3School of Computing and KI for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST) We introduce a semi-automatic protocol for shape analysis on brain structures, including image segmentation using open software, and further group-wise shape analysis using an automated modeling package. Here, we demonstrate each step of the 3D shape analysis protocol with hippocampal segmentation from brain MR images. Bioengineering Traction Microscopy Integrated with Microfluidics for Chemotactic Collective Migration Hwanseok Jang1, Jongseong Kim1, Jennifer H. Shin2, Jeffrey J. Fredberg3, Chan Young Park3, Yongdoo Park1 1Department of Biomedical Sciences, Korea University, 2Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 3Department of Environmental Health, Harvard T.H. Chan School of Public Health Collective cell migration in development, wound healing, and cancer metastasis is often guided by the gradients of growth factors or signaling molecules. Described here is an experimental system combining traction microscopy with a microfluidic system and a demonstration of how to quantify the mechanics of collective migration under biochemical gradient. Biochemistry Studying RNA Interactors of Protein Kinase RNA-Activated during the Mammalian Cell Cycle Sujin Kim1, Minjeong Kang1, Yoosik Kim1 1Department of Chemical and Biomolecular Engineering and KI for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST) We present experimental approaches for studying RNA-interactors of double-stranded RNA binding protein kinase RNA-activated (PKR) during the mammalian cell cycle using HeLa cells. This method utilizes formaldehyde to crosslink RNA-PKR complexes and immunoprecipitation to enrich PKR-bound RNAs. These RNAs can be further analyzed through high-throughput sequencing or qRT-PCR. Engineering Preparation of Graphene Liquid Cells for the Observation of Lithium-ion Battery Material Joon Ha Chang*1, Jun Young Cheong*1, Hyeon Kook Seo1, Il-Doo Kim1, Jong Min Yuk1 1Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology Here, we present a protocol for the fabrication and preparation of a graphene liquid cell for in situ transmission electron microscopy observation, along with a synthesis of electrode materials and electrochemical battery cell tests. Chemistry Preparation of Poly(pentafluorophenyl acrylate) Functionalized SiO2 Beads for Protein Purification Sura Kim1, Jayoung Ku1,2, Jaemin Park1, Raisa Kharbash1,2, Sheng Li1 1Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 2KI for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST) A protocol for the preparation of poly(pentafluorophenyl acrylate) (poly(PFPA)) grafted silica beads is presented. The poly(PFPA) functionalized surface is then immobilized with antibodies and used successfully for the protein separation through immunoprecipitation. Immunology and Infection Label-Free Identification of Lymphocyte Subtypes Using Three-Dimensional Quantitative Phase Imaging and Machine Learning Jonghee Yoon1, YoungJu Jo2,3,4,7, Young Seo Kim3,4,5, Yeongjin Yu2,3, Jiyeon Park6, Sumin Lee4, Wei Sun Park2,3, YongKeun Park2,3,4 1Department of Physics, University of Cambridge, 2Department of Physics, Korea Advanced Institute of Science and Technology, 3KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology, 4Tomocube, Inc., 5Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 6Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 7Department of Applied Physics, Stanford University We describe a protocol for the label-free identification of lymphocyte subtypes using quantitative phase imaging and a machine learning algorithm. Measurements of 3D refractive index tomograms of lymphocytes present 3D morphological and biochemical information for individual cells, which is then analyzed with a machine-learning algorithm for identification of cell types. Bioengineering Construction of Modular Hydrogel Sheets for Micropatterned Macro-scaled 3D Cellular Architecture Jaejung Son1, Chae Yun Bae1, Je-Kyun Park1 1Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST) We describe the fabrication of micropatterned hydrogel sheets using a simple process, which can be assembled and manipulated in a freestanding form. Using these modular hydrogel sheets, a simple macro-scaled 3D cell culture system can be generated with a controlled cellular microenvironment.
