Peking University 26 articles published in JoVE Engineering Fabrication of polydimethylsiloxane (PDMS)-Based Flexible Surface-Enhanced Raman Scattering (SERS) Substrate for Ultrasensitive Detection Guanzhou Lin1, Jia Zhu2, Yang Wang1, Bingquan Yang1,3, Shisong Xiong1,3, Jinwen Zhang1, Wengang Wu1 1National Key Laboratory of Advanced Micro and Nano Manufacture Technology, School of Integrated Circuits, Peking University, 2School of Electronic Engineering and Computer Science, Peking University, 3School of Software and Microelectronics, Peking University This protocol describes a fabrication method for a flexible substrate for surface-enhanced Raman scattering. This method has been used in the successful detection of low concentrations of R6G and Thiram. Behavior An Automated Method for Assessing Visual Acuity in Infants and Toddlers Using an Eye-Tracking System Jing Wen1, Bikun Yang2, Jinshi Cui2, Li Wang3, Xiaoqing Li1 1Department of Pediatric Ophthalmology, Peking University First Hospital, Peking University Children Vison Institute, Peking University, 2School of Intelligence Science and Technology, Peking University, 3School of Psychological and Cognitive Sciences and Beijing Key Laboratory of Behavior and Mental Health, Peking University In this paper, we present a novel automated method for assessing visual acuity in infants and toddlers by using an eye-tracking system. Biology A Calcium Phosphate-Induced Mouse Abdominal Aortic Aneurysm Model Siting Zhang*1, Zeyu Cai*1, Xu Zhang1, Tianfeng Ma2, Wei Kong1 1Department of Physiology and Pathophysiology, School of Basic Medical Sciences; Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, 2Department of Vascular and Endovascular Surgery, the First Medical Centre, Chinese PLA General Hospital This protocol describes a calcium phosphate-induced abdominal aortic aneurysm (AAA) mouse model to study the pathological features and molecular mechanisms of AAAs. Biology In Vivo Vascular Permeability Detection in Mouse Submandibular Gland Xiangdi Mao1, Sainan Min2, Qihua He3, Xin Cong1 1Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, and Beijing Key Laboratory of Cardiovascular Receptors Research, 2Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Reseah Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, 3State Key Laboratory of Natural and Biomimetic Drugs, Peking University In the present protocol, the endothelial barrier function of the submandibular gland (SMG) was evaluated by injecting different molecular weighted fluorescent tracers into the angular veins of test animal models in vivo under a two-photon laser-scanning microscope. Neuroscience Measurement of Oxygen Consumption Rate in Acute Striatal Slices from Adult Mice Lianteng Zhi1, Jingyu Zhao1, David Jaffe1, Yuanxin Chen1, Ninghan Wang1,2, Qi Qin1, Erin L. Seifert3, Chenjian Li4, Hui Zhang1 1Department of Neuroscience, Thomas Jefferson University, 2School of Biomedical Engineering, Drexel University, 3Department of Pathology, MitoCare Center, Thomas Jefferson University, 4School of Life Sciences, Peking University Oxygen consumption rate (OCR) is a common proxy for mitochondrial function and can be used to study different disease models. We developed a new method using a Seahorse XF analyzer to directly measure the OCR in acute striatal slices from adult mice that is more physiologically relevant than other methods. Medicine Augmented Reality Navigation-Guided Core Decompression for Osteonecrosis of Femoral Head Qi Wang*1,3, Qiuyuan Wang*2,3, Ran Ding3, Youjie Yao4, Junjun Pan5, Weiguo Wang3 1China-Japan Friendship School of Clinical Medicine, Peking University, 2Graduate School of Beijing University of Chinese Medicine, 3Department of Orthopedic Surgery, Beijing Key Lab of Immunes-Mediated Inflammatory Disease, China-Japan Friendship Hospital, 4Beijing Normal University, 5State Key Laboratory of Virtual Reality Technology and Systems, Beihang University Augmented reality technology was applied to core decompression for osteonecrosis of the femoral head to realize real-time visualization of this surgical procedure. This method can effectively improve the safety and precision of core decompression. Genetics A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data Zhencheng Fang1,2, Hongwei Zhou1,3 1Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, 2Center for Quantitative Biology, Peking University, 3State Key Laboratory of Organ Failure Research, Southern Medical University This tutorial describes a simple method to construct a deep learning algorithm for performing 2-class sequence classification of metagenomic data. Biochemistry Single-Molecule Imaging of EWS-FLI1 Condensates Assembling on DNA Linyu Zuo*1, Jiawei Ding*1, Zhi Qi1 1Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University Here, we describe the use of the single-molecule imaging method, DNA Curtains, to study the biophysical mechanism of EWS-FLI1 condensates assembling on DNA. Genetics Chromosome Screening of Human Preimplantation Embryos by Using Spent Culture Medium: Sample Collection and Chromosomal Ploidy Analysis Jin Huang*1,2,3,4, Yaxin Yao*5, Jialin Jia1,2,3,4, Xiaohui Zhu1,2,3,4, Jieliang Ma5, Jing Wang5, Ping Liu1,2,3,4, Sijia Lu5 1Centre for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, 2National Clinical Research Center for Obstetrics and Gynecology(Peking University Third Hospital), 3Ministry of Education, Key Laboratory of Assisted Reproduction (Peking University), 4Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, 5Department of Clinical Research, Yikon Genomics Co. Ltd. The present study reports a protocol for chromosome screening of human embryos that uses spent culture medium, which avoids embryo biopsy and enables chromosome ploidy identification using NGS. The present article presents the detailed procedure, including the preparation of culture medium, whole genome amplification (WGA), next-generation sequencing (NGS) library preparation, and data analysis. Engineering Graphene-Assisted Quasi-van der Waals Epitaxy of AlN Film on Nano-Patterned Sapphire Substrate for Ultraviolet Light Emitting Diodes Xiang Zhang*1,2, Zhaolong Chen*3, Hongliang Chang1,2, Jianchang Yan1,2, Shenyuan Yang2,4, Junxi Wang1,2, Peng Gao5, Tongbo Wei1,2 1State Key Laboratory of Solid-State Lighting, Institute of Semiconductors, Chinese Academy of Sciences, 2Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Science, 3Center for Nanochemistry (CNC), Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, 4State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, 5Electron Microscopy Laboratory, School of Physics, Peking University A protocol for graphene-assisted growth of high-quality AlN films on nano-patterned sapphire substrate is presented. Biology Nucleofection and In Vivo Propagation of Chicken Eimeria Parasites Chunhui Duan1, Xinming Tang1, Dandan Hu1, Sixin Zhang1, Jie Liu1, Feifei Bi1, Zhenkai Hao1, Jingxia Suo1, Ying Yu1, Min Wang1, Pei Sun1, Liying Du2, Xun Suo1, Xianyong Liu1 1National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, 2School of Life Sciences, Peking University Here, we provided a method to achieve stable transfection of chicken Eimeria parasites by nucleofecting sporozoites or second-generation merozoites. Genetically modified eimerian parasites expressing heterologous antigenic genes could be used as vaccine delivery vehicles. Genetics A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants Ying Wang*1,2, Zheng Kuang*1,2, Lei Li2, Xiaozeng Yang1 1Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, 2State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University A bioinformatics pipeline, namely miRDeep-P2 (miRDP2 for short), with updated plant miRNA criteria and an overhauled algorithm, could accurately and efficiently analyze microRNA transcriptomes in plants, especially for species with complex and large genomes. Medicine Invasive Hemodynamic Assessment for the Right Ventricular System and Hypoxia-Induced Pulmonary Arterial Hypertension in Mice Fuliang Luo1, Xin Wang1, Xiaokang Luo1, Bo Li1, Desheng Zhu2, Hansong Sun3, Yue Tang1 1Beijing Key Laboratory of Pre-clinical Research and Evaluation for Cardiovascular Implant Materials, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Centre for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 2Laboratory Animal Center, Peking University, 3Center of Cardiac Surgery for Adults, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Centre for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College Here, we present a protocol to perform an invasive hemodynamic assessment of the right ventricle and pulmonary artery in mice using an open-chest surgery approach. Neuroscience Identifying Cell Surface Markers of Primary Neural Stem and Progenitor Cells by Metabolic Labeling of Sialoglycan Qing-Ran Bai*1, Lu Dong*2, Qin Shen1 1Brain and Spinal Cord Innovative Research Center of Tongji Hospital, School of Life Sciences and Technology, Tongji University and Frontier Science Research Center for Stem Cells of Ministry of Education, 2College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University Presented here is a protocol that combines an in vitro neural-endothelial co-culture system and metabolic incorporation of sialoglycan with bioorthogonal functional groups to expand primary neural stem and progenitor cells and label their surface sialoglycoproteins for imaging or mass-spectrometry analysis of cell surface markers. Neuroscience Use of In Vivo Single-fiber Recording and Intact Dorsal Root Ganglion with Attached Sciatic Nerve to Examine the Mechanism of Conduction Failure Honghui Mao*1,2, Xiuchao Wang*1,3, Wen Chen4, FengYu Liu5, You Wan5, Sanjue Hu1, Junling Xing1,6 1Department of Neurobiology, School of Basic Medicine, Fourth Military Medical University, 2Department of Toxicology, School of Public Health, ShanXi Medical University, 3Department of Psychology, Fourth Military Medical University, 4Department of Neurobiology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, 5Neuroscience Research Institute, Key Lab for Neuroscience, Ministry of Education/National Health Commission, Peking University, 6Department of Radiation Biology, Faculty of Preventive Medicine, Fourth Military Medical University Single-fiber recording is an effective electrophysiological technique that is applicable to the central and peripheral nervous systems. Along with the preparation of intact DRG with the attached sciatic nerve, the mechanism of conduction failure is examined. Both protocols improve the understanding of the peripheral nervous system's relationship with pain. Behavior Simultaneous Recordings of Cortical Local Field Potentials and Electrocorticograms in Response to Nociceptive Laser Stimuli from Freely Moving Rats Lupeng Yue1,2, Fengrui Zhang3, Xuejing Lu1,2, You Wan4,5,6, Li Hu1,2,7 1CAS Key Laboratory of Mental Health, Institute of Psychology, 2Department of Psychology, University of Chinese Academy of Sciences, 3Research Center of Brain Cognitive Neuroscience, Liaoning Normal University, 4Neuroscience Research Institute, Peking University, 5Department of Neurobiology, School of Basic Medical Sciences, Peking University, 6Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, 7Department of Pain Management, State Key Clinical Specialty in Pain Medicine, Second Affiliated Hospital of Guangzhou Medical University We developed a technique that simultaneously records both electrocorticography and local field potentials in response to nociceptive laser stimuli from freely moving rats. This technique helps establish a direct relationship of electrocortical signals at the mesoscopic and macroscopic levels, which facilitates the investigation of nociceptive information processing in the brain. Biochemistry Capture and Identification of RNA-binding Proteins by Using Click Chemistry-assisted RNA-interactome Capture (CARIC) Strategy Rongbing Huang*1,2, Mengting Han*1,2, Liying Meng1,3, Xing Chen1,2,3,4,5 1College of Chemistry and Molecular Engineering, Peking University, 2Beijing National Laboratory for Molecular Sciences, Peking University, 3Peking-Tsinghua Center for Life Sciences, Peking University, 4Synthetic and Functional Biomolecules Center, Peking University, 5Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University A detailed protocol for applying the click chemistry-assisted RNA-interactome capture (CARIC) strategy to identify proteins binding to both coding and noncoding RNAs is presented. Cancer Research Immunophenotyping of Orthotopic Homograft (Syngeneic) of Murine Primary KPC Pancreatic Ductal Adenocarcinoma by Flow Cytometry Xiaoyu An*1,2, Xuesong Ouyang*1, Hui Zhang1, Tingting Li1, Yu-yang Huang1, Zhiyuan Li1, Demin Zhou2, Qi-Xang Li1,2 1Crown Bioscience Inc., 2State Key Laboratory of Natural and Biomimetic Drugs, Peking University The experimental procedure on the immunophenotyping of murine orthotopic PDAC homografts aims at profiling the tumor immuno-microenvironment. Tumors are orthotopically implanted via surgery. Tumors of 200–600 mm3 in size were harvested and dissociated to prepare single-cell suspensions, followed by multi-immune marker FACS analysis using different fluorescently-labeled antibodies. Developmental Biology Single-cell Transcriptomic Analyses of Mouse Pancreatic Endocrine Cells Lin-Chen Li*1,2, Xin-Xin Yu*1,2, Yu-Wei Zhang*1, Ye Feng*1,3, Wei-Lin Qiu*1,3, Cheng-Ran Xu1 1College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 2Academy for Advanced Interdisciplinary Studies, Peking University, 3PKU-Tsinghua-NIBS Graduate Program, Peking University We describe a method for the isolation of endocrine cells from embryonic, neonatal and postnatal pancreases followed by single-cell RNA sequencing. This method allows analyses of pancreatic endocrine lineage development, cell heterogeneity and transcriptomic dynamics. Developmental Biology Nanoparticle-mediated siRNA Gene-silencing in Adult Zebrafish Heart Chenglu Xiao1, Fang Wang2, Junjie Hou1, Xiaojun Zhu1, Ying Luo2, Jing-Wei Xiong1 1Beijing Key Laboratory of Cardiometabolic Molecular Medicine, State Key Laboratory of Natural and Biomimetic Drugs, Institute of Molecular Medicine, Peking University, 2Department of Biomedical Engineering, College of Engineering, Peking University It remains a major challenge to develop conditional gene-knockout or effective gene-knockdown in adult zebrafish organs. Here we report a protocol for performing nanoparticle-mediated siRNA gene-silencing in adult zebrafish heart, thus providing a new loss-of-function method for studying adult organs in zebrafish and other model organisms. Neuroscience In Vivo Monitoring of Circadian Clock Gene Expression in the Mouse Suprachiasmatic Nucleus Using Fluorescence Reporters Long Mei1,2, Cheng Zhan2, Eric Erquan Zhang2 1PTN Joint Graduate Program, School of Life Sciences, Peking University, 2National Institute of Biological Sciences, Beijing This newly developed fluorescence-based technology enables long-term monitoring of the transcription of circadian clock genes in the suprachiasmatic nucleus (SCN) of freely moving mice in real-time and at a high temporal resolution. Chemistry Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy Jing Guo1, Sifan You1, Zhichang Wang1, Jinbo Peng1, Runze Ma1, Ying Jiang1,2 1International Center for Quantum Materials, School of Physics, Peking University, 2Collaborative Innovation Center of Quantum Matter Here, we present a protocol to investigate the structure and dynamics of interfacial water at the atomic scale, in terms of submolecular resolution imaging, molecular manipulation, and single-bond vibrational spectroscopy. Environment Data Processing Methods for 3D Seismic Imaging of Subsurface Volcanoes: Applications to the Tarim Flood Basalt Lei Wang1, Wei Tian2, Yongmin Shi2 1College of Engineering, Peking University, 2School of Earth and Space Sciences, Peking University Three-dimensional (3D) reflection seismology is a powerful method for imaging subsurface volcanoes. By using industrial 3D seismological data from the Tarim Basin, we illustrate how to extract the sills and the conduits of subsurface volcanoes from seismic data cubes. Developmental Biology A Standardized Method for Measuring Internal Lung Surface Area via Mouse Pneumonectomy and Prosthesis Implantation Zhe Liu1,2, Siling Fu2,3, Nan Tang2 1Department of Life Sciences, Peking University, 2National Institute of Biological Sciences, Beijing, 3Graduate School of Peking Union Medical College Internal lung surface area (ISA) is a critical criterion for assessing lung morphology and physiology in lung diseases and injury-induced alveolar regeneration. We describe here a standardized method that can minimize the measurement bias for ISA in both lung pneumonectomy and prosthesis implantation mouse models. Bioengineering Scaffold-supported Transplantation of Islets in the Epididymal Fat Pad of Diabetic Mice Kai Wang*1, Xi Wang*1, Cheng-sheng Han*2, Liang-yi Chen2, Ying Luo1 1Department of Biomedical Engineering, Peking University, 2Institute of Molecular Medicine, Peking University This protocol demonstrates murine islet isolation and seeding onto a decellularized scaffold. Scaffold-supported islets were transplanted into the epididymal fat pad of streptozotocin (STZ)-induced diabetic mice. Islets survived at the transplantation site and reversed the hyperglycemic condition. Biology Using Microfluidic Devices to Measure Lifespan and Cellular Phenotypes in Single Budding Yeast Cells Ke Zou1,2, Diana S. Ren2, Qi Ou-yang1,3, Hao Li2, Jiashun Zheng2 1The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, 2Department of Biochemistry and Biophysics, University of California, San Francisco, 3Peking-Tsinghua Center for Life Sciences at Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University This article presents a protocol optimized for the production of microfluidic chips and the setup of microfluidic experiments to measure the lifespan and cellular phenotypes of single yeast cells.