Peking University

23 articles published in JoVE

• Biology

  
  A Calcium Phosphate-Induced Mouse Abdominal Aortic Aneurysm Model Siting Zhang*¹, Zeyu Cai*¹, Xu Zhang¹, Tianfeng Ma², Wei Kong^{1 1}Department 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 Cong^{1 1}Department 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 Wang^1,2, Qi Qin¹, Erin L. Seifert³, Chenjian Li⁴, Hui Zhang^{1 1}Department 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 Wang^{3 1}China-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 Fang^1,2, Hongwei Zhou^{1,3 1}Microbiome 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 Qi^{1 1}Center 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.

• 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 Chang^1,2, Jianchang Yan^1,2, Shenyuan Yang^2,4, Junxi Wang^1,2, Peng Gao⁵, Tongbo Wei^{1,2 1}State 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 Liu^{1 1}National 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 Yang^{1 1}Beijing 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 Tang^{1 1}Beijing 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 Shen^{1 1}Brain 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 Xing^{1,6 1}Department 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 Yue^1,2, Fengrui Zhang³, Xuejing Lu^1,2, You Wan^4,5,6, Li Hu^{1,2,7 1}CAS 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 Meng^1,3, Xing Chen^{1,2,3,4,5 1}College 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 Li^{1,2 1}Crown 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 Xu^{1 1}College 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 Xiong^{1 1}Beijing 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 Mei^1,2, Cheng Zhan², Eric Erquan Zhang^{2 1}PTN 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 Jiang^{1,2 1}International 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 Shi^{2 1}College 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 Liu^1,2, Siling Fu^2,3, Nan Tang^{2 1}Department 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 Luo^{1 1}Department 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 Zou^1,2, Diana S. Ren², Qi Ou-yang^1,3, Hao Li², Jiashun Zheng^{2 1}The 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.