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University of North Carolina, Chapel Hill

22 ARTICLES PUBLISHED IN JoVE

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Biology

The Production of C. elegans Transgenes via Recombineering with the galK Selectable Marker
Yue Zhang *1, Luv Kashyap *2, Annabel A. Ferguson 2, Alfred L. Fisher 2
1Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 2Department of Medicine, Division of Geriatric Medicine and Pittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh

The ability to produce transgenes for Caenorhabditis elegans using genomic DNA carried by fosmids is particularly attractive as all of the native regulatory elements are retained. Described is a simple and robust procedure for the production of transgenes via recombineering with the galK selectable marker.

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Biology

Flow Cytometric Analysis of Bimolecular Fluorescence Complementation: A High Throughput Quantitative Method to Study Protein-protein Interaction
Li Wang 1, Graeme K. Carnegie 1
1Department of Pharmacology, University of Illinois at Chicago

Flow cytometric analysis of Bimolecular Fluorescence Complementation provides a high throughput quantitative method to study protein-protein interaction. This methodology can be applied to mapping protein binding sites and for screening factors that regulate protein-protein interaction.

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Biology

Massively Parallel Reporter Assays in Cultured Mammalian Cells
Alexandre Melnikov 1, Xiaolan Zhang 1, Peter Rogov 1, Li Wang 1, Tarjei S. Mikkelsen 1
1Broad Institute

The genetic reporter assay is a well-established and powerful tool for dissecting the relationship between DNA sequences and their gene regulatory activities. Coupling candidate regulatory elements to reporter genes that carry identifying sequence tags enables massive parallelization of these assays.

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Developmental Biology

Improved Generation of Induced Cardiomyocytes Using a Polycistronic Construct Expressing Optimal Ratio of Gata4, Mef2c and Tbx5
Li Wang 1, Ziqing Liu 1, Chaoying Yin 1, Yang Zhou 1, Jiandong Liu 1, Li Qian 1
1Department of Pathology and Laboratory Medicine, McAllister Heart Institute, University of North Carolina, Chapel Hill

We describe here a protocol for the generation of iCMs using retrovirus-mediated delivery of Gata4, Tbx5 and Mef2c in a polycistronic construct. This protocol yields a relatively homogeneous population of reprogrammed cells with improved efficiency and quality and is valuable for future studies of iCM reprogramming.

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Developmental Biology

Isolation and Characterization of Single Cells from Zebrafish Embryos
Leigh Ann Samsa 1,2, Nicole Fleming 2,3, Scott Magness 1, Li Qian 2,3, Jiandong Liu 2,3
1Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, 2McAllister Heart Institute, University of North Carolina at Chapel Hill, 3Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill

This protocol describes a method for isolating single cells from zebrafish embryos, enriching for cells of interest, capturing zebrafish cells in microfluidic based single cell multiplex systems, and assessing gene expression from single cells.

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Immunology and Infection

Dextran Enhances the Lentiviral Transduction Efficiency of Murine and Human Primary NK Cells
Arash Nanbakhsh 1, Brad Best 2, Matthew Riese 3, Sridhar Rao 4, Li Wang 5, Jeffrey Medin 6, Monica S. Thakar 6, Subramaniam Malarkannan 1,5,6,7
1Laboratory of Molecular Immunology and Immunotherapy, Blood Research Institute, The Blood Center of Wisconsin, 2Vector Core Lab, Blood Research Institute, The Blood Center of Wisconsin, 3Laboratory of Lymphocyte Biology, Blood Research Institute, The Blood Center of Wisconsin, 4Laboratory of Stem Cell Transcriptional Regulation, Blood Research Institute, The Blood Center of Wisconsin, 5Department of Microbiology and Immunology, The Medical College of Wisconsin, 6Department of Pediatrics, The Medical College of Wisconsin, 7Department of Medicine, The Medical College of Wisconsin

The goal of this study was to formulate technologies that allow for successful gene transduction in primary natural killer (NK) cells. The dextran-mediated lentiviral transduction of human or mouse primary NK cells results in higher gene expression efficiencies. This method of gene transduction will vastly improve NK cell genetic manipulation.

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Environment

Production and Measurement of Organic Particulate Matter in a Flow Tube Reactor
Yue Zhang 1,2, Pengfei Liu 1, Zhaoheng Gong 1, Franz M. Geiger 3, Scot T. Martin 1,4
1School of Engineering and Applied Sciences, Harvard University, 2Department of Environmental Science and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, 3Department of Chemistry, Northwestern University, 4Department of Earth and Planetary Sciences, Harvard University

This paper describes the operation procedure for the flow tube reactor and related data collection. It shows the protocols for setting the experiments, recording data and generating the number-diameter distribution as well as the particle mass information, which gives useful information about chemical and physical properties of the organic aerosols.

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Environment

Production and Measurement of Organic Particulate Matter in the Harvard Environmental Chamber
Yue Zhang 1,2, Zhaoheng Gong 1, Suzane de Sa 1, Adam P. Bateman 1, Yingjun Liu 1, Yongjie Li 1, Franz M. Geiger 3, Scot T. Martin 1,4
1School of Engineering and Applied Sciences, Harvard University, 2Department of Environmental Science and Engineering, Gillings School of Global Public Health, University of North Carolina, 3Department of Chemistry, Northwestern University, 4Department of Earth and Planetary Sciences, Harvard University

This paper describes operation procedures for the Harvard Environmental Chamber (HEC) and related instrumentation for measuring gaseous and particle species. The environmental chamber is used to produce and study secondary organic species produced from the organic precursors, especially related to atmospheric organic particulate matter.

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Immunology and Infection

Generation of Monoclonal Antibodies Against Natural Products
Yue Zhang 1, Peng Cao 2, Fang Lu 3, Xin Yan 4, Bingqian Jiang 3, Jinjun Cheng 3, Huihua Qu 5
1School of Life Science, Beijing University of Chinese Medicine, 2Third Affiliated Hospital, Beijing University of Chinese Medicine, 3School of Basic Medical Sciences, Beijing University of Chinese Medicine, 4School of Chinese Materia Medica, Beijing University of Chinese Medicine, 5Center of Scientific Experiment, Beijing University of Chinese Medicine

This article provides a detailed protocol for the preparation and evaluation of monoclonal antibodies against natural products for use in various immunoassays. This procedure includes immunization, cell fusion, indirect competitive ELISA for positive clone screening, and monoclonal hybridoma preparation. The specifications for antibody characterization using MALDI-TOF-MS and ELISA analyses are also provided.

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Behavior

A Conflict Model of Reward-seeking Behavior in Male Rats
Shaofei Jiang 1,2, Yue Zhang 1,2, Xigeng Zheng 1,2, Haoshuang Luo 1,2, Zhengkui Liu 1,2, Yunjing Bai 1,2
1CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 2Department of Psychology, University of Chinese Academy of Sciences

This conflict model is used to measure the impairment of inhibitory control after exposure to addictive drugs, or other factors that may influence inhibitory control. A sexual stimulus and an aversive obstacle are concurrently presented, thus male rats have to conquer the obstacle to approach the sexual reward.

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Immunology and Infection

Coincubation Assay for Quantifying Competitive Interactions between Vibrio fischeri Isolates
Lauren Speare 1, Alecia N. Septer 1
1Department of Marine Sciences, University of North Carolina, Chapel Hill

Bacteria encode diverse mechanisms for engaging in interbacterial competition. Here, we present a culture-based protocol for characterizing competitive interactions between bacterial isolates and how they impact the spatial structure of a mixed population.

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Bioengineering

Using Multilayered Hydrogel Bioink in Three-Dimensional Bioprinting for Homogeneous Cell Distribution
Nan Chen 1,2, Kai Zhu 1,2, Shiqiang Yan 3,4, Junmin Li 1,2, Tianyi Pan 4, Mieradilijiang Abudupataer 1,2, Fazle Alam 4, Xiaoning Sun 1,2, Li Wang 3,4, Chunsheng Wang 1,2
1Department of Cardiac Surgery and Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, 2Shanghai Institute of Cardiovascular Diseases, 3Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, 4Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, Shanghai Medical College, Fudan University

Here, we developed a novel multilayered modified strategy for liquid-like bioinks (gelatin methacryloyl with low viscosity) to prevent the sedimentation of encapsulated cells.

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Bioengineering

Microfluidic Model to Mimic Initial Event of Neovascularization
Ping Zhao 1, Xing Zhang 1, Xiao Liu 1, Li Wang 4, Haoran Su 1, Liyi Wang 1, Dongrui Zhang 1, Xiaoyan Deng 3, Yubo Fan 1,2
1Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Chinese Education Ministry, School of Biological Science and Medical Engineering, Beihang University, 2School of Engineering Medicine, Beihang University, 3Artificial Intelligence Key Laboratory of Sichuan Province, School of Automation and Information Engineering, Sichuan University of Science and Engineering, 4Beijing Research Center of Urban System Engineering

Here, we provide a microfluidic chip and an automatically controlled, highly efficient circulation microfluidic system that recapitulates the initial microenvironment of neovascularization, allowing endothelial cells (ECs) to be stimulated by high luminal shear stress, physiological level of transendothelial flow, and various vascular endothelial growth factor (VEGF) distribution simultaneously.

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Biochemistry

Development of a Lateral Flow Immunochromatographic Strip for Rapid and Quantitative Detection of Small Molecule Compounds
Yue Zhang *1, Peng Cao *2, Fang Lu 1, Jinjun Cheng 3, Huihua Qu 4
1School of Life Science, Beijing University of Chinese Medicine, 2Third Affiliated Hospital, Beijing University of Chinese Medicine, 3National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, 4Center of Scientific Experiment, Beijing University of Chinese Medicine

Development of a Lateral Flow Immunochromatographic Strip for Rapid and Quantitative Detection of Small Molecule Compounds

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Biology

Quantification of Interbacterial Competition using Single-Cell Fluorescence Imaging
Stephanie Smith 1, Alecia N. Septer 1
1Department of Earth, Marine, and Environmental Sciences, University of North Carolina

This manuscript describes a method for using single-cell fluorescence microscopy to visualize and quantify bacterial competition in coculture.

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Genetics

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
Chengming Xu *1, Riqing Wei *2, Hui Lin 1, Leiyu Deng 1, Li Wang 3, Deyang Li 4, Honghui Den 5, Wensong Qin 1, Ping Wen 1, Ying Liu 1, Yingsong Wu 2, Qiang Ma 2, Jinliang Duan 1
1Centre for Women, Children, and Reproduction, Guangxi Key Laboratory of Metabolic Diseases Research, 2Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, 3Department of Obstetrics and Gynecology, Chinese PLA General Hospital, 4Clinical Laboratory, Northern Theater Air Force Hospital, 5Guangzhou Darui Reproduction Technology Co., Ltd.

The protocol presents the overall in-lab procedures required in pre-implantation genetic testing for aneuploidy on a semiconductor-based next-generation sequencing platform. Here we present the detailed steps of whole genome amplification, DNA fragment selection, library construction, template preparation, and sequencing working flow with representative results.

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Neuroscience

Intraventricular Drug Delivery and Sampling for Pharmacokinetics and Pharmacodynamics Study
Sara Oberrauch 1, Jing Lu 1, Linda Cornthwaite-Duncan 1, Maytham Hussein 1, Jian Li 2, Gauri Rao 3, Tony Velkov 1
1Department of Biochemistry & Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, 2Department of Microbiology, Biomedicine Discovery Institute, Monash University, 3UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill

Delivery of therapeutics directly into the central nervous system is one way of circumventing the blood-brain barrier. The present protocol demonstrates intracerebroventricular injection for subsequent collection of cerebrospinal fluid and bodily organs. This facilitates the investigation of drug pharmacokinetics and pharmacodynamics in animal models for developing new treatments.

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Neuroscience

Analysis of Astrocyte Territory Volume and Tiling in Thick Free-Floating Tissue Sections
Alex R. Eaker 1, Katherine T. Baldwin 1,2
1Neuroscience Center, University of North Carolina, Chapel Hill, 2Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill

This protocol describes methods for sectioning, staining, and imaging free-floating tissue sections of the mouse brain, followed by a detailed description of the analysis of astrocyte territory volume and astrocyte territory overlap or tiling.

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Cancer Research

Ex Vivo Organoid Model of Adenovirus-Cre Mediated Gene Deletions in Mouse Urothelial Cells
Dongbo Xu 1, Li Wang 1, Kyle Wieczorek 1, Yanqing Wang 2, Xiaojing Zhang 2, David W. Goodrich 2, Qiang Li 1,2
1Department of Urology, Roswell Park Comprehensive Cancer Center, 2Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center

This protocol describes the process of the generation and characterization of mouse urothelial organoids harboring deletions in genes of interest. The methods include harvesting mouse urothelial cells, ex vivo transduction with adenovirus driving Cre expression with a CMV promoter, and in vitro as well as in vivo characterization.

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Neuroscience

Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy
Felix A. Kyere *1,2, Ian Curtin *1,2, Oleh Krupa 1,2, Carolyn M. McCormick 1,2, Mustafa Dere 3, Sarah Khan 3,7, Minjeong Kim 7, Tzu-Wen Winnie Wang 4,5,6, Qiuhong He 4,5,6, Guorong Wu 3, Yen-Yu Ian Shih 4,5,6, Jason L. Stein 1,2
1UNC Neuroscience Center, University of North Carolina, Chapel Hill, 2Department of Genetics, University of North Carolina, Chapel Hill, 3Department of Psychiatry, University of North Carolina, Chapel Hill, 4Center for Animal Magnetic Resonance Imaging, The University of North Carolina at Chapel Hill, 5Biomedical Research Imaging Center, The University of North Carolina at Chapel Hill, 6Department of Neurology, The University of North Carolina at Chapel Hill, 7Department of Computer Science, The University of North Carolina at Greensboro

This protocol describes methods for conducting magnetic resonance imaging, clearing, and immunolabeling of intact mouse brains using iDISCO+, followed by a detailed description of imaging using light-sheet microscopy, and downstream analyses using NuMorph.

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Immunology and Infection

Rat Burn Model to Study Full-Thickness Cutaneous Thermal Burn and Infection
Rajnikant Sharma 1, Shekhar Yeshwante 1, Quentin Vallé 1, Maytham Hussein 2, Varsha Thombare 2, Sean Michael McCann 1, Robert Maile 3,4,5, Jian Li 6, Tony Velkov 2, Gauri Rao 1
1UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 2Department of Biochemistry & Pharmacology, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, 3Department of Microbiology & Immunology, University of North Carolina School of Medicine, 4Department of Surgery, University of North Carolina at Chapel Hill, 5Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, 6Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University

A model mimicking the clinical scenario of burn injury and infection is necessary for furthering burn research. The present protocol demonstrates a simple and reproducible rat burn infection model comparable to that in humans. This facilitates the study of burn and infections following burn for developing new topical antibiotic treatments.

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Neuroscience

Clinical Indications for Rapid Sequence MRI in Pediatric Neurosurgical Patients and the Limitations and Barriers to Implementation
Deveney Franklin 1, Candace Barr 1, Diana Nguyen 1, Declan O’Shaughnessy 2, Olivia E. Gilbert 1,3, Carolyn Quinsey 1,3
1School of Medicine, University of North Carolina, Chapel Hill, 2Department of Radiology, University of North Carolina at Chapel Hill, 3Department of Neurosurgery, University of North Carolina at Chapel Hill

Here, we present a protocol to increase the use of rapid sequence magnetic resonance imaging (RS-MRI) for pediatric patients for spine, traumatic brain injury (TBI), and hydrocephalus while documenting limitations and barriers to universal implementation.

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