Brown University View Institution's Website 29 articles published in JoVE Chemistry Stable Aqueous Suspensions of Manganese Ferrite Clusters with Tunable Nanoscale Dimension and Composition Samuel Effman*1, Shawn Avidan*1, Zhen Xiao*1, Vicki Colvin1,2 1Department of Chemistry, Brown University, 2Center for Biomedical Engineering, School of Engineering, Brown University We report a one-pot hydrothermal synthesis of manganese ferrite clusters (MFCs) that offers independent control over material dimension and composition. Magnetic separation allows rapid purification while surface functionalization using sulfonated polymers ensures the materials are non-aggregating in biologically relevant medium. The resulting products are well positioned for biomedical applications. Bioengineering Assembly of Cell Mimicking Supported and Suspended Lipid Bilayer Models for the Study of Molecular Interactions Christina M. Bailey-Hytholt1, Veronica LaMastro2, Anita Shukla2 1Department of Chemical Engineering, Worcester Polytechnic Institute, 2Center for Biomedical Engineering, School of Engineering, Brown University This protocol describes the formation of cell mimicking uni-lipid and multi-lipid vesicles, supported lipid bilayers, and suspended lipid bilayers. These in vitro models can be adapted to incorporate a variety of lipid types and can be used to investigate various molecule and macromolecule interactions. Neuroscience Generation of Human Neurons and Oligodendrocytes from Pluripotent Stem Cells for Modeling Neuron-Oligodendrocyte Interactions Benedetta Assetta*1, Changyong Tang*1,2, Jing Bian*3, Ryan O'Rourke1, Kevin Connolly1, Thomas Brickler3, Sundari Chetty3,4, Yu-Wen Alvin Huang1,5,6 1Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 2Department of Neurology, The Third Affiliated Hospital of Sun Yat-Sen University, 3Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, 4Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, 5Department of Neurology, Warren Alpert Medical School of Brown University, 6Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University The neuron-glial interactions in neurodegeneration are not well understood due to inadequate tools and methods. Here, we describe optimized protocols to obtain induced neurons, oligodendrocyte precursor cells, and oligodendrocytes from human pluripotent stem cells and provide examples of the values of these methods in understanding cell-type-specific contributions in Alzheimer’s disease. Immunology and Infection Assessment of Acute Wound Healing using the Dorsal Subcutaneous Polyvinyl Alcohol Sponge Implantation and Excisional Tail Skin Wound Models. Meredith J. Crane1, William L. Henry Jr1, Holly L. Tran1, Jorge E. Albina2, Amanda M. Jamieson1 1Department of Molecular Microbiology & Immunology, Brown University, 2Division of Surgical Research, Department of Surgery, Rhode Island Hospital and The Warren Alpert School of Medicine of Brown University Here, two murine wound healing models are described, one designed to assess cellular and cytokine wound healing responses and the other to quantify the rate of wound closure. These methods can be used with complex disease models such as diabetes to determine mechanisms of various aspects of poor wound healing. Cancer Research Real-Time Monitoring of Human Glioma Cell Migration on Dorsal Root Ganglion Axon-Oligodendrocyte Co-Cultures John P. Zepecki1, Kristin M. Snyder2, Nikos Tapinos1,3 1Molecular Neuro-oncology Laboratory, Brown University, Rhode Island Hospital, 2University of Minnesota, College of Veterinary Medicine, 3Department of Neurosurgery, Brown University Here we present an ex-vivo mixed monolayer culture system for the study of human glioma cell (hGC) migration in real-time. This model provides the ability to observe interactions between hGCs and both myelinated and non-myelinated axons within a compartmentalized chamber. Behavior Paw-Print Analysis of Contrast-Enhanced Recordings (PrAnCER): A Low-Cost, Open-Access Automated Gait Analysis System for Assessing Motor Deficits Hayley A. Bounds1, Devon L. Poeta1, Petra M. Klinge3, Rebecca D. Burwell1,2 1Cognitive, Linguistic & Psychological Sciences, Brown University, 2Department of Neuroscience, Brown University, 3Department of Neurosurgery, Warren Alpert Medical School, Brown University We describe a novel gait analysis system, Paw-Print Analysis of Contrast-Enhanced Recordings (PrAnCER), an open-access automated system for the quantification of gait characteristics in rats that utilizes a novel semitransparent floor to automatically quantify gait. This system was validated using the haloperidol model of Parkinson’s Disease. Biology Combined Nucleotide and Protein Extractions in Caenorhabditis elegans Joslyn Mills1, Erin McConnell1, Joshua A. Leitão1, Louis R. Lapierre1 1Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Here, we present a protocol for the isolation of RNA, DNA, and protein from the same sample, in an effort to reduce variation, improve reproducibility, and facilitate interpretations. Bioengineering Custom Engineered Tissue Culture Molds from Laser-etched Masters Nicholas J. Kaiser1, Fabiola Munarin1, Kareen L.K. Coulombe1 1Center for Biomedical Engineering,, Brown University Herein we present a rapid, facile, and low-cost method for fabricating custom polydimethylsiloxane molds that can be used for producing hydrogel-based engineered tissues with complex geometries. We additionally describe results from mechanical and histological assessments conducted on engineered cardiac tissues produced using this technique. Engineering The Diffusion of Passive Tracers in Laminar Shear Flow Manuchehr Aminian1,2, Francesca Bernardi1, Roberto Camassa1, Daniel M. Harris1,3, Richard M. McLaughlin1 1Department of Mathematics, University of North Carolina at Chapel Hill, 2Department of Mathematics, Colorado State University, 3School of Engineering, Brown University A protocol for the study of the diffusion of passive tracers in laminar pressure-driven flow is presented. The procedure is applicable to various capillary pipe geometries. Bioengineering A Millimeter Scale Flexural Testing System for Measuring the Mechanical Properties of Marine Sponge Spicules Michael A. Monn1, Jarod Ferreira1, Jianzhe Yang1, Haneesh Kesari1 1School of Engineering, Brown University We present a protocol for performing three-point bending tests on sub-millimeter scale fibers using a custom-built mechanical testing device. The device can measure forces ranging from 20 µN up to 10 N and can therefore accommodate a variety of fiber sizes. Immunology and Infection SILAC Based Proteomic Characterization of Exosomes from HIV-1 Infected Cells Collins Cheruiyot1, Zemplen Pataki1, Robert Williams1, Bharat Ramratnam2,3, Ming Li3 1Brown University, 2COBRE Center for Cancer Research, Lifespan Laboratories, Rhode Island and Miriam Hospitals, 3Division of Infectious Diseases, Department of Medicine, Warren Alpert Medical School, Brown University Here, we describe a quantitative proteomics method using the technique of stable isotope labeling by amino acids in cell culture (SILAC) to analyze the effects of HIV-1 infection on host exosomal proteomes. This protocol can be easily adapted to cells under different stress or infection conditions. Environment Automated, High-resolution Mobile Collection System for the Nitrogen Isotopic Analysis of NOx Paul K. Wojtal1,2, David J. Miller2,3, Mary O'Connor1, Sydney C. Clark2,3, Meredith G. Hastings2,3 1Department of Chemistry, Brown University, 2Institute at Brown for Environment and Society, Brown University, 3Department of Earth, Environmental, and Planetary Sciences, Brown University Previous work suggests that the nitrogen isotopic composition of atmospheric nitrogen oxides might distinguish the influence of different sources in the environment. We report on an automated, mobile, field-based method for the high collection efficiency of atmospheric NOx for N isotopic analysis at an hourly time resolution. Immunology and Infection Qualitative and Quantitative Assays for Detection and Characterization of Protein Antimicrobials M. Heath Farris1, Kara A. Ford2, Richard C. Doyle3 1Department of Advanced Technology, The MITRE Corporation, 2Center for Biomedical Engineering, Brown University, 3The MITRE Corporation Here, we present protocols to rapidly screen and characterize enzymes for antimicrobial activity. The microslide diffusion assay and the dye-release assay utilize target bacterial substrates for qualitative and quantitative enzymatic activity evaluation. Developmental Biology Preparation of Mitochondrial Enriched Fractions for Metabolic Analysis in Drosophila Eugenia Villa-Cuesta1, David M. Rand2 1Biology Department, Adelphi University, 2Department of Ecology and Evolutionary Biology, Brown University Mitochondria play central roles in the regulation of metabolism and homeostasis. Subtle changes in mitochondrial metabolism that affect organismal physiology could be difficult to detect in whole organism metabolomics studies. Here we describe an isolation method that enhances the detection of subtle metabolic shifts in Drosophila melanogaster. Medicine Murine Isolated Heart Model of Myocardial Stunning Associated with Cardioplegic Arrest Brenda Cordeiro1, Richard Clements1,2 1Cardiothoracic Surgery Research Center, Brown University, 2Rhode Island Hospital and Alpert Medical School, Brown University The goal of this protocol to assess myocardial stunning following ischemic cardioplegic arrest in rodents. Bioengineering Planar Gradient Diffusion System to Investigate Chemotaxis in a 3D Collagen Matrix David A. Stout1, Jennet Toyjanova2, Christian Franck3 1Department of Mechanical and Aerospace Engineering, California State University, Long Beach, 2Ximedica, 3School of Engineering, Brown University Cell migration is an important part of human development and life. In order to understand the mechanisms that can alter cell migration, we present a planar gradient diffusion system to investigate chemotaxis in a 3D collagen matrix, which allows one to overcome modern diffusion chamber limitations of existing assays. Behavior Assessment and Evaluation of the High Risk Neonate: The NICU Network Neurobehavioral Scale Barry M. Lester1,2, Lynne Andreozzi-Fontaine1,2, Edward Tronick3, Rosemarie Bigsby1,2 1Center for the Study of Children at Risk, Alpert Medical School, Brown University, 2Women & Infants Hospital of Rhode Island, 3University of Massachusetts, Boston The NICU Network Neurobehavioral Scale (NNNS) was developed as an assessment for the at-risk infant. The purpose of this article is to describe the NNNS, provide video examples of the NNNS procedures and discuss the ways in which the exam has been used. Behavior Automated Visual Cognitive Tasks for Recording Neural Activity Using a Floor Projection Maze Tara K. Jacobson*1, Jonathan W. Ho*1, Brendon W. Kent1, Fang-Chi Yang1, Rebecca D. Burwell1,2 1Department of Cognitive, Linguistic & Psychological Sciences, Brown University, 2Department of Neuroscience, Brown University We describe protocols for training rats for chronic electrophysiological recordings in fully automated cognitive tasks on a Floor Projection Maze. Neuroscience Automated High-throughput Behavioral Analyses in Zebrafish Larvae Holly Richendrfer1, Robbert Créton1 1Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Our laboratory developed a novel high-throughput automated imaging system that is useful for the detection of several different behaviors in 7-day-old zebrafish larvae. The system can be used for detecting subtle changes in behavior after the larvae have been exposed to environmental toxicants or pharmaceuticals. Bioengineering Design of a Biaxial Mechanical Loading Bioreactor for Tissue Engineering Bahar Bilgen1,2, Danielle Chu3, Robert Stefani1, Roy K. Aaron1,2 1Department of Orthopaedics, The Warren Alpert Brown Medical School of Brown University and the Rhode Island Hospital, 2Center for Restorative and Regenerative Medicine, VA Medical Center, Providence, RI, 3University of Texas Southwestern Medical Center We designed a novel mechanical loading bioreactor that can apply uniaxial or biaxial mechanical strain to a cartilage biocomposite prior to transplantation into an articular cartilage defect. Neuroscience In Vivo Two-photon Imaging Of Experience-dependent Molecular Changes In Cortical Neurons Vania Y. Cao1,2, Yizhou Ye1, Surjeet S. Mastwal1, David M. Lovinger3, Rui M. Costa4, Kuan H. Wang1 1Unit on Neural Circuits and Adaptive Behaviors, Genes Cognition and Psychosis Program, National Institute of Mental Health, 2Department of Neuroscience, Brown University - National Institutes of Health Graduate Partnership Program, 3Section on Synaptic Pharmacology, Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, 4Champalimaud Neuroscience Programme, Champalimaud Center for the Unknown Experience-dependent molecular changes in neurons are essential for the brain's ability to adapt in response to behavioral challenges. An in vivo two-photon imaging method is described here that allows the tracking of such molecular changes in individual cortical neurons through genetically encoded reporters. Neuroscience Methods for Study of Neuronal Morphogenesis: Ex vivo RNAi Electroporation in Embryonic Murine Cerebral Cortex Sofia B. Lizarraga1,2,3, Kathryn R. Coser1,2, Mark Sabbagh1,2, Eric M. Morrow1,2,3 1Department of Molecular, Cellular Biology and Biochemistry, Brown University, 2Institute for Brain Science, Brown University, 3Department of Psychiatry and Human Behavior, Warren Alpert School of Medicine, Brown University To conduct a rapid assessment of the function of genes in the development of cerebral cortex, we describe methods involving the ex vivo electroporation of plasmids co-expressing inhibitory RNA (RNAi) and GFP in murine embryonic cortex. This protocol is amenable to the study of various aspects of neurodevelopment such as neurogenesis, neuronal migration and neuronal morphogenesis including dendrite and axon outgrowth. Bioengineering An Experimental System to Study Mechanotransduction in Fetal Lung Cells Yulian Wang1, Zheping Huang1, Pritha S. Nayak1, Juan Sanchez-Esteban1 1Women & Infants Hospital of Rhode Island, Alpert Medical School of Brown University Mechanical forces play a key role in lung development and lung injury. Here, we describe a method to isolate rodent fetal lung type II epithelial cells and fibroblasts and to expose them to mechanical stimulation using an in vitro system. Biology Visualizing RNA Localization in Xenopus Oocytes James A. Gagnon1, Kimberly L. Mowry1 1Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University Visualization of in vivo RNA transport is accomplished by microinjection of fluorescently labeled RNA transcripts into Xenopus oocytes, followed by confocal microscopy. Biology A Protocol for the Production of KLRG1 Tetramer Stephanie C. Terrizzi1, Cindy Banh1, Laurent Brossay1 1Department of Molecular Microbiology and Immunology, Brown University This protocol describes the production of KLRG1 tetramer, which is a powerful tool for the analysis of KLRG1 ligands. Biology A Practical Approach to Genetic Inducible Fate Mapping: A Visual Guide to Mark and Track Cells In Vivo Ashly Brown1, Stephen Brown2, Debra Ellisor2, Nellwyn Hagan1, Elizabeth Normand1, Mark Zervas2 1Department of Neuroscience, Division of Biology and Medicine, Brown University, 2Department of Molecular Biology, Cell Biology and Biochemistry, Division of Biology and Medicine, Brown University Genetic Inducible Fate Mapping (GIFM) marks and tracks cells with fine spatial and temporal control in vivo and elucidates how cells from a specific genetic lineage contribute to developing and adult tissues. Demonstrated here are the techniques required to fate map E12.5 mouse embryos for epifluorescent and explant analysis. Biology A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA Katherine H. Watkins1, Allan Stewart1, William G. Fairbrother1,2 1Department of Molecular and Cellular Biology, Brown University, 2Center for Computational Molecular Biology, Brown University Due to the transient nature of pre-mRNA, it can be difficult to isolate and study in vivo. Here, we present a novel in vitro approach to investigate RNA-protein interactions using a synthetic oligo pool that tiles across selected regions of pre-mRNA. Biology The MODS method for diagnosis of tuberculosis and multidrug resistant tuberculosis Mark F Brady1, Jorge Coronel2, Robert H Gilman3, David AJ Moore4 1The Warren Alpert Medical School of Brown University, 2Laboratorio de Investigacion de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, 3Department of International Health, Johns Hopkins Bloomberg School of Public Health, 4Wellcome Trust Centre for Clinical Tropical Medicine, Imperial College London The microscopic-observation drug-susceptibility (MODS) assay is a low-cost, low-tech tool for high-performance detection of tuberculosis (TB) and multidrug-resistant tuberculosis (MDRTB). This video describes the MODS liquid media culture method. Biology Gene-gun Transfection of Hippocampal Neurons Powrnima Joshi1, Anna Dunaevsky1 1Dept of Neuroscience, Brown University