Georgia Institute of Technology

30 articles published in JoVE

• Biochemistry

  
  The Peel-Blot Technique: A Cryo-EM Sample Preparation Method to Separate Single Layers From Multi-Layered or Concentrated Biological Samples Matthew C. Johnson*^1,2, Arshay J. Grant*¹, Ingeborg Schmidt-Krey^{1,3 1}School of Biological Sciences, Georgia Institute of Technology, ²Department of Structural Biology, Genentech, ³School of Chemistry and Biochemistry, Georgia Institute of Technology The peel-blot technique is a cryo-EM grid preparation method that allows for the separation of multilayered and concentrated biological samples into single layers to reduce thickness, increase sample concentration, and facilitate image processing.

• Neuroscience

  
  Systems Analysis of the Neuroinflammatory and Hemodynamic Response to Traumatic Brain Injury Rowan O. Brothers*¹, Sara Bitarafan*^2,3, Alyssa F. Pybus^1,3, Levi B. Wood*^1,2,3, Erin M. Buckley*^{1,4,5 1}Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, ²George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, ³Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, ⁴Department of Pediatrics, Emory University School of Medicine, ⁵ This protocol presents methods to characterize the neuroinflammatory and hemodynamic response to mild traumatic brain injury and to integrate these data as part of a multivariate systems analysis using partial least squares regression.

• Bioengineering

  
  Formulation and Acoustic Modulation of Optically Vaporized Perfluorocarbon Nanodroplets Andrew Zhao¹, Jeungyoon Lee², Stanislav Emelianov^{1,3 1}Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, ²School of Electrical Engineering, Georgia Institute of Technology, ³Department of Biomedical Engineering and School of Electrical Engineering, Georgia Institute of Technology and Emory University Optically activated perfluorocarbon nanodroplets show promise in imaging applications outside of the vascular system. This article will demonstrate how to synthesize these particles, crosslink polyacrylamide phantoms, and modulate the droplets acoustically to enhance their signal.

• Environment

  
  Methane Hydrate Crystallization on Sessile Water Droplets Abigail M. Johnson¹, Yumeng Zhao², Jongchan Kim², Sheng Dai², Jennifer B. Glass^{1 1}Earth and Atmospheric Sciences, Georgia Institute of Technology, ²Civil and Environmental Engineering, Georgia Institute of Technology We describe a method to form gas hydrate on sessile water droplets to study the effects of various inhibitors, promoters, and substrates on the hydrate crystal morphology.

• Behavior

  
  Behavioral Assessment of Visual Function via Optomotor Response and Cognitive Function via Y-Maze in Diabetic Rats Kaavya Gudapati*^1,2, Anayesha Singh*^1,3, Danielle Clarkson-Townsend^1,4, Stephen Q. Phillips¹, Amber Douglass¹, Andrew J. Feola^1,2, Rachael S. Allen^{1,2 1}Center for Visual and Neurocognitive Rehabilitation, Atlanta VA Medical Center, ²Department of Biomedical Engineering, Georgia Institute of Technology, ³Department of Neuroscience, Emory University, ⁴Gangarosa Department of Environmental Health, Emory University Neural degeneration in both eyes and brain as a result of diabetes can be observed through behavioral tests carried out on rodents. The Y-maze, a measure of spatial cognition, and the optomotor response, a measure of visual function, both provide insight into potential diagnoses and treatments.

• Bioengineering

  
  In vivo Structural Assessments of Ocular Disease in Rodent Models using Optical Coherence Tomography Rachael S. Allen^1,2, Katie Bales^1,3, Andrew Feola^1,2, Machelle T Pardue^{1,2,3 1}Center of Excellence for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Medical Center, ²Department of Biomedical Engineering, Georgia Institute of Technology, ³Department of Ophthalmology, Emory University Here, we describe the use of spectral-domain optical coherence tomography (SD-OCT) to visualize retinal and ocular structures in vivo in models of retinal degeneration, glaucoma, diabetic retinopathy, and myopia.

• Biochemistry

  
  Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling Ryan C. Oliver¹, Swe-Htet Naing², Kevin L. Weiss¹, Sai Venkatesh Pingali¹, Raquel L. Lieberman², Volker S. Urban^{1 1}Neutron Scattering Division, Oak Ridge National Laboratory, ²School of Chemistry and Biochemistry, Georgia Institute of Technology This protocol demonstrates how to obtain a low-resolution ab initio model and structural details of a detergent-solubilized membrane protein in solution using small-angle neutron scattering with contrast-matching of the detergent.

• Medicine

  
  Porcine As a Training Module for Head and Neck Microvascular Reconstruction Mohammad Ali Alessa*^1,2, Sang Hyun Kwak*², Young Woo Lee², Mi-Lan Kang³, Hak-Joon Sung^3,4, Soon Hyun Ahn⁵, Eun Chang Choi², Won Shik Kim^{5 1}Department of Otolaryngology, Head and Neck Surgery, King Abdullah Medical City, ²Department of Otorhinolaryngology, Yonsei University, College of Medicine, ³Severance Biomedical Science Institute, Yonsei University, College of Medicine, ⁴The George W.Woodruff School of Mechanical Engineering, Georgia Institute of Technology, ⁵Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University College of Medicine Here we present a protocol for the use of the pig superior epigastric artery perforator flap as a learning module for head and neck microvascular reconstruction.

• Bioengineering

  
  Nanosensors to Detect Protease Activity In Vivo for Noninvasive Diagnostics Brandon Alexander Holt¹, Quoc D. Mac¹, Gabriel A. Kwong^{1,2,3,4,5 1}Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, ²Parker H. Petit Institute of Bioengineering and Bioscience, ³Institute for Electronics and Nanotechnology, Georgia Tech, ⁴Integrated Cancer Research Center, Georgia Tech, ⁵The Georgia Immunoengineering Consortium, Emory University and Georgia Tech Proteases are tightly regulated enzymes involved in fundamental biological processes, and dysregulated protease activity drives progression of complex diseases such as cancer. This method's goal is to create nanosensors that measure protease activity in vivo by producing a cleavage signal that is detectable from host urine and discriminates disease.

• Bioengineering

  
  Melt Electrospinning Writing of Three-dimensional Poly(ε-caprolactone) Scaffolds with Controllable Morphologies for Tissue Engineering Applications Felix M. Wunner¹, Onur Bas¹, Navid T. Saidy¹, Paul D. Dalton², Elena M. De-Juan Pardo¹, Dietmar W. Hutmacher^{1,3,4 1}ARC ITTC in Additive Biomanufacturing, Institute for Health and Biomedical Innovation (IHBI), Queensland University of Technology (QUT), ²Department for Functional Materials in Medicine and Dentistry and Bavarian Polymer Institute, University of Würzburg, ³Institute for Advanced Study, Technical University of Munich (TUM), ⁴George W Woodruff School of Mechanical Engineering, Georgia Institute of Technology This protocol serves as a comprehensive guideline to fabricate scaffolds via electrospinning with polymer melts in a direct writing mode. We systematically outline the process and define the appropriate parameter settings for achieving targeted scaffold architectures.

• Chemistry

  
  Continuous Flow Chemistry: Reaction of Diphenyldiazomethane with p-Nitrobenzoic Acid Alex Aw¹, Marshall Fritz², Jonathan W. Napoline¹, Pamela Pollet¹, Charles L. Liotta^{1 1}School of Chemistry & Biochemistry, Georgia Institute of Technology, ²School of Chemical & Biomolecular Engineering, Georgia Institute of Technology Flow chemistry carries environmental and economic advantages by leveraging superior mixing, heat transfer and cost benefits. Herein, we provide a blueprint to transfer chemical processes from batch to flow mode. The reaction of diphenyldiazomethane (DDM) with p-nitrobenzoic acid, conducted in batch and flow, was chosen for proof of concept.

• Genetics

  
  Quantification of Information Encoded by Gene Expression Levels During Lifespan Modulation Under Broad-range Dietary Restriction in C. elegans Dhaval S Patel*¹, Giovanni Diana*¹, Eugeni V. Entchev¹, Mei Zhan^2,3,4, Hang Lu^2,3,4, QueeLim Ch'ng^{1 1} Here, we present a framework to relate broad-range dietary restriction to gene expression and lifespan. We describe protocols for broad-range dietary restriction and for quantitative imaging of gene expression under this paradigm. We further outline computational analyses to reveal underlying information processing features of the genetic circuits involved in food-sensing.

• Bioengineering

  
  Microfluidic Platform with Multiplexed Electronic Detection for Spatial Tracking of Particles Ningquan Wang¹, Ruxiu Liu¹, A. Fatih Sarioglu^{1,2,3 1}School of Electrical and Computer Engineering, Georgia Institute of Technology, ²Institute of Electronics and Nanotechnology, Georgia Institute of Technology, ³Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology We demonstrate a microfluidic platform with an integrated surface electrode network that combines resistive pulse sensing (RPS) with code division multiple access (CDMA), to multiplex detection and sizing of particles in multiple microfluidic channels.

• Developmental Biology

  
  Development of an Ethanol-induced Fibrotic Liver Model in Zebrafish to Study Progenitor Cell-mediated Hepatocyte Regeneration Mianbo Huang¹, Jin Xu¹, Chong Hyun Shin^{1 1}School of Biology, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology Sustained fibrosis with deposition of excessive extracellular matrix proteins leads to cirrhosis. Alcohol abuse is one of the main causes of severe liver disease. We established an ethanol-induced zebrafish fibrotic liver model to study the mechanisms and strategies of promoting hepatocyte regeneration upon alcohol-induced injury.

• Bioengineering

  
  Fluorescence Biomembrane Force Probe: Concurrent Quantitation of Receptor-ligand Kinetics and Binding-induced Intracellular Signaling on a Single Cell Yunfeng Chen*¹, Baoyu Liu*², Lining Ju*³, Jinsung Hong*¹, Qinghua Ji^4,5, Wei Chen⁶, Cheng Zhu^{1 1}Woodruff School of Mechanical Engineering, Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, ²Coulter Department of Biomedical Engineering, Georgia Institute of Technology, ³Charles Perkins Centre, The University of Sydney, ⁴Institute of Biophysics, Laboratory of RNA Biology, Chinese Academy of Sciences, ⁵University of Chinese Academy of Sciences, ⁶School of Medicine and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University We describe a technique for concurrently measuring force-regulated single receptor-ligand binding kinetics and real-time imaging of calcium signaling in a single T lymphocyte.

• Medicine

  
  Experimental and Imaging Techniques for Examining Fibrin Clot Structures in Normal and Diseased States Natalie K. Fan¹, Philip M. Keegan¹, Manu O. Platt^1,2, Rodney D. Averett^{2,3 1}Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University School of Medicine, ²Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, ³George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology In this manuscript, experimental techniques, including blood preparation, confocal microscopy, and lysis rate analysis, to examine the morphological differences between normal and abnormal clot structures due to diseased states are presented.

• Biology

  
  Studying DNA Looping by Single-Molecule FRET Tung T. Le¹, Harold D. Kim^{1 1}School of Physics, Georgia Institute of Technology This study presents a detailed experimental procedure to measure looping dynamics of double-stranded DNA using single-molecule Fluorescence Resonance Energy Transfer (FRET). The protocol also describes how to extract the looping probability density called the J factor.

• Chemistry

  
  High-pressure Sapphire Cell for Phase Equilibria Measurements of CO₂/Organic/Water Systems Pamela Pollet¹, Amy L. Ethier², James C. Senter², Charles A. Eckert², Charles L. Liotta^{1 1}School of Chemistry and Biochemistry, Georgia Institute of Technology, ²School of Chemical and Biomolecular Engineering, Georgia Institute of Technology The high pressure sapphire cell apparatus is a unique tool to study, without sampling, phase behavior under a wide range of pressures. Using a cathetometer, very precise volume measurements can be recorded to measure liquid expansion and phase composition. Thus, this synthetic method enables the study of (1) phase equilibria of multi-component mixtures and (2) the partition behavior of catalyst or model compounds as a function of pressure.

• Chemistry

  
  Conducting Miller-Urey Experiments Eric T. Parker¹, James H. Cleaves^2,3, Aaron S. Burton⁴, Daniel P. Glavin⁵, Jason P. Dworkin⁵, Manshui Zhou¹, Jeffrey L. Bada⁶, Facundo M. Fernández^{1 1}School of Chemistry and Biochemistry, Georgia Institute of Technology, ²Earth-Life Science Institute, Tokyo Institute of Technology, ³Institute for Advanced Study, ⁴Astromaterials Research and Exploration Science Directorate, NASA Johnson Space Center, ⁵Goddard Center for Astrobiology, NASA Goddard Space Flight Center, ⁶Geosciences Research Division, Scripps Institution of Oceanography, University of California at San Diego The Miller-Urey experiment was a pioneering study regarding the abiotic synthesis of organic compounds with possible relevance to the origins of life. Simple gases were introduced into a glass apparatus and subjected to an electric discharge, simulating the effects of lightning in the primordial Earth’s atmosphere-ocean system. The experiment was conducted for one week, after which, the samples collected from it were analyzed for the chemical building blocks of life.

• Bioengineering

  
  Cell Squeezing as a Robust, Microfluidic Intracellular Delivery Platform Armon Sharei¹, Nahyun Cho¹, Shirley Mao¹, Emily Jackson¹, Roberta Poceviciute¹, Andrea Adamo¹, Janet Zoldan², Robert Langer^1,2, Klavs F Jensen^{1 1}Department of Chemical Engineering, Massachusetts Institute of Technology, ²David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Rapid mechanical deformation of cells has emerged as a promising, vector-free method for intracellular delivery of macromolecules and nanomaterials. This protocol provides detailed steps on how to use the system for a broad range of applications.

• Bioengineering

  
  Imaging of Biological Tissues by Desorption Electrospray Ionization Mass Spectrometry Rachel V. Bennett*¹, Chaminda M. Gamage*¹, Facundo M. Fernández^{1 1}School of Chemistry and Biochemistry, Georgia Institute of Technology Desorption electrospray ionization mass spectrometry (DESI-MS) is an ambient method by which samples, including biological tissues, can be imaged with minimal sample preparation. By rastering the sample below the ionization probe, this spray-based technique provides sufficient spatial resolution to discern molecular features of interest within tissue sections.

• Medicine

  
  Surgical Technique for Spinal Cord Delivery of Therapies: Demonstration of Procedure in Gottingen Minipigs Thais Federici¹, Carl V. Hurtig¹, Kentrell L. Burks¹, Jonathan P. Riley¹, Vibhor Krishna², Brandon A. Miller¹, Eric A. Sribnick¹, Joseph H. Miller³, Natalia Grin¹, Jason J. Lamanna^1,4,5, Nicholas M. Boulis^{1 1}Department of Neurosurgery, Emory University, ²Department of Neuroscience, Medical University of South Carolina, ³Division of Neurosurgery, University of Alabama, Birmingham, ⁴Department of Biomedical Engineering, Georgia Institute of Technology, ⁵Department of Biomedical Engineering, Emory University Short visual description of the surgical technique and device used for the delivery of (gene and cell) therapies into the spinal cord. The technique is demonstrated in the animal but is entirely translatable and currently being used for human application.

• Engineering

  
  Compact Quantum Dots for Single-molecule Imaging Andrew M. Smith¹, Shuming Nie^{1,2 1}Department of Biomedical Engineering, Emory University, ²Department of Chemistry, Georgia Institute of Technology We describe the preparation of colloidal quantum dots with minimized hydrodynamic size for single-molecule fluorescence imaging. Compared to conventional quantum dots, these nanoparticles are similar in size to globular proteins and are optimized for single-molecule brightness, stability against photodegradation, and resistance to nonspecific binding to proteins and cells.

• Engineering

  
  Probing and Mapping Electrode Surfaces in Solid Oxide Fuel Cells Kevin S. Blinn¹, Xiaxi Li¹, Mingfei Liu¹, Lawrence A. Bottomley², Meilin Liu^{1 1}Center for Innovative Fuel Cells and Battery Technologies, School of Materials Science and Engineering, Georgia Institute of Technology, ²School of Chemistry and Biochemistry, Georgia Institute of Technology We present a unique platform for characterizing electrode surfaces in solid oxide fuel cells (SOFCs) that allows simultaneous performance of multiple characterization techniques (e.g. in situ Raman spectroscopy and scanning probe microscopy alongside electrochemical measurements). Complementary information from these analyses may help to advance toward a more profound understanding of electrode reaction and degradation mechanisms, providing insights into rational design of better materials for SOFCs.

• Bioengineering

  
  Endothelialized Microfluidics for Studying Microvascular Interactions in Hematologic Diseases David R. Myers*^1,2,3,4, Yumiko Sakurai*^1,2,3,4, Reginald Tran^1,2,3,4, Byungwook Ahn^1,2,3,4, Elaissa Trybus Hardy^1,2,3,4, Robert Mannino^1,2,3,4, Ashley Kita^1,2,3,4, Michelle Tsai^1,2,3,4, Wilbur A. Lam^{1,2,3,4 1}Department of Pediatrics, Emory University School of Medicine, ²Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, ³Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, ⁴Winship Cancer Institute of Emory University A method to culture an endothelial cell monolayer throughout the entire inner 3D surface of a microfluidic device with microvascular-sized channels (<30 μm) is described. This in vitro microvasculature model enables the study of biophysical interactions between blood cells, endothelial cells, and soluble factors in hematologic diseases.

• Biology

  
  Expression Analysis of Mammalian Linker-histone Subtypes Magdalena Medrzycki¹, Yunzhe Zhang¹, Kaixiang Cao¹, Yuhong Fan^{1 1}School of Biology and the Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology We describe a set of assays to analyze expression levels of H1 linker histones. mRNA of individual H1 genes are quantitatively measured by random primer based reverse transcription followed by real-time PCR, whereas protein quantification of H1 histones is achieved by HPLC analysis.

• Bioengineering

  
  Adhesion Frequency Assay for In Situ Kinetics Analysis of Cross-Junctional Molecular Interactions at the Cell-Cell Interface Veronika I. Zarnitsyna¹, Cheng Zhu^{1 1}Biomedical Engineering Department, Georgia Institute of Technology An adhesion frequency assay for measuring receptor-ligand interaction kinetics when both molecules are anchored on the surfaces of the interacting cells is described. This mechanically-based assay is exemplified using a micropipette-pressurized human red blood cell as adhesion sensor and integrin αLβ2 and intercellular adhesion molecule-1 as interacting receptors and ligands.

• Biology

  
  Generation of RNA/DNA Hybrids in Genomic DNA by Transformation using RNA-containing Oligonucleotides Ying Shen¹, Francesca Storici^{1 1}School of Biology, Georgia Institute of Technology This work shows how to form an RNA/DNA hybrid at the chromosomal level and reveal transfer of genetic information from RNA to genomic DNA in yeast cells.

• Biology

  
  Assessing Two-dimensional Crystallization Trials of Small Membrane Proteins for Structural Biology Studies by Electron Crystallography Matthew C. Johnson*¹, Frederik Rudolph*^1,2, Tina M. Dreaden*³, Gengxiang Zhao*¹, Bridgette A. Barry³, Ingeborg Schmidt-Krey^{1,3 1}School of Biology, Georgia Institute of Technology, ²Department of Molecular Pharmacology, RWTH Aachen University, ³School of Chemistry and Biochemistry, Georgia Institute of Technology Evaluating two-dimensional (2D) crystallization trials for the formation of ordered membrane protein arrays is a highly critical and difficult task in electron crystallography. Here we describe our approach in screening for and identifying 2D crystals of predominantly small membrane proteins in the range of 15 – 90kDa.

• Neuroscience

  
  Simultaneous fMRI and Electrophysiology in the Rodent Brain Wen-ju Pan^1,2, Garth Thompson^1,2, Matthew Magnuson^1,2, Waqas Majeed^1,2, Dieter Jaeger³, Shella Keilholz^{1,2 1}Biomedical Engineering, Emory University, ²Biomedical Engineering, Georgia Institute of Technology, ³Biology, Emory University We have developed a method for simultaneous functional magnetic resonance imaging and electrophysiological recording in the rodent brain, providing a platform for the investigation of the relationship between neural activity and the blood oxygenation level dependent (BOLD) MRI signal.