University of Texas, Dallas View Institution's Website 19 articles published in JoVE Bioengineering 4D Light-sheet Imaging of Zebrafish Cardiac Contraction Xinyuan Zhang1, Alireza Saberigarakani1, Milad Almasian1, Sohail Hassan1, Manasa Nekkanti1, Yichen Ding1,2,3 1Department of Bioengineering, The University of Texas at Dallas, 2Center for Imaging and Surgical Innovation, The University of Texas at Dallas, 3Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center This protocol utilizes light-sheet imaging to investigate cardiac contractile function in zebrafish larvae and gain insights into cardiac mechanics through cell tracking and interactive analysis. Bioengineering Tools for Surface Treatment of Silicon Planar Intracortical Microelectrodes Olivia K. Krebs1,2, Gaurav Mittal1,2, Shreya Ramani1,2, Jichu Zhang1,2, Andrew J. Shoffstall1,2, Stuart F. Cogan3, Joseph J. Pancrazio3, Jeffrey R. Capadona1,2 1Department of Biomedical Engineering, Case Western Reserve University, 2Advanced Platform Technology Center, Rehabilitation Research and Development, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 3Department of Bioengineering, The University of Texas at Dallas The present protocol describes tools for handling silicon planar intracortical microelectrodes during treatments for surface modification via gas deposition and aqueous solution reactions. The assembly of the components used to handle the devices throughout the procedure is explained in detail. Genetics Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies Belle M. Sharon1, Neha V. Hulyalkar1, Vivian H. Nguyen1, Philippe E. Zimmern2, Kelli L. Palmer1, Nicole J. De Nisco1 1Department of Biological Sciences, University of Texas at Dallas, 2Department of Urology, University of Texas Southwestern Medical Center This protocol details a comprehensive approach for the culturing, sequencing, and de novo hybrid genome assembly of urinary bacteria. It provides a reproducible procedure for the generation of complete, circular genome sequences useful in studying both chromosomal and extrachromosomal genetic elements contributing to urinary colonization, pathogenesis, and antimicrobial resistance dissemination. Behavior Investigating Migraine-Like Behavior Using Light Aversion in Mice Mengya Wang1, Bianca N. Mason2, Levi P. Sowers3,4, Adisa Kuburas4, Brandon J. Rea3,4, Andrew F. Russo3,4,5 1Department of Neuroscience and Pharmacology, University of Iowa, 2School of Behavioral and Brain Sciences, University of Texas at Dallas, 3Center for the Prevention and Treatment of Visual Loss, Veterans Administration Health Center, Iowa City, IA, 4Department of Molecular Physiology and Biophysics, University of Iowa, 5Department of Neurology, University of Iowa Rodents are not able to report migraine symptoms. Here, we describe a manageable test paradigm (light/dark and open field assays) to measure light aversion, one of the most common and bothersome symptoms in patients with migraines. Neuroscience Dural Stimulation and Periorbital von Frey Testing in Mice As a Preclinical Model of Headache Bianca N. Mason1, Amanda Avona1, Jacob Lackovic1, Gregory Dussor1 1School of Brain and Behavioral Sciences and Center for Advanced Pain Studies, University of Texas at Dallas The most notable symptom of migraine is severe head pain, and it is hypothesized that this is mediated by sensory neurons innervating the meninges. Here, we present a method to locally apply substances to the dura in a minimally invasive manner while using facial hypersensitivity as an output. Bioengineering Production of Membrane-Filtered Phase-Shift Decafluorobutane Nanodroplets from Preformed Microbubbles Darrah A. Merillat1, Arvin Honari1, Shashank R. Sirsi1,2 1Department of Bioengineering, The University of Texas at Dallas, 2Department of Radiology, The University of Texas Southwestern This protocol describes a method of generating large volumes of lipid encapsulated decafluorobutane microbubbles using probe-tip sonication and subsequently condensing them into phase-shift nanodroplets using high-pressure extrusion and mechanical filtration. Neuroscience Preparation of Peripheral Nerve Stimulation Electrodes for Chronic Implantation in Rats Camilo A. Sanchez1, Jackson Brougher2, Kim C. Rahebi3, Catherine A. Thorn2 1Department of Bioengineering, University of Texas at Dallas, 2School of Behavioral and Brain Sciences, University of Texas at Dallas, 3Texas Biomedical Device Center, University of Texas at Dallas Existing approaches for constructing chronically implantable peripheral nerve cuff electrodes for use in small rodents often require specialized equipment and/or highly trained personnel. In this protocol we demonstrate a simple, low-cost approach for fabricating chronically implantable cuff electrodes, and demonstrate their effectiveness for vagus nerve stimulation (VNS) in rats. Biology Detection of Tissue-resident Bacteria in Bladder Biopsies by 16S rRNA Fluorescence In Situ Hybridization Michael L. Neugent*1, Jashkaran Gadhvi*1, Kelli L. Palmer1, Philippe E. Zimmern2, Nicole J. De Nisco1 1Department of Biological Sciences, University of Texas at Dallas, 2Department of Urology, University of Texas Southwestern Medical Center This protocol is for the unbiased detection of tissue-associated bacteria in patient biopsies by 16S rRNA in situ hybridization and confocal microscopy. Bioengineering In Vivo Two-Color 2-Photon Imaging of Genetically-Tagged Reporter Cells in the Skin Thomas A. Szabo-Pardi1, Nilesh M. Agalave1, Ashley T. Andrew1, Michael D. Burton1 1School of Brain and Behavioral Science, Center for Advanced Pain Studies, University of Texas at Dallas Morphological changes occur in immune responsive fibroblast cells following activation and promote alterations in cellular recruitment. Utilizing 2-photon imaging in conjunction with a genetically engineered Fibroblast-specific protein 1 (FSP1)-cre; tdTomato floxed-stop-floxed (TB/TB) mouse line and green fluorescently tagged lipopolysaccharide-FITC, we can illustrate highly specific uptake of lipopolysaccharide in dermal fibroblasts and morphological changes in vivo. Bioengineering Environmental Dynamic Mechanical Analysis to Predict the Softening Behavior of Neural Implants Seyed Mahmoud Hosseini1, Walter E. Voit1,2,3, Melanie Ecker2,3,4 1Department of Chemistry and Biochemistry, University of Texas at Dallas, 2Department of Materials Science and Engineering, University of Texas at Dallas, 3Center for Engineering Innovation, University of Texas at Dallas, 4Department of Bioengineering, University of Texas at Dallas To allow reliable predictions of the softening of polymeric substrates for neural implants in an in vivo environment, it is important to have a reliable in vitro method. Here, the use of dynamic mechanical analysis in phosphate buffered saline at body temperature is presented. Bioengineering Making Conjugation-induced Fluorescent PEGylated Virus-like Particles by Dibromomaleimide-disulfide Chemistry Zhuo Chen1, Stacey T. Detvo2, Elizabeth Pham3, Jeremiah J. Gassensmith4 1Department of Chemistry & Biochemistry, University of Texas at Dallas, 2Undergraduate Biology, University of Texas at Dallas, 3Undergraduate Healthcare Studies, University of Texas at Dallas, 4Departments of Chemistry & Biochemistry and Biomedical Engineering, University of Texas at Dallas Here, we present a procedure to fluorescently functionalize the disulfides on Qβ VLP with dibromomaleimide. We describe Qβ expression and purification, the synthesis of dibromomaleimide-functionalized molecules, and the conjugation reaction between dibromomaleimide and Qβ. The resulting yellow fluorescent conjugated particle can be used as a fluorescence probe inside cells. Behavior The Knob Supination Task: A Semi-automated Method for Assessing Forelimb Function in Rats Samuel D. Butensky1, Thelma Bethea1, Joshua Santos1, Anil Sindhurakar1, Eric Meyers2,3, Andrew M. Sloan2,3, Robert L. Rennaker II2,3, Jason B. Carmel1,4,5 1Burke Medical Research Institute, 2Texas Biomedical Center, The University of Texas at Dallas, 3Erik Jonsson School of Engineering and Computer Science, The University of Texas at Dallas, 4Brain and Mind Research Institute, Weill Cornell Medical College, 5Departments of Neurology and Pediatrics, Weill Cornell Medical College This manuscript describes a semi-automated task that quantifies supination in rats. Rats reach, grasp, and supinate a spherical manipulandum. The rat is rewarded with a pellet if the turn angle exceeds a criterion set by the user. This task increases throughput, sensitivity to injury, and objectivity compared to traditional tasks. Chemistry Self-assembling Morphologies Obtained from Helical Polycarbodiimide Copolymers and Their Triazole Derivatives Oleg V. Kulikov1, Dumindika A. Siriwardane1, Gregory T. McCandless1, Samsuddin F. Mahmood1, Bruce M. Novak1 1Department of Chemistry and Biochemistry, University of Texas at Dallas Here, we present a protocol to prepare and visualize secondary structures (e.g., fibers, toroidal architectures, and nano-spheres) derived from helical polycarbodiimides. The morphology characterized by both atomic force microscopy (AFM) and scanning electron microscopy (SEM) was shown to depend on molecular structure, concentration, and the solvent of choice. Behavior Vagus Nerve Stimulation as a Tool to Induce Plasticity in Pathways Relevant for Extinction Learning Jessica E. Childs1, Amanda C. Alvarez-Dieppa1, Christa K. McIntyre1, Sven Kroener1 1School of Behavioral and Brain Sciences, The University of Texas at Dallas Vagus nerve stimulation (VNS) has emerged as a tool to induce targeted synaptic plasticity in the forebrain to modify a range of behaviors. This protocol describes how to implement VNS to facilitate the consolidation of fear extinction memory. Engineering Atomically Traceable Nanostructure Fabrication Josh B. Ballard1, Don D. Dick2, Stephen J. McDonnell3, Maia Bischof4, Joseph Fu5, James H. G. Owen1, William R. Owen1, Justin D. Alexander1, David L. Jaeger4, Pradeep Namboodiri5, Ehud Fuchs1, Yves J. Chabal3, Robert M. Wallace3, Richard Reidy4, Richard M. Silver5, John N. Randall1, James Von Ehr1 1Zyvex Labs, 2Department of Physics, University of Texas at Dallas, 3Department of Materials Science and Engineering, University of Texas at Dallas, 4Materials Science and Engineering, University of North Texas, 5National Institute of Standards and Technology We report a protocol for combining the atomic metrology of the Scanning Tunneling Microscope for surface patterning with selective Atomic Layer Deposition and Reactive Ion Etching. Using a robust process involving numerous atmospheric exposures and transport, 3D nanostructures with atomic metrology are fabricated. Biology Measurement of Heme Synthesis Levels in Mammalian Cells Jagmohan Hooda1, Maksudul Alam1, Li Zhang1 1Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas Altered intracellular heme levels are associated with common diseases such as cancer. Thus, there is a need to measure heme biosynthesis levels in diverse cells. The goal of this protocol is to provide a fast and sensitive method to measure and compare the levels of heme synthesis in different cells. Engineering Ambient Method for the Production of an Ionically Gated Carbon Nanotube Common Cathode in Tandem Organic Solar Cells Alexander B. Cook1,2, Jonathan D. Yuen2, Joseph W. Micheli1, Albert G. Nasibulin3, Anvar Zakhidov1,2 1Physics Department, The University of Texas at Dallas, 2The NanoTech Institute, The University of Texas at Dallas, 3Department of Applied Physics, Aalto University School of Science A method of fabricating, in ambient conditions, organic photovoltaic tandem devices in a parallel configuration is presented. These devices feature an air-processed, semi-transparent, carbon nanotube common cathode. Biology A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types Haipeng Xing1, Willey Liao1,2, Yifan Mo1,2, Michael Q. Zhang2,3 1Department of Applied Mathematics & Statistics, Stony Brook University, 2Computational Biology and Bioinformatics, Cold Spring Harbor Laboratory, 3Department of Molecular and Cell Biology, University of Texas at Dallas Our Bayesian Change Point (BCP) algorithm builds on state-of-the-art advances in modeling change-points via Hidden Markov Models and applies them to chromatin immunoprecipitation sequencing (ChIPseq) data analysis. BCP performs well in both broad and punctate data types, but excels in accurately identifying robust, reproducible islands of diffuse histone enrichment. Medicine Eye Tracking Young Children with Autism Noah J. Sasson1, Jed T. Elison2 1School of Behavioral and Brain Sciences, University of Texas at Dallas, 2Carolina Institute for Developmental Disabilities, School of Medicine, University of North Carolina at Chapel Hill Eye tracking has long been used to study gaze patterns in typically-developing individuals, but recent technological advancements have made its use with clinical populations, including autism, more feasible. While eye-tracking young children with autism can offer insight into early symptom manifestations, it involves methodological challenges. Suggestions for best practices are provided.
