Oak Ridge National Laboratory

23 articles published in JoVE

• Engineering

  
  Forming Micro-and Nano-Plastics from Agricultural Plastic Films for Employment in Fundamental Research Studies Anton F. Astner¹, Douglas G. Hayes¹, Hugh M. O'Neill², Barbara R. Evans³, Sai Venkatesh Pingali², Volker S. Urban², Timothy M. Young^{4 1}Department of Biosystems Engineering and Soil Science, University of Tennessee, ²Neutron Scattering, Oak Ridge National Laboratory, ³Chemical Sciences Divisions, Oak Ridge National Laboratory, ⁴Center for Renewable Carbon, The University of Tennessee We show the formation and dimensional characterization of micro- and nanoplastics (MPs and NPs, respectively) using a stepwise process of mechanical milling, grinding, and imaging analysis.

• Bioengineering

  
  Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems Jaime Lorenzo N. Dinglasan^1,3, David T. Reeves^2,3, Robert L. Hettich³, Mitchel J. Doktycz^{3 1}Graduate School of Genome Science & Technology, University of Tennessee Knoxville, ²Bredesen Center for Interdisciplinary Research, University of Tennessee Knoxville, ³Biosciences Division, Oak Ridge National Laboratory The protocols describe high-performance liquid chromatography methods coupled to refractive index or mass spectrometric detection for studying metabolic reactions in complex lysate-based cell-free systems.

• Engineering

  
  Performing In Situ Closed-Cell Gas Reactions in the Transmission Electron Microscope Kinga A. Unocic¹, Dale K. Hensley¹, Franklin S. Walden², Wilbur C. Bigelow³, Michael B. Griffin⁴, Susan E. Habas⁴, Raymond R. Unocic¹, Lawrence F. Allard^{5 1}Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, ²Protochips Inc., ³Department of Materials Science & Engineering, University of Michigan, ⁴Catalytic Carbon Transformation & Scale-up, National Renewable Energy Laboratory, ⁵Materials Science & Technology Division, Oak Ridge National Laboratory Here, we present a protocol for performing in situ TEM closed-cell gas reaction experiments while detailing several commonly used sample preparation methods.

• Chemistry

  
  Picometer-Precision Atomic Position Tracking through Electron Microscopy Leixin Miao¹, Adrian Chmielewski¹, Debangshu Mukherjee², Nasim Alem^{1 1}Department of Materials Science & Engineering, The Pennsylvania State University, ²Center for Nanophase Materials Sciences, Oak Ridge National Laboratory This work presents a workflow for atomic position tracking in atomic resolution transmission electron microscopy imaging. This workflow is performed using an open-source Matlab app (EASY-STEM).

• Biology

  
  Neutron Radiography and Computed Tomography of Biological Systems at the Oak Ridge National Laboratory's High Flux Isotope Reactor Hassina Z. Bilheux*¹, Maria Cekanova*^2,3,4, Jeffrey M. Warren*⁵, Matthew J. Meagher⁶, Ryan D. Ross⁶, Jean C. Bilheux^1,7, Singanallur Venkatakrishnan⁸, Jiao Y.Y. Lin^1,9, Yuxuan Zhang¹, Matthew R. Pearson^9,10, Erik Stringfellow^{1 1}Neutron Scattering Division, Oak Ridge National Laboratory, ²College of Veterinary Medicine, The University of Tennessee, ³UT-ORNL Graduate School of Genome, Science and Technology, The University of Tennessee, ⁴Integrity Laboratories, ⁵Environmental Sciences Division, Oak Ridge National Laboratory, ⁶Department of Cell & Molecular Medicine, Rush Medical College, Rush University, ⁷Computer Science and Mathematics Division, Oak Ridge National Laboratory, ⁸Electrification and Energy Infrastructures Division, Oak Ridge National Laboratory, ⁹Now at Second Target Station Project, Oak Ridge National Laboratory, ¹⁰Neutron Technologies Division, Oak Ridge National Laboratory This manuscript describes a protocol for neutron radiography and computed tomography of biological samples using a High Flux Isotope Reactor (HFIR) CG-1D beamline to measure a metal implant in a rat femur, a mouse lung, and an herbaceous plant root/soil system.

• Environment

  
  Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures Jeremy R. Chen See^1,2, Olivia Wright¹, Lavinia V. Unverdorben^1,2, Nathan Heibeck¹, Stephen M. Techtmann³, Terry C. Hazen^4,5, Regina Lamendella^{1,2 1}Department of Biology, Juniata College, ²Wright Labs, LLC, ³Department of Biological Sciences, Michigan Technological University, ⁴Biosciences Division, Oak Ridge National Laboratory, ⁵Department of Civil and Environmental Engineering, University of Tennessee Here, we present a protocol to investigate the impacts of hydraulic fracturing on nearby streams by analyzing their water and sediment microbial communities.

• Chemistry

  
  Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures Gabriela C. Schröder^1,2, Flora Meilleur^{1,2 1}Department of Molecular and Structural Biochemistry, North Carolina State University, ²Neutron Scattering Division, Oak Ridge National Laboratory Neutron protein crystallography is a structural technique that permits the localization of hydrogen atoms, thereby providing important mechanistic details of protein function. We present here the workflow for mounting a protein crystal, neutron diffraction data collection, structure refinement and analysis of the neutron scattering length density maps.

• Neuroscience

  
  Computer-based Multitaper Spectrogram Program for Electroencephalographic Data Christopher B. O'Brien¹, Helen A. Baghdoyan^1,2,3, Ralph Lydic^{1,2,3 1}Department of Psychology, University of Tennessee, ²Department of Anesthesiology, University of Tennessee, ³Oak Ridge National Laboratory This protocol provides an open source, compiled MATLAB program that generates multitaper spectrograms for electroencephalographic data.

• Bioengineering

  
  Assembly and Characterization of Biomolecular Memristors Consisting of Ion Channel-doped Lipid Membranes Joseph S. Najem^1,2, Graham J. Taylor^2,3, Nick Armendarez⁴, Ryan J. Weiss⁵, Md Sakib Hasan⁵, Garrett S. Rose⁵, Catherine D. Schuman⁶, Alex Belianinov⁷, Stephen A. Sarles², C. Patrick Collier^{2,3,7 1}Joint Institute for Biological Sciences, Oak Ridge National Laboratory, ²Department of Mechanical, Aerospace and Biomedical Engineering, University of Tennessee, ³Bredesen Center for Interdisciplinary Research, University of Tennessee, ⁴Department of Biosystems and Agriculture Engineering, University of Kentucky, ⁵Department of Electrical Engineering and Computer Science, University of Tennessee, ⁶Computer Science and Mathematics Division, Oak Ridge National Laboratory, ⁷Center for Nanophase Materials Sciences, Oak Ridge National Laboratory Soft, low-power, biomolecular memristors leverage similar composition, structure, and switching mechanisms of bio-synapses. Presented here is a protocol to assemble and characterize biomolecular memristors obtained from insulating lipid bilayers formed between water droplets in oil. The incorporation of voltage-activated alamethicin peptides results in memristive ionic conductance across the membrane.

• Engineering

  
  A Silicon-tipped Fiber-optic Sensing Platform with High Resolution and Fast Response Guigen Liu*¹, Qiwen Sheng*¹, Weilin Hou², Matthew L. Reinke³, Ming Han^{1,4 1}Department of Electrical and Computer Engineering, Michigan State University, ²Naval Research Laboratory, Stennis Space Center, ³Oak Ridge National Laboratory, ⁴Department of Electrical and Computer Engineering, University of Nebraska-Lincoln This work reports an innovative silicon-tipped fiber-optic sensing platform (Si-FOSP) for high-resolution and fast-response measurement of a variety of physical parameters, such as temperature, flow, and radiation. Applications of this Si-FOSP span from oceanographic research, mechanical industry, to fusion energy research.

• 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.

• Engineering

  
  Fabricating Reactive Surfaces with Brush-like and Crosslinked Films of Azlactone-Functionalized Block Co-Polymers Mohammadali Masigol¹, Niloy Barua¹, Bradley S. Lokitz², Ryan R. Hansen^{1 1}Chemical Engineering Department, Kansas State University, ²Center for Nanophase Materials Sciences, Oak Ridge National Laboratory Surface fabrication methods for patterned deposition of nanometer thick brushes or micron thick, crosslinked films of an azlactone block co-polymer are reported. Critical experimental steps, representative results, and limitations of each method are discussed. These methods are useful for creating functional interfaces with tailored physical features and tunable surface reactivity.

• Chemistry

  
  Monitoring the Effects of Illumination on the Structure of Conjugated Polymer Gels Using Neutron Scattering Brian Morgan¹, Samantha J. Rinehart¹, Mark D. Dadmun^{1,2 1}Department of Chemistry, University of Tennessee, Knoxville, ²Chemical Sciences Division, Oak Ridge National Laboratory A protocol for the analysis of gels formed from the optoelectronic conjugated polymer poly(3-hexylthiophene-2,5-diyl) (P3HT) using small and ultra-small angle neutron scattering in both the presence and absence of illumination is presented.

• Bioengineering

  
  Imaging the Root Hair Morphology of Arabidopsis Seedlings in a Two-layer Microfluidic Platform Jayde A. Aufrecht^1,2, Jennifer M. Ryan³, Sahar Hasim⁴, David P. Allison^2,3, Andreas Nebenführ³, Mitchel J. Doktycz^1,2, Scott T. Retterer^{1,2 1}Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, ²Bioscience Division and Center for Nanophase Materials Sciences, Oak Ridge national Laboratory, ³Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, ⁴Department of Microbiology, University of Tennessee This article demonstrates how to culture Arabidopsis thaliana seedlings in a two-layer microfluidic platform that confines the main root and root hairs to a single optical plane. This platform can be used for real-time optical imaging of fine root morphology as well as for high-resolution imaging by other means.

• Bioengineering

  
  Assembly and Tracking of Microbial Community Development within a Microwell Array Platform Andrea C. Timm¹, Michelle C. Halsted², Jared L. Wilmoth¹, Scott T. Retterer^{1,3 1}Biosciences Division, Oak Ridge National Laboratory, ²Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, ³Center for Nanophase Materials Sciences, Oak Ridge National Laboratory The development of microbial communities depends on a combination of factors, including environmental architecture, member abundance, traits, and interactions. This protocol describes a synthetic, microfabricated environment for the simultaneous tracking of thousands of communities contained in femtoliter wells, where key factors such as niche size and confinement can be approximated.

• Immunology and Infection

  
  A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy Cora Miquel Guennoc¹, Christophe Rose², Frédéric Guinnet¹, Igor Miquel¹, Jessy Labbé³, Aurélie Deveau^{1 1}Interactions Arbres – Microorganismes, UMR1136, INRA Université de Lorraine, ²Ecologie et Ecophysiologie Forestières - PTEF, UMR 1137, INRA Université de Lorraine, ³Biosciences Division, Oak Ridge National Laboratory This protocol describes a new method to grow and qualitatively analyze bacterial biofilms on fungal hyphae by confocal and electron microscopy.

• Chemistry

  
  Sulfate Separation by Selective Crystallization with a Bis-iminoguanidinium Ligand Charles A. Seipp^1,2, Neil J. Williams^1,3, Radu Custelcean^{1 1}Chemical Sciences Division, Oak Ridge National Laboratory, ²Department of Chemistry, The University of Texas at Austin, ³Department of Chemistry, The University of Tennessee A protocol for in situ aqueous synthesis of a bis(iminoguanidinium) ligand and its utilization in selective separation of sulfate is presented.

• Chemistry

  
  Functionalization of Single-walled Carbon Nanotubes with Thermo-reversible Block Copolymers and Characterization by Small-angle Neutron Scattering Youngkyu Han¹, Suk-kyun Ahn^2,3, Zhe Zhang^1,4, Gregory S. Smith¹, Changwoo Do^{1 1}Biology and Soft Matter Division, Neutron Science Directorate, Oak Ridge National Laboratory, ²Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, ³Department of Polymer Science and Engineering, Pusan National University, ⁴Jülich Center for Neutron Science, Forschungszentrum Jülich A method for the functionalization of carbon nanotubes with structure-tunable polymeric encapsulation layers and structural characterization using small-angle neutron scattering is presented.

• Bioengineering

  
  Sealable Femtoliter Chamber Arrays for Cell-free Biology Sarah Elizabeth Norred^1,2, Patrick M. Caveney^1,2, Scott T. Retterer^1,2, Jonathan B. Boreyko^1,2, Jason D. Fowlkes^2,3, Charles Patrick Collier², Michael L. Simpson^{1,2,3 1}Bredesen Center, University of Tennessee, Knoxville, ²Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, ³Department of Materials Science and Engineering, University of Tennessee, Knoxville A microfabricated device with sealable femtoliter-volume reaction chambers is described. This report includes a protocol for sealing cell-free protein synthesis reactants inside these chambers for the purpose of understanding the role of crowding and confinement in gene expression.

• Environment

  
  High-throughput Fluorometric Measurement of Potential Soil Extracellular Enzyme Activities Colin W. Bell¹, Barbara E. Fricks¹, Jennifer D. Rocca¹, Jessica M. Steinweg², Shawna K. McMahon³, Matthew D. Wallenstein^{1 1}Natural Resource Ecology Laboratory, Colorado State University, ²Biosciences Division, Oak Ridge National Laboratory, ³Department of Bioengineering, University of Colorado To measure potential rates of soil extracellular enzyme activities, synthetic substrates that are bound to a fluorescent dye are added to soil samples. Enzyme activity is measured as the fluorescent dye is released from the substrate by an enzyme-catalyzed reaction, where higher fluorescence indicates more substrate degradation.

• Biology

  
  Autonomously Bioluminescent Mammalian Cells for Continuous and Real-time Monitoring of Cytotoxicity Tingting Xu¹, Dan M. Close², James D. Webb³, Steven A. Ripp^2,3, Gary S. Sayler^{1,2,3 1}The Joint Institute for Biological Sciences, Oak Ridge National Laboratory, ²490 BioTech, Inc., ³The Center for Environmental Biotechnology, The University of Tennessee, Knoxville Mammalian cells expressing the bacterial bioluminescence gene cassette (lux) produce light autonomously. The resulting bioluminescent dynamics upon chemical exposure have been demonstrated to reflect the treatment effects on cellular growth and metabolism, making these cells an inexpensive, continuous, real-time toxicity screening tool that can easily be adapted for high-throughput automation.

• Engineering

  
  Fabrication of Spatially Confined Complex Oxides Hangwen Guo^1,2, Thomas Z. Ward^{1 1}Materials Science and Technology Division, Oak Ridge National Laboratory, ²Department of Physics & Astronomy, University of Tennessee, Knoxville We describe the use of pulsed laser deposition (PLD), photolithography and wire-bonding techniques to create micrometer scale complex oxides devices. The PLD is utilized to grow epitaxial thin films. Photolithography and wire-bonding techniques are introduced to create practical devices for measurement purposes.

• Bioengineering

  
  Bacterial Immobilization for Imaging by Atomic Force Microscopy David P. Allison^1,2, Claretta J. Sullivan³, Ninell Pollas Mortensen^1,2, Scott T. Retterer^1,4, Mitchel Doktycz^{1,4 1}Biological and Nanoscale Systems Group, Biosciences Division, Oak Ridge National Laboratory, ²Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, ³Department of Surgery, Eastern Virginia Medical School, ⁴Center for Nanophase Materials Sciences Division, Oak Ridge National Laboratory Live Gram-negative and Gram-positive bacteria can be immobilized on gelatin-coated mica and imaged in liquid using Atomic Force Microscopy (AFM).