Lawrence Berkeley National Laboratory View Institution's Website 34 articles published in JoVE Biochemistry Streptavidin-Affinity Grid Fabrication for Cryo-Electron Microscopy Sample Preparation Trinity Cookis1, Paul Sauer2,3, Simon Poepsel4,5, Bong-Gyoon Han6, Dominik A. Herbst1,2,6, Robert Glaeser6, Eva Nogales1,2,3,6 1Department of Molecular and Cell Biology, University of California, Berkeley, 2California Institute for Quantitative Biology (QB3), University of California, Berkeley, 3Howard Hughes Medical Institute, University of California, Berkeley, 4Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, University of Cologne, 5Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, 6Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory A step-by-step protocol for fabricating streptavidin affinity grids is provided for use in structural studies of challenging macromolecular samples by cryo-electron microscopy. Environment Bioprospecting of Extremophilic Microorganisms to Address Environmental Pollution Giovanni Gallo1,2, Martina Aulitto1,3, Patrizia Contursi1,4, Danila Limauro1,4, Simonetta Bartolucci1, Gabriella Fiorentino1,4 1Department of Biology, University of Naples Federico II, 2Institute of Polymers, Composites and Biomaterials (IPCB), Consiglio Nazionale delle Ricerche CNR, 3Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, 4BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II The isolation of heavy metal-resistant microbes from geothermal springs is a hot topic for the development of bioremediation and environmental monitoring biosystems. This study provides a methodological approach for isolating and identifying heavy metal tolerant bacteria from hot springs. Engineering Determining the Mechanical Strength of Ultra-Fine-Grained Metals Jianing Xu*1,2, Yanju Wang*2, Jinyuan Yan3, Bin Chen1,2 1School of Science, Harbin Institute of Technology, 2Center for High Pressure Science and Technology Advanced Research, 3Advanced Light Source, Lawrence Berkeley National Lab The protocol presented here describes the high-pressure radial diamond-anvil-cell experiments and analyzing the related data, which are essential for obtaining the mechanical strength of the nanomaterials with a significant breakthrough to the traditional approach. Biochemistry Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers Mowei Zhou1, Shadan H. Abdali1, David Dilworth2, Lifeng Liu2, Benjamin Cole2, Neha Malhan1, Amir H. Ahkami1, Tanya E. Winkler1, Joy Hollingsworth3, Julie Sievert3, Jeff Dahlberg3, Robert Hutmacher4,5, Mary Madera6, Judith A. Owiti6, Kim K. Hixson1, Peggy G. Lemaux6, Christer Jansson1, Ljiljana Paša-Tolić1 1Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 2DOE-Joint Genome Institute, Lawrence Berkeley Laboratory, 3Kearney Agricultural Research and Extension Center, University of California Agriculture and Natural Resources, 4West Side Research and Extension Center, University of California, 5Department of Plant Sciences, University of California, Davis, 6Department of Plant and Microbial Biology, University of California, Berkeley The protocol has been developed to effectively extract intact histones from sorghum leaf materials for profiling of histone post-translational modifications that can serve as potential epigenetic markers to aid engineering drought resistant crops. Bioengineering Generating a Fractal Microstructure of Laminin-111 to Signal to Cells Camila Hochman-Mendez1, Tatiana Coelho-Sampaio2, Ariel J. Kent3, Jamie L. Inman3, Mina J. Bissell3, Claire Robertson4 1Regenerative Medicine Research, Texas Heart Institute, 2Institute of Biomedical Sciences, Federal University of Rio de Janeiro, 3Biological Systems and Engineering, Lawrence Berkeley National Lab, 4Materials Engineering Division, Lawrence Livermore National Lab We describe three methods to generate Ln1 polymers with fractal properties that signal to cells differently compared to unpolymerized Ln1. Engineering Synchrotron X-ray Microdiffraction and Fluorescence Imaging of Mineral and Rock Samples Camelia V. Stan1, Nobumichi Tamura1 1Advanced Light Source, Lawrence Berkeley National Laboratory We describe a beamline setup meant to carry out rapid two-dimensional x-ray fluorescence and x-ray microdiffraction mapping of single crystal or powder samples using either Laue (polychromatic radiation) or powder (monochromatic radiation) diffraction. The resulting maps give information about strain, orientation, phase distribution, and plastic deformation. Chemistry Using Graphene Liquid Cell Transmission Electron Microscopy to Study in Situ Nanocrystal Etching Matthew R. Hauwiller1, Justin C. Ondry1, A. Paul Alivisatos1,2,3,4 1Department of Chemistry, University of California-Berkeley, 2Department of Material Science and Engineering, University of California-Berkeley, 3Kavli Energy NanoScience Institute, 4Materials Sciences Division, Lawrence Berkeley National Laboratory Graphene liquid cell electron microscopy can be used to observe nanocrystal dynamics in a liquid environment with greater spatial resolution than other liquid cell electron microscopy techniques. Etching premade nanocrystals and following their shape using graphene liquid cell Transmission Electron Microscopy can yield important mechanistic information about nanoparticle transformations. Chemistry Elemental-sensitive Detection of the Chemistry in Batteries through Soft X-ray Absorption Spectroscopy and Resonant Inelastic X-ray Scattering Jinpeng Wu1,2, Shawn Sallis2,3, Ruimin Qiao2, Qinghao Li2,4, Zengqing Zhuo2,5, Kehua Dai2,6, Zixuan Guo2,7, Wanli Yang2 1Geballe Laboratory for Advanced Materials, Stanford University, 2Advanced Light Source, Lawrence Berkeley National Laboratory, 3Department of Materials Science and Engineering, Binghamton University, 4School of Physics, National Key Laboratory of Crystal Materials, Shandong University, 5School of Advanced Materials, Peking University Shenzhen Graduate School, 6School of Metallurgy, Northeastern University, 7Department of Chemical Engineering, University of California-Santa Barbara Here, we present a protocol for typical experiments of soft X-ray absorption spectroscopy (sXAS) and resonant inelastic X-ray scattering (RIXS) with applications in battery material studies. Engineering Electric-field Control of Electronic States in WS2 Nanodevices by Electrolyte Gating Feng Qin1, Toshiya Ideue1, Wu Shi2, Yijin Zhang3,4, Ryuji Suzuki1, Masaro Yoshida5, Yu Saito1, Yoshihiro Iwasa1,5 1Quantum-Phase Electronics Center (QPEC) and Department of Applied Physics, The University of Tokyo, 2Materials Sciences Division, Lawrence Berkeley National Laboratory, 3Institute of Scientific and Industrial Research, Osaka University, 4Max Planck Institute for Solid State Research, 5RIKEN Center for Emergent Matter Science (CEMS) Here, we present a protocol to control the carrier number in solids by using the electrolyte. Environment Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions Jian Gao1,2, Joelle Sasse1,2, Kyle M. Lewald1,2, Kateryna Zhalnina1,2, Lloyd T. Cornmesser1,2, Todd A. Duncombe3, Yasuo Yoshikuni2, John P. Vogel2, Mary K. Firestone4, Trent R. Northen1,2 1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 2Joint Genome Institute, Department of Energy, 3Joint BioEnergy Institute, 4Department of Environmental Science Policy and Management, University of California This article describes detailed protocols for ecosystem fabrication of devices (EcoFABs) that enable the studies of plants and plant-microbe interactions in highly controlled laboratory conditions. Biochemistry Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE Venkataramana R. Pidatala*1,2, Amir Mahboubi*1,2, Jenny C. Mortimer1,2 1Joint BioEnergy Institute, 2Environmental and Systems Biology, BioSciences Division, Lawrence Berkeley National Laboratory A protocol for the structural analysis of polysaccharides by gel electrophoresis (PACE), using mannan as an example, is described. Chemistry Low Pressure Vapor-assisted Solution Process for Tunable Band Gap Pinhole-free Methylammonium Lead Halide Perovskite Films Carolin M. Sutter-Fella*1,2,3, Yanbo Li*1,4, Nicola Cefarin1,5,6, Aya Buckley1,7, Quynh Phuong Ngo8,9, Ali Javey2,3, Ian D. Sharp1, Francesca M. Toma1 1Joint Center for Artificial Photosynthesis, Chemical Sciences Division, Lawrence Berkeley National Laboratory, 2Electrical Engineering and Computer Sciences, University of California, Berkeley, 3Materials Science Division, Lawrence Berkeley National Laboratory, 4Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 5Department of Physics, Graduate School of Nanotechnology, University of Trieste, 6TASC Laboratory, IOM-CNR - Istituto Officina dei Materiali, 7Department of Chemistry, University of California, Berkeley, 8Materials Science and Engineering, University of California, Berkeley, 9Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory Here, we present a protocol for the synthesis of CH3NH3I and CH3NH3Br precursors and the subsequent formation of pinhole-free, continuous CH3NH3PbI3-xBrx thin films for the application in high efficiency solar cells and other optoelectronic devices. Engineering Printing Fabrication of Bulk Heterojunction Solar Cells and In Situ Morphology Characterization Feng Liu1, Sunzida Ferdous2, Xianjian Wan1, Chenhui Zhu3, Eric Schaible3, Alexander Hexemer3, Cheng Wang3, Thomas P. Russell1,2 1Materials Sciences Division, Lawrence Berkeley National Laboratory, 2Department of Polymer Science and Engineering, University of Massachusetts, Amherst, 3Advanced Light Source, Lawrence Berkeley National Laboratory Here, we present a protocol to fabricate organic thin film solar cells using a mini-slot die coater and related in-line structure characterizations using synchrotron scattering techniques. Chemistry Synthesis of a Water-soluble Metal–Organic Complex Array Purnandhu Bose1, Pradip K. Sukul1, Omar M. Yaghi2,3,4, Kentaro Tashiro1 1International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 2Department of Chemistry, University of California–Berkeley, 3Materials Sciences Division, Lawrence Berkeley National Laboratory, 4Kavli Energy NanoSciences Institute at Berkeley, University of California–Berkeley A potential general method for the synthesis of water-soluble multimetallic peptidic arrays containing a predetermined sequence of metal centers is presented. Engineering Using Synchrotron Radiation Microtomography to Investigate Multi-scale Three-dimensional Microelectronic Packages Holly D. Carlton1, John W. Elmer1, Yan Li2, Mario Pacheco2, Deepak Goyal2, Dilworth Y. Parkinson3, Alastair A. MacDowell3 1Materials Engineering Division, Lawrence Livermore National Laboratory, 2Assembly Test and Technology Development Failure Analysis Labs, Intel Corporation, 3Advanced Light Source, Lawrence Berkeley National Laboratory For this study synchrotron radiation micro-tomography, a non-destructive three-dimensional imaging technique, is employed to investigate an entire microelectronic package with a cross-sectional area of 16 x 16 mm. Due to the synchrotron's high flux and brightness the sample was imaged in just 3 min with an 8.7 µm spatial resolution. Engineering Failure Analysis of Batteries Using Synchrotron-based Hard X-ray Microtomography Katherine J. Harry1,2, Dilworth Y. Parkinson3, Nitash P. Balsara2,4,5 1Department of Materials Science and Engineering, University of California Berkeley, 2Materials Science Division, Lawrence Berkeley National Laboratory, 3Advanced Light Source Division, Lawrence Berkeley National Laboratory, 4Department of Chemical and Biomolecular Engineering, University of California Berkeley, 5Environmental Energy Technology Division, Lawrence Berkeley National Laboratory Synchrotron-based hard X-ray microtomography is used to image the electrochemical growth of dendrites from a lithium metal electrode through a solid polymer electrolyte membrane. Engineering Fabrication of Gate-tunable Graphene Devices for Scanning Tunneling Microscopy Studies with Coulomb Impurities Han Sae Jung1,2, Hsin-Zon Tsai1, Dillon Wong1, Chad Germany1, Salman Kahn1, Youngkyou Kim1,3, Andrew S. Aikawa1, Dhruv K. Desai1, Griffin F. Rodgers1, Aaron J. Bradley1, Jairo Velasco Jr.1, Kenji Watanabe4, Takashi Taniguchi4, Feng Wang1,5,6, Alex Zettl1,5,6, Michael F. Crommie1,5,6 1Department of Physics, University of California at Berkeley, 2Department of Chemistry, University of California at Berkeley, 3Department of Chemical and Biomolecular Engineering, University of California at Berkeley, 4National Institute for Materials Science (Japan), 5Materials Sciences Division, Lawrence Berkeley National Laboratory, 6Kavli Energy NanoSciences Institute, University of California at Berkeley and Lawrence Berkeley National Laboratory This paper details the fabrication process of a gate-tunable graphene device, decorated with Coulomb impurities for scanning tunneling microscopy studies. Mapping the spatially dependent electronic structure of graphene in the presence of charged impurities unveils the unique behavior of its relativistic charge carriers in response to a local Coulomb potential. Chemistry Preparation of Highly Porous Coordination Polymer Coatings on Macroporous Polymer Monoliths for Enhanced Enrichment of Phosphopeptides Alexandros Lamprou1, Hongxia Wang1,4, Adeela Saeed2, Frantisek Svec1, David Britt1, Fernando Maya3 1The Molecular Foundry, E. O. Lawrence Berkeley National Laboratory, 2Institute of Chemical Sciences, Bahauddin Zakariya University, 3Department of Chemistry, University of the Balearic Islands, 4Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology A procedure for the preparation of porous hybrid separation media composed of a macroporous polymer monolith internally coated by a high surface area microporous coordination polymer is presented. Bioengineering Production and Targeting of Monovalent Quantum Dots Daeha Seo*1,2,3, Justin Farlow*4,5,6, Kade Southard1,4,7, Young-wook Jun1,7, Zev J. Gartner4,5,6,7 1Department of Otolaryngology, University of California, San Francisco, 2Department of Chemistry, University of California, Berkeley, 3Materials Science Division, Lawrence Berkeley National Laboratory, 4Department of Pharmaceutical Chemistry, University of California, San Francisco, 5Tetrad Graduate Program, University of California, San Francisco, 6Center for Systems and Synthetic Biology, University of California, San Francisco, 7Chemistry and Chemical Biology Graduate Program, University of California, San Francisco We provide detailed instructions for the preparation of monovalent targeted quantum dots (mQDs) from phosphorothioate DNA of defined length. DNA wrapping occurs in high yield, and therefore, products do not require purification. We demonstrate the use of the SNAP tag to target mQDs to cell-surface receptors for live-cell imaging applications. Bioengineering From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data Wen-Ting Tsai1, Ahmed Hassan1, Purbasha Sarkar2, Joaquin Correa1,3, Zoltan Metlagel1, Danielle M. Jorgens1, Manfred Auer1,2 1Life Sciences Division, Lawrence Berkeley National Laboratory, 2Joint Bioenergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 3National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory The bottleneck for cellular 3D electron microscopy is feature extraction (segmentation) in highly complex 3D density maps. We have developed a set of criteria, which provides guidance regarding which segmentation approach (manual, semi-automated, or automated) is best suited for different data types, thus providing a starting point for effective segmentation. Biology DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems Lara Rajeev1, Eric G. Luning1, Aindrila Mukhopadhyay1 1Physical Biosciences Division, Lawrence Berkeley National Laboratory This video article describes an in vitro microarray based method to determine the gene targets and binding sites for two component system response regulators. Engineering Flame Experiments at the Advanced Light Source: New Insights into Soot Formation Processes Nils Hansen1, Scott A. Skeen1, Hope A. Michelsen1, Kevin R. Wilson2, Katharina Kohse-Höinghaus3 1Combustion Research Facility, Sandia National Laboratories, 2Chemical Sciences Division, Advanced Light Source, Lawrence Berkeley National Laboratory, 3Physikalische Chemie I, Universität Bielefeld Gas sampling from laboratory-scale flames with online analysis of all species by mass spectrometry is a powerful method to investigate the complex mixture of chemical compounds occurring during combustion processes. Coupled with tunable soft ionization via synchrotron-generated vacuum-ultraviolet radiation, this technique provides isomer-resolved information and potentially fragment-free mass spectra. Biology Histochemical Staining of Arabidopsis thaliana Secondary Cell Wall Elements Prajakta Pradhan Mitra1,2, Dominique Loqué1,2 1Feedstocks Division, Joint Bioenergy Institute, 2Physical Biosciences Division, Lawrence Berkeley National Laboratory Plant cell wall composition varies between tissue types and can include lignin, cellulose, hemicelluloses, and pectin. Various staining techniques have been developed to visualize differences at the cell-type level. This paper is a compilation of commonly used cell wall staining techniques. Bioengineering Lipid Bilayer Vesicle Generation Using Microfluidic Jetting Christopher W. Coyne1, Karan Patel1, Johanna Heureaux1, Jeanne Stachowiak3, Daniel A. Fletcher4,5, Allen P. Liu1,2 1Department of Mechanical Engineering, University of Michigan, 2Department of Biomedical Engineering, University of Michigan, 3Department of Biomedical Engineering, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 4Department of Bioengineering, University of California, Berkeley, 5Physical Biosciences Division, Lawrence Berkeley National Laboratory Microfluidic jetting against a droplet interface lipid bilayer provides a reliable way to generate vesicles with control over membrane asymmetry, incorporation of transmembrane proteins, and encapsulation of material. This technique can be applied to study a variety of biological systems where compartmentalized biomolecules are desired. Chemistry Seeded Synthesis of CdSe/CdS Rod and Tetrapod Nanocrystals Karthish Manthiram*1,4, Brandon J. Beberwyck*2,4, Dmitri V. Talapin5,6, A. Paul Alivisatos2,3,4 1Department of Chemical Engineering, UC Berkeley, 2Department of Materials Science and Engineering, UC Berkeley, 3Department of Chemistry, UC Berkeley, 4Materials Sciences Division, Lawrence Berkeley National Laboratory, 5Department of Chemistry, University of Chicago, 6Center for Nanoscale Materials, Argonne National Laboratory A protocol for the seeded synthesis of rod-shaped and tetrapod-shaped multicomponent nanostructures consisting of CdS and CdSe is presented. Engineering Setting Limits on Supersymmetry Using Simplified Models Christian Gütschow1, Zachary Marshall2,3 1Department of Physics and Astronomy, University College London, 2CERN, 3Physics Division, Lawrence Berkeley National Laboratories This paper demonstrates a protocol for recasting experimental simplified model limits into conservative and aggressive limits on an arbitrary new physics model. Publicly available LHC experimental results can be recast in this manner into limits on almost any new physics model with a supersymmetry-like signature. Engineering Characterization of Electrode Materials for Lithium Ion and Sodium Ion Batteries Using Synchrotron Radiation Techniques Marca M. Doeff1, Guoying Chen1, Jordi Cabana1,2, Thomas J. Richardson1, Apurva Mehta3, Mona Shirpour1, Hugues Duncan1, Chunjoong Kim1, Kinson C. Kam4, Thomas Conry5 1Environmental Energy Technologies Division, Lawrence Berkeley National Laboratory, 2Department of Chemistry, University of Illinois at Chicago, 3Stanford Synchrotron Radiation Lightsource, 4Haldor Topsøe A/S, 5PolyPlus Battery Company We describe the use of synchrotron X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) techniques to probe details of intercalation/deintercalation processes in electrode materials for Li-ion and Na-ion batteries. Both in situ and ex situ experiments are used to understand structural behavior relevant to the operation of devices Biology Using High Resolution Computed Tomography to Visualize the Three Dimensional Structure and Function of Plant Vasculature Andrew J. McElrone1,2, Brendan Choat3, Dilworth Y. Parkinson4, Alastair A. MacDowell4, Craig R. Brodersen5 1U.S. Department of Agriculture, 2Department of Viticulture and Enology, University of California - Davis, 3Hawkesbury Institute for the Environment, University of Western Sydney, 4Advanced Light Source, Lawrence Berkeley National Lab, 5Citrus Research & Education Center, University of Florida High resolution x-ray computed tomography (HRCT) is a non-destructive diagnostic imaging technique that can be used to study the structure and function of plant vasculature in 3D. We demonstrate how HRCT facilitates exploration of xylem networks across a wide range of plant tissues and species. Medicine Processing of Human Reduction Mammoplasty and Mastectomy Tissues for Cell Culture Mark A. LaBarge1, James C. Garbe1, Martha R. Stampfer1 1Life Science Division, Lawrence Berkeley National Laboratory A method to process human mammary surgical discard material is described. Processed tissue, in the form of organoids, can be stored frozen indefinitely or placed in culture for long-term growth. This method enables experimental examination of normal human epithelial cell biology, and the effects of exogenous perturbations. Engineering Revealing Dynamic Processes of Materials in Liquids Using Liquid Cell Transmission Electron Microscopy Kai-Yang Niu1, Hong-Gang Liao1, Haimei Zheng1 1Materials Sciences Division, Lawrence Berkeley National Laboratory We have developed a self-contained liquid cell, which allows imaging through liquids using a transmission electron microscope. Dynamic processes of nanoparticles in liquids can be revealed in real time with sub-nanometer resolution. Engineering Molecular Beam Mass Spectrometry With Tunable Vacuum Ultraviolet (VUV) Synchrotron Radiation Amir Golan1, Musahid Ahmed1 1Chemical Sciences Division, Lawrence Berkeley National Laboratory A molecular beam coupled to tunable vacuum ultraviolet photoionization mass spectrometer at a synchrotron provides a convenient tool to explore the electronic structure of isolated gas phase molecules and clusters. Proton transfer mechanisms in DNA base dimers were elucidated with this technique. Biology Fabrication and Use of MicroEnvironment microArrays (MEArrays) Chun-Han Lin1,2, Jonathan K. Lee1, Mark A. LaBarge1 1Life Science Division, Lawrence Berkeley National Laboratory, 2Department of Comparative Biochemistry, University of California, Berkeley A combinatorial functional screening method for gaining insights into the impacts of the molecular composition of microenvironments on cellular functions is described. The method takes advantage of existing microarray-based technologies to generate arrays of defined combinatorial microenvironments that support cell adhesion and functional analysis. Bioengineering Solid-phase Submonomer Synthesis of Peptoid Polymers and their Self-Assembly into Highly-Ordered Nanosheets Helen Tran1, Sarah L. Gael1, Michael D. Connolly1, Ronald N. Zuckermann1 1Molecular Foundry, Lawrence Berkeley National Laboratory A simple and general manual peptoid synthesis method involving basic equipment and commercially available reagents is outlined, enabling peptoids to be easily synthesized in most laboratories. The synthesis, purification and characterization of an amphiphilic peptoid 36mer is described, as well as its self-assembly into highly-ordered nanosheets. Biology Label-free in situ Imaging of Lignification in Plant Cell Walls Martin Schmidt1, Pradeep Perera1, Adam M. Schwartzberg2, Paul D. Adams3, P. James Schuck2 1Energy Biosciences Institute, University of California, Berkeley, 2Molecular Foundry, Lawrence Berkeley National Laboratory, 3Physical Biosciences Division, Lawrence Berkeley National Laboratory A method based on confocal Raman microscopy is presented that affords label-free visualization of lignin in plant cell walls and comparison of lignification in different tissues, samples or species.
