Pacific Northwest National Laboratory 19 articles published in JoVE Engineering Balloon Tag Manufacturing Technique for Sensor Fish and Live Fish Recovery Aljon Salalila1, Jayson Martinez1, Ashlynn Tate1, Noe Acevedo1, Marsobyn Salalila1, Zhiqun Daniel Deng1 1Energy and Environment Directorate, Pacific Northwest National Laboratory A protocol is presented for designing and manufacturing balloon tags to recover Sensor Fish and live fish, allowing assessment of their physical condition and biological performance in hydraulic structures. The method optimizes balloon tag performance by considering factors such as balloon volume, inflation/deflation times, component selection, and the characteristics of the injected water. Biochemistry Resin-Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation Matthew J. Gaffrey1, Nicholas J. Day1, Xiaolu Li2, Wei-Jun Qian1 1Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, 2Bioproducts Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University Protein thiol oxidation has significant implications under normal physiological and pathophysiological conditions. We describe the details of a quantitative redox proteomics method, which utilizes resin-assisted capture, isobaric labeling, and mass spectrometry, enabling site-specific identification and quantification of reversibly oxidized cysteine residues of proteins. 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. Chemistry High-Temperature and High-Pressure In situ Magic Angle Spinning Nuclear Magnetic Resonance Spectroscopy Nicholas R. Jaegers1, Wenda Hu2, Yong Wang1, Jian Zhi Hu1 1Pacific Northwest National Laboratory, 2Washington State University The molecular structures and dynamics of solids, liquids, gases, and mixtures are of critical interest to diverse scientific fields. High-temperature, high-pressure in situ MAS NMR enables detection of the chemical environment of constituents in mixed phase systems under tightly controlled chemical environments. Chemistry Imaging Corrosion at the Metal-Paint Interface Using Time-of-Flight Secondary Ion Mass Spectrometry Jennifer Yao1, Anthony Guzman2, Zihua Zhu3, Xiao-Ying Yu1 1Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 2Energy and Environment Directorate, Pacific Northwest National Laboratory, 3Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Time-of-flight secondary ion mass spectrometry is applied to demonstrate the chemical mapping and corrosion morphology at the metal-paint interface of an aluminum alloy after being exposed to a salt solution compared with a specimen exposed to air. Environment Implantation of a New Micro Acoustic Tag in Juvenile Pacific Lamprey and American Eel Robert Mueller1, Stephanie Liss1, Z. Daniel Deng1 1Earth Systems Science Division, Pacific Northwest National Laboratory This article illustrates the procedure for implanting a micro acoustic tag in juvenile Pacific Lamprey and American Eel. Our application is based on laboratory trials, which indicate that acoustic tags can be successfully implanted with no apparent effects on swimming ability or survival and minimal tag loss. Environment Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures Malak M. Tfaily*1,2, Rachel M. Wilson*3, Heather M. Brewer1, Rosalie K. Chu1, Heino M. Heyman4, David W. Hoyt1, Jennifer E. Kyle5, Samuel O. Purvine1 1Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 2Department of Soil, Water and Environmental Science, University of Arizona, 3Department of Earth Ocean and Atmospheric Sciences, Florida State University, 4Bruker Daltonics Inc., 5Biological Sciences Division, Pacific Northwest National Laboratory This protocol describes a single throughput for complementary analytical and omics techniques culminating in a fully-paired characterization of natural organic matter and microbial proteomics in different ecosystems. This approach permits robust comparisons for identifying metabolic pathways and transformations important for describing greenhouse gas production and predicting responses to environmental change. Biology Micropuncture of Bowman's Space in Mice Facilitated by 2 Photon Microscopy Katsuyuki Matsushita1, Kirsti Golgotiu1, Daniel J. Orton2, Richard D. Smith2, Karin D. Rodland2, Paul D. Piehowski2, Michael P. Hutchens1,3 1Anesthesiology & Perioperative Medicine, Oregon Health & Science University, 2Environmental and Biological Services Division, Pacific Northwest National Laboratory, 3Operative Care Division, Portland Veterans Affairs Medical Center We present use of 2-photon microscopy to place a micropipette within Bowman's urinary space in mice, combining 2 foundational techniques of renal physiology. Use of 2-photon microscopy overcomes critical limitations of conventional microscopy for micropuncture renal physiology studies. Chemistry Ligand-Mediated Nucleation and Growth of Palladium Metal Nanoparticles Saeed Mozaffari*1, Wenhui Li*1, Coogan Thompson1, Sergei Ivanov2, Soenke Seifert3, Byeongdu Lee4, Libor Kovarik5, Ayman M. Karim1 1Department of Chemical Engineering, Virginia Polytechnic Institute and State University, 2Center for Integrated Nanotechnologies, Los Alamos National Laboratory, 3Advanced Photon Source, Argonne National Laboratory, 4X-ray Science Division, Argonne National Laboratory, 5Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory The main goal of this work is to elucidate the role of capping agents in regulating the size of palladium nanoparticles by combining in situ small angle x-ray scattering (SAXS) and ligand-based kinetic modeling. Chemistry The MPLEx Protocol for Multi-omic Analyses of Soil Samples Carrie D. Nicora*1, Kristin E. Burnum-Johnson*1, Ernesto S. Nakayasu1, Cameron P. Casey1, Richard A. White III1, Taniya Roy Chowdhury1, Jennifer E. Kyle1, Young-Mo Kim1, Richard D. Smith1, Thomas O. Metz1, Janet K. Jansson1, Erin S. Baker1 1Biological Sciences Division, Pacific Northwest National Laboratory A protocol is presented for simultaneously extracting metabolites, proteins, and lipids from a single soil sample, allowing reduced sample preparation times and enabling multi-omic mass spectrometry analyses of samples with limited quantities. Engineering In Situ High Pressure Hydrogen Tribological Testing of Common Polymer Materials Used in the Hydrogen Delivery Infrastructure Edward R. Duranty1, Timothy J. Roosendaal1, Stan G. Pitman1, Joseph C. Tucker1, Stanley L. Owsley Jr.1, Jonathan D. Suter1, Kyle James Alvine1 1Energy and Environment Directorate, Pacific Northwest National Laboratory A test methodology for quantifying tribological properties of polymers used in hydrogen infrastructure service is demonstrated and characteristic results for a common elastomer are discussed. Chemistry In Situ Characterization of Boehmite Particles in Water Using Liquid SEM Juan Yao1, Bruce W. Arey1, Li Yang1, Fei Zhang1, Rachel Komorek1, Jaehun Chun1, Xiao-Ying Yu1 1Earth & Biological Sciences Directorate, Pacific Northwest National Laboratory We present a procedure for real-time imaging and elemental composition analysis of boehmite particles in deionized water by in situ liquid Scanning Electron Microscopy. Chemistry In Situ Characterization of Shewanella oneidensis MR1 Biofilms by SALVI and ToF-SIMS Rachel Komorek1, Wenchao Wei1, Xiaofei Yu2, Eric Hill1, Juan Yao1, Zihua Zhu2, Xiao-Ying Yu1 1Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 2Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory This article presents a method for growing a biofilm for in situ time-of-flight secondary ion mass spectrometry for chemical mapping in its hydrated state, enabled by a microfluidic reactor, System for Analysis at the liquid Vacuum Interface. The Shewanella oneidensis MR-1 with green fluorescence protein was used as a model. Chemistry A Protocol for Electrochemical Evaluations and State of Charge Diagnostics of a Symmetric Organic Redox Flow Battery Wentao Duan*1,2, Rama S. Vemuri*1,3, Dehong Hu3, Zheng Yang1,4, Xiaoliang Wei1,2 1Joint Center for Energy Storage Research (JCESR), 2Energy & Environment Directorate, Pacific Northwest National Laboratory, 3Earth & Biological Systems Directorate, Pacific Northwest National Laboratory, 4Physical & Computational Sciences Directorate, Pacific Northwest National Laboratory We present the protocols for electrochemically evaluating a symmetric non-aqueous organic redox flow battery and for diagnosing its state of charge using FTIR. Biochemistry Biomass Conversion to Produce Hydrocarbon Liquid Fuel Via Hot-vapor Filtered Fast Pyrolysis and Catalytic Hydrotreating Huamin Wang1, Douglas C. Elliott1, Richard J. French2, Steve Deutch2, Kristiina Iisa2 1Chemical and Biological Process Development, Pacific Northwest National Laboratory (PNNL), 2National Bioenergy Center, National Renewable Energy Laboratory (NREL) Experimental methods for fast pyrolysis of lignocellulosic biomass to produce bio-oils and for the catalytic hydrotreating of bio-oils to produce fuel range hydrocarbons are presented. Hot-vapor filtration during fast pyrolysis to remove fine char particles and inorganic contaminants from bio-oil was also assessed. Bioengineering Qualitative Characterization of the Aqueous Fraction from Hydrothermal Liquefaction of Algae Using 2D Gas Chromatography with Time-of-flight Mass Spectrometry Balakrishna Maddi1, Ellen Panisko1, Karl Albrecht1, Daniel Howe1 1Chemical & Biological Process Development, Pacific Northwest National Laboratory A two-dimensional gas chromatography-time-of-flight mass spectrometry method is described for characterization of the aqueous fraction of bio-crude produced from hydrothermal liquefaction of algae. This protocol can also be employed to analyze the aqueous fraction of liquid products from fast pyrolysis, catalytic fast pyrolysis, catalytic deoxygenation and hydro-treating. Chemistry In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS Jiachao Yu1, Yufan Zhou*2, Xin Hua*1, Zihua Zhu2, Xiao-Ying Yu1 1Fundamental & Computational Sciences Directorate, Pacific Northwest National Laboratory, 2Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory This work presents a protocol for liquid handling and sample introduction to a microchannel for in situ time-of-flight secondary ion mass spectrometry analysis of protein biomolecules in an aqueous solution. Immunology and Infection Electroporation of Functional Bacterial Effectors into Mammalian Cells Ryan L. Sontag1, Cosmin Mihai2, Galya Orr2, Alexei Savchenko3, Tatiana Skarina3, Hong Cui3, John R. Cort1, Joshua N. Adkins1, Roslyn N. Brown4 1Biological Sciences Division, Pacific Northwest National Laboratory, 2Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, 3Structural Proteomics Group, Ontario Center for Structural Proteomics, University of Toronto, 4Center for Bioproducts and Bioenergy, Washington State University Electroporation was used to insert purified bacterial virulence effector proteins directly into living eukaryotic cells. Protein localization was monitored by confocal immunofluorescence microscopy. This method allows for studies on trafficking, function, and protein-protein interactions using active exogenous proteins, avoiding the need for heterologous expression in eukaryotic cells. Chemistry In Situ SIMS and IR Spectroscopy of Well-defined Surfaces Prepared by Soft Landing of Mass-selected Ions Grant E. Johnson1, K. Don Dasitha Gunaratne1, Julia Laskin1 1Physical Sciences Division, Pacific Northwest National Laboratory Soft landing of mass-selected ions onto surfaces is a powerful approach for the highly-controlled preparation of novel materials. Coupled with analysis by in situ secondary ion mass spectrometry (SIMS) and infrared reflection absorption spectroscopy (IRRAS), soft landing provides unprecedented insights into the interactions of well-defined species with surfaces.