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Pacific Northwest National Laboratory

37 ARTICLES PUBLISHED IN JoVE

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Biology

Human Pancreatic Islet Isolation: Part I: Digestion and Collection of Pancreatic Tissue
Meirigeng Qi 1, Barbara Barbaro 1, Shusen Wang 1, Yong Wang 1, Mike Hansen 1, Jose Oberholzer 1
1Department of Surgery, University of Illinois, Chicago

Achieving high quality and appropriate quantity of human islets is one of the prominent prerequisites for successful islet transplantation. In this video, we describe step by step the procedures for human pancreatic islet isolation (part I: digestion and collection of pancreatic tissue) using a modified automated method.

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Biology

Human Pancreatic Islet Isolation: Part II: Purification and Culture of Human Islets
Meirigeng Qi 1, Barbara Barbaro 1, Shusen Wang 1, Yong Wang 1, Mike Hansen 1, Jose Oberholzer 1
1Department of Surgery, University of Illinois, Chicago

Achieving high quality and appropriate quantity of human islets is one of the prominent prerequisites for successful islet transplantation. In this video, we describe step by step the procedures for human pancreatic islet isolation (part II: purification and culture of human islets) using a modified automated method.

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Biology

A Multi-Parametric Islet Perifusion System within a Microfluidic Perifusion Device
Adeola F. Adewola 1, Yong Wang 1, Tricia Harvat 1, David T. Eddington 2, Dongyoung Lee 1, Jose Oberholzer 1,2
1Department of Surgery, University of Illinois, Chicago, 2Department of Bioengineering, University of Illinois, Chicago

A microfluidic islet perifusion device was developed for the assessment of dynamic insulin secretion of multiple islets and simultaneous fluorescence imaging of calcium influx and mitochondrial potential changes.

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Bioengineering

Quantitative and Temporal Control of Oxygen Microenvironment at the Single Islet Level
Joe Fu-Jiou Lo 1, Yong Wang 2,3, Zidong Li 1, Zhengtuo Zhao 1, Di Hu 1, David T. Eddington 3, Jose Oberholzer 2,3
1Department of Mechanical Engineering, University of Michigan-Dearborn, 2Department of Surgery/Transplant, University of Illinois at Chicago, 3Department of Bioengineering, University of Illinois at Chicago

Microfluidic oxygen control confers more than just convenience and speed over hypoxic chambers for biological experiments. Especially when implemented via diffusion through a membrane, microfluidic oxygen can provide simultaneous liquid and gas phase modulations at the microscale-level. This technique enables dynamic multi-parametric experiments critical for studying islet pathophysiology.

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Chemistry

In Situ SIMS and IR Spectroscopy of Well-defined Surfaces Prepared by Soft Landing of Mass-selected Ions
Grant E. Johnson 1, K. Don Dasitha Gunaratne 1, Julia Laskin 1
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.

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Biology

Fluorescence Imaging with One-nanometer Accuracy (FIONA)
Yong Wang *1,2, En Cai *1,2, Janet Sheung 1,2, Sang Hak Lee 1,2, Kai Wen Teng 2,3, Paul R. Selvin 1,2,3
1Department of Physics, University of Illinois at Urbana-Champaign, 2Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, 3Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign

Single fluorophores can be localized with nanometer precision using FIONA. Here a summary of the FIONA technique is reported, and how to carry out FIONA experiments is described.

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Immunology and Infection

Electroporation of Functional Bacterial Effectors into Mammalian Cells
Ryan L. Sontag 1, Cosmin Mihai 2, Galya Orr 2, Alexei Savchenko 3, Tatiana Skarina 3, Hong Cui 3, John R. Cort 1, Joshua N. Adkins 1, Roslyn N. Brown 4
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.

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Bioengineering

Qualitative Characterization of the Aqueous Fraction from Hydrothermal Liquefaction of Algae Using 2D Gas Chromatography with Time-of-flight Mass Spectrometry
Balakrishna Maddi 1, Ellen Panisko 1, Karl Albrecht 1, Daniel Howe 1
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.

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Chemistry

In Situ Characterization of Hydrated Proteins in Water by SALVI and ToF-SIMS
Jiachao Yu 1, Yufan Zhou *2, Xin Hua *1, Zihua Zhu 2, Xiao-Ying Yu 1
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.

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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 Hu 3, Zheng Yang 1,4, Xiaoliang Wei 1,2
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.

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Chemistry

In Situ Characterization of Shewanella oneidensis MR1 Biofilms by SALVI and ToF-SIMS
Rachel Komorek 1, Wenchao Wei 1, Xiaofei Yu 2, Eric Hill 1, Juan Yao 1, Zihua Zhu 2, Xiao-Ying Yu 1
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.

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Chemistry

In Situ Characterization of Boehmite Particles in Water Using Liquid SEM
Juan Yao 1, Bruce W. Arey 1, Li Yang 1, Fei Zhang 1, Rachel Komorek 1, Jaehun Chun 1, Xiao-Ying Yu 1
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.

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Cancer Research

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing
Xiaoxing Lv 1, Meiru Zhao 1, Yuting Yi 1, Lucheng Zhang 1, Yanfang Guan 1, Tao Liu 1, Ling Yang 1, Rongrong Chen 1, Jianhui Ma 1, Xin Yi 1
1Geneplus-Beijing Institute

This manuscript describes a technique for detecting mutations of low frequency in ctDNA, ER-Seq. This method is differentiated by its unique use of two-directional error correction, a special background filter, and efficient molecular acquirement.

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Neuroscience

Whole-cell Currents Induced by Puff Application of GABA in Brain Slices
Yangjian Feng *1,2, Binliang Tang *1,2, Ming Chen 2, Li Yang 1,3,4,5
1School of Psychology, South China Normal University, 2School of Life Sciences, South China Normal University, 3Brain Science Institute, South China Normal University, 4Center for Studies of Psychological Application, South China Normal University, 5Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University

We describe the puff technique, by which pharmacological reagents can be administered during whole-cell patch-clamp recording, and highlight various aspects of the features that are crucial for its success.

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Engineering

In Situ High Pressure Hydrogen Tribological Testing of Common Polymer Materials Used in the Hydrogen Delivery Infrastructure
Edward R. Duranty 1, Timothy J. Roosendaal 1, Stan G. Pitman 1, Joseph C. Tucker 1, Stanley L. Owsley Jr. 1, Jonathan D. Suter 1, Kyle James Alvine 1
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.

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Chemistry

The MPLEx Protocol for Multi-omic Analyses of Soil Samples
Carrie D. Nicora *1, Kristin E. Burnum-Johnson *1, Ernesto S. Nakayasu 1, Cameron P. Casey 1, Richard A. White III 1, Taniya Roy Chowdhury 1, Jennifer E. Kyle 1, Young-Mo Kim 1, Richard D. Smith 1, Thomas O. Metz 1, Janet K. Jansson 1, Erin S. Baker 1
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.

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Medicine

A Doxorubicin-induced Cardiomyopathy Model in Adult Zebrafish
Xiao Ma *1,2,3, Yonghe Ding *2,3, Yong Wang 2,3,4, Xiaolei Xu 1,2,3
1Clinical and Translational Sciences Track, Mayo Clinic Graduate School of Biomedical Sciences, 2Department of Biochemistry and Molecular Biology, Mayo Clinic, 3Division of Cardiovascular Diseases, Mayo Clinic, 4Institute of Life Science, Beijing University of Chinese Medicine

A method to generate a doxorubicin-induced cardiomyopathy model in adult zebrafish (Danio rerio) is described here. Two alternative ways of intraperitoneal injection are presented and conditions to reduce variations among different experimental groups are discussed.

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Education

Ligand-Mediated Nucleation and Growth of Palladium Metal Nanoparticles
Saeed Mozaffari *1, Wenhui Li *1, Coogan Thompson 1, Sergei Ivanov 2, Soenke Seifert 3, Byeongdu Lee 4, Libor Kovarik 5, Ayman M. Karim 1
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.

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Biology

Micropuncture of Bowman's Space in Mice Facilitated by 2 Photon Microscopy
Katsuyuki Matsushita 1, Kirsti Golgotiu 1, Daniel J. Orton 2, Richard D. Smith 2, Karin D. Rodland 2, Paul D. Piehowski 2, Michael P. Hutchens 1,3
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.

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Neuroscience

Preparation of Acute Spinal Cord Slices for Whole-cell Patch-clamp Recording in Substantia Gelatinosa Neurons
Mengye Zhu 1, Daying Zhang 1, Sicong Peng 2, Nana Liu 2, Jing Wu 2, Haixia Kuang 2, Tao Liu 2,3
1Department of Pain, First Affiliated Hospital of Nanchang University, 2Department of Pediatrics, First Affiliated Hospital of Nanchang University, 3Center for Laboratory Medicine, First Affiliated Hospital of Nanchang University

Here, we describe the essential steps for whole-cell patch-clamp recordings made from substantia gelatinosa (SG) neurons in the in vitro spinal cord slice. This method allows the intrinsic membrane properties, synaptic transmission and morphological characterization of SG neurons to be studied.

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Neuroscience

Diagnosis of Hirschsprung's Disease by Immunostaining Rectal Suction Biopsies for Calretinin, S100 Protein and Protein Gene Product 9.5
Shuiqing Chi 1, Mijing Fang 1, Kang Li 1, Li Yang 2, Shao-tao Tang 1
1Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 2Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center

This protocol describes the process of immunostaining rectal suction biopsies for calretinin, S100 protein, and protein gene product 9.5. This novel adjuvant diagnostic method for Hirschsprung's disease has preferable sensitivity and specificity rates.

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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. Brewer 1, Rosalie K. Chu 1, Heino M. Heyman 4, David W. Hoyt 1, Jennifer E. Kyle 5, Samuel O. Purvine 1
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.

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Developmental Biology

A Mini-Invasive Internal Fixation Technique for Studying Immobilization-Induced Knee Flexion Contracture in Rats
Shihai Jiang *1, Xiaoyou Yi *3, Yuansen Luo 2, Dongjie Yu 1, Yuangao Liu 1, Fei Zhang 1,4, Lei Zhu 2, Kun Wang 1
1Department of Joint and Trauma Surgery, The Third Affiliated Hospital of Sun Yat-sen University, 2Department of Plastic Surgery, The Third Affiliated Hospital of Sun Yat-sen University, 3Department of Bone Surgery, Tungwah Hospital of Sun Yat-sen University, 4Department of Othopaedic Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University

Here, we present a protocol to describe a minimally invasive technique for knee joint immobilization in a rat model. This reproducible protocol, basing on muscle-gap separation modus and the mini-incision skill, is suitable for studying the underlying molecular mechanism of acquired joint contracture.

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Immunology and Infection

Co-staining Blood Vessels and Nerve Fibers in Adipose Tissue
Xin Li 1, Zhengmei Mao 2, Li Yang 1, Kai Sun 1
1Center for Metabolic and Degenerative Diseases, the Brown Foundation of Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 2Microscopy Core, the Brown Foundation of Institute of Molecular Medicine, University of Texas Health Science Center at Houston

New blood vessel formation and sympathetic innervation play pivotal roles in adipose tissue remodeling. However, there remain technical issues in visualizing and quantitatively measuring adipose tissue. Here we present a protocol to successfully label and quantitatively compare the densities of blood vessels and nerve fibers in different adipose tissues.

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Environment

Implantation of a New Micro Acoustic Tag in Juvenile Pacific Lamprey and American Eel
Robert Mueller 1, Stephanie Liss 1, Z. Daniel Deng 1
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.

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Neuroscience

Evaluation of Hemisphere Lateralization with Bilateral Local Field Potential Recording in Secondary Motor Cortex of Mice
Yunan Chen 1,2, Ming Li 3, Ying Zheng 3, Li Yang 1
1School of Life Sciences, Guangzhou University, 2Institute for Brain Research and Rehabilitation, South China Normal University, 3School of Life Sciences, South China Normal University

We present in vivo electrophysiological recording of the local field potential (LFP) in bilateral secondary motor cortex (M2) of mice, which can be applied to evaluate hemisphere lateralization. The study revealed altered levels of synchronization between the left and right M2 in APP/PS1 mice compared to WT controls.

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Chemistry

Imaging Corrosion at the Metal-Paint Interface Using Time-of-Flight Secondary Ion Mass Spectrometry
Jennifer Yao 1, Anthony Guzman 2, Zihua Zhu 3, Xiao-Ying Yu 1
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.

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Cancer Research

A Human Peripheral Blood Mononuclear Cell (PBMC) Engrafted Humanized Xenograft Model for Translational Immuno-oncology (I-O) Research
Zhuo Li *1, Xiao Yang *1, Yilu Zhang 1, Xiaolong Yang 1, Xinxin Cui 1, Yanjuan Zhang 1, Wenfeng Gong 1, Huichen Bai 1, Ning Liu 1, Zhiyu Tang 1, Mingming Guo 1, Kang Li 1, Tong Zhang 1, Lai Wang 1, Xiaomin Song 1
1BeiGene (Beijing) Co., Ltd.

We describe a human peripheral blood mononuclear cell (PBMC) — based humanized xenograft mouse model for translational immuno-oncology research. This protocol could serve as a general guideline for establishing and characterizing similar models for I-O therapy assessment.

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Developmental Biology

Whole-Mount In Situ Hybridization in Zebrafish Embryos and Tube Formation Assay in iPSC-ECs to Study the Role of Endoglin in Vascular Development
Yong Wang *1, Ding Zhang *2, Fang Zhou 2, Meijun Zhou 2, Qiujie Li 1, Jingyu Chen 3, Jun Yang 1,2
1Department of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, 2Department of Cell Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, 3Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University

Presented here is a protocol for whole-mount in situ RNA hybridization analysis in zebrafish and tube formation assay in patient-derived induced pluripotent stem cell-derived endothelial cells to study the role of endoglin in vascular formation.

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Medicine

OP-IVM: Combining In vitro Maturation after Oocyte Retrieval with Gynecological Surgery
Tao Liu *1,2,3,4,5, Xueling Song *1,2,3,4,5, Xiaoying Zheng *1,2,3,4,5, Liying Yan 1,2,3,4,5, Caihong Ma 1,2,3,5, Rong Li 1,2,3,4,5, Jie Yan 1,2,3,4,5, Jie Qiao 1,2,3,4,5
1Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, 2National Clinical Research Center for Obstetrics and Gynecology, 3Key Laboratory of Assisted Reproduction, Ministry of Education, 4Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, 5Research Units of Comprehensive Diagnosis and Treatment of Oocyte Maturation Arrest, Chinese Academy of Medical Sciences

In vitro maturation (IVM) before gynecological operation (OP-IVM) combines IVM following oocyte retrieval with routine gynecological surgery and serves as an extension of conventional IVM applications for fertility preservation.

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Biochemistry

Isolation of Histone from Sorghum Leaf Tissue for Top Down Mass Spectrometry Profiling of Potential Epigenetic Markers
Mowei Zhou 1, Shadan H. Abdali 1, David Dilworth 2, Lifeng Liu 2, Benjamin Cole 2, Neha Malhan 1, Amir H. Ahkami 1, Tanya E. Winkler 1, Joy Hollingsworth 3, Julie Sievert 3, Jeff Dahlberg 3, Robert Hutmacher 4,5, Mary Madera 6, Judith A. Owiti 6, Kim K. Hixson 1, Peggy G. Lemaux 6, Christer Jansson 1, Ljiljana Paša-Tolić 1
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.

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JoVE Core

High-Temperature and High-Pressure In situ Magic Angle Spinning Nuclear Magnetic Resonance Spectroscopy
Nicholas R. Jaegers 1, Wenda Hu 2, Yong Wang 1, Jian Zhi Hu 1
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.

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Biochemistry

Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells
Kendall Martin 1, Tong Zhang 1, Pengfei Zhang 2, William B. Chrisler 1, Fillmore L. Thomas 3, Fen Liu 4, Tao Liu 1, Wei-Jun Qian 1, Richard D. Smith 1, Tujin Shi 1
1Biological Sciences Division, Pacific Northwest National Laboratory, 2NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, 3Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 4Department of Critical Care Medicine, The First Affiliated Hospital of Nanchang University

A protein carrier-assisted one-pot sample preparation coupled with liquid chromatography (LC) - selected reaction monitoring (SRM) termed cLC-SRM is a convenient method for multiplexed targeted proteomics analysis of small numbers of cells, including single cells. It capitalizes on using excessive exogenous protein as a carrier and high-specificity LC-SRM for targeted quantification.

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Chemistry

Visualizing Solution Structure at Solid-Liquid Interfaces using Three-Dimensional Fast Force Mapping
Elias Nakouzi 1, Sakshi Yadav 1, Benjamin A. Legg 1, Shuai Zhang 1,2, Jinhui Tao 1, Christopher J. Mundy 1,3, Gregory K. Schenter 1,4, Jaehun Chun 1,5, James J. De Yoreo 1,2
1Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, 2Department of Materials Science and Engineering, University of Washington, 3Department of Chemical Engineering, University of Washington, 4Department of Chemistry, Washington State University, 5CUNY City College of New York

Here, we present a protocol for using three-dimensional fast force mapping - an atomic force microscopy technique - for visualizing solution structure at solid-liquid interfaces with the subnanometer resolution by mapping the tip-sample interactions within the interfacial region.

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Biochemistry

Resin-Assisted Capture Coupled with Isobaric Tandem Mass Tag Labeling for Multiplexed Quantification of Protein Thiol Oxidation
Matthew J. Gaffrey 1, Nicholas J. Day 1, Xiaolu Li 2, Wei-Jun Qian 1
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.

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Engineering

Balloon Tag Manufacturing Technique for Sensor Fish and Live Fish Recovery
Aljon Salalila 1, Jayson Martinez 1, Ashlynn Tate 1, Noe Acevedo 1, Marsobyn Salalila 1, Zhiqun Daniel Deng 1
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.

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Behavior

Handling and Tagging Techniques for Implanting Juvenile American Shad with a New Acoustic Microtransmitter
Katherine A Deters 1, Jill M Janak 1, Robert P Mueller 1, Brandon T Boehnke 1, Zhiqun Daniel Deng 1
1Earth Systems Science Division, Pacific Northwest National Laboratory

This article provides a detailed procedure for optimal handling practices and implantation of an acoustic micro transmitter into juvenile American shad. The results of our laboratory study suggest that these tagging techniques could be implemented in field studies of juvenile American shad with a high probability of survival.

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