James Evans

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using microcrystal electron diffraction (MicroED)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

Project type

Cryo-EM Only

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain…

The molecular basis for the role of apolipoprotein A-II in cholesterol and triglyceride metabolism

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Melchior

Project type

Cryo-EM Only

Apolipoprotein (apo)A-II is an abundant human plasma protein primarily in high-density lipoproteins (HDL) but also in very low density lipoproteins (VLDL) and chylomicrons. Despite a large literature…

Enhancing biopreparedness through a model system to understand the molecular mechanisms that lead to pathogenesis and disease transmission

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Margaret Cheung-Wyker

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision…

Accelerating cryo-EM screening at EMSL by 25-fold

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Cryo-Electron Microscopy (cryo-EM) is a powerful structural biology technique since it does not require crystallization (unlike X-ray), does not require ultrahigh purity (unlike NMR) and provides…

Enhancing EMSL’s cryo-EM capability through a novel high pressure freezing workflow to improve throughput and sample quality

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Trevor Moser

Cryo-focused ion beam/scanning electron microscopy (cryo-FIB/SEM) is an essential sample preparation technique for creating thin sections (500nm or less) of cells and tissues for cryo-transmission…

Project Title: Protein Structure Without Purification

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Purification remains a major technical and temporal bottleneck for protein annotation especially for membrane, filamentous and heterocomplex assembling proteins. If a target protein in a mixed…

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using microcrystal electron diffraction (MicroED)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain…

Biomineralization and Biosequestration Mechanisms at Life's Upper Temperatures: A Reappraisal using Novel CryoEM Techniques

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sherry Cady

Though microbes can indirectly and metabolically transform, sequester, and transport (i) ions, (ii) organic and inorganic complexes, and (iii) precipitates via a wide range of mechanisms,…

Native Mass Spectrometry Enabled Electron Microscopy for Visual Proteomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jared Shaw

Develop a soft-landing capability for native protein complexes coupled with electron microscopy (EM) to enable visual proteomics. Sample heterogeneity greatly limits the resolution of 3D structures…

Advanced High Resolution and Dynamic in-situ TEM/STEM Observations of Materials Processes

Lead Institution

University of Liverpool

Principal Investigator

Nigel Browning

The first goal of this research program is to develop a robust method to quantify the atomic scale changes in structure, composition and bonding that occur at interfaces under a variety of…

Manganese biomineralization by the bacterial protein complex Mnx

Lead Institution

University of Washington

Principal Investigator

Bradley Tebo

Project type

Large-Scale EMSL Research

Manganese-oxide mineral formation by bacterial oxidation of dissolved Mn(II) is an important process in aquatic and soil environments and is a key part of the global Mn cycle. The Mn bio-oxides…

An Experimental and Modeling Investigation of Solidification and Microstructural Evolution in Magnesium Alloys using in situ Techniques

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Aashish Rohatgi

The goal of this proposal is to understand the microstructural evolution during non-equilibrium, rapid solidification of a molten magnesium-aluminum-zinc (AZ91) alloy, and during its subsequent heat…

Solving the Structure of Eukaryotic Type III Glutamine Synthetase Assembles

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

There are three major classes of the enzyme Glutamine Synthetase (GS) that share widely conserved active-site residues but vary in average protein length, oligomeric assembly state and cofactor…

Correlative Imaging and Spectroscopy of Biological Systems and Structural Dynamics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

The overall objective of this project is to create an integrative capability for combining dynamic transmission electron microscopy with femtosecond x-ray diffraction, in situ and automated secondary…

Dynamic TEM

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Achieving a holistic, molecular-level understanding of the structure, function and mechanism of cellular machinery remains a formidable scientific challenge. While over 100,000 protein structures…

Systems Biology Through an Integrated Multimodal Imaging and Analysis Framework

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Organisms have evolved a number of spatially localized processes to efficiently break down, absorb, and use necessary metabolites. Although progress has been made in identifying the genes that are…

Application of machine learning to APT data to trace nanoscale protein structure

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Daniel Perea

The objective of this project is the development and application of deep learning algorithms aimed at extracting molecular structure within Atom Probe Tomography (APT) data collected from protein…

Carbon, Oxide, Metal Sequestration Mechanisms of Hot Springs Microbial Communities: Establishing a Technical Platform for Chemical Imaging Investigation

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sherry Cady

Though microbes can indirectly and metabolically transform, sequester, and transport (i) ions, (ii) organic and inorganic complexes, and (iii) precipitates via a wide range of mechanisms,…

Tomography of Pseudarthrobacter chlorophenolicus

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Subcellular structures and macromolecular complexes can be revealed through cryo electron tomography of whole cells. Pseudarthrobacter chlorophenolicus is a soil bacterium which has novel metabolic…

An Experimental and Modeling Investigation of Solidification and Microstructural Evolution in Magnesium Alloys using in situ Techniques

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Aashish Rohatgi

The goal of this proposal is to understand the microstructural evolution during non-equilibrium, rapid solidification of a molten magnesium-aluminum-zinc (AZ91) alloy, and during its subsequent heat…

Integrated multi-modal approach for structure and function determination of lignin-forming protein complexes isolated from plants

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

We propose to apply an integrated multi-modal structural biology approach to investigate a biosynthetic protein complex in plants that is hypothesized to organize and guide lignin biosynthesis via…

Correlative High-Resolution Imaging and Spectroscopy to Characterize the Structure and Biogeochemical Function of Microbial Biofilms

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Matthew Marshall

Project type

Exploratory Research

This proposal leverages knowledge and experience gained from DOE-funded research to elucidate the mechanisms involved in dissimilatory metal reduction, as well as, microscale imaging and analytical…

Systems Biology Through an Integrated Multimodal Imaging and Analysis Framework

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Organisms have evolved a number of spatially localized processes to efficiently break down, absorb, and use necessary metabolites. Although progress has been made in identifying the genes that are…

Opportunities linking omics and structural biology at PNNL: Excelling at Cryo-EM

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

We were recently funded jointly by EMSL and DOE/BER to purchase, install and operate a new Krios G3i cryo-TEM at EMSL. By funding the system jointly, the new microscope would become available to EMSL…

Characterization of Catalyst Materials in the Electron and Atom Probe Microscopes

Lead Institution

Argonne National Laboratory

Principal Investigator

Ilke Arslan

Project type

Exploratory Research

The aim of this proposal is to combine existing techniques in the electron and atom-probe microscopes to afford novel methods for a fundamental understanding of catalyst interactions with atomic…

An Experimental and Modeling Investigation of Solidification and Microstructural Evolution in Magnesium Alloys using in situ Techniques

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Aashish Rohatgi

The goal of this proposal is to understand the microstructural evolution during non-equilibrium, rapid solidification of a molten magnesium-aluminum-zinc (AZ91) alloy, and during its subsequent heat…

Accurately predict the spatial arrangement of protein complexes from subtomogram images through physics-informed machine learning

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Margaret Cheung-Wyker

Deducing three-dimensional (3D) structures of molecular assemblies from cryo-electron tomography (cryoET) data provides an unprecedented level of detail about biological systems in their native…

Advanced High Resolution and Dynamic in-situ TEM/STEM Observations of Materials Processes

Lead Institution

University of Liverpool

Principal Investigator

Nigel Browning

The first goal of this research program is to develop a robust method to quantify the atomic scale changes in structure, composition and bonding that occur at interfaces under a variety of…

Unraveling New Pathways for Carbon Capture to Enhance Lipid-Biomass Feedstocks

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Organisms have evolved a number of spatially localized processes to efficiently break down, absorb, and use necessary metabolites. Although progress has been made in identifying the genes that are…

Towards proteome-wide assessment of cellular landscapes

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

We will develop a novel workflow to characterize proteome-wide structural changes of cellular landscapes between different cell states (or cell types). The goal is to bridge the gap between cellular…

EMSL/FCSD Scientific Partner Proposal on the Dynamics of Biological and Catalytic Systems

Lead Institution

University of Liverpool

Principal Investigator

Nigel Browning

Project type

Scientific Partner

The goal of this Scientific Partner Proposal is to develop the capability to observe “live” biological and catalytic processes in the dynamic transmission electron microscope (DTEM). Live biological…

Integrated multi-omic analysis of high lipid accumulation in the oleaginous green microalgae Ostreococcus tauri to engineer metabolic pathways for improved triacylglycerol feedstocks

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Project type

Exploratory Research

Our proposed mutli-omic approach will empower a comprehensive understanding of cellular pathways linking carbon, nitrogen and phosphate metabolism in the microalga Ostreococcus tauri. The use of this…

Assessment of EUV Atom Probe Tomography for Mass Spectral Analysis of Biomolecules

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Daniel Perea

A Local Electrode Atom Probe (LEAP) Atom utilizing a pulsed, coherent, extreme ultraviolet (EUV) source will be used for the first time for mass-spectral and 3D atomic-scale reconstruction analysis…

Correlative Imaging and Spectroscopy of Biological Systems and Structural Dynamics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

The overall objective of this project is to create an integrative capability for combining dynamic transmission electron microscopy with femtosecond x-ray diffraction, in situ and automated secondary…

Visualizing pathways in cells for more accurate biodesign

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

In this Capability Development Focus project, we plan to acquire label-free whole cell three-dimensional (3D) tomograms of the two primary organisms of interest for the FY18 Subcellular SSA thrust…

The molecular basis for the role of apolipoprotein A-II in cholesterol and triglyceride metabolism

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Melchior

Apolipoprotein (apo)A-II is an abundant human plasma protein primarily in high-density lipoproteins (HDL) but also in very low density lipoproteins (VLDL) and chylomicrons. Despite a large literature…

Correlative Imaging and Spectroscopy of Biological Systems and Structural Dynamics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

The overall objective of this project is to create an integrative capability for combining dynamic transmission electron microscopy with femtosecond x-ray diffraction, in situ and automated secondary…

Collaborative Access Team: Pacific Northwest Cryo-EM Center (PNCC)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

PNNL will create and operate the Pacific Northwest Center for Cryo-EM (PNCC), a state-of-the-art national center for cryo-electron microscopy (Cryo-EM) that will rapidly and efficiently collect and…

Virtual Proteomics (ViP): Integrative modeling of protein assemblies in a cell with constraints from proteomic data and reconstructed images from cryo-electron tomography

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Margaret Cheung-Wyker

The objective of the proposed research is to advance the spatial knowledge of higher-order protein assemblies in a cell by integrating improved image reconstruction from cryo-electron tomography and…

An Experimental and Modeling Investigation of Solidification and Microstructural Evolution in Magnesium Alloys using in situ Techniques

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Aashish Rohatgi

The goal of this proposal is to understand the microstructural evolution during non-equilibrium, rapid solidification of a molten magnesium-aluminum-zinc (AZ91) alloy, and during its subsequent heat…

Joining Systems Biology and Bioimaging on Same Cells

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

We plan to develop a new capability at EMSL for coupling bioimaging and systems biology analysis of the same exact cells. The use of the highly simplified and smallest free-living eukaryote…

Validation and functional characterization of transcription factors in wheat using cell-free protein
expression and high-throughput sequencing technologies

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Irina El Khoury

This study aims to validate and functionally characterize a family of transcription factors to understand the differences in their deoxyribonucleic acid binding preferences and their potential impact…

Multi-scale investigation of the nitrogen fixation mechanism of Mo-dependent nitrogenase

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Simone Raugei

Project type

Large-Scale EMSL Research

We propose to use EMSL NMR and supercomputing resources to gain a molecular level understanding of how substrate binding, electron, and proton delivery is controlled by the nitrogenase metalloenzyme…

The structure of pseudoenzyme PDX1.2 and its complex with active enzyme PDX1.3

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Aim - Determine the high-resolution structure of the protein PDX1.2 alone and in complex with PDX1.3. PDX1.2 is an important pseudo-enzyme with regulatory roles in vitamin B6 biosynthesis. It…

Detergent-free extraction of membrane proteins and lipids from native cells

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Melchior

Membrane proteins account for >30% of most genomes, yet only make up <4% of reported high-resolution structures in the protein data bank. Current approaches for isolating membrane proteins from…

Systems Biology Through an Integrated Multimodal Imaging and Analysis Framework

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Organisms have evolved a number of spatially localized processes to efficiently break down, absorb, and use necessary metabolites. Although progress has been made in identifying the genes that are…

PNCC Database Capability Development

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

This is a capability development proposal to work on the data transfer between PNCC in Oregon and MyEMSL.

Projects