H Wiley

Inferring Kinetic Models for Large-Scale Biochemical Networks

Lead Institution

University of Washington

Principal Investigator

Herbert Sauro

Project type

Large-Scale EMSL Research

Mechanistic models of cell networks that accurately predict changes in input-output dynamics and outcomes upon perturbation have the potential to facilitate a greater understanding of the…

FRET Screening of Protein-Protein Interactions in Shewanella (Orr GTL-Imaging, PNNL/ORNL Scope #43930)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Galya Orr

Project type

Exploratory Research

Fluorescence resonance energy transfer (FRET) imaging and spectroscopy techniques will be used to identify specific molecular interactions among proteins in Shewanella. The techniques incorporate…

Regulation of Cell Surface Ligand Dynamics (Orr LDRD-BSI, PNNL Scope #90001)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Galya Orr

Project type

Exploratory Research

We will develop a set of new imaging technologies that can directly visualize ligand oligomerization as well as interaction with other cell surface molecules. We expect to observe an increase in…

FRET-Based Molecular Dynamics Simulation of Membrane-Receptor Activation

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Galya Orr

Project type

Large-Scale EMSL Research

This proposal is a continuation of research pursued under EMSL User Proposals #6494 and #6493. Membrane receptors are activated upon the binding of small ligand molecules to specific sites in their…

Regulatory dynamics of microbial communities

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

H Wiley

Project type

Large-Scale EMSL Research

This is a proposal to conduct work in EMSL in support of the Foundational Scientific Focus Area (FSFA) research program at Pacific Northwest National Laboratory. This large-scale research program…

Isoprene Research Campaign: Making Isoprene from Biomass Material using Bacillus Species

Lead Institution

Washington State University Tri-Cities

Principal Investigator

Birgitte Ahring

Project type

Research Campaign

The overarching goal of this project is to understand the pathway of isoprene production in Bacillus subtilis, to serve as the basis for genetically modifying the pathway to substantially increase…

Untangling the Complexity of Microbial Networks by Using Simplified Natural Communities

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

H Wiley

The overall goal of this proposal is to understand the dynamics of both microbial populations and their gene regulatory networks in response to environmental perturbations and to elucidate mechanisms…

Untangling the complexity of phototroph-heterotroph interactions in the lab and in the field

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

H Wiley

Project type

Large-Scale EMSL Research

Despite the fact that ubiquitous microbial interspecies interactions form the foundation of energy flow as well as the biogeochemical cycling of carbon and other elements within natural environments,…

Quantifying the functional and structural states of dynamic microbial communities

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Fredrickson

Project type

Large-Scale EMSL Research

The overall goal of this proposal is to provide a quantitative framework in which to compare species-resolved patterns of gene expression, allowing comparison of the effects of perturbations of…

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…

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…

Biosystems Analysis for Determining the Impact of Nutrient Uptake on Autotroph-Heterotroph Interactions within Cyanobacterial Consortia

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

Project type

Large-Scale EMSL Research

The exchange of carbon and other nutrients between microorganisms is a key factor in the establishment of microbial interactions and trophic levels. Depending upon the nutrient, the establishment of…

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…

Reverse Sensitivity Analysis for Identifying Predictive Proteomics Signatures of
Cancer

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Weijun Qian

Cancer is a complex disease in which genetic disruptions in cell signaling networks are known to play a significant role. A major aim of cancer systems biology is to build models that can predict the…

Single Molecule Approach for Understanding EGFR Molecular Interactions (Orr LDRD-FRET, PNNL Scope #48287)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Galya Orr

Project type

Exploratory Research

We will use cutting edge fluorescence imaging techniques to study the molecular interactions of EGFR with other molecules in the pathway to better understand its role in determining cell fate.

Genomes-to-Life Protein Complex Isolation Capability

Lead Institution

Western University of Health Sciences

Principal Investigator

Thomas Squier

Project type

Exploratory Research

We have established a pilot proteomics facility in support of the "Goal 1" of the Department of Energy's Genomes to Life program, which seeks to identify 80% of the protein complexes…

Genomes-to-Life Protein Complex Isolation Capability

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Brian Hooker

We have established a pilot proteomics facility. The primary aim of this facility is to develop new approaches for rapid, robust isolation of protein complexes as well as develop methods to analyze…

EMSL Science Overview

H Wiley

Projects

Inferring Kinetic Models for Large-Scale Biochemical Networks

FRET Screening of Protein-Protein Interactions in Shewanella (Orr GTL-Imaging, PNNL/ORNL Scope #43930)

Regulation of Cell Surface Ligand Dynamics (Orr LDRD-BSI, PNNL Scope #90001)

FRET-Based Molecular Dynamics Simulation of Membrane-Receptor Activation

Regulatory dynamics of microbial communities

Isoprene Research Campaign: Making Isoprene from Biomass Material using Bacillus Species

Untangling the Complexity of Microbial Networks by Using Simplified Natural Communities

Untangling the complexity of phototroph-heterotroph interactions in the lab and in the field

Quantifying the functional and structural states of dynamic microbial communities

Systems Biology Through an Integrated Multimodal Imaging and Analysis Framework

Systems Biology Through an Integrated Multimodal Imaging and Analysis Framework

Biosystems Analysis for Determining the Impact of Nutrient Uptake on Autotroph-Heterotroph Interactions within Cyanobacterial Consortia

Systems Biology Through an Integrated Multimodal Imaging and Analysis Framework

Reverse Sensitivity Analysis for Identifying Predictive Proteomics Signatures of
Cancer

Single Molecule Approach for Understanding EGFR Molecular Interactions (Orr LDRD-FRET, PNNL Scope #48287)

Genomes-to-Life Protein Complex Isolation Capability

Genomes-to-Life Protein Complex Isolation Capability