Thomas Metz

Discovery and Biological Signatures of Microbiome-Derived Xanthohumol (XN) Metabolites and their Role in Ameliorating Inflammatory Bowel Disease (IBD)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

The limitations of current therapies for treatment of inflammatory bowel disease (IBD) underscore the need for new therapeutic modalities that both target the inflamed gut and the microbial dysbiosis…

Mammary and milk microbiomes and metabolomes - Understanding early variation and impacts on risk for mammary inflammation and mastitis

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Exclusive breastfeeding for at least 4 mo is considered the optimal form of nutrition for most newborns, yet many women experience substantial roadblocks in meeting this goal. One of the most common…

CPTAC Proteome Characterization Center

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Tao Liu

The overall objective of the PNNL Proteome Characterization Center (PCC) is to comprehensively characterize human tumor samples provided by the National Cancer Institute (NCI), and to integrate the…

Cyanobacteria Membrane Biology Grand Challenge: Systems Analysis of the Dynamics of Membrane Architecture, Composition, and Function- Proteomic, Metabolomic, and Metallomic Characterization

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jon Jacobs

Project type

Grand Challenge

The strain Cyanothece sp. ATCC 51142, isolated from benthic waters off the coast near Galveston, Texas, is a unicellular strain approximately 4-7 &#956;m in diameter along the major axis. This…

Optimizing Oil Production in Oleaginous Yeast by Cell-Wide Measurements and Genome-Based Models

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Scott Baker

Develop tools for cell-wide measurement of metabolites and lipids, which, along with transcriptional data, will allow the construction of genome-scale metabolic models, as well as models of…

Optimizing Oil Production in Oleaginous Yeast by Cell-Wide Measurements and Genome-Based Models

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Scott Baker

The team at PNNL is using a combination of flow cytometry, microscopy and lipidomics to establish baseline cell biological and metabolite data on lipid production by the W29 strain of Yarrowia…

Pan-Omics Technology Development, Implementation, and Application to GSP Systems Biology Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The BER Genome Science Program aims to understand complex biological and environmental systems across spatial and temporal scales to develop predictive knowledge relevant to DOE mission challenges…

FSFA: MOSAIC -- Metabolic and Spatial Interactions in Communities FY18 proposal

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Errol Robinson

This EMSL user proposal is to support the MOSAIC DOE BER funded FSFA at PNNL. The primary activities involving EMSL are a set of BSSD demonstration tasks focusing on key science questions and related…

Mapping Nutrient Flow through a Plant-Microbe Symbiont System using Stable Isotope Probing under Drought and Salinity Stress

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

Red alder (Alnus rubra) is one of the fastest growing, commercially important, hardwood species for biomass/timber production in North America, and is also involved in a nitrogen-fixation symbiosis…

Does the brain differentially alter metabolic and immunologic programs in the bone marrow in a pathogen-specific manner?

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Sneha Couvillion

: A wide variety of pathogens present an acute survival challenge in humans, and our ability to rapidly and precisely respond to these pathogens is critical to our survival as a species. Although…

High Resolution 1H NMR Metabolomics Using Slow and Ultra Slow Magic Angle Spinning

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jian-zhi Hu

Project type

Large-Scale EMSL Research

Recently, we developed new so-called slow-MAS (magic angle spinning) NMR techniques that significantly enhance the spectral information in biofluids, intact excised tissues, organs and live small…

Biological Systems Interactions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Fredrickson

SPECIFIC AIMS: The overall objective of the proposed research is to acquire a predictive understanding of how microbial interactions impart stability, fitness, and functional efficiency to microbial…

Pan-Omics Technology Development, Implementation, and Application to GSP Systems Biology Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The BER Genome Science Program aims to understand complex biological and environmental systems across spatial and temporal scales to develop predictive knowledge relevant to DOE mission challenges…

Establishment of a Robust Method for Soil Metabolomics Analysis

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vanessa Bailey

Project type

Limited Scope

The objective of this work is to adapt current evolving protocols for metabolomics analyses to soil samples. As chemical perturbations are primarily detected on a molecular level, the metabolome will…

BetaMarker: Biomarkers of Beta Cell Stress in Type 1 Diabetes

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Type 1 diabetes (T1D) is generally accepted to result from impaired immune tolerance, leading to the autoimmune destruction of islet beta cells. However, the durable preservation of beta cell…

Pacific Northwest Advanced Compound Identification Core

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

The capability to chemically identify thousands of metabolites and other chemicals in clinical samples will revolutionize the search for environmental, dietary, and metabolic determinants of disease…

Prediction of response in soil microbiome carbon utilization to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

This project is directed under the “Phenotypic Response of the Soil Microbiome to Environmental Perturbations” SFA project awarded to Pacific Northwest National Laboratory. The goal of the SFA is to…

LC-MS-based metabolomics for computational toxicology

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

The goal of this project is to assist the Environmental Protection Agency in analyzing samples from a fish-model of environmental exposure. LC-MS-based metabolomics will be utilized to help develop…

Mapping soil carbon from cradle to grave: using comparative transcriptomics, proteomics and metabolite analysis to identify the microbial blueprint for root-enhanced decomposition of organic matter.

Lead Institution

University of California, Berkeley

Principal Investigator

Mary Firestone

Project type

FICUS Research

In this JGI-EMSL project, we will investigate how living roots impact the functional capacity of the detritosphere (litter and surrounding soil) microbiome that is actively mediating decomposition…

BetaMarker: Biomarkers of Beta Cell Stress in Type 1 Diabetes

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Type 1 diabetes (T1D) is generally accepted to result from impaired immune tolerance, leading to the autoimmune destruction of islet beta cells. However, the durable preservation of beta cell…

The effect of monoclonal antibodies against HSP60 on Histoplasma capsulatum extracellular vesicles

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Ernesto Nakayasu

The capacity of the human fungal pathogen Histoplasma capsulatum (Hc) to cause severe invasive disease is attributed to the fungus’ ability to subvert host responses, especially in the setting of…

Agile BioFoundry

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Kristin Burnum-Johnson

This proposed EMSL Resource Owner project, is a sub-project supporting two DOE-EERE-BETO supported PNNL projects: FY16-17 four-national laboratory “Agile BioFoundry” (ABF) seed project and a larger…

Pacific Northwest Advanced Compound Identification Core

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

The capability to chemically identify thousands of metabolites and other chemicals in clinical samples will revolutionize the search for environmental, dietary, and metabolic determinants of disease…

Pacific Northwest Advanced Compound Identification Core

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

The capability to chemically identify thousands of metabolites and other chemicals in clinical samples will revolutionize the search for environmental, dietary, and metabolic determinants of disease…

A Systems Biology Approach to Emerging Respiratory Viral Diseases

Lead Institution

University of Washington

Principal Investigator

Michael Katze

This Systems Biology Program will comprehensively analyze and model the molecular and cellular events and pathogen-host interactions that occur during the course of respiratory virus infection. Our…

Metabolomics of Mixed Microbial Communities: Understanding the Influence of Gut Microbiota on Host Energy Regulation.

Lead Institution

Arizona State University

Principal Investigator

Rosa Krajmalnik-Brown

Understanding the complex relationships in mixed microbial communities and host-microbiome interactions directly addresses the EMSL Science Theme of Biological Interactions and Dynamics: “Developing…

INFLUENCE OF GUT MICROBIOME-HOST INTERACTIONS ON STRESS INDUCED BY ALTERED
SLEEP PATTERNS.

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Janet Jansson

The proposed research will address how altered sleep cycles, such as that experienced in a submarine environment, impacts the gut microbiome (GM) with important implications towards the long-term…

Integrated Capability for Metabolomics and Fluxomics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Nancy Washton

The goal of this project is to develop an integrated cyberinfrastructure that can be used to demonstrate a novel, end-to-end metabolomics and fluxomics use case: Isotopically Non-STationary…

The effect of monoclonal antibodies against HSP60 on Histoplasma capsulatum extracellular vesicles

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Ernesto Nakayasu

The capacity of the human fungal pathogen Histoplasma capsulatum (Hc) to cause severe invasive disease is attributed to the fungus’ ability to subvert host responses, especially in the setting of…

METABOLOMICS ANALYSES OF THE MICROBIOME FOR DEFENSE HEALTH

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

PNNL will perform both targeted and untargeted metabolomics analyses of human fecal samples to assess the role of diet and dietary components on host health.

Metabolomics analyses of the microbiome for defense health

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

PNNL will perform both targeted and untargeted metabolomics analyses of human fecal samples to assess the role of diet and dietary components on host health.

High-Throughput Proteomics: Applications and Development (PNNL Scope #40601 and #43488)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Gordon Anderson

This project involves the application and development of high-throughput proteomics and quantitative measurement capabilities within biological systems. More so, application measurements will be…

Optimizing Oil Production in Oleaginous Yeast by Cell-Wide Measurements and Genome-Based Models

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Scott Baker

The team at PNNL is using a combination of flow cytometry, microscopy and lipidomics to establish baseline cell biological and metabolite data on lipid production by the W29 strain of Yarrowia…

Control of methane and carbon dioxide emissions by sulfur biogeochemistry in terrestrial ecosystems

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Project type

Large-Scale EMSL Research

Freshwater wetlands are responsible for 40% of the methane emissions worldwide. Despite very low amounts of ambient sulfate, these ecosystems often support high rates of sulfate reduction, rivaling…

A Molecular Atlas of the Developing Lung

Lead Institution

National Institutes of Health

Principal Investigator

Charles Ansong

The United States is one of the top nations for prematurely born infants and has a correspondingly high dayone infant mortality rate. Expanding our understanding of alveologenesis is a critical step…

BetaMarker: Biomarkers of Beta Cell Stress in Type 1 Diabetes

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Type 1 diabetes (T1D) is generally accepted to result from impaired immune tolerance, leading to the autoimmune destruction of islet beta cells. However, the durable preservation of beta cell…

BRAVE Agile: WSU-Signatures of Metabolic Dysregulation from Sleep Cycle Disruption

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Fatigue induced by sleep deprivation, sleep cycle disturbance, or a combination of the two is common in first responder populations. Sleep cycle disruption shifts central and peripheral "clocks…

OHSU-PNNL Northwest Co-laboratory for Integrated Omics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jon Jacobs

An essential component of the OHSU-PNNL Northwest CoLaboratory for Integrated Omics (CoLab) is the collaborative pursuit of joint research projects that leverage the compelling biomedical model…

Pacific Northwest Regional Center of Excellence (PNWRCE)Proteomics, Metabolomics, and Lipidomics Core

Lead Institution

Oregon Health & Science University

Principal Investigator

Jay Nelson

This Pacific Northwest Regional Center of Excellence (PNWRCE) exists in NIAID Region X. The two inter-related but distinct PNWRCE themes that have been selected reflect not only the scientific…

Diagnosis of sub-clinical cryptic group A streptococcal myonecrosis

Lead Institution

Boise VA Medical Center

Principal Investigator

Amy Bryant

Invasive group A streptococcal (GAS) infections associated with shock, multi-organ failure, necrotizing fasciitis with myonecrosis, and death emerged worldwide in the mid-1980s prompting an official…

Enabling Agile Biomanufacturing with Leading Edge Analytical Biology

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Mark Butcher

This proposed EMSL User project supports a larger multi-lab "Agile Biomanufacturing" project (LBNL, PNNL, SNL). Through the EMSL’s leading edge analytical biology, GC and LC mass…

Deciphering Microbial Communication Through Metabolites

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

This project will establish a Metabolomics Center at PNNL that will develop the advanced measurement capabilities necessary to define the metabolic processes of microbiomes and determine how these…

Deciphering Microbial Communication Through Metabolites

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

This project will establish a Metabolomics Center at PNNL that will develop the advanced measurement capabilities necessary to define the metabolic processes of microbiomes and determine how these…

Prediction of response in soil microbiome carbon utilization to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

Project type

FICUS Research

The goal of this project is to attain a systems level understanding of the soil microbiome and its phenotypic response to changing moisture through a tractable, spatially explicit examination of the…

Multi-platform 'Omics Analysis to Determine TB Vaccine Correlates

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jennifer Kyle

In recent years, mass spectrometry-based integrated multi-omics analyses have allowed for powerful interrogations of patient samples, and the identification of correlates of risk for tuberculosis…

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…

Modeling Host Responses to Understand Severe Human Virus Infections

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Richard Smith

This comprehensive and highly integrated systems biology program seeks to delineate the complex host responses that determine the outcome of infections with potentially lethal viruses. To achieve…

Developing Signatures that Relate Fecal Microbiome Characteristics with Patient Phenotype

Lead Institution

Arizona State University

Principal Investigator

Rosa Krajmalnik-Brown

The exploration of the human microbiome is currently an area of keen interest to NIH and biotech firms, and has been explored by many researchers using either NMR or MS metabolomics or 16S rDNA…

Modeling Host Responses to Understand Severe Human Virus Infections

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Richard Smith

This comprehensive and highly integrated systems biology program seeks to delineate the complex host responses that determine the outcome of infections with potentially lethal viruses. To achieve…

Modeling Host Responses to Understand Severe Human Virus Infections

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Richard Smith

This comprehensive and highly integrated systems biology program seeks to delineate the complex host responses that determine the outcome of infections with potentially lethal viruses. To achieve…

Projects