Thomas Metz | Environmental Molecular Sciences Laboratory

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…

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…

Evaluation of type 1 diabetes biomarker candidates in plasma samples of the DAISY cohort

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Ernesto Nakayasu

Type 1 diabetes (T1D) is a devastating disease that reduce the life expectancy by over one decade. Its treatment is based solely on exogenous insulin administration and there is no cure or remission…

Proteomics analysis of ovulation in primates

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Sneha Couvillion

To perform a parallel genomic (RNAseq, University of Oregon) and proteomic (PNNL) assessment of the ovarian follicle in the period prior to and at different time points after an ovulatory stimulus (i…

A Systems Biology Approach to Infectious Diseases Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

Project type

Exploratory Research

We describe an integrated program for coupling advanced capabilities in high-throughput transcriptomics, proteomics, and metabolomics with a comprehensive informatics infrastructure and a…

Effects of Silymarin on the Metabolome

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Silymarin (SM)-derived natural products interact with mammalian biomolecules in a specific and productive manner to cause changes in signal transduction and gene expression in a cell to protect the…

Metabolomics of Mixed Microbial Communities: Understanding the Influence of Gut Microbiota

Lead Institution

Arizona State University

Principal Investigator

Rosa Krajmalnik-Brown

Combining NMR data and Mass Spec data with biostatistics and bioinformatics will enhance the impact of phylogenetic analysis, biochemical mechanistic studies, and mathematical modeling currently…

Proteomics Laboratory for The Environmental Determinants of Diabetes in the Young

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Type 1 diabetes mellitus (T1D) is a common autoimmune disease in children and results from autoimmune destruction of insulin-producing pancreatic ?-cells triggered by complex interactions of…

OHSU-PNNL NORTHWEST CO-LABORATORY FOR INTEGRATED OMICS

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Karin Rodland

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…

MKP1 regulates plant metabolite signals that induce bacterial virulence: How and where are these signals controlled?

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

PNNL will perform both untargeted and targeted metabolomics analyses of plant exudate and tissue samples to assess mechanisms of altered resistance in MKP1

Reconstructing the Mycobacterium Tuberculosis Metabolic Model

Lead Institution

National Institute of Allergy and Infectious Diseases

Principal Investigator

Clifton Barry

Project type

Large-Scale EMSL Research

Tuberculosis (TB) kills 3 million people every year, and the rising tide of drug-resistant TB threatens to overwhelm global health programs. New and improved drugs are urgently needed to shorten the…

Protein markers to type 1 diabetes progression

Lead Institution

University of North Carolina Greensboro

Principal Investigator

Qibin Zhang

Type 1 diabetes (T1D) results from autoimmune destruction of insulin-producing pancreatic ?-cells – a long asymptomatic period spanning many months to years. Currently, autoantibodies to islet cell…

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…

Agile BioFoundry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jon Magnuson

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…

Yarrowia lipolytica for biotechnology and synthetic biology

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…

Proteomics Laboratory for The Environmental Determinants of Diabetes in the Young

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Type 1 diabetes mellitus (T1D) is a common autoimmune disease in children and results from autoimmune destruction of insulin-producing pancreatic ?-cells triggered by complex interactions of…

A Systems Biology Approach to Infectious Diseases Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

Project type

Exploratory Research

We describe an integrated program for coupling advanced capabilities in high-throughput transcriptomics, proteomics, and metabolomics with a comprehensive informatics infrastructure and a…

Global Forensic Chemical Exposure Assessment for the Environmental Exposome

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

The absence of methodology for making unique chemical identifications of 100’s or 1000s of chemicals in a single analysis is the most significant obstacle to the global assessment of chemical…

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…

Predictive Modeling of Viral Pathogenesis

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The interactions between a host and a pathogen are complex, representing a molecular interplay that results in either health or disease as an outcome. Understanding the nuances of these interactions…

Prediction of soil microbiome phenotypic responses to changing moisture conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jason McDermott

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…

Modeling Host Responses to Understand Severe Human Virus Infections

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

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…

Development of High Throughput Global Metabolomics Approaches based upon Mass Spectrometry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Project type

Exploratory Research

The term 'metabolome' refers to the entire complement of all small molecular weight metabolites and related species at a given time for a system of interest. Quantitative metabolomic…

Projects