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…

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…

GC-MS Analysis of Alkaline Cellulose Degradation Products

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Cort

Project type

Exploratory Research

Degradation of cellulose and other polysaccharides in alkaline conditions and at elevated temperatures yields mixtures of compounds containing carboxylic acid and/or alcohol functional groups. These…

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…

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…

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…

Agile BioFoundry

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Scott Baker

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…

Comprehensive comparison of taxonomic composition and metabolic functioning in oxygenic and anoxygenic microbial mats of Yellowstone hot springs

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

This proposal focuses on comparing a rare, but evolutionarily important, modern laminated microbial mat formed exclusively by anoxygenic photosynthetic microorganisms and a well-studied mat formed by…

Advanced Proteomics and Metabolomics Studies of Type 1 Diabetes

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Project type

Exploratory Research

In this four year two phase (R21/R33) project we will apply advanced proteomic and metabolomic nanoflow liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry technologies…

NMR-based metabolomics of the enteropathogens Salmonella and Yersinia

Lead Institution

Washington State University Tri-Cities

Principal Investigator

Kathleen McAteer

Project type

Large-Scale EMSL Research

The goal of this research is to analyze and reconstruct intercellular and intracellular networks in Salmonella and Yersinia using multiple types of -omics data. Although we hope to gain a more…

Development of an Integrated EMSL MS and NMR Metabolic Flux Analysis Capability In Support of Systems Biology: Test Application for Biofuels Production

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Nancy Isern

An important element in the production of biofuels is the metabolic engineering process required to maximize the production of renewable biofuel molecules from fermentable substrates. Biofuel…

Undiagnosed Diseases Network Metabolomics Core

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

A state of the art metabolomics core will be a vital part of the Undiagnosed Diseases Network (UDN). However, in order for the UDN to realize it’s the full potential it is essential that the…

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…

Identification of Metabolite Toxins

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

David Wunschel

This project will collect data on ion-mobility, accurate mass and compound fragmentation data using an ESI-IMS-MS/MS system for a number of metabolite toxins and structurally similar compounds. This…

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…

Advanced Proteomics and Metabolomics Studies of Type 1 Diabetes

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

In this four year two phase (R21/R33) project we will apply advanced proteomic and metabolomic nanoflow liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry technologies…

Evaluation of the specificity and early diagnostic value of novel peptide biomarkers of Type 1 Diabetes

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Type 1 diabetes (T1D) results from autoimmune destruction of insulin-producing pancreatic B-cells triggered by complex interactions of environmental factors in genetically predisposed individuals. …

Type 1 Diabetes Mellitus: Correlating the Gastrointestinal Microbiome, Urinary Proteome and Metabolome

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Type 1 diabetes mellitus (T1D) is characterized by autoimmune destruction of the insulin producing ?-cells of pancreatic islets. It is believed that T1D results from complex interactions between…

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…

Development of high-throughput metabolomics technologies: Application to studying the flowering time in Arabidopsis thaliana

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

David Hoyt

The future trajectory of metabolomics and its applications largely depends on the analytical capabilities of NMR and MS and their combination. Although the use of both NMR and MS methods is…

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…

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…

Development of Metabolomics for Biomarker Discovery

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Thomas Metz

Project type

Exploratory Research

Metabolomics is a holistic approach to the study of a biological system’s metabolite complement (often generalized to include essentially all small molecules), and its practice is anticipated to…

Projects