Lee Ann McCue

The National Microbiome Data Collaborative: improving metaproteomics methods and processing capabilities

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Paul Piehowski

We will improve and streamline the metaproteomics analysis workflow used by both EMSL and the NMDC. Generating gold-standard proteomics data will support algorithmic improvements for the inference of…

High performance sequence analysis for data-intensive bioinformatics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Christopher Oehmen

Project type

Grand Challenge

Volume of sequence data available through public repositories are growing almost exponentially in time. Currently, the nonredundant protein database doubles in size approximately every 2 years. At…

SyPro Poplar: Improving Poplar Biomass Production under Abiotic Stress Conditions: an
Integrated Omics, Bioinformatics, Synthetic Biology and Genetic Engineering Approach

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Amir Ahkami

To engineer bioenergy crops that can grow in dry, marginal lands, this project will introduce into poplar trees tolerance to different environmental stresses such as water deficit, high soil salinity…

Does Forest-to-Pasture conversion decrease functional turnover across space? – Measuring the effects of deforestation on the Amazon rainforest soil microbiome

Lead Institution

University of California, Davis

Principal Investigator

Jorge Rodrigues

Project type

Limited Scope

The Amazon rainforest plays an essential role in CO2 sequestration. Yet, the impact of anthropogenic activities on microbial communities that participate in this biochemical process needs…

The National Microbiome Data Collaborative: improving metaproteomics methods and processing capabilities

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Lee Ann McCue

We will improve and streamline the metaproteomics analysis workflow used by both EMSL and the NMDC. Generating gold-standard proteomics data will support algorithmic improvements for the inference of…

Signatures of Environmental Perturbation - Microbial Community and Organic Matter Resilience

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vanessa Bailey

The goal of this project is to use advanced statistical tools developed by PNNL Signature Discovery Initiative to discover one or more signatures that indicate impaired resilience of the soil carbon…

Signatures of Environmental Perturbation - Microbial Community and Organic Matter Resilience - Computing Adendum

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vanessa Bailey

The goal of this project is to use advanced statistical tools developed by PNNL Signature Discovery Initiative to discover one or more signatures that indicate impaired resilience of the soil carbon …

Evaluation of the Adaptation and Acclimation of Hypersaline Lithifying Microbial Mats to Salinity Disturbance in the Great Salt Lake Ecosystem

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

Project type

Large-Scale EMSL Research

Multiple capabilities at EMSL will be applied to mat microbial communities present along a salinity gradient between the North and South arms of the Great Salt Lake, UT. These lithifying microbial…

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…

Exploring the Molecular Driving Forces for f-Element Complexation and Organization in Mixed Solvents at Interfaces

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Sue Clark

Project type

Special Science

This project will examine changes in the solvation of trivalent actinide (An3+) and lanthanide (Ln3+) cations in binary solvents during complexation with an emphasis on characterizing the speciation…

Signatures of Environmental Perturbation - Microbial Community and Organic Matter Resilience

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vanessa Bailey

The goal of this project is to use advanced statistical tools developed by PNNL Signature Discovery Initiative to discover one or more signatures that indicate impaired resilience of the soil carbon …

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…

Pore- to Core-Scale Research to Inform Ecosystem-Scale Soil C Biogeochemistry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vanessa Bailey

Project type

Large-Scale EMSL Research

The spatial separation of soil organic carbon (SOC), microbes, and extracellular activity is an important mechanism of SOC protection in soils that exists at the soil pore (micron-mm) scale. The…

PhenoAccess: Physiological Phenotyping of Brachypodium Accessions

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Amir Ahkami

Although the effects of elevated CO2 on plant growth, physiology and metabolism has been investigated thoroughly, the underlying integrated organismal, cellular and molecular mechanisms of these…

Drivers of Microbial Community Development and Persistence in Deep Subsurface Shales

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Lee Ann McCue

Hydraulic fracturing, the extraction of oil and gas from deep shale reservoirs via high-pressure injection of fluids, is now a critical part of the US energy portfolio. Microbial communities…

Development of computational pipeline to integrate protein structure/function discovery with genome scale model

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Marat Valiev

The project is focused on developing a computational pipeline that connects genome scale model to protein structure/function at the molecular level. It addresses an immediate need of the Subcellular…

SyPro Poplar: Improving Poplar Biomass Production under Abiotic Stress Conditions: an
Integrated Omics, Bioinformatics, Synthetic Biology and Genetic Engineering Approach

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Amir Ahkami

To engineer bioenergy crops that can grow in dry, marginal lands, this project will introduce into poplar trees tolerance to different environmental stresses such as water deficit, high soil salinity…

Stable Isotope Probing Informatics Infrastructure for High Throughput Analyses

Lead Institution

Michigan State University

Principal Investigator

James Moran

The ability to identify, quantify and trace organic compounds through a soil ecosystem is essential for characterization of the molecular mechanisms that regulate biomolecule interactions with soil…

Identifying and Quantifying Sources of Variability in FTICR

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Allison Thompson

Many EMSL users are requesting Fourier transform ion cyclotron resonance (FTICR) soil organic matter (SOM) data. However, there are many circumstances where results are unexpected and experts…

Projects