Mary Lipton

Development of an Environmental-Focused DIA Pipeline for HTP Proteomics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Isaac Attah

Currently, metaproteomics workflows are hindered by sample complexity which necessitates fractionation of the sample meaning one sample can require 12 to 24 MS analyses. Data dependent workflows …

Determining how metabolic regulation can improve biofuel and bioproduct accumulation

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Photosynthetic organisms are promising sustainable sources of biofuels and bioproducts to help meet growing global needs. Microalgae utilize solar energy, consume CO2, can be cultivated on non-arable…

Modeling microbial community metabolic interactions in hypersaline ecosystems

Lead Institution

Duke University

Principal Investigator

Amy Schmid

Project type

Exploratory Research

The proposed research will test the hypothesis that hypersaline microbial communities interact to maintain stability despite changes in salinity and nutrient availability. Hypersaline-adapted Archaea…

Determination of the proteins induced in mutant forms of Deinococcus radiodurans after exposure to hydrogen peroxide

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kwong Kwok Wong

Project type

Exploratory Research

The extraordinary repair mechansims of D. radiodurans allow the organism to survive even after exposure to extremely large doses of ionizing radiation. Although it is clear that the DNA is…

proteomics study of Corynebacterium glutamicum.

Lead Institution

Research Institute of Innovative Technology for the Earth

Principal Investigator

Alain Vertes

Project type

Limited Scope

Under a previous user proposal, we have initiated the proteomic characterization of this organism using the living-cell reaction process to characterize the interaction cell growth and metabolism…

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…

DNA- Protein Kinase Complex: Defining the participants

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Steven Yannone

Project type

Exploratory Research

We are primarily interested in looking for novel and known DNA-PK associated proteins. We plan to use purified monoclonal antibodies that recognize either Ku80 or DNA-PKcs and make small affinity…

Understanding microbial dynamics in a biostimulated aquifer using combined Omics approaches

Lead Institution

University of California, Berkeley

Principal Investigator

Jillian Banfield

Project type

Large-Scale EMSL Research

At the Rifle Integrated Field Research Challenge (IFRC) site in Colorado, carbon amendments to the subsurface are used to stimulate growth of the indigenous microbial community. The microbial…

An Integrated Omics Guided Approach to Lignification and Gravitational Responses: The Final Frontier

Lead Institution

Washington State University

Principal Investigator

Norman Lewis

Integrated “omics” approaches are increasingly urgently needed to robustly pursue incisive hypotheses in biological systems, while concomitantly gaining better understanding of global ramifications…

Defining the in vitro phosporylation osites of DNA protein kinase (catalytic subunit)

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Doug Chan

Project type

Exploratory Research

We are in the process of identifying all the in vitro phosphorylation sites on DNA-PKcs.? Because the protein is so large, we were never able to identify the sites by the classical method (isolation…

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…

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…

Proteomic analysis of wild type and soil-colonization deficient strains of Pseudomonas fluorescens

Lead Institution

Tufts University School of Medicine

Principal Investigator

Stuart Levy

Project type

Exploratory Research

Proteomic analysis of wild type and soil-colonization deficient strains of Pseudomonas fluorescens A significant step towards developing effective genetically modified-microbes for bioremediation…

Comparative metaproteomics and metametabolomics of the biomass-degrading microbial community that inhabits the cow rumen

Lead Institution

University of California, Davis

Principal Investigator

Matthias Hess

Project type

Large-Scale EMSL Research

Lignocellulosic plant material is one of the most promising sources of sustainable liquid transportation fuels but the recalcitrant nature of the plant cell wall and the cost of biomass-degrading…

Tracing rhizosphere carbon exchange processes and nutrient interactions

Lead Institution

Michigan State University

Principal Investigator

James Moran

Rhizodeposition represents the largest flux of photosynthetically derived organic matter into soil for most terrestrial systems and, in so doing, serves as a major point of connection between…

Great Lakes Bioenergy Research Center

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

The researchers of the GLBRC will utilize state of the art proteomics facilities resident at the Pacific Northwest National Laboratory that allow for rapid global determination of protein expression…

Linking Microbial Communities to Subsurface Geochemistry and Hydrology at the Field-Scale

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Stegen

Project type

Large-Scale EMSL Research

Background and Key Challenges: A major challenge in subsurface science is understanding how microbial communities, geochemistry, and hydrology interactively govern the fate and transport of…

High throughput generation of small molecule probes for discovery of unique cellular functions using Substrate Activity Screening

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sankarganesh Krishnamoorthy

We propose a method to demystify the massive catalog of proteins-of-unknown-function accumulated by recent advances in genome sequencing by direct assignment of function. We will query enzyme…

Proteomic Characterization of Yersinia pestis

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Project type

Exploratory Research

Proteomic profiling of pathogenic microbes: Expand the knowledge base of the threat to enable better intervention and treatment after exposure. This project will: 1) Leverage the state of the art…

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…

Harnessing Biomineralization Potential of Metal-Oxidizing Bacteria for REE Synthesis

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alex Beliaev

Although redox reactions and enzymes participating in the extracellular oxidation of Fe and Mn are identified, little is known about the biomineralization mechanisms that facilitate formation…

ShewFed

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Project type

Exploratory Research

Bacterial strains such as Shewanella oneidensis strain MR-1 are key organisms in the bioremediation of metals due to their ability to enzymatically reduce and precipitate a diverse range of heavy…

Biomolecular Mechanisms for Microbe-Fe(III) Oxide Interactions in Geobacter species

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Project type

Exploratory Research

The most promising strategy for the in situ bioremediation of radioactive groundwater contaminants that has been identified by the NABIR program is to stimulate the activity of dissimilatory metal…

Identifying the key organisms, pathways and locations of hydrogen fermentation from lignocellulosic biomass in wood-feeding Passalid beetles.

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Eoin Brodie

Project type

Large-Scale EMSL Research

Passalid beetles, such as Odontotaenius disjunctus, are subsocial insects that process large amounts of woody biomass by feeding on triturated wood. With the development of symbiotic relationships…

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…

FedEx1

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alex Beliaev

Project type

Exploratory Research

Bacterial strains such as Shewanella oneidensis strain MR-1 are key organisms in the bioremediation of metals due to their ability to enzymatically reduce and precipitate a diverse range of heavy…

Deinococcus radiodurans

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Project type

Exploratory Research

The most significant defining characteristic of D. radiodurans is its ability to resist the lethal effects of DNA damaging agents such as ionizing radiation, UV radiation, hydrogen peroxide and…

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…

Nanopore Platforms for Protein Analysis

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jayde Aufrecht

Nanopore-based protein sensing has the potential to revolutionize the field of proteomics by providing single-molecule protein sequencing at amino acid level resolution. However, even if nanopore…

Shew strains

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Metal reducing members of the Shewanella genus carry out a variety of processes important to the U.S. department of Energy (DOE) missions including the bioremediation of metals (Fe, Mn, Cr) and…

Shewanella oneidensis

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Project type

Exploratory Research

Bacterial strains such as Shewanella oneidensis strain MR-1 are key organisms in the bioremediation of metals due to their ability to enzymatically reduce and precipitate a diverse range of heavy…

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…

Proteomics of Burkholderia mallei

Lead Institution

University of Medicine and Dentistry, New Jersey Medical School

Principal Investigator

Steven Schutzer

Project type

Exploratory Research

Burkholderia mallei is the cause of glanders. There is no rapid discriminating diagnostic assay, no vaccine, and reliable therapy. Gaps in our understanding and rapid diagnostics for the microbe can…

Low Dose

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Project type

Exploratory Research

Although it is clear that understanding the protein complement of the cell is extremely important in understanding the function of the cell, the next stop in the further interpretion of pathways…

Organic N Turnover in Soil: An Overlooked Component of C Cycling

Lead Institution

Oregon State University

Principal Investigator

David Myrold

Project type

Large-Scale EMSL Research

It is now generally accepted that most of the organic matter in soils consists of materials that have been processed by the microbial community. Indeed, "necromass"--the remains of dead…

Proteomics of in stiu Biostimulated Sediments

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Philip Long

Project type

Exploratory Research

The proteomics facility will be used for the detection of peptides/proteins belonging to metal-reducing bacteria in sediment samples from naturally-occurring microbial communities. The bacteria…

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…

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…

NBACC: Host/pathogen interactions (PNNL Scope # 49488, Lipton's NBACC Host project)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Determine the host pathogen interactions from Yersinia pestis infected into rat animal models. In collaboration with Walter Reed Army research center, rats will be infected with Yersina pestis and…

Rhodobacter sphaerodies

Lead Institution

University of Wisconsin, Madison

Principal Investigator

Timothy Donohue

Project type

Exploratory Research

Rhodobacter sphaerodies 2.4.1. is a-3 purple nonsulfur eubacterium with an extensive metabolic repertoire. Under anaerobic conditions, it is able to grow by photosynthesis, respiration and…

Integrated Stable Isotope Probing for the Comprehensive Quantitative- Characterization of Biological Dynamics and Elemental Cycling

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Biological organisms dynamically function in relationship to their environment and neighboring organisms, creating a continual interplay that constitutes the ecological state. Fundamental…

Identification of Metal Reductases (NABIR)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

Project type

Exploratory Research

Central to the NABIR goal to develop the scientific basis for in situ remediation of radioactive contaminants is the fundamental understanding of microorganisms with dissmilatory metal reducing…

Post-translational modification of key proteins during exposure of intact prokaryotic and eukaryotic cells to organomercurials.

Lead Institution

University of Georgia

Principal Investigator

Anne Summers

Project type

Large-Scale EMSL Research

Mercury (Hg) contaminates many DOE sites, notably Oak Ridge National Laboratory (ORNL) where its effects have been monitored for decades. Hg is also released from fossil fuels and minimization of…

Stable Isotope Probing Overarching Infrastructure to Integrate and Stabilize Technologies

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

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

Application of High-Throughput Proteomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

The understanding of how cells function at the systems level will greatly benefit from the development of new approaches capable of making global measurements of protein expression (proteome). 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…

New Method for Sequential Extraction of Microbes and Biomolecules from Soil

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

The goal of this project is to develop a sequential extraction method that is based on the affinity of biomolecules and microbes to soil particles. By using sequentially harsher extractions, we will…

Biomarker discovery in pathogens by proteomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mary Lipton

The ability to respond adequately to a biological threat requires not only rapid and accurate detection, but also a detailed understanding of the threat agent to determine the appropriate response…

Examinations of Cell Surface Layer Proteins in the Thermophilic Thermotogales Bacteria to Determine Their Roles in Polysaccharide Hydrolysis

Lead Institution

University of Connecticut

Principal Investigator

Kenneth Noll

Project type

Large-Scale EMSL Research

We propose to characterize the protein constituents of the outer surface layer of cells of the hyperthermophilic bacterium Thermotoga maritima and its relatives and examine their roles in the…

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…

Projects