William Chrisler

Algal Productivity Enhancements by Rapid Screening and Selection of Improved Biomass and Lipid Producing Phototrophs (APEX)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Erin Bredeweg

This project uses a multi-pronged approach to improve oil content in algae capable of sustaining high areal biomass productivities in outdoor ponds. This includes mutagenesis techniques (EMS, ARTP)…

An integrated pest management approach to algal crop protection based on metagenomic characterization, antimicrobial peptides, and adaptive laboratory evolution

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Erin Bredeweg

This project uses a multi-pronged approach to improve pest management in open air algal cultivation, an important crop strategy for decarbonization. This includes identification of the most…

Using culture-independent methods to link active compound-specific carbon degradation to greenhouse gas production and recycling in natural populations of permafrost microbes

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

The initial focus of this work will be to improve sample handling of microbial samples to aid in FISH, Imaging Mass Spectrometry, and other spatially-resolved analyses. In initial efforts, we will…

Development of a single-cell top-down proteomics platform for understanding rhizobial infection process

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ying Zhu

We aim to extend EMSL’s leading capability in ultrasensitive/single cell proteomics to measure intact proteins in individual plant cells. We will address major challenges in ultrasensitive top down…

Identification of plant host and microbe model system for study of rhizophagy cycle

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

Rhizophagy (“root eating”) is a process by which plants actively uptake soil microbes into their roots and use oxidative degradation to extract micronutrients from the cells. This phenomenon has been…

Next generation microfluidics platform for high throughput single cell proteomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ying Zhu

The project aims to improve both sensitivity and throughput in single cell proteomics through the development of a microfluidic platform that leverages current technology. A hybrid picowell/nanowell…

A Molecular Atlas of the Developing Lung

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Richard Corley

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…

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…

In situ mesoscale imaging of biofilm dynamics using SALVI

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

Xiao-Ying Yu

Understanding how metabolic pathways are interconnected and controlled at the subcellular scale within living systems with coexisting macromolecules in a cell that has complex structure, dynamics,…

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…

Rhizosphere Underground:
Unraveling the Role of Microbes in Stabilizing Carbon Pools in Soils

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

Microorganisms are fundamental to biogeochemical cycling, as microbial metabolism significantly contributes to the regulation of terrestrial carbon and nitrogen cycling. However, the impact of the…

Spatially resolved chemical proteomics for linking enzymatic activity to omics phenotyping in heterogeneous microbial communities

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

We will connect chemical probes and nanoPOTS to rapidly identify microbial species and essential protein functions in structured microbial communities. We will use aggregation induced emission (AIE)…

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…

Single-Cell Characterization of Microbiomes via Split-Pool Ligation Transcriptomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alex Beliaev

While single-cell technologies are rapidly becoming a standard for measuring expression in eukaryotic organisms, their utility for prokaryotes is facing substantial technical barriers including…

Microbial Community Dynamics and Plant Phenomics with Single-Cell Gene Expression and Imaging Mass Spectrometry

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Galya Orr

The inherent heterogeneity of biological systems, including microbial communities or cell populations, limits the questions that can be resolved by averaged cell population measurements, which lump…

Deep UV laser ablation system for spatial single-cell proteomics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

William Chrisler

Laser capture microdissection (LCM) is the key capability for spatially resolved omicss. However, commercially available LCM systems are designed for mammalian tissues and feature UV lasers (330 nm),…

The CCMEE - Culture Collection of Microorganisms from Extreme Environments as a platform for biodiversity research at EMSL

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sherry Cady

PNNL is home to the CCMEE (Culture Collection of Microorganisms from Extreme Environments), a unique microbial extremophile culture collection. The CCMEE was transferred to EMSL from the University…

Nanoliter-scale Affinity Purification Mass Spectrometry for Small Numbers of Hair Cells

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ying Zhu

The molecular mechanisms of mechanotransduction function of hair cells in auditory system and the vestibular system are largely undefined due to the scarcity of hair cells and the lack of sensitive…

The Lignin Enigma: Turning the Corner

Lead Institution

Washington State University

Principal Investigator

Norman Lewis

Project type

Large-Scale EMSL Research

Lignins (Nature's second most abundant terrestrial plant substances) provide structural support for plants to stand upright, to conduct water/nutrients, and as barriers to opportunistic…

A streamlined platform for phosphoproteome mapping of human tissues

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Tujin Shi

Recent technological advances in genomics, transcriptomics, and proteomics allow for rapid generation of comprehensive 3D-human tissue maps for biomolecules DNAs, RNAs, and proteins at the single…

The CCMEE - Culture Collection of Microorganisms from Extreme Environments as a platform for biodiversity research at EMSL

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sherry Cady

PNNL is home to the CCMEE (Culture Collection of Microorganisms from Extreme Environments), a unique microbial extremophile culture collection. The CCMEE was transferred to EMSL from the University…

A scalable mass spectrometry platform for proteome mapping of brain tissues

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Tujin Shi

The brain is the most complex organ in the mammalian body. Bulk analysis obscures heterogeneity of cell types present even in the smallest brain regions. Multi-omics single-cell resolution 3D…

Detecting Seismically-Sustained Deep Subsurface CH4-cycling Chemolithoautotrophic Microbial Communities Using Multi-Omic Analyses and NanoSIMS

Lead Institution

Princeton University

Principal Investigator

Tullis Onstott

Project type

FICUS Research

The specific objective of the proposed JGI/EMSL project is to document the microbial ecosystem of an active fault zone at 3.5 to 3.6 kilometers depth in South Africa. More specifically, the goal is…

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…

InterCom

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

We intend to identify how molecular interactions at the intercellular level participate in controlling carbon assimilation, allocation and transformation in the plant-microbe-soil system (Fig. 1),…

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…

Yarrowia lipolytica for biotechnology and synthetic biology

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Erin Bredeweg

The team at PNNL is using a combination of flow cytometry, microscopy and lipidomics/metabolomics to establish baseline cell biological and metabolite data on DNA agility in eukaryotic organisms, and…

Projects