Lye Meng Markillie

Accelerating cryo-EM screening at EMSL by 25-fold

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

Cryo-Electron Microscopy (cryo-EM) is a powerful structural biology technique since it does not require crystallization (unlike X-ray), does not require ultrahigh purity (unlike NMR) and provides…

Transcriptome analysis of methanotrophic microbe Methylotuvimicrobium alcaliphilum 20ZR during cultivation in the presence of rare-earth elements.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Lye Meng Markillie

Owing to their unique physical properties, rare-earth elements (REEs) are key resources for developing new clean and advanced manufacturing technologies. Most of these elements, however, are not…

High throughput single cell multiomics platform

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

In this collaborative project, PNNL and Scienion will co-develop an integrated microfluidic technology to co-measure the transcriptome and proteome in single cells. The technology will enable us to…

Rhizosphere Research Campaign: The plant-soil interface - understanding dynamic interactions in the context of environmental change

Lead Institution

University of Missouri - Columbia

Principal Investigator

Gary Stacey

Project type

Research Campaign

The ultimate, long-term goal is to determine what drives source-sink relationships that control the cycling of plant nutrients belowground. To fully appreciate the complexities of this dynamic…

Validation and functional characterization of transcription factors in wheat using cell-free protein
expression and high-throughput sequencing technologies

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Irina El Khoury

This study aims to validate and functionally characterize a family of transcription factors to understand the differences in their deoxyribonucleic acid binding preferences and their potential impact…

Multi-Omics Evaluation of Tripartite Associations in Red Alder Roots: Integrated Transcriptomics, Proteomics, Metabolomics and Metabolite Imaging of Red Alder Symbiotic Associations in Root Tissue

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

This proposal presents the unique opportunity to conduct the first ever integrated multi-omics and imaging evaluation of the Alnus rubra (red alder tree)/Frankia alni (bacteria)/Alpova diplophloeus …

Automating Microbial Community Phenotyping within Synthetic Soil Aggregates

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jayde Aufrecht

Microbial hotspots are the sites of nearly all biogeochemical transformations (BGT) in the soil. Unfortunately, the small size (µm to mm) and transient existence (hours to days) of microbial…

Single-Bacterium Transcriptomics Using Nanoliter Microfluidic Droplets

Lead Institution

Brigham Young University

Principal Investigator

Ryan Kelly

RNA-seq has been emerging as an advanced approach to the characterization and quantification of transcriptomes using next-generation sequencing technologies. Nevertheless, most studies target to…

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…

Elucidating synergistic plant-bacteria metabolic pathways for alleviating iron deficiency

Lead Institution

Oregon State University

Principal Investigator

Rene Boiteau

Nutrient mobilization from soil minerals is critical for plant growth, particularly in marginal lands with high pH soils or low phosphate availability. One way that rhizospheric bacteria enhance…

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…

Reprogramming Plant Gene Regulatory Networks for Source-to-Sink Carbon Allocation

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Amir Ahkami

The regulation of carbon partitioning between source and sink tissues plays a critical role in plant growth and development. Plant productivity is enhanced by sink strength and source activity, which…

Extracellular Research Thrust for EMSL SSA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

This project will develop a conceptual framework that defines the biotic and abiotic mechanisms regulating the persistence of mineral associated organic matter (OM). The specific goals are to…

Mapping Nutrient Flow through a Plant-Microbe Symbiont System using Stable Isotope Probing under Drought and Salinity Stress

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

Red alder (Alnus rubra) is one of the fastest growing, commercially important, hardwood species for biomass/timber production in North America, and is also involved in a nitrogen-fixation symbiosis…

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…

High throughput and in-depth single-cell proteomics for plant cells

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ying Zhu

In support of the "Single-cell biology" value stream in EMSD/EMSL DigiPhen Motivation, we propose to develop a high throughput and in-depth single-cell proteomics platform. We aim to…

Elucidation of the Roles of Diazotrophic EndoPopulus: Endophyte Communities in Promoting Productivity and Resilience of Populus through Systems Biology Approaches (EndoPopulus)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Amir Ahkami

The plant microbiome, including microbial endophytes living within plants and the epiphytes living on the plant surface, has a profound influence on the productivity and resilience of the host plant…

Nanoscale Characterization of Nanomaterial - Cell Interactions

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Galya Orr

Project type

Large-Scale EMSL Research

This proposal is a continuation of research pursued under EMSL User Proposal #17690. The extensive use of amorphous silica nanoparticles (NPs) in the industry, and the growing use of carbon nanotubes…

Integrated single-cell transcriptomics and proteomics platform

Lead Institution

Scienion

Principal Investigator

Joshua Cantlon-Bruce

Project type

Scientific Partner

In this partner project, Scienion and EMSL teams will work together to develop an integrated single-cell transcriptomics and proteomics platform. The platform will enable us to simultaneously profile…

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…

Bio-printed microbial habitats for high-throughput, in situ metaphenomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jayde Aufrecht

Outside of laboratory cultures microorganisms live in micro-structured environments which provide non-competitive spatial niches critical to maintaining genotypic and phenotypic diversity in the…

Transcriptional and epigenetic regulation following ionizing radiation exposure in a skin model system

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

David Stenoien

Project type

Exploratory Research

Dynamic post-translational modifications (PTMs) occurring on histones play essential roles in regulating transcription of specific target genes and in the epigenetic reprogramming occurring during…

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…

Isoprene Research Campaign: Making Isoprene from Biomass Material using Bacillus Species

Lead Institution

Washington State University Tri-Cities

Principal Investigator

Birgitte Ahring

Project type

Research Campaign

The overarching goal of this project is to understand the pathway of isoprene production in Bacillus subtilis, to serve as the basis for genetically modifying the pathway to substantially increase…

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…

EMSL Science Overview

Lye Meng Markillie

Projects

Accelerating cryo-EM screening at EMSL by 25-fold

Transcriptome analysis of methanotrophic microbe Methylotuvimicrobium alcaliphilum 20ZR during cultivation in the presence of rare-earth elements.

High throughput single cell multiomics platform

Rhizosphere Research Campaign: The plant-soil interface - understanding dynamic interactions in the context of environmental change

Validation and functional characterization of transcription factors in wheat using cell-free protein
expression and high-throughput sequencing technologies

Multi-Omics Evaluation of Tripartite Associations in Red Alder Roots: Integrated Transcriptomics, Proteomics, Metabolomics and Metabolite Imaging of Red Alder Symbiotic Associations in Root Tissue

Automating Microbial Community Phenotyping within Synthetic Soil Aggregates

Single-Bacterium Transcriptomics Using Nanoliter Microfluidic Droplets

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

Elucidating synergistic plant-bacteria metabolic pathways for alleviating iron deficiency

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

Reprogramming Plant Gene Regulatory Networks for Source-to-Sink Carbon Allocation

Extracellular Research Thrust for EMSL SSA

Mapping Nutrient Flow through a Plant-Microbe Symbiont System using Stable Isotope Probing under Drought and Salinity Stress

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

High throughput and in-depth single-cell proteomics for plant cells

Elucidation of the Roles of Diazotrophic EndoPopulus: Endophyte Communities in Promoting Productivity and Resilience of Populus through Systems Biology Approaches (EndoPopulus)

Nanoscale Characterization of Nanomaterial - Cell Interactions

Integrated single-cell transcriptomics and proteomics platform

Regulatory dynamics of microbial communities

Bio-printed microbial habitats for high-throughput, in situ metaphenomics

Transcriptional and epigenetic regulation following ionizing radiation exposure in a skin model system

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

Isoprene Research Campaign: Making Isoprene from Biomass Material using Bacillus Species

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