Amir Ahkami

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…

Molecular Phenotyping of Brachypodium to Provide Metabolic and Functional Linkages to the Plant-Atmosphere-Soil-Systems (iPASS) Model

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

This proposal aims to provide the fundamental molecular characterization necessary to develop a model which ultimately links phenotypic measurements to the atmospheric processes and soil…

Deciphering exopolysaccharide functional specificity via visualization of chemical motifs that mediate microbial-microenvironment interactions in soil micromodels

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Dusan Velickovic

Exopolysaccharides (EPS) are carbohydrate-based matrices of microbial biofilms that microbes use to adapt to their surroundings. The chemical structure of EPS, even within single species biofilms,…

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…

A new capability for high-resolution 3D imaging of soil structure and soil chemistry in the rhizosphere

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Tamas Varga

We aim to answer the following critical questions about the rhizosphere: (i) What is the distribution of important nutrient elements like P in the soil and around the root? (ii) How much of the…

MS imaging of cell wall N- and O-linked glycans in interaction between roots and soil-borne microbes

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christopher Anderton

We propose to address a critical barrier in deciphering rhizosphere communication, specifically that of the role of glycans (a modifiable moiety of glycoproteins) in these processes. The first aim of…

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…

3D Root Cartography of Molecular-Microbe Interactions

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

We intend to develop a pipeline for simultaneous 3D spatial imaging of metabolites and microorganisms on plant roots, generating a molecular and microbial 3D-cartography of the root system. By…

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…

Molecular Phenotyping of Plants & Microbes (MolPheno) for the PRedicting Ecosystem Resilience through Multiscale and Integrative Science (PREMIS) initiative

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

This proposal aims to provide the fundamental molecular characterization necessary to develop a model which ultimately links phenotypic measurements to the soil biogeochemistry associated with…

Targeted spatial metabolomics: an automated approach to identifying and analyzing single cells in situ

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christopher Anderton

Tissue-scale or cell-population-level analysis (i.e., ‘bulk analysis’) yields averaged abundance data that can mask critical information about the state of individual cells. Through a recently ended…

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…

Imaging and Analysis of Root System Architecture with an Automated Non-invasive Phenotyping System

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Amir Ahkami

We will deploy a Non-invasive Automated Root Imager (NARI) System for the capture and image analysis of root traits to EMSL user community. The NARI system is partially assembled and once completed…

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…

Toward plant spatial hormonomics: multiple phytohormone profiling by derivatization assisted-ionization enhanced targeted MALDI MS imaging

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Dusan Velickovic

Phytohormones are physiologically important small molecules that regulate diverse processes as chemical messengers within plants and in plant communications with environments. However, the complex…

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…

EMSL Science Overview

Amir Ahkami

Projects

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

Molecular Phenotyping of Brachypodium to Provide Metabolic and Functional Linkages to the Plant-Atmosphere-Soil-Systems (iPASS) Model

Deciphering exopolysaccharide functional specificity via visualization of chemical motifs that mediate microbial-microenvironment interactions in soil micromodels

PhenoAccess: Physiological Phenotyping of Brachypodium Accessions

A new capability for high-resolution 3D imaging of soil structure and soil chemistry in the rhizosphere

MS imaging of cell wall N- and O-linked glycans in interaction between roots and soil-borne microbes

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

3D Root Cartography of Molecular-Microbe Interactions

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

Molecular Phenotyping of Plants & Microbes (MolPheno) for the PRedicting Ecosystem Resilience through Multiscale and Integrative Science (PREMIS) initiative

Targeted spatial metabolomics: an automated approach to identifying and analyzing single cells in situ

Next generation microfluidics platform for high throughput single cell proteomics

Imaging and Analysis of Root System Architecture with an Automated Non-invasive Phenotyping System

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)

Toward plant spatial hormonomics: multiple phytohormone profiling by derivatization assisted-ionization enhanced targeted MALDI MS imaging

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