Pubudu Handakumbura

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using microcrystal electron diffraction (MicroED)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

Project type

Cryo-EM Only

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain…

Advanced Plant Experiment-09 (APEX 09) - C4 Space

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Pubudu Handakumbura

Advanced Plant Experiment-09 (APEX 09) the C4 photosynthesis in Space (C4 Space) project examines how microgravity affects C3 and C4 plant metabolism. Plants capture atmospheric CO2 and convert it…

Integrated Pennycress Resilience Project (IPReP)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Pubudu Handakumbura

Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop for the 80 million-acre U.S. Midwest Corn Belt and other temperate regions including the Pacific Northwest…

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using microcrystal electron diffraction (MicroED)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain…

Persistence Control SFA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Robert Egbert

Emergent genomic tools present transformational opportunities for the U.S. bioeconomy, including potential to design synthetic rhizosphere microbiomes to generate secure, sustainable, stress-tolerant…

Understanding the Interactions of the Plant Root and Plant Growth Promoting Bacteria with Unique Correlative Surface Imaging Tools

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Zihua Zhu

This research aims to achieve the following objectives: 1) integrate surface tools and apply them in submicron chemical mapping of the plant-microbe interface; 2) provide novel in vivo analysis of…

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…

Exploring Genotypic Diversity for Functional Trait Variance

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Bryan Stanfill

By establishing genome-phenome maps for Brachypodium and Setaria, we will seek to unravel how information in the plant genome translates to traits and responses at the plant and experimental…

Consortium for Advanced Sorghum Phenomics (CASP)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

The mission of the proposed project is to accelerate breeding of biomass sorghum to maximize terminal compositional (e.g., lignocellulosic) yield under drought and saline field conditions using novel…

EPICON: Epigenetic Control of Drought Acclimation in Sorghum

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

Genetic manipulation of crops to increase the presence or intensity of desirable traits has been critical to increasing agricultural productivity. These changes have primarily involved modification…

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…

The Effects of Earthworms on Ecosystem Multifunctionality (E3M)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

In a collaborative endeavor between EMSL and the CNRS Ecotron facility in Monpellier, France, we are launching a pilot project, E3M, to explore how Ecotron’s Macrocosm platform with ecosystem-scale…

Profiling protease activities in sorghum under drought stress and recovery

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

We will investigate proteases as signatures of plant drought stress by using in vivo activity-based protein profiling to identify and evaluate the contributions of distinct serine and cysteine…

EPICON: Epigenetic Control of Drought Acclimation in Sorghum

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

Genetic manipulation of crops to increase the presence or intensity of desirable traits has been critical to increasing agricultural productivity. These changes have primarily involved modification…

Persistence Control SFA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Robert Egbert

Emergent genomic tools present transformational opportunities for the U.S. bioeconomy, including potential to design synthetic rhizosphere microbiomes to generate secure, sustainable, stress-tolerant…

Molecular Mechanism of PGPR-Plant Associations

Lead Institution

University of Missouri - Columbia

Principal Investigator

Gary Stacey

Project type

Large-Scale EMSL Research

A large body of literature attests to the plant growth promotion effects of various endophytic bacteria, including significant increases in crop yield. These studies include the possible impact of…

High-throughput rhizosphere biosensor development

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Elmore

The development of robust quantitative in situ bacterial biosensors that report on inter-organismal rhizosphere signaling, soil conditions, and plant health remains a pivotal goal for the research…

EPICON: Epigenetic Control of Drought Acclimation in Sorghum

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

Genetic manipulation of crops to increase the presence or intensity of desirable traits has been critical to increasing agricultural productivity. These changes have primarily involved modification…

Integrated Pennycress Resilience Project (IPReP)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Pubudu Handakumbura

Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop for the 80 million-acre U.S. Midwest Corn Belt and other temperate regions including the Pacific Northwest…

GoBrachy: Developing a Metabolite-Trait Association Network Model for Carbon Allocation in Brachypodium

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

Aboveground biomass (AGBM) and belowground biomass (BGBM) of Brachypodium lines will be harvested at week seven and parallel lines will be allowed to grow to senescence (B. distachyon) or longer (B…

C4 Photosynthesis in Space (C4Space)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Pubudu Handakumbura

C4 plants like maize (Zea mays) and sorghum (Sorghum bicolor) have a more efficient photosynthesis than C3 plants such as wheat (Triticum aestivum) and rice (Oryza sativa) due to a CO2-concentrating…

Consortium for Advanced Sorghum Phenomics (CASP)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

The mission of the proposed project is to accelerate breeding of biomass sorghum to maximize terminal compositional (e.g., lignocellulosic) yield under drought and saline field conditions using novel…

Multimodal Chemical Imaging Across Scales to Visualize Metabolic Pathways in Live Plants and Microbial Systems

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Scott Lea

We will develop a novel spectral imaging platform (“BioImager”) that may be used to image and identify biomolecules involved in both microbial and plant metabolic processes through different chemical…

EPICON: Epigenetic Control of Drought Acclimation in Sorghum

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christer Jansson

Genetic manipulation of crops to increase the presence or intensity of desirable traits has been critical to increasing agricultural productivity. These changes have primarily involved modification…

Persistence Control SFA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Robert Egbert

Emergent genomic tools present transformational opportunities for the U.S. bioeconomy, including potential to design synthetic rhizosphere microbiomes to generate secure, sustainable, stress-tolerant…

PRedicting ecosystem Resilience through Multiscale and Innovative Science (PREMIS) Initiative: Molecular Phenotyping of Plants & Microbes (MolPheno)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

The MolPheno project will establish molecular (metabolite and protein) profiles from plants exposed to fresh water-replete or -deprived conditions. Metabolite profiling will include tissue-specific…

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),…

Projects