Ljiljana Pasa-Tolic

Genome-Enabled Characterization of Orphan Receptor-Like Kinases in Plants

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

This research will characterize the functions and clients (i.e., substrates) of receptor-like kinases (RLKs) of Arabidopsis, rice, and soybean. Objective 1 will reveal RLK functions by combing…

Unlocking the molecular basis of plant-pathogen interactions to create resilient bioenergy crops

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

In the winning 2023-DOE BRAVE (Biopreparedness Research Virtual Environment) Proposal (LAB-23-2955), awarded to co-PI Ljiljana Pasa-Tolic (EMSL/PNNL), PI Qun Liu (BNL), and other co-PI:, Clint Magill…

Spatial Metabolomics and Glycomics for Human Kidneys

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christopher Anderton

Acute kidney injury (AKI) and chronic kidney disease (CKD) are major contributors to overall morbidity and mortality in patients in the US. However, we lack a clear understanding of the major…

Spatially resolved characterization of proteoforms for functional proteomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

Differentiated cells have distinctive patterns of epigenetic marks including various post-translational modifications (PTMs) on histones that may work in concert to control transcriptional programs…

Developing automatic gain control for organic matter analyses by FTICR-MS

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Kevin Zemaitis

Three commercial FTICR-MS instruments (Bruker; 7T, 12T, and 15T) routinely support organic matter (OM) analyses in EMSL. Generally speaking, the quality of data produced is inherently linked to the…

Massive single-cell proteomics for cancer biology

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

Single-cell technologies have become the cornerstone of biomedical and cell biology research. Next- generation sequencing-based technologies have enabled large-scale characterization of transcript…

Spatially-resolved proteome mapping of senescent cells and their tissue microenvironment at single-cell resolution

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

Cellular senescence is a permanent state of cell cycle arrest induced by many different stresses. Although senescent cells (SNCs) have been demonstrated with beneficial roles in normal physiological…

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…

Proteomic study of Transthyretin Protein

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

The project will establish a scientific partnership between the cardiomyopathy section at OHSU and mass spectrometry facility at PNNL which leverages the strengths of OHSU Cardiomyopathy center …

An integrated workflow for identification and quantitation of intact phosphoproteins

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

Multisite protein modifications involving phosphorylation alone or in combination with other post-translational modifications (PTMs) play an essential role in regulating protein activity. Hence,…

High resolution and Mass Accuracy Capability (HRMAC) Development Project

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

David Koppenaal

Fourier transform ion cyclotron mass spectrometry (FTICR-MS), the highest performance mass spectrometry technique, is uniquely valued as a research tool for analytical applications requiring the…

Characterization of an Expressed Bacterial Mn(II,III)-Oxidizing Multicopper Oxidase Complex and its Mn Oxide Products

Lead Institution

University of Washington

Principal Investigator

Bradley Tebo

Project type

Large-Scale EMSL Research

Microbial Mn(II) oxidation is an important environmental process that links the biogeochemical cycle of Mn with the cycling of C, N, P, and many trace metals and radionuclides. Microbes that oxidize…

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…

MICROBES PERSIST: SYSTEMS BIOLOGY OF THE SOIL MICROBIOME

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

Soils store more carbon than the atmosphere and biosphere combined, yet the mechanisms that regulate soil C remain elusive. While plant roots are the initial source of carbon (C) that enters…

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…

Epigenetic engineering to increase expression of novel feedstocks and lignocellulolytic enzymes

Lead Institution

Oregon State University

Principal Investigator

Michael Freitag

Project type

Large-Scale EMSL Research

Responses to environmental stimuli, e.g. changes in nutritional status, require space- and time-dependent transcription of genes in the context of chromatin, the assembly of DNA and proteins that…

Development and refinement of an in situ 'molecular microscope' utilizing ultrahigh resolution mass spectrometry

Lead Institution

University of Missouri - Columbia

Principal Investigator

Gary Stacey

The ability to elucidate complex metabolic behavior of living organisms in situ and with cellular resolution is a bioanalytical grand challenge that is yet to be realized. Mass spectrometry imaging …

FSFA: MOSAIC—Metabolic and Spatial Interactions in Communities

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Errol Robinson

This EMSL user proposal is to support the MOSAIC DOE BER funded FSFA at PNNL. The primary activities involving EMSL are a set of BSSD demonstration tasks focusing on key science questions and related…

Advanced 21T FTICR MS instrumentation and methods for functional proteomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

William Kew

The 21T FTICR-MS at the EMSL provides extremely high mass accuracy and resolution enabling superior depth of characterization for natural organic matter and intact mass measurement of denatured…

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…

Untangling the complexity of phototroph-heterotroph interactions in the lab and in the field

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

H Wiley

Project type

Large-Scale EMSL Research

Despite the fact that ubiquitous microbial interspecies interactions form the foundation of energy flow as well as the biogeochemical cycling of carbon and other elements within natural environments,…

Integration of Substrate Oxidation with Protein Synthesis and Cellular Signaling in a Complex Biological System

Lead Institution

Seattle Children's Research Institute

Principal Investigator

Michael Portman

These investigations will explore the complex interactions involved in cellular metabolism, protein synthesis, and cell signaling. We will use complex models to link intra-cellular regulatory…

FSFA: MOSAIC -- Metabolic and Spatial Interactions in Communities FY18 proposal

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Errol Robinson

This EMSL user proposal is to support the MOSAIC DOE BER funded FSFA at PNNL. The primary activities involving EMSL are a set of BSSD demonstration tasks focusing on key science questions and related…

COVID-19: High-throughput SARS-CoV-2-Human protein-protein interactome and drug discovery on a nanowell array chip

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ying Zhu

The project aims to develop a high throughput and multiplex affinity purification mass spectrometry (AP-MS) assay by seamless integration of protein microarray and nanoscale proteomics. We will…

Collaborative research projects in the PNNL NIH NCRR P41 Biomedical Technology Research Center 'Proteomics research resource for integrative biology'

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

David Camp

Collaborative research projects in the PNNL NIH NCRR P41 Biomedical Technology Research Center 'Proteomics research resource for integrative biology'

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Jon Jacobs

Collaborative research projects in the PNNL NIH NCRR P41 Biomedical Technology Research Center 'Proteomics research resource for integrative biology'

New Mesoscale Multi-Modal Imaging Of Cellular Communication Between Microbe And Plant In The Rhizosphere -- A Pilot Project

Lead Institution

University of Missouri - Columbia

Principal Investigator

Richard Ferrieri

The interaction between plants and their environment is of key importance in promoting sustainable, healthy, and robust plant growth. Underlying the ability of plants to cope with a variety of…

Development and refinement of an in situ 'molecular microscope' utilizing ultrahigh resolution mass spectrometry

Lead Institution

University of Missouri - Columbia

Principal Investigator

Gary Stacey

The ability to elucidate complex metabolic behavior of living organisms in situ and with cellular resolution is a bioanalytical grand challenge that is yet to be realized. Mass spectrometry imaging …

Spatial Metabolomics and Glycomics for Human Kidneys

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christopher Anderton

Acute kidney injury (AKI) and chronic kidney disease (CKD) are major contributors to overall morbidity and mortality in patients in the US. However, we lack a clear understanding of the major…

Innovative Molecular Imaging Using Spatially Controlled Ionization Combined with High Performance FT-ICR Mass Spectrometry

Lead Institution

Maastricht University

Principal Investigator

Ronald Heeren

Project type

Scientific Partner

The objective of this proposed 3 year EMSL-FOM institute AMOLF partnership is to incorporate C60 SIMS and MALDI ionization techniques with a 9.4 Tesla FT-ICR mass spectrometer to enable and enhance…

Substrate Oxidation and Protein Synthesis Integration in a Complex Biological System

Lead Institution

Seattle Children's Research Institute

Principal Investigator

Michael Portman

These investigations will explore the complex interactions involved in cellular metabolism and protein synthesis in accordance with the EMSL Science Theme: Biological Interactions and Dynamics. We…

Development and refinement of an in situ 'molecular microscope' utilizing ultrahigh resolution mass spectrometry

Lead Institution

University of Missouri - Columbia

Principal Investigator

Gary Stacey

The ability to elucidate complex metabolic behavior of living organisms in situ and with cellular resolution is a bioanalytical grand challenge that is yet to be realized. Mass spectrometry imaging …

Advancing ecosystem understanding of carbon turnover and storage through molecular characterization

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

EMSL Staff Proposal: The coupling between concurrently changing carbon (C) and nitrogen (N) cycles remains a key uncertainty in understanding feedbacks between the terrestrial C cycle and climate…

Spatially resolved characterization of proteoforms for functional proteomics

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

Differentiated cells have distinctive patterns of epigenetic marks including various post-translational modifications (PTMs) on histones that may work in concert to control transcriptional programs…

Development of the Integrated MetaPROteomics Viewer (IMPROV) Software Toolkit

Lead Institution

University of British Columbia

Principal Investigator

Steven Hallam

Project type

Scientific Partner

Beyond the periphery of our senses exists an infinitely diverse microbial world. This microcosm extends into every imaginable habitat, thrives under powerful extremes, and helps create and sustain…

High resolution and Mass Accuracy Capability (HRMAC) Development Project

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

David Koppenaal

Access to other FTMS instrumentation is important o successfully and rapidly implement first science applications, to facilitate parallel testing of spectrometer subsystems, and to perform cross…

High Resolution and Mass Accuracy Capability (HRMAC) Development Project

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

David Koppenaal

Access to other FTMS instrumentation is important o successfully and rapidly implement first science applications, to facilitate parallel testing of spectrometer subsystems, and to perform cross…

In-Depth Proteome Mapping of the Tumor Microenvironment with Single-Cell Resolution

Lead Institution

Brigham Young University

Principal Investigator

Ryan Kelly

The development of effective therapies for cancer requires a deep molecular understanding of tumor heterogeneity by advanced omics technologies with spatially resolved measurements. Unfortunately,…

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),…

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…

Insights into peatland carbon cycling derived from integration of Omics with biogeochemical profiling

Lead Institution

Michigan Technological University

Principal Investigator

Evan Kane

Project type

Large-Scale EMSL Research

Peatlands are one of the most important ecosystems providing feedbacks to the climate system because they store a large component (>30%) of the world's soil C stocks. Peatlands also are found…

Rhizosphere processes at molecular to core scale

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Nancy Hess

The amount of C in soil far exceeds the C content of atmosphere as well as the amount C stored above ground as plant biomass. The C fluxes between atmosphere and biomass are huge, many orders of…

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…

Towards proteome-wide assessment of cellular landscapes

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

We will develop a novel workflow to characterize proteome-wide structural changes of cellular landscapes between different cell states (or cell types). The goal is to bridge the gap between cellular…

Development of High Throughput Proteomic Production Operations (PNNL Scope # 40601, Dick Smith's OBER Proteomics)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Nancy Colton

This project is developing the capability for high throughput and quantitative measurements of microbial proteomes along with the informatics capabilities necessary to support such applications. Some…

Identification and quantification of biomarkers of malaria infection.

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

This application is for the continuation of the currently closed proposal 8211 "Membrane proteins of placental parasites". We have a joint grant proposal between Richard D. Smith and Michal…

Soybean Proteomics

Lead Institution

University of Missouri - Columbia

Principal Investigator

Gary Stacey

Project type

Large-Scale EMSL Research

The USA is one of the world's largest producers of soybean (Glycine max), which is important as a source of animal feed, oil and, more recently, for biodiesel production. In recognition of this…

Probing complex microbiomes using mass spectrometry and sequencing capabilities to understand how microbiomes are influenced by their environment

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Stephen Callister

This proposal will utilize next generation sequencing and mass spectrometry (MS) capabilities to address key knowledge gaps in our functional understanding of how complex microbiomes influence and…

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…

Virtual Proteomics (ViP): Integrative modeling of protein assemblies in a cell with constraints from proteomic data and reconstructed images from cryo-electron tomography

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Margaret Cheung-Wyker

The objective of the proposed research is to advance the spatial knowledge of higher-order protein assemblies in a cell by integrating improved image reconstruction from cryo-electron tomography and…

Projects