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 …

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…

Technology development in support of NCRR

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Nancy Colton

The Pacific Northwest National Laboratory (PNNL) has built a facility that already stands at the forefront of proteomic research. Moreover, the Center is uniquely poised for future developments. We…

Cross-talk between DNA methylation and histone post-translational modifications in Arabidopsis

Lead Institution

Indiana University - Bloomington

Principal Investigator

Craig Pikaard

Project type

Large-Scale EMSL Research

In eukaryotes, chromosomal DNA must be highly compacted by proteins in order to fit within the confines of the nucleus, yet must also allow the DNA to be accessible for transcription, replication and…

Structural and functional analyses of multi-protein complexes regulating genotype to phenotype translations in plants

Lead Institution

Indiana University - Bloomington

Principal Investigator

Craig Pikaard

Project type

Large-Scale EMSL Research

DNA-dependent RNA polymerases decode genetic information stored in DNA by converting the information into RNA. This enzymatic activity, known as transcription, is a critical step in the process by…

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…

Spatial Metabolomics 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…

Mechanistic studies of AAP and capsid assembly of AAV vectors

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

Adeno-associated viruses (AAV) have become increasingly popular as vectors for human gene therapy. However, the requirement for high vector doses needed to achieve therapeutic efficacy poses a…

Collaborative Research Projects Supported by the NCRR P41 Resource Center

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

David Camp

Project type

Large-Scale EMSL Research

The Proteomics Resource Center for Integrative Biology at PNNL was established in 2003 and builds on the unique instrumentation and the infrastructure provided by PNNLs EMSL facility. The mission of…

Mass Spectrometry Imaging of Microbial Communities

Lead Institution

University of California, San Diego

Principal Investigator

Pieter Dorrestein

Project type

Large-Scale EMSL Research

Despite our significant technological advancements, the solutions to many of humanities lingering problems such as bioremediation of toxic heavy metal environmental contaminants, creation of…

Quantifying the functional and structural states of dynamic microbial communities

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Fredrickson

Project type

Large-Scale EMSL Research

The overall goal of this proposal is to provide a quantitative framework in which to compare species-resolved patterns of gene expression, allowing comparison of the effects of perturbations of…

Pan-Omics Technology Development, Implementation, and Application to GSP Systems Biology Research

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Joshua Adkins

The BER Genome Science Program aims to understand complex biological and environmental systems across spatial and temporal scales to develop predictive knowledge relevant to DOE mission challenges…

Metabolic regulation of O-GlcNAc and cardiac function during hypertrophy

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

Despite treatment advances, half of patients suffering from heart failure die within five years of diagnosis, while those who survive may live with severe disabilities. Cardiac hypertrophy poses a…

High-throughput native mass spectrometry as experimental validation for in silico drug design

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Mowei Zhou

Enzyme functions can often be modulated via interaction with small molecules. For example, inhibitors are actively sought in the pharmaceutical industry to block protein targets and treat diseases…

Subunit structures of Arabidopsis RNA Polymerase IV complexes

Lead Institution

Indiana University - Bloomington

Principal Investigator

Craig Pikaard

Project type

Large-Scale EMSL Research

All eukaryotes have three conventional nuclear DNA-dependent RNA polymerases, abbreviated as Pol I, Pol II and Pol III. Pol I transcribe 45S pre-rRNA, pol II transcribes mRNAs and pol III…

Integrating intact protein proteomics with ChIP-Seq for identification and functional characterization of epigenetic histone modifications

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

David Stenoien

Project type

Large-Scale EMSL Research

Biological systems are exceedingly more complex than defined by the genome due to differential protein expression and degradation, altered mRNA splicing, and the presence of multiple post…

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…

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

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…

Microbes persist: Systems biology of the soil microbiome

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ljiljana Pasa-Tolic

Microorganisms play key roles in soil carbon turnover and stabilization of persistent organic matter via their metabolic activities, cellular biochemistry, and extracellular products. Microbial…

Protein modifications associated with hibernation.

Lead Institution

University of Colorado

Principal Investigator

Lois Epperson

Project type

Limited Scope

Liver samples from the hibernator, golden-mantled ground squirrel, when separated by 2D gel electrophoresis, demonstrate a quantifiable and as yet undefined physical modification that manifests…

Systematic Characterization of Protein Glycosylation of Bacteria Cell Surface Proteins

Lead Institution

University of Oklahoma

Principal Investigator

Si Wu

The overall goal of this proposal is to develop an integrated top-down and bottom-up approach for bacterial glycoprotein profiling assisted by accurate glycan structure identification, which will be…

A combined top-down and bottom-up glycoproteome analysis of O-glycoform diversity of the secretome of the lignocellulose degrading fungus Neurospora crassa

Lead Institution

University of California, Berkeley

Principal Investigator

Christopher Somerville

Project type

Special Science

Enzymatic hydrolysis of (ligno)cellulose by cellulases is key for the production of second generation biofuels which represent a long-standing leading theme in the field of sustainable energy…

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 …

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

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Christopher Anderton

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 …

Identification and Validation of Protein Profiles Associated with Therapy-Resistance in Breast Cancer

Lead Institution

Erasmus University Medical Center, Rotterdam

Principal Investigator

Arzu Umar

Project type

Large-Scale EMSL Research

Successful treatment of breast cancer is hampered by the occurrence of drug resistance in approximately 50% of patients with advanced recurrent disease. The ultimate goal of proposed work is to…

Identification and relative expression of membrane proteins in breast cancer cell lines

Lead Institution

University of California, San Francisco

Principal Investigator

Anil Patwardhan

Project type

Exploratory Research

Overview Phase 1: Protein identification in the ?sub-proteome? mixtures from these cell lines will be accomplished using a combination of separation techniques, LC-ESI-MS/MS, and database search and…