Erika Zink
A5042766841- Methane Hydrates and Related Phenomena
- Seismic Waves and Analysis
- Earthquake Detection and Analysis
- Superconducting Materials and Applications
- Geophysics and Gravity Measurements
- Ionosphere and magnetosphere dynamics
- Seismology and Earthquake Studies
- Astrophysics and Cosmic Phenomena
- Solar and Space Plasma Dynamics
- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Neonatal Respiratory Health Research
- Gut microbiota and health
- Enzyme-mediated dye degradation
- Legume Nitrogen Fixing Symbiosis
- Diet and metabolism studies
- Glycosylation and Glycoproteins Research
- Advanced Chemical Sensor Technologies
- Microbial Metabolism and Applications
- Analytical Chemistry and Chromatography
- Plant-Microbe Interactions and Immunity
- Biofuel production and bioconversion
- Epigenetics and DNA Methylation
- MicroRNA in disease regulation
Pacific Northwest National Laboratory
2015-2024
Environmental Molecular Sciences Laboratory
2016-2020
Battelle
2010-2018
Richland College
2016-2017
Significance Drought remains a critical obstacle to meeting the food demands of coming century. Understanding interplay between drought stress, plant development, and microbiome is central this challenge. Here, we demonstrate that causes enrichment distinct set microbes in roots, composed almost entirely monoderms, which lack outer membranes have thick cell walls. We under drought, roots increase production many metabolites, monoderms inhabiting drought-treated rhizosphere exhibit increased...
Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification metabolomic data on 99 treatment-naive GBMs provides insights GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 PLCG1) as potential switches mediating oncogenic pathway activation, well targets for EGFR-, TP53-, RB1-altered tumors. Immune...
This report demonstrates the use of bioinformatic and chemometric tools on liquid chromatography-mass spectrometry (LC-MS) data for discovery trace forensic signatures sample matching ten stocks nerve-agent precursor known as methylphosphonic dichloride (dichlor). XCMS, a software tool primarily used in bioinformatics, was to comprehensively search find candidate LC-MS peaks set dichlor samples. These were down selected group 34 impurity peaks. Hierarchal cluster analysis factor demonstrated...
Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for catabolism remain unclear. Improved understanding biological process would aid our collective knowledge both carbon cycling microbial strategies valorize value-added compounds. Here, we examine modifications exoproteome three...
Fungal ligninolytic enzymes are able to depolymerize solid lignin and the presence of an aromatic catabolic bacterium enhances this effect.
Abstract Lung immaturity is a major cause of morbidity and mortality in premature infants. Understanding the molecular mechanisms driving normal lung development could provide insights on how to ameliorate disrupted development. While transcriptomic proteomic analyses have been previously reported, characterization changes lipidome lacking. Lipids play significant roles lung, such as dipalmitoylphosphatidylcholine pulmonary surfactant; however, many specific lipid species development, well...
ATP synthase, H+ transporting, mitochondrial F1 complex, δ subunit (ATP5F1D; formerly ATP5D) is a of synthase and plays an important role in coupling proton translocation production. Here, we describe two individuals, each with homozygous missense variants ATP5F1D, who presented episodic lethargy, metabolic acidosis, 3-methylglutaconic aciduria, hyperammonemia. Subject 1, for c.245C>T (p.Pro82Leu), recurrent decompensation starting the neonatal period, subject 2, c.317T>G (p.Val106Gly),...
Laser capture microdissection (LCM)-enabled region-specific tissue analyses are critical to better understand complex multicellular processes. However, current proteomics workflows entail several manual sample preparation steps and challenged by the microscopic mass-limited samples generated LCM, impacting measurement robustness, quantification throughput. Here, we coupled LCM with a workflow that provides fully automated analysis of proteomes from microdissected tissues. Benchmarking...
Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic environmental causes disease. However, surveillance chemical exposure disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, application expansive space. Here, we present a novel for small molecule analyses addresses these requirements by combining solid-phase extraction with ion...
An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of carbon utilization in R. reconstructed the genome-scale metabolic network . High-quality models model organisms orthologous protein mapping were used build draft reconstruction. The reconstruction was manually curated using functional annotation data including transcriptomics, proteomics, metabolomics, RB-TDNA...
Introduction Phosphorus (P) deficiency in plants creates a variety of metabolic perturbations that decrease photosynthesis and growth. is especially challenging for the production bioenergy feedstock plantation species, such as poplars ( Populus spp.), where fertilization may not be practically or economically feasible. While phenotypic effects P are well known, molecular mechanisms underlying whole-plant tissue-specific responses to deficiency, particular commercially valuable hardwoods,...
Silymarin, a characterized extract of the seeds milk thistle (Silybum marianum), suppresses cellular inflammation. To define how this occurs, transcriptional profiling, metabolomics, and signaling studies were performed in human liver T cell lines. Cellular stress metabolic pathways modulated within 4 h silymarin treatment: activation Activating Transcription Factor (ATF-4) adenosine monophosphate protein kinase (AMPK) inhibition mammalian target rapamycin (mTOR) signaling, latter being...
Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, lignin-degrading accessory that synergistically drive litter decomposition in the environment. While secretome studies model organisms such as Phanerochaete chrysosporium Aspergillus species have greatly expanded our knowledge these few extended characterization to environmental isolates or conducted side-by-side comparisons diverse species. Thus, mechanisms carbon...
The continued emergence and spread of infectious agents is great concern, systems biology approaches to disease research can advance our understanding host–pathogen relationships facilitate the development new therapies vaccines.
Adaptation to respiration at birth depends upon the synthesis of pulmonary surfactant, a lipid-protein complex that reduces surface tension air-liquid interface in alveoli and prevents lung collapse during ventilatory cycle. Herein, we demonstrated gene encoding subunit endoplasmic reticulum membrane complex, EMC3, also known as TMEM111 (Emc3/Tmem111), was required for murine surfactant function birth. Conditional deletion Emc3 embryonic epithelial cells disrupted packaging lipids proteins,...
Adaptation to air breathing after birth is dependent upon the synthesis and secretion of pulmonary surfactant by alveolar type 2 (AT2) cells. Surfactant, a complex mixture phospholipids proteins, secreted into alveolus, where it reduces collapsing forces at air-liquid interface maintain lung volumes during ventilatory cycle. ABCA3, an ATP-dependent Walker domain containing transport protein, required for function birth. Mutations in ABCA3 cause severe deficiency respiratory failure newborn...
Abstract Cell type-resolved proteome analyses of the brain, heart and liver have been reported, however a similar effort on lipidome is currently lacking. Here we applied liquid chromatography-tandem mass spectrometry to characterize major lung cell types isolated from human donors, representing first map any organ. We coupled this with proteomics same samples (available at Lungmap.net). Complementary substantiated functional identity cells. Lipidomics showed significant variations in across...
The gut microbiome plays an important role in the mammalian host and when proper balance helps protect health prevent disease. Host environmental stress its influence on microbiome, health, disease is emerging area of research. Exposures to unnatural light cycles are becoming increasingly common due travel shift work. However, much remains unknown about how these changes health. This information needed understand predict relationship between response altered sleep cycles. In present study,...
Manganese (Mn) oxides are among the strongest oxidants and sorbents in environment, Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic microbially-mediated processes. While white-rot Basidiomycete fungi oxidize using laccases manganese peroxidases association with lignocellulose degradation, mechanisms by which filamentous Ascomycete a physiological role for these organisms remain poorly understood. Here we use combination of chemical in-gel assays bulk mass spectrometry...