A5032336803- Microbial Community Ecology and Physiology
- Advanced Proteomics Techniques and Applications
- Marine and coastal ecosystems
- Mass Spectrometry Techniques and Applications
- Pharmaceutical and Antibiotic Environmental Impacts
- Advanced biosensing and bioanalysis techniques
- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Geology and Paleoclimatology Research
- Marine Biology and Ecology Research
- Photodynamic Therapy Research Studies
- Geological formations and processes
- Pluripotent Stem Cells Research
- Water Quality Monitoring Technologies
- bioluminescence and chemiluminescence research
- Biosensors and Analytical Detection
- Microbial Fuel Cells and Bioremediation
- Heme Oxygenase-1 and Carbon Monoxide
- 3D Printing in Biomedical Research
- Radical Photochemical Reactions
- Electron Spin Resonance Studies
- Sulfur Compounds in Biology
- Algal biology and biofuel production
- Advanced Chemical Sensor Technologies
- Spectroscopy and Quantum Chemical Studies
University of Washington
2017-2024
Fred Hutch Cancer Center
2021-2023
Center for Urban Waters
2020
University of Washington Tacoma
2020
ETH Zurich
2013-2016
University of St. Thomas - Minnesota
2007-2012
University of Minnesota
2007
In U.S. Pacific Northwest coho salmon (
Cysteine (Cys) plays numerous key roles in the biogeochemistry of natural waters. Despite its importance, a full assessment Cys abiotic transformation kinetics, products and pathways under environmental conditions has not been conducted. This study is mechanistic evaluation photochemical nonphotochemical (dark) transformations solutions containing chromophoric dissolved organic matter (CDOM). The results show that underwent both dark irradiated conditions. Under conditions, rates were...
Summary Extracellular vesicles are small (~50–200 nm diameter) membrane‐bound structures released by cells from all domains of life. While abundant in the oceans, their functions, both for themselves and emergent ecosystem, remain a mystery. To better characterize these particles – prerequisite determining function we analysed lipid, protein, metabolite content produced marine cyanobacterium Prochlorococcus . We show that exports diverse array cellular compounds into surrounding seawater...
Amino acids, peptides and proteins are central building blocks of life key importance in the biogeochemistry aquatic ecosystems. In sunlit surface waters, amino acid-based molecules at different levels structural organization susceptible to transformation by both direct photochemical reactions indirect processes caused photochemically produced reactive oxygen species (e.g. hydroxyl radical or singlet oxygen). Photochemical can thereby affect availability these crucial nutrient sources...
Photochemical transformations greatly affect the stability and fate of amino acids (AAs) in sunlit aquatic ecosystems. Whereas direct phototransformation dissolved AAs is well investigated, their indirect photolysis presence chromophoric organic matter (CDOM) poorly understood. In systems, CDOM may act both as sorbent for photosensitizer, creating microenvironments with high concentrations photochemically produced reactive intermediates, such singlet oxygen (1O2). This study provides a...
It has long been appreciated that the photooxidation kinetics of amino acid (AA) residues in an intact protein differ from those free AAs due to differences local steric microenvironment, such as its location three-dimensional structure. Yet there are only a few studies have quantified effect structure on photochemical reactivity residues. This is important for predicting phototransformation rates aquatic environments where combined forms (e.g., oligopeptides and proteins) more abundant than...
Sulfur-oxidizing bacteria from the SUP05 clade are abundant in anoxic and oxygenated marine waters that appear to lack reduced sources of sulfur for cell growth. This raises questions about how these chemosynthetic survive across oxygen gradients their mode survival impacts environment. Here, we use growth experiments, proteomics, cryo-electron tomography show a isolate, "Candidatus Thioglobus autotrophicus," is amorphous shape several times larger stores considerably more intracellular when...
Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery candidate and costly validation studies. Due dearth multiplexable assays, generally only few are tested, success rate is accordingly low. Previously, mass spectrometry-based approaches have been used fill this gap but feature poor quantitative performance were limited hundreds proteins. Here, we demonstrate capability an internal standard...
Summary A hallmark of the SUP05 clade marine Gammaproteobacteria is ability to use energy obtained from reduced inorganic sulfur fuel autotrophic fixation carbon using RuBisCo. However, some also have genetic potential for heterotrophic growth, raising questions about roles in cycle. We used genomic reconstructions, physiological growth experiments and proteomics characterize central metabolism Candidatus Thioglobus singularis strain PS1, a representative that has autotrophy heterotrophy....
Bacitracin is a mixture of nonribosomal peptides (NRPs) that extensively used as an antibiotic in both human and veterinary medicine. Despite its widespread use over the past six decades, very few studies have addressed environmental fate bacitracin zinc-bacitracin complexes. In this study, photochemical transformation components (i.e., cyclic dodecapeptides) aquatic environment was investigated. A high resolution mass spectrometry (HRMS)-based approach enabled monitoring degradation...
The environmental photochemical kinetics of tylosin, a common veterinary macrolide antibiotic and growth promoter, were investigated under simulated sunlight. An efficient, reversible photoisomerization was characterized using kinetic, mass spectrometry, proton nuclear magnetic resonance data. confirmed to occur by rotation about the distal alkene ketodiene functionality. Concurrent forward (quantum yield = 0.39 ± 0.09) back 0.32 0.08) reactions lead equilibrium near tylosin/photoisomer...
Immunotherapies are revolutionizing cancer care, producing durable responses and potentially cures in a subset of patients. However, response rates low for most tumors, grade 3/4 toxicities not uncommon, our current understanding tumor immunobiology is incomplete. While hundreds immunomodulatory proteins the microenvironment shape anti-tumor response, few them can be reliably quantified. To address this need, we developed multiplex panel targeted proteomic assays targeting 52 peptides...
Photooxidation is an important abiotic transformation pathway for amino acids (AAs) in sunlit waters. Although dissolved free AAs are well studied, the photooxidation of combined (DCAAs) remains poorly investigated. This study a systematic investigation effect neighboring photostable AA residues (i.e., aliphatic, cationic, anionic, or aromatic residues) on environmental indirect photochemical histidine (His) His-containing oligopeptides. The pKa values His studied oligopeptides were found to...
Introduction Immunotherapy is an effective treatment for a subset of cancer patients, and expanding the benefits immunotherapy to all patients will require predictive biomarkers response immune-related adverse events (irAEs). To support correlative studies in clinical trials, we are developing highly validated assays quantifying immunomodulatory proteins human biospecimens. Methods Here, developed panel novel monoclonal antibodies incorporated them into novel, multiplexed, immuno-multiple...
Mesoscale eddies significantly alter open ocean environments such as those found in the subtropical gyres that cover a large fraction of global ocean. Previous studies have explored eddy effects on biogeochemistry and microbial community composition but not molecular particulate organic matter. This study reports absolute concentration 67 metabolites relative abundances for 640 features, measured using liquid chromatography-mass spectrometry (LC-MS) following both targeted untargeted...
Abstract Mesoscale eddies significantly alter open ocean environments such as those found in the subtropical gyres that cover a large fraction of global ocean. Previous studies have explored eddy effects on biogeochemistry and microbial community composition but not molecular particulate organic matter. This study reports absolute concentration 67 metabolites relative abundances for 640 features to understand how mesoscale impact metabolome North Pacific Subtropical Gyre during two cruises...
Abstract Peptides are identified using a de novo‐discovery approach in suspended and sinking particles from the eastern tropical North Pacific oxygen‐deficient zone (ODZ) culture of dominant autotroph region, cyanobacterium Prochlorococcus . The benchmarking experiment with shows novo peptides to be taxonomically specific, thus value augmenting database‐driven approaches. Analysis reveals presence fungal proteins deep that were not our original search database, contributing growing...
Targeted mass spectrometry (MS)-based proteomic assays, such as multiplexed multiple reaction monitoring (MRM)-MS enable sensitive and specific quantification of proteotypic peptides stoichiometric surrogates for proteins. Efforts are underway to expand the use MRM-MS assays in clinical environments, which requires a reliable strategy monitor proteolytic digestion efficiency within individual samples. Towards this goal, extended stable isotope-labeled standard (SIS) (hE), incorporate native...