A5048045559- Metabolomics and Mass Spectrometry Studies
- Microbial Community Ecology and Physiology
- Marine and coastal ecosystems
- Isotope Analysis in Ecology
- Coral and Marine Ecosystems Studies
- Geology and Paleoclimatology Research
- Marine and coastal plant biology
- Cephalopods and Marine Biology
- Data Analysis with R
- Statistical Methods and Inference
- Analytical Chemistry and Chromatography
- Statistical Methods in Clinical Trials
- Computational Drug Discovery Methods
- Methane Hydrates and Related Phenomena
- Scientific Computing and Data Management
- Cell Image Analysis Techniques
- Geological formations and processes
- Advanced Proteomics Techniques and Applications
- Alcohol Consumption and Health Effects
- Natural Products and Biological Research
- Marine Biology and Ecology Research
- Protist diversity and phylogeny
- Statistical Methods and Bayesian Inference
- Data Mining Algorithms and Applications
- Oceanographic and Atmospheric Processes
University of Washington
2020-2024
University of California, Berkeley
2017-2020
Planetary Science Institute
2017
Glycine betaine (GBT) is a compatible solute in high concentrations marine microorganisms. As component of labile organic matter, GBT has complex biochemical potential as substrate for microbial use that unconstrained the environment. Here we determine uptake kinetics and metabolic fate two natural communities North Pacific characterized by different nitrate concentrations. Dissolved had maximum rates 0.36 0.56 nM h-1 with half-saturation constants 79 11 low stations respectively. During...
Metabolites, the small, polar, organic molecules that are products of metabolism, represent ultimate expression marine microbial genomes. Metabolites include primary metabolites, such as amino acids and nucleobases, participate in central metabolic processes, secondary often more structurally complex play roles toxins, hormones, infochemicals regulating interactions communities. Marine metabolites have potential for a range applications healthcare (antibacterial, antiviral, etc.) industry...
Abstract Microbial eukaryotes, critical links in aquatic food webs, are unicellular, but some, such as choanoflagellates, form multicellular colonies. Are there consequences to predator avoidance of being unicellular vs. forming larger colonies? Choanoflagellates share a common ancestor with animals and used model organisms study the evolution multicellularity. Escape size from protozoan predators is suggested selective factor favoring Heterotrophic protozoans categorized suspension feeders,...
Mass spectrometry (MS) is a powerful tool for measuring biomolecules, but the data produced often difficult to handle computationally because it stored as ragged array. In R, this format typically encoded in complex S4 objects built around environments, requiring an extensive background R perform even simple tasks. However, adoption of tidy [@wickham2014] provides alternate structure that highly intuitive and works neatly with base functions common packages, well other programming languages....
Chromatographic peakpicking continues to represent a significant bottleneck in automated LC-MS workflows. Uncontrolled false discovery rates and the lack of manually-calibrated quality metrics require researchers visually evaluate individual peaks, requiring large amounts time breaking replicability. This problem is exacerbated noisy environmental datasets for novel separation methods such as hydrophilic interaction columns metabolomics, creating demand simple, intuitive, robust metric peak...
<title>Abstract</title> The efficacy of the marine biological carbon pump is tied to new production phytoplankton which require nitrogen and phosphorus grow. Globally, nitrate phosphate are delivered from deep surface waters incorporated into biomass at molar ratios near 16:1, N:P “Redfield ratio.” Latitudinally, particulate vary, often attributed two mechanisms: variations in microbial community composition physiological acclimation. How these mechanisms influence plankton growth...
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...
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...
Allelopathic macroalgae have been shown to significant negative effects on corals via the transfer of toxic compounds. The interaction that takes place between allelopathic and other algae, however, has not studied in detail. Here, Chlorodesmis fastigiata were analyzed. These first tested complete coral macroalgal individuals over several days, then small samples species when exposed isolated toxins. However, neither experiment found either Sargassum mangarevense or Boodlea kaeneana due...
Allelopathic macroalgae have been shown to significant negative effects on corals via the transfer of toxic compounds. The interaction that takes place between allelopathic and other algae, however, has not studied in detail. Here, Chlorodesmis fastigiata were analyzed. These first tested complete coral macroalgal individuals over several days, then small samples species when exposed isolated toxins. However, neither experiment found either Sargassum mangarevense or Boodlea kaeneana due...
Abstract Background Chromatographic peakpicking continues to represent a significant bottleneck in automated LC-MS workflows. Uncontrolled false discovery rates and the lack of manually-calibrated quality metrics require researchers visually evaluate individual peaks, requiring large amounts time breaking replicability. This problem is exacerbated noisy environmental datasets for novel separation methods such as hydrophilic interaction columns metabolomics, creating demand simple, intuitive,...