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Garcia, Whitney L.

Publications and source records attributed to Garcia, Whitney L..

Activity-Based Protein Profiling to Probe Relationships between Cytochrome P450 Enzymes and Early-Age Metabolism of Two Polycyclic Aromatic Hydrocarbons (PAHs): Phenanthrene and Retene

A growing body of literature has linked early life exposures to polycyclic aromatic hydrocarbons (PAH) with adverse neurodevelopmental effects. Once in the body, metabolism serves as a powerful mediator of PAH toxicity by bioactivating and detoxifying PAH metabolites. Since enzyme expression and activity varies considerably throughout human development, we evaluated infant metabolism of PAHs as a potential contributing factor to PAH susceptibility. Here, we measured and compared rates of phenanthrene and retene (two primary PAH constituents of woodsmoke) metabolism in human hepatic microsomes from individuals ≤21 months of age to a pooled sample (n = 200) consisting primarily of adults. We used activity-based protein profiling (ABPP) to characterize cytochrome P450 enzymes (CYPs) in the same hepatic microsome samples. Once incubated in microsomes, phenanthrene demonstrated rapid depletion. Best fit models for phenanthrene metabolism demonstrated either 1 or 2 phases, depending on the sample, indicating that multiple enzymes could metabolize phenanthrene. We observed no statistically significant differences in phenanthrene metabolism as a function of age, although samples from the youngest individuals had the slowest phenanthrene metabolism rates. We observed slower rates of retene metabolism compared to phenanthrene also in multiple phases. Rates of retene metabolism increased in an age-dependent manner until adult (pooled) levels were achieved at ~12 mo. ABPP identified 28 unique CYPs among all samples, and we observed lower amounts of active CYPs in individuals ≤21 months of age compared to the pooled sample. Phenanthrene metabolism correlated to CYPs 1A1, 1A2, 2C8, 4A22, 3A4, and 3A43 and activities and retene metabolism correlated to CYPs 1A1, 1A2, and 2C8 activities measured by ABPP and vendor-supplied substrate marker activities. These results will aid efforts to determine human health risk and susceptibility to PAHs exposures during early life.

59 BASIC BIOLOGICAL SCIENCES↗

Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes

Abstract Host‐associated and environmental microbiomes play central roles in human health, biogeochemical cycling, response to ecosystem change, and agriculture. Scientific approaches that can reveal the functional activities that contribute to observed phenotypes are needed in microbiome research. Broad characterization of the functional activity of microbes within microbiomes is currently hampered by approaches that rely on inference of function from metagenomes or indirect measurements. Activity‐based protein profiling is uniquely positioned to overcome these challenges and reveal the protein‐level mechanisms associated with microbiome phenotypes. In this review we describe the progress made to date using ABPP in gut microbiome, plant‐microbe interaction, and soil microbiome research, and suggest how ABPP data can be coupled with advanced computational methods to enable phenotype prediction and bioengineering of microbiomes for applied purposes.

59 BASIC BIOLOGICAL SCIENCES↗

Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism

Organic matter (OM) metabolism in freshwater ecosystems is a critical source of uncertainty in global biogeochemical cycles, yet the processes regulating aerobic respiration in aquatic environments remain poorly understood. Aerobic respiration is typically predicted through kinetic controls such as organic carbon and oxygen concentrations, while assuming thermodynamic regulation has no influence. The role of OM thermodynamics has been mainly explored under anaerobic conditions; however, recent observations have suggested that thermodynamic properties of OM may influence aerobic respiration rates. Here, we explicitly test OM thermodynamics as a key regulator of aerobic respiration. We pair controlled microcosm experiments with ultrahigh-resolution OM characterization to show that aerobic respiration increases with OM thermodynamic favorability under carbon limitation. We also demonstrate a shift in the regulation of aerobic respiration from OM thermodynamics to nitrogen content when carbon is in excess, highlighting a central role for OM thermodynamics particularly in carbon-limited ecosystems. This illuminates a structural gap in aquatic biogeochemical models by demonstrating that both kinetic and thermodynamic constraints can modulate aerobic respiration. Our work therefore proposes a new conceptual model in which thermodynamic and nutrient limitations dually control aerobic respiration.

54 ENVIRONMENTAL SCIENCES↗