Dataset Information

Modeling of Contaminant Biodegradation and Compound-Specific Isotope Fractionation in Chemostats at Low Dilution Rates.

ABSTRACT: We present a framework to model microbial transformations in chemostats and retentostats under transient or quasi-steady state conditions. The model accounts for transformation-induced isotope fractionation and mass-transfer across the cell membrane. It also verifies that the isotope fractionation ? can be evaluated as the difference of substrate-specific isotope ratios between inflow and outflow. We explicitly considered that the dropwise feeding of substrate into the reactor at very low dilution rates leads to transient behavior of concentrations and transformation rates and use this information to validate conditions under which a quasi-steady state treatment is justified. We demonstrate the practicality of the code by modeling a chemostat experiment of atrazine degradation at low dilution/growth rates by the strain Arthrobacter aurescens TC1. Our results shed light on the interplay of processes that control biodegradation and isotope fractionation of contaminants at low (?g/L) concentration levels. With the help of the model, an estimate of the mass-transfer coefficient of atrazine through the cell membrane was achieved (0.0025 s^-1).

SUBMITTER: Gharasoo M

PROVIDER: S-EPMC6986770 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Publications

Modeling of Contaminant Biodegradation and Compound-Specific Isotope Fractionation in Chemostats at Low Dilution Rates.

Gharasoo Mehdi M Ehrl Benno N BN Cirpka Olaf A OA Elsner Martin M

Environmental science & technology 20190107 3

We present a framework to model microbial transformations in chemostats and retentostats under transient or quasi-steady state conditions. The model accounts for transformation-induced isotope fractionation and mass-transfer across the cell membrane. It also verifies that the isotope fractionation ϵ can be evaluated as the difference of substrate-specific isotope ratios between inflow and outflow. We explicitly considered that the dropwise feeding of substrate into the reactor at very low diluti ...[more]

PMID: 30339002

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Project description:No consensus has been reached on the proper time to add stable-isotope labeled (SIL) peptides in protein cleavage isotope dilution mass spectrometry workflows. While quantifying 24 monolignol pathway enzymes in the xylem tissue of Populus trichocarpa, we compared the protein concentrations obtained when adding the SIL standard peptides concurrently with the enzyme or after quenching of the digestion (i.e. postdigestion) and observed discrepancies for nearly all tryptic peptides investigated. In some cases, greater than 30-fold differences were observed. To explain these differences and potentially correct for them, we developed a mathematical model based on pseudo-first-order kinetics to account for the dynamic production and decay (e.g. degradation and precipitation) of the native peptide targets in conjunction with the decay of the SIL peptide standards. A time course study of the digests confirmed the results predicted by the proposed model and revealed that the discrepancy between concurrent and postdigestion introduction of the SIL standards was related to differential decay experienced by the SIL peptide and the native peptide in each method. Given these results, we propose concurrent introduction of the SIL peptide is most appropriate, though not free from bias. Mathematical modeling of this method reveals that overestimation of protein quantities would still result when rapid peptide decay occurs and that this bias would be further exaggerated by slow proteolysis. We derive a simple equation to estimate the bias for each peptide based on the relative rates of production and decay. According to this equation, nearly half of the peptides evaluated here were estimated to have quantitative errors greater than 10% and in a few cases over 100%. We conclude that the instability of peptides can often significantly bias the protein quantities measured in protein cleavage isotope dilution mass spectrometry-based assays and suggest peptide stability be made a priority when selecting peptides to use for quantification.

Dataset Information

Modeling of Contaminant Biodegradation and Compound-Specific Isotope Fractionation in Chemostats at Low Dilution Rates.

Publications

Modeling of Contaminant Biodegradation and Compound-Specific Isotope Fractionation in Chemostats at Low Dilution Rates.

Similar Datasets

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