Journal: Microbiology Spectrum

Article Title: Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities

doi: 10.1128/spectrum.04006-23

Figure Lengend Snippet: Complete experimentally-derived nutrient utilization phenome of R. mucilaginosa DSM20746. ( A ) Utilization of individual nutrients by the bacterium across four Biolog phenotypic microarrays. Bacterial growth was measured by OD at 590 nm. ( B ) Numerical summary nutrient sources experimentally tested in each Biolog phenotype microarray (PM), classified into those resulting in bacterial growth and those that R. mucilaginosa could not utilize. ( C ) Categorization of all tested phosphorous sources during the high-throughput Biolog assay. Utilization of totally 31 phosphorus sources resulted in positive phenotype (green chart), while the cell exhibited an inability to utilize the remaining 28 (orange chart).

Article Snippet: We independently confirmed the Biolog nutrient utilization data by testing the ability of DSM20746 to grow on minimal media in the presence of 10 compounds (see Materials and Methods, ).

Techniques: Derivative Assay, Microarray, High Throughput Screening Assay

Journal: Microbiology Spectrum

Article Title: Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities

doi: 10.1128/spectrum.04006-23

Figure Lengend Snippet: Predictive accuracy performance of i RM23NL using nutrient utilization data. Only substrates that exhibited complete mapping to both BiGG and model identifiers could be analyzed. Green represents correct predictions, and orange represents inconsistent predictions. The overall prediction accuracy of i RM23NL was computed using .

Article Snippet: We independently confirmed the Biolog nutrient utilization data by testing the ability of DSM20746 to grow on minimal media in the presence of 10 compounds (see Materials and Methods, ).

Techniques:

Journal: Computational and Structural Biotechnology Journal

Article Title: Dissecting carbon metabolism of Yarrowia lipolytica type strain W29 using genome-scale metabolic modelling

doi: 10.1016/j.csbj.2022.05.018

Figure Lengend Snippet: Comparison of Biolog assay (left columns) and model predictions before (middle columns) and after curation (right columns). Red indicates either growth predicted by model i Yli21 or nutrient utilization examined by Biolog assays) while white indicates neither growth nor nutrient utilization. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: For Biolog nutrient utilization assay, synthetic minimal media (7.5 g·L −1 ammonium sulfate, 14.4 g·L −1 potassium dihydrogen phosphate, 0.5 g·L −1 magnesium sulfate heptahydrate, 20 g·L −1 glucose, trace metal and vitamin solution, pH 6.0) was used , .

Techniques: Comparison

Journal: BMC Systems Biology

Article Title: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

doi: 10.1186/1752-0509-8-79

Figure Lengend Snippet: Conflicts between EcoCyc–18.0–GEM growth predictions and experimental carbon source utilization data for aerobic growth on Biolog PM plates at 37°C

Article Snippet: Aerobic Biolog PM nutrient utilization assay results were compiled from four different datasets captured in EcoCyc: (1) from our own experiments; (2) from a dataset obtained from B. Bochner; and from the recent publications of (3) AbuOun et al. [ ] and (4) Yoon et al. [ ].

Techniques: Expressing

Journal: BMC Systems Biology

Article Title: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

doi: 10.1186/1752-0509-8-79

Figure Lengend Snippet: Conflicts between EcoCyc–18.0–GEM growth predictions and experimental nitrogen source utilization data for aerobic growth on Biolog PM plates at 37°C

Article Snippet: Aerobic Biolog PM nutrient utilization assay results were compiled from four different datasets captured in EcoCyc: (1) from our own experiments; (2) from a dataset obtained from B. Bochner; and from the recent publications of (3) AbuOun et al. [ ] and (4) Yoon et al. [ ].

Techniques:

Journal: BMC Systems Biology

Article Title: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

doi: 10.1186/1752-0509-8-79

Figure Lengend Snippet: Conflicts between EcoCyc–18.0–GEM growth predictions and experimental sulfur source utilization data for aerobic growth on Biolog PM plates at 37°C

Article Snippet: Aerobic Biolog PM nutrient utilization assay results were compiled from four different datasets captured in EcoCyc: (1) from our own experiments; (2) from a dataset obtained from B. Bochner; and from the recent publications of (3) AbuOun et al. [ ] and (4) Yoon et al. [ ].

Techniques: De-Phosphorylation Assay

Journal: BMC Systems Biology

Article Title: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

doi: 10.1186/1752-0509-8-79

Figure Lengend Snippet: Conflicts between EcoCyc–18.0–GEM growth predictions and experimental sulfur source utilization data for aerobic growth on Biolog PM plates at 37°C

Article Snippet: Aerobic Biolog PM nutrient utilization assay results were compiled from four different datasets captured in EcoCyc: (1) from our own experiments; (2) from a dataset obtained from B. Bochner; and from the recent publications of (3) AbuOun et al. [ ] and (4) Yoon et al. [ ].

Techniques: Activity Assay

Journal: BMC Systems Biology

Article Title: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

doi: 10.1186/1752-0509-8-79

Figure Lengend Snippet: Conflicts between EcoCyc–18.0–GEM growth predictions and experimental carbon source utilization data for aerobic growth on Biolog PM plates at 37°C

Article Snippet: Anaerobic Biolog PM nutrient utilization assay results were obtained from B. Bochner.

Techniques: Expressing

Journal: BMC Systems Biology

Article Title: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

doi: 10.1186/1752-0509-8-79

Figure Lengend Snippet: Conflicts between EcoCyc–18.0–GEM growth predictions and experimental nitrogen source utilization data for aerobic growth on Biolog PM plates at 37°C

Article Snippet: Anaerobic Biolog PM nutrient utilization assay results were obtained from B. Bochner.

Techniques: