biolog phenotype microarray plates pm2  (Biolog Inc)

Journal: Nature Communications

Article Title: Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome

doi: 10.1038/s41467-023-39982-5

Figure Lengend Snippet: a Workflow for A. fumigatus strain-specific GEM reconstructions. Colors indicate strains and associated metabolic models. b – g Characteristics of pan-GEM reconstruction for A. fumigatus . b Counts of pan-GEM components for included genes, reactions, and metabolites. c Contribution of macromolecules in one unit of biomass (Supplementary Data ). d Distribution of pan-GEM reactions across major pathway categories (Supplementary Data ). e Distribution of pan-GEM reactions across nine compartments (Supplementary Data ). f Growth prediction accuracy of pan-GEM for A. fumigatus wild-type (Af293) and four mutant strains using phenotypic microarray data ( n = 5 in total, bars show mean and standard error of mean, Supplementary Data ). C: carbon, N: nitrogen, P: phosphorus, S: sulfur. g Confusion matrix of pan-GEM accuracy in predicting the essentiality of 20 genes according to the literature (see Results and Methods). h Experimental values compared to simulated growth rate values under normoxic and hypoxic conditions (Supplementary Data has experimental and simulated secretion values). Source data for Fig. 1b–h are provided in the Source Data file.

Article Snippet: Phenotypic microarrays were performed using Biolog Phenotypic Microarray plates PM1, PM2, PM3, and PM4 (Biolog Inc., Hayward, CA, USA) prepared following the manufacturer’s protocol for filamentous fungi, including resuspending conidia in filamentous fungi (FF) media and the addition of 0.16 ml of Biolog Redox Dye D to the master mix of each plate to quantify fungal metabolic activity.

Techniques: Mutagenesis, Microarray