pm2 phenotype microarray plates  (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

Journal: mSystems

Article Title: Insights into the metabolic specificities of pathogenic strains from the Ralstonia solanacearum species complex

doi: 10.1128/msystems.00083-23

Figure Lengend Snippet: Number of carbon (resp. nitrogen) sources which can support growth for each wild-type strain ( A ) and phcA mutant strain ( B ). *, phcA mutant strain. Carbon sources were divided as sustaining a fast growth or a slow growth. Strains were grouped by phylotypes. The trophic preferences were assessed using Biolog phenotype microplates PM1, PM2-A, and PM3-B and an in-house script, which detect automatically if there is growth or fast growth (see Materials and Methods for details).

Article Snippet: Phenotyping was performed using Biolog Phenotype Microarray plates PM1, PM2-A, and PM3-B following the manufacturer’s protocol.

Techniques: Mutagenesis

Journal: Scientific Reports

Article Title: Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams

doi: 10.1038/s41598-019-52846-7

Figure Lengend Snippet: Heatmap showing the number of carbon substrates supporting growth in the various compound categories as measured by reduction of a tetrazolium dye on Biolog phenotype microarray plates 1 and 2. Isolates Tessaracoccus SUR-6 and Pseudomonas SYD-2 are not included as they appeared unable to grow under the conditions supplied by the Biolog assay.

Article Snippet: Biolog phenotype microarray plates PM1 and PM2 were used to characterise the catabolic capabilities of the coal seam bacterial isolates under aerobic metabolisms.

Techniques: Microarray