Journal: Genome Biology and Evolution

Article Title: Massive Gene Loss in the Fungus Sporothrix epigloea Accompanied a Shift to Life in a Glucuronoxylomannan-based Gel Matrix

doi: 10.1093/gbe/evaf015

Figure Lengend Snippet: Carbon utilization assays of strains S. epigloea CBS 119000, S. epigloea CBS 573.63, and S. eucalyptigena CBS 140593 using Biolog Phenotype MicroArray™ plate PM1 with a total of 95 carbon sources.

Article Snippet: We used Biolog © Phenotype MicroArray TM plates to test the substrate utilization of the two S. epigloea strains and S. eucalyptigena CBS 140593 obtained through the Westerdijk Fungal Biodiversity Institute.

Techniques: Microarray

Journal: Genome Biology and Evolution

Article Title: Massive Gene Loss in the Fungus Sporothrix epigloea Accompanied a Shift to Life in a Glucuronoxylomannan-based Gel Matrix

doi: 10.1093/gbe/evaf015

Figure Lengend Snippet: Carbon utilization assays of strains S. epigloea CBS 119000, S. epigloea CBS 573.63, and S. eucalyptigena CBS 140593 using Biolog Phenotype MicroArray™ plate PM1 with a total of 95 carbon sources.

Article Snippet: Carbon and nitrogen utilization assays were conducted with Biolog's Phenotype MicroArray TM plates PM1 and PM2 with a total of 190 carbon sources ( online).

Techniques: Microarray

Journal: NPJ Systems Biology and Applications

Article Title: Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source

doi: 10.1038/s41540-024-00480-z

Figure Lengend Snippet: A Serial dilution plating for growth on solid agar medium supplemented with rich (LB) or p -CA minimal medium. Abbreviated genotypes are indicated to the left of each image. B The native PP_0897 promoter was replaced with two different low abundance promoters and the impact on viability in rich medium or M9 p- CA minimal medium was quantified. C P. putida strains assayed for indigoidine production in M9 60 mM p -CA medium at the indicated time points following induction with 1.5% arabinose (w/v). Control is WT P. putida harboring genome integrated indigoidine pathway cassette and ∆PP_0897 is the single gene deletion strain. Strain D1b_gf ∆PP_0897 did not grow nor produced in M9 p- CA medium. D P. putida strains with promoter-varied PP_0897 expression assayed for indigoidine production. Specific indigoidine yield (mg/CFU) was calculated by normalizing the indigoidine with the number of total viable cells at 24 h. E P. putida strains with promoter-varied PP_0897 expression with or without induction of the indigoidine pathway in M9 60 mM p- CA, sampled at 24 h and 48 h for glutamate and indigoidine (Supplementary Fig. ). F , G Strains D1b_gf with or without ∆PP_0897 were transformed with an empty vector plasmid or a plasmid containing a P BAD -PP_0897 construct. F Growth in M9 60 mM p- CA medium with basal BAD promoter induction without inducer ( F ) or with 1.5% (w/v) arabinose ( G ) in 24 well microtiter dishes. Strain genotypes are indicated above each panel. Measurements are average of at least three independent replicates. Error bars represent mean ± S.D. ( n = 4) in ( C – E ). The shaded area represents mean ± S.D. ( n = 3) in ( F , G ).

Article Snippet: A BIOLOG TM phenotype microarray assay (Cat. No. 12111, & Cat. No. 12112, Hayward CA) was conducted using strain D1b_gf ΔPP_0897.

Techniques: Serial Dilution, Control, Produced, Expressing, Transformation Assay, Plasmid Preparation, Construct

Journal: NPJ Systems Biology and Applications

Article Title: Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source

doi: 10.1038/s41540-024-00480-z

Figure Lengend Snippet: A Overall workflow of the simulations performed to model the permissible flux space limiting growth coupled production. Proteomics data, the D1b_gf reduced model, and the iMAT algorithm are used to develop context-specific models, which are then used for sensitivity analysis. A double robustness analysis is applied to determine the tradeoff between growth represented as biomass formation flux, fumarase flux, and glutamine exchange reaction flux, removing glutamine from the system represented as glutamine flux. Double robustness analysis 3D plots of the genome-scale metabolic model (GSMM) of P. putida WT (iJN1462) ( B ), context-specific D1b_gf reduced model ( C ) and context-specific D1b_gf P PP_0415 -PP_0897 model (iMAT_PP_0415p_PP_0897) ( D ). A red box indicates the region of interest replotted in the detailed view. The units for fumarase and glutamine flux are mmol/gDCW/h, and the unit for biomass is h −1 . Infinity (Inf) represents unconstrained flux for the reaction and may have a variable value based on the definition of bounds for a GSMM.

Article Snippet: A BIOLOG TM phenotype microarray assay (Cat. No. 12111, & Cat. No. 12112, Hayward CA) was conducted using strain D1b_gf ΔPP_0897.

Techniques:

Journal: NPJ Systems Biology and Applications

Article Title: Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source

doi: 10.1038/s41540-024-00480-z

Figure Lengend Snippet: A Initial auxotrophy analysis and complementation via ectopic plasmid expression of the Design 1 cutset strain, D1b_gf ∆PP_0897 transformed with P BAD - PP_0897 Refer to Fig. for complementation of the PP_0897 deletion mutant on M9 p -CA medium. B Heatmap showing selected BIOLOG TM metabolite sources that rescued growth under different media conditions including basal media supplemented with 50 mM p -CA and/or 100 mM l -malate.

Article Snippet: A BIOLOG TM phenotype microarray assay (Cat. No. 12111, & Cat. No. 12112, Hayward CA) was conducted using strain D1b_gf ΔPP_0897.

Techniques: Plasmid Preparation, Expressing, Transformation Assay, Mutagenesis

Journal: NPJ Systems Biology and Applications

Article Title: Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source

doi: 10.1038/s41540-024-00480-z

Figure Lengend Snippet: A Model validation using BIOLOG TM phenotyping. Blue dots indicate each of the 190 metabolites tested (refer to Supplementary Table for details), and the light blue shaded region shows the accurately predicted metabolites, including 16 true positives and 75 true negatives. Red dots indicate the subset of metabolites that successfully rescued growth when fed both p -CA and l -malate. B Double robustness analysis on mixed carbon source utilization for growth and production. C – E Strains D1b_gf and D1b_gf ∆PP_0897 were fed three carbon sources, 50 mM p -CA, 100 mM malate, and 100 mM alanine. Samples were analyzed at the indicated time points for growth and metabolic profiles. C Optical density (OD 600 ) was monitored every 4 h. D Glutamate concentrations for strains D1b_gf and D1b_gf ∆PP_0897, intracellular and extracellular values pooled together. E Consumption profiles of the three carbon sources (malate, alanine, and p -CA) from the culture medium were monitored at the indicated time points using LC–MS. Error bars represent mean ± S.D. ( n = 3) in ( C ). The shaded region represents mean ± S.D. ( n = 3) in ( D and E ).

Article Snippet: A BIOLOG TM phenotype microarray assay (Cat. No. 12111, & Cat. No. 12112, Hayward CA) was conducted using strain D1b_gf ΔPP_0897.

Techniques: Liquid Chromatography with Mass Spectroscopy

Journal: bioRxiv

Article Title: Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi

doi: 10.1101/2024.12.09.627583

Figure Lengend Snippet:

Article Snippet: Phenotype MicroArray TM (Biolog Inc.) screens for carbon (PM1 and PM2A plates) and nitrogen (PM3B plates) sources were used to identify additional differential phenotypic markers.

Techniques: Microarray

Journal: bioRxiv

Article Title: Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi

doi: 10.1101/2024.12.09.627583

Figure Lengend Snippet: Heat map of Phenotype MicroArray TM (PM) results for carbon and nitrogen source utilization by PAM 2766 T , R. equi DSM 20307 T and R. equi 103S (PAM 1126). Bacterial inocula were grown at 30°C in TSB until the stationary phase and then suspended in mReMM mineral medium and transferred to the PM plates. Incubabion was performed at 30°C with OD 590 monitored every 15 min for 48 hours in an OmniLog reader. Strains were tested in duplicate and results were analysed using OmniLog software. Maximum growth is represented in graded colours from lowest (black) to highest (yellow). Red arrows indicate differential utilization of a substrate between PAM 2766 T and R. equi. Black arrows in the PM1 and PM2A plates indicate a carbon source utilized by the three tested bacteria (see Table S2 for detailed results). Asterisks indicate false positive reactions in the PM2A plate previously reported in ref. .

Article Snippet: Phenotype MicroArray TM (Biolog Inc.) screens for carbon (PM1 and PM2A plates) and nitrogen (PM3B plates) sources were used to identify additional differential phenotypic markers.

Techniques: Microarray, Software, Bacteria