Journal: bioRxiv

Article Title: Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments

doi: 10.1101/2023.02.28.530341

Figure Lengend Snippet: (A) Lineage tracking data of haploid Bulk Fitness Assay, hBFA, for lineages evolved in fluconazole, clotrimazole, and glycerol/ethanol. Each column represents a replicate. The columns are grouped together by the evolution environment: fluconazole, clotrimazole, glycerol/ethanol. Each row represents the “Test Environment”. Each line represents one lineage evolved in the home environments that corresponds with its column group. The color of the line indicates the test environment in which that lineage was remeasured. (B) Lineage tracking data of diploid Bulk Fitness Assay, dBFA, for lineages evolved in fluconazole, clotrimazole, and glycerol/ethanol. (C) Lineage tracking data of combined Bulk Fitness Assay, cBFA, for lineages evolved in fluconazole, clotrimazole, and glycerol/ethanol.

Article Snippet: Conditions with 0.2M NaCl (Fisher Scientific - BP358-212), 0.8M NaCl, 21°C, 2% Glycerol (Fisher - G33-4) + 2 % Ethanol (Goldshield - 412804), Fluconazole 13 µM (4 mg/L, Acros Organics #455480050), Clotrimazole 6 µM (or 2 mg/L, Chem-Impex International #01311) were performed with 48 hour transfers at Stanford.

Techniques:

Journal: bioRxiv

Article Title: Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments

doi: 10.1101/2023.02.28.530341

Figure Lengend Snippet: These heatmaps show the fitnesses of all lineages including lineages that had the same mutation and were collapsed into a single row using the median fitnesses in . The number at the end of the name represents numerical barcode identification number. (A) Mutations identified in clotrimazole 1N measured in hBFA, (B) Mutations identified in clotrimazole 2N measured in dBFA, (C) Mutations identified in fluconazole 2N measured in cBFA, (D) Mutations identified in fluconazole 2N measured in dBFA, (E) Mutations identified in glycerol/ethanol 1N measured in hBFA, (F) Mutations identified in glycerol/ethanol 2N measured in cBFA.

Article Snippet: Conditions with 0.2M NaCl (Fisher Scientific - BP358-212), 0.8M NaCl, 21°C, 2% Glycerol (Fisher - G33-4) + 2 % Ethanol (Goldshield - 412804), Fluconazole 13 µM (4 mg/L, Acros Organics #455480050), Clotrimazole 6 µM (or 2 mg/L, Chem-Impex International #01311) were performed with 48 hour transfers at Stanford.

Techniques: Mutagenesis

Journal: bioRxiv

Article Title: Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments

doi: 10.1101/2023.02.28.530341

Figure Lengend Snippet: The columns are the home environments that lineages evolved in and the rows are the test environments in which their fitnesses were remeasured. X axis is the fitness of the lineages remeasured in the BFA in their home environment. Y axis is the fitness of the lineages in a non-home environment. No fitness remeasurements are available from BFAs grown in clotrimazole.

Article Snippet: Conditions with 0.2M NaCl (Fisher Scientific - BP358-212), 0.8M NaCl, 21°C, 2% Glycerol (Fisher - G33-4) + 2 % Ethanol (Goldshield - 412804), Fluconazole 13 µM (4 mg/L, Acros Organics #455480050), Clotrimazole 6 µM (or 2 mg/L, Chem-Impex International #01311) were performed with 48 hour transfers at Stanford.

Techniques:

Journal: bioRxiv

Article Title: Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments

doi: 10.1101/2023.02.28.530341

Figure Lengend Snippet: Distribution of Fitness Effects for Fitness Estimates of All Adaptive Diploid Lineages remeasured in Clotrimazole, Fluconazole, and Glycerol/Ethanol: The distribution of fitness effects for all adaptive diploid lineages remeasured in clotrimazole, fluconazole, and glycerol/ethanol. The gray vertical line delineates the fitness threshold of the top 10% of mutants that were evolved in the labeled environment. The red line delineated the top fitness of all mutants that were evolved in the labeled environment. The y axis delineates the percentage of mutants that have a specific fitness (x axis).

Article Snippet: Conditions with 0.2M NaCl (Fisher Scientific - BP358-212), 0.8M NaCl, 21°C, 2% Glycerol (Fisher - G33-4) + 2 % Ethanol (Goldshield - 412804), Fluconazole 13 µM (4 mg/L, Acros Organics #455480050), Clotrimazole 6 µM (or 2 mg/L, Chem-Impex International #01311) were performed with 48 hour transfers at Stanford.

Techniques: Labeling

Journal: bioRxiv

Article Title: Far From Home: Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments

doi: 10.1101/2023.02.28.530341

Figure Lengend Snippet: Heatmaps Representing Pleiotropic Profiles of Adaptive Mutant Lineages from populations evolved in clotrimazole. Each heatmap shows the lineages evolved in a particular condition and their fitness remeasurements in a specific bulk fitness assay. Each square on the heatmap shows the average fitness of the lineage measured in each environment (columns) for approximately 40 generations, specifically for mutant lineages we identified in (rows). The “+” indicates that in that lineage there are other background mutations, the “++” indicates that this specific mutation was observed in multiple lineages and what is shown in the row is the median fitness of all the lineages that have that mutation. (A) shows the haploids and (B) shows the diploids from the fluconazole evolutions.

Article Snippet: Conditions with 0.2M NaCl (Fisher Scientific - BP358-212), 0.8M NaCl, 21°C, 2% Glycerol (Fisher - G33-4) + 2 % Ethanol (Goldshield - 412804), Fluconazole 13 µM (4 mg/L, Acros Organics #455480050), Clotrimazole 6 µM (or 2 mg/L, Chem-Impex International #01311) were performed with 48 hour transfers at Stanford.

Techniques: Mutagenesis

Journal: Oncology Letters

Article Title: Survivin expression as an independent predictor of overall survival in malignant peritoneal mesothelioma

doi: 10.3892/ol.2020.11505

Figure Lengend Snippet: Demographic patient characteristics (n=60).

Article Snippet: Specimens were incubated overnight at 4°C with primary antibodies against the following molecules: Survivin (dilution, 1:100; rabbit monoclonal, clone EP119; OriGene Technologies, Inc.; cat. no. S1130), CD146 (dilution, 1:100; rabbit monoclonal, clone EP54; OriGene Technologies, Inc.; cat. no. GTX34461) and Ki-67 (dilution, 1:200; rabbit monoclonal, clone EP5; OriGene Technologies, Inc.; cat. no. GTX16667).

Techniques:

Journal: Oncology Letters

Article Title: Survivin expression as an independent predictor of overall survival in malignant peritoneal mesothelioma

doi: 10.3892/ol.2020.11505

Figure Lengend Snippet: Representative IHC images of CD146, survivin and Ki-67 expression. Expression of CD146 in epithelioid MPeM: (A) Negative; (B) 1+; (C) 2+; (D) 3+. Expression of CD146 in non-epithelioid MPeM: (E) Negative; (F) 1+; (G) 2+; (H) 3+. Expression of survivin in epithelioid MPeM: (I) Negative; (J) 1+; (K) 2+; (L) 3+. Expression of survivin in non-epithelioid MPeM: (M) Negative; (N) 1+; (O) 2+; (P) 3+. Expression of Ki-67 in epithelioid MPeM: (Q) Lower expression; (R) higher expression. Expression of Ki-67 in non-epithelioid MPeM: (S) Lower expression; (T) higher expression. Staining of CD146 was observed in the cytoplasm and cell membrane, staining of survivin was found in the nucleus and cytoplasm, while Ki-67 staining was nuclear. Magnification, ×400. IHC, immunohistochemistry; MPeM, malignant peritoneal mesothelioma.

Article Snippet: Specimens were incubated overnight at 4°C with primary antibodies against the following molecules: Survivin (dilution, 1:100; rabbit monoclonal, clone EP119; OriGene Technologies, Inc.; cat. no. S1130), CD146 (dilution, 1:100; rabbit monoclonal, clone EP54; OriGene Technologies, Inc.; cat. no. GTX34461) and Ki-67 (dilution, 1:200; rabbit monoclonal, clone EP5; OriGene Technologies, Inc.; cat. no. GTX16667).

Techniques: Expressing, Staining, Membrane, Immunohistochemistry

Journal: Oncology Letters

Article Title: Survivin expression as an independent predictor of overall survival in malignant peritoneal mesothelioma

doi: 10.3892/ol.2020.11505

Figure Lengend Snippet: Association and differences of survivin and CD146 expression with clinicopathologic parameters and Ki-67LI in patients with malignant peritoneal mesothelioma.

Article Snippet: Specimens were incubated overnight at 4°C with primary antibodies against the following molecules: Survivin (dilution, 1:100; rabbit monoclonal, clone EP119; OriGene Technologies, Inc.; cat. no. S1130), CD146 (dilution, 1:100; rabbit monoclonal, clone EP54; OriGene Technologies, Inc.; cat. no. GTX34461) and Ki-67 (dilution, 1:200; rabbit monoclonal, clone EP5; OriGene Technologies, Inc.; cat. no. GTX16667).

Techniques: Expressing

Journal: Oncology Letters

Article Title: Survivin expression as an independent predictor of overall survival in malignant peritoneal mesothelioma

doi: 10.3892/ol.2020.11505

Figure Lengend Snippet: Survivin (A) CD146 (C) and Ki-67 (E) expression is absent in normal mesothelium. Survivin (B) CD146 (D) and Ki-67 (F) expression is absent in peritonitis specimens (B, D, F). Magnification ×400.

Article Snippet: Specimens were incubated overnight at 4°C with primary antibodies against the following molecules: Survivin (dilution, 1:100; rabbit monoclonal, clone EP119; OriGene Technologies, Inc.; cat. no. S1130), CD146 (dilution, 1:100; rabbit monoclonal, clone EP54; OriGene Technologies, Inc.; cat. no. GTX34461) and Ki-67 (dilution, 1:200; rabbit monoclonal, clone EP5; OriGene Technologies, Inc.; cat. no. GTX16667).

Techniques: Expressing

Journal: Oncology Letters

Article Title: Survivin expression as an independent predictor of overall survival in malignant peritoneal mesothelioma

doi: 10.3892/ol.2020.11505

Figure Lengend Snippet: Univariate and multivariate analyses of factors affecting OS in patients with malignant peritoneal mesothelioma.

Article Snippet: Specimens were incubated overnight at 4°C with primary antibodies against the following molecules: Survivin (dilution, 1:100; rabbit monoclonal, clone EP119; OriGene Technologies, Inc.; cat. no. S1130), CD146 (dilution, 1:100; rabbit monoclonal, clone EP54; OriGene Technologies, Inc.; cat. no. GTX34461) and Ki-67 (dilution, 1:200; rabbit monoclonal, clone EP5; OriGene Technologies, Inc.; cat. no. GTX16667).

Techniques:

Journal: Oncology Letters

Article Title: Survivin expression as an independent predictor of overall survival in malignant peritoneal mesothelioma

doi: 10.3892/ol.2020.11505

Figure Lengend Snippet: Kaplan-Meier survival curves for different predictors. (A) Ki-67 grade 2 expression; (B) CD146 grade 4 expression; (C) survivin grade 4 expression; (D) forest plot of disease-free survival hazard ratios of major subgroups (exploratory analysis). Dashed lines represent median survival. PCI, peritoneal cancer index. Treatment protocols 0, best supportive care; Treatment protocols 1, intraperitoneal chemotherapy; Treatment protocols 2, systemic chemotherapy. *P<0.05. ***P<0.001.

Article Snippet: Specimens were incubated overnight at 4°C with primary antibodies against the following molecules: Survivin (dilution, 1:100; rabbit monoclonal, clone EP119; OriGene Technologies, Inc.; cat. no. S1130), CD146 (dilution, 1:100; rabbit monoclonal, clone EP54; OriGene Technologies, Inc.; cat. no. GTX34461) and Ki-67 (dilution, 1:200; rabbit monoclonal, clone EP5; OriGene Technologies, Inc.; cat. no. GTX16667).

Techniques: Expressing