Journal: ACS chemical neuroscience

Article Title: Passage Variation of PC12 Cells Results in Inconsistent Susceptibility to Externally Induced Apoptosis

doi: 10.1021/acschemneuro.6b00208

Figure Lengend Snippet: Optimization and validation of etoposide-induced cell death in PC12 cells (passage 9–13). 50 × 103 cells/well. (a) Approximately 50% cell death was observed after 48 h. Four replicates per experiment. Values are represented as mean ± SD. Multiple t test, Holm-Sidak method, alpha = 5.000%, ****p < 0.0001. (b) Fluorescence measured after 48 h. Flupirtine at 3 μM concentration rescued the cells from apoptosis. Experiment repeated thrice. Values are represented as mean ± SD. Unpaired two-tailed t test, 95% CI, ****p < 0.0001 in comparison to vehicle. ####p < 0.0001 in comparison to etoposide treatment.

Article Snippet: 5 Etoposide (Chem-Impex International, 28435) was stored as a working stock solution of 150 μ g/mL at −20 °C for up to 3 months.

Techniques: Fluorescence, Concentration Assay, Two Tailed Test, Comparison

Journal: ACS chemical neuroscience

Article Title: Passage Variation of PC12 Cells Results in Inconsistent Susceptibility to Externally Induced Apoptosis

doi: 10.1021/acschemneuro.6b00208

Figure Lengend Snippet: NGF differentiated PC12 cells show a statistically significant difference in sensitivity to apoptosis induced by etoposide between early and late passages at 72 h post insult. (a) Passage 10. Three replicates per experiment. Values are represented as mean ± SD. One-way ANOVA, Dunnett test, 95% CI. ****p < 0.0001. (b) Passage 17. Three replicates per experiment. Values are represented as mean ± SD. One-way ANOVA, Dunnett test, 95% CI. ****p < 0.0001. (c) Comparison of 72 h etoposide treatment in passage 10 and 17 PC12 cells differentiated using NGF. Unpaired two-tailed t test, 95% CI, ****p < 0.0001.

Article Snippet: 5 Etoposide (Chem-Impex International, 28435) was stored as a working stock solution of 150 μ g/mL at −20 °C for up to 3 months.

Techniques: Comparison, Two Tailed Test

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: Cellular and Molecular Bioengineering

Article Title: Re-engineering Antimicrobial Peptides into Oncolytics Targeting Drug-Resistant Ovarian Cancers

doi: 10.1007/s12195-020-00626-z

Figure Lengend Snippet: Chemotherapeutic synergy. (a) Isobolograms of MAD1 and Doxorubicin (Dox), Paclitaxel (Ptx) or Cisplatin (Cis) combinatorial synergy in OVCAR-3 (left) and NCI/ADR-RES (right) cells. Fractional inhibitory concentration (FIC) < 1 and < 0.5 represent additive and synergistic effects, respectively. (b) Comparison of Dox and Cis IC50 towards NCI/ADR-RES as either a monotherapy (ADR-RES, black) or in combination with 20 μM MAD1 (ADR-RES + MAD1, grey). Activity of each drug as a monotherapy in pre-resistant OVCAR-3 (OVCAR-3, white) cells shown for comparison. (c–f) Indicated ovarian cancer cell line or patient-derived ovarian carcinoma cells were cultured in ultra-low attachment conditions and treated for 48 h with 2 μM cisplatin or 4 μM MAD1 alone and in combination. Data represent volume in arbitrary units (a.u.) and median.

Article Snippet: 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT), Fmoc-protected amino acids, N,N 0 -diisopropylcarbodiimide (DIC), O-(7-Azabenzotriazol-1-yl)-N,N,N’,N’-tetramethyluronium hexafluorophosphate (HATU), N,N -dimethylformamide (DMF), and Paclitaxel were purchased from Chem-Impex International, Inc. RPMI-1640, M199, trypsin and EDTA solution, Antibiotic-Antimycotic Solution, ultra-low attachment (ULA) plates, and 1× phosphate buffered saline (PBS) were purchased from Corning.

Techniques: Concentration Assay, Comparison, Activity Assay, Derivative Assay, Cell Culture