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5 protocols using xf dmem medium ph 7

1

Measuring ARPE-19 Cells Mitochondrial Respiration

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The oxygen consumption rate (OCR) was measured using an XFe96 Extracellular Flux Analyzer (Seahorse Bioscience, Inc., Billerica, MA, USA). ARPE-19 cells were seeded in XFe96 cell culture plates (96-well) at a density of 2 × 104 cells/well and incubated overnight. On day 6, the ARPE-19 cells were treated with LPS (10 µg/mL) for 48 hours with or without fursultiamine for the final 24 hours. The assay medium consisted of XF DMEM Medium pH 7.4 (Agilent Technologies, Santa Clara, CA, USA) supplemented with 5.5 mM Seahorse XF 1.0 M glucose solution, 9 mM Seahorse XF 100 mM pyruvate solution, and 1 mM Seahorse XF 200 mM glutamine solution. Sigma-Aldrich inhibitors and uncouplers were used at the following concentrations: oligomycin A (1 µM), carbonyl cyanide 4-(trifluoro-methoxy) phenylhydrazone (FCCP, 0.5 µM), rotenone (1 µM), and antimycin A (1 µM). To normalize by cell number, 4′,6-diamidino-2-phenylindole (DAPI)-stained cells were counted automatically by ImageXpress Micro Confocal Microscopy (Molecular Devices, San Jose, CA, USA).
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2

Glycolytic Activity Profiling of NK Cells

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The extracellular acidification rate (ECAR), which indicates glycolytic activities was analyzed using the Seahorse Glycolysis Stress Test (Agilent) on a Seahorse XFe96 Analyzer (Agilent) according to the manufacturer’s protocol. Briefly, conditioned NK cells were harvested, washed using prewarmed supplemented RPMI medium, and plated on XF96 cell culture microplates (Agilent) coated with poly-d-lysine (Thermo Fisher Scientific) to adhere the cells on the microplate surface. Prior to the assay, the RPMI medium was replaced with XF DMEM Medium, pH 7.4 (Agilent), supplemented with 2 mM glutamine (Agilent). At indicated time points, ECAR was measured in the basal condition and in response to 10 mM glucose, 6 mM oligomycin and 50 mM 2-DG (Agilent).
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3

Assessing Graphene's Impact on Cellular Metabolism

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We used the Seahorse XFe-96 analyzer (Agilent Technologies, Santa Clara, CA, USA) to evaluate the effect of graphene on cellular metabolic function. Cells were treated for eight weeks with different concentrations of graphene, then harvested and seeded in the Seahorse XF cell culture microplates at a density of 15,000 cells per well one day prior to measurement. Before the measurement, we replaced the cell culture medium with the assay medium (bicarbonate-free XF DMEM Medium pH 7.4, Agilent Technologies, Santa Clara, CA, USA) supplemented with 4 mM L-glutamine, 1 mM pyruvate, and 1 g/L D-glucose. The cells were then incubated in a CO2-free incubator for one hour at 37 °C. After measuring the basal respiration, we performed a mitochondrial stress test by sequential additions of 1 μM oligomycin, 1.2 μM carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone (FCCP), and 1 μM rotenone-antimycin A mixture. The differences between OCR (oxygen consumption rate) values in response to respiratory modulators were used to calculate mitochondrial respiratory parameters such as ATP-related respiration and spare respiratory capacities. The changes in ECAR (extracellular acidification rate) were used to calculate glycolytic parameters (spare glycolytic capacity).
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4

Measuring Cellular Respiration in iPSCs and NPCs

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Cellular Consumption Respiration (OCR) was analyzed using the Flux Analyzer XFe96 (Agilent-Seahorse) device. We seeded iPSCs or NPCs on Matrigel-coated Seahorse XF96 cell plates. The test was carried out using the Seahorse XF Cell Mito Stress Test Kit (Agilent). Before measurements, cells were washed and incubated for 1 h at 37 °C in CO2-free conditions in XF DMEM Medium, pH 7.4 (Agilent), previously warmed and supplemented with pyruvate, glucose, and glutamine at final concentrations of 1mM, 10mM, and 2 mM, respectively. Subsequently, various drugs were sequentially injected to reach the following final concentrations: oligomycin (1.5 μM), carbonyl-cyanide-p-trifluoro-methoxy phenylhydrazone (FCCP 20 μM), and a combination of rotenone/antimycin A (0.5 μM each). FCCP concentration was previously optimized through titration. Following the completion of the measurement, all wells in the p96 plate were stained with Hoechst (1:100) for 30 min at room temperature. The number of cells per well was quantified for data normalization using the Cytation 5 image reader. The data obtained were processed using software provided by the manufacturer: seahorseanalytics.agilent.com (accessed on 20 October 2022).
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5

Measuring Mitochondrial and Glycolytic ATP Production

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Mitochondrial and glycolytic ATP production rates were measured on the same Seahorse bioanalyzers. SH-SY5Y cells were plated at a concentration of 6 × 104 cells/well, and assay measurements were performed using the Seahorse XF Real-Time ATP Rate Assay Kit (Agilent, Santa Clara, CA, USA, Catalog #103592-100) and XF DMEM medium, pH 7.4 (Agilent, Catalog #103575-100), with addition of 10 mM glucose, 1 mM pyruvate and 2 mM glutamine as per the manufacturer’s instructions. Briefly, basal OCR and proton efflux rate were measured following serial injections of oligomycin (1.5 μM) and a mix of rotenone and antimycin A (0.5 μM each), which were used for the calculation of the mitochondrial and glycolytic ATP production rates. Bioenergetics values were calculated using the Agilent XF/Seahorse ATP rate assay Report Generator version 4.0.17.
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