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48 protocols using powerwave

1

Measuring Yeast Growth Arrest under H2O2 Stress

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Yeast cells were grown in YE5S at 30 °C to an OD600 of 0.5 in flasks, then cultures were diluted to an OD600 of 0.05 and growth proceeded in flasks for 20–30 min, to an OD600 of 0.1. We then transferred 100-µL samples to 96-well plates in duplicates, added or not 2 mM or 10 mM H2O2, and OD600 were automatically recorded to generate growth curves using a the Power Wave microplate scanning spectrophotometer (Bio-Tek, Winooski, VT, USA) and Gen5 software version 1.04.5, as previously described [25 (link)]. We calculated the time of “arrest after H2O2” by subtracting the minutes required to reach an absorbance at 600 nm of 0.5 between 2 mM H2O2-treated and untreated cultures, as previously described [26 (link)].
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2

Cytotoxicity Evaluation of Gallic Acid and Extracts

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EXT and standard analytical concentrations were tested to select the highest non-toxic concentrations for further experiments. B16F10 cells were seeded in 96-well plates at a density of 1 × 104 cells per well and incubated for 48 h. Then, cells were treated with GA and EXT. The concentrations of the EXT tested were 0.001, 0.01, 0.05, 0.1, 1, and 10 μg/mL (m/v) using DMSO as a solvent and GA was used at 10, 25, 50, 100, 200, and 400 μM. Cells incubated with vehicle only were considered as untreated controls. After 48 h, cells were washed with PBS, fresh DMEM was supplemented with FBS, and 5 mg/mL MTT was added, followed by plate incubation for 4 h in the dark. Once the MTT solution was carefully removed, DMSO was added to dissolve the formed formazan crystals. A spectrophotometer of microplates (BioTek, PowerWave, VT, USA) was used to read the microplate at 570 nm. After deducting the optical density obtained from the blank (DMSO), the analysis was carried out. Data were normalized to the untreated controls, considered 100% viability, representing the mean ± SD of three independent experiments.
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3

Bradford Protein Quantification in Microplate

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The protein concentration was determined according to the Bradford Method [28 (link)], using an adapted 96-well plate approach. Bovine serum albumin was used as standard, with a working protein concentration linear range of 0 to 1 mg·mL−1, in 50 mM Potassium phosphate buffer (pH 7). The protocol entailed, in triplicate, 5 µL of the protein standard/diluted sample was added to an individual well. The negative control was 5 µL of the buffer (50 mM Potassium phosphate, pH 7) in place of the protein standard/diluted sample. Subsequently, 250 µL of the Bradford reagent (Sigma) was added to each well sequentially, using a multichannel pipette, and the mixtures were thoroughly mixed by using the mixing cycle on the microplate spectrophotometer (Bio-Tek PowerWave) for 10 s and incubated at room temperature for 20 min. The resulting absorbance was measured at 595 nm against the blank and the absorbance of the unknown protein concentration was determined in comparison to the standards.
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4

Western Blot Protein Quantification and Analysis

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Proteins were homogenized from snap frozen tissue using a tissue lysis buffer described previously [23 (link)]. The protein concentration was then quantified using a Bicinchinonic Acid Assay (BCA) (ThermoScientific, Wilmington, DE). The samples plus standards were incubated at 37°C and then read using a PowerWave plate reader (BioTek, Winooski, VT) at 562 nm. The sample concentration was extrapolated using the slope of the standard curve and was used to assure equal loading. The protein homogenate was mixed with a sample buffer and loaded onto a polyacrylamide gel (5% stacking, 12% resolving) and run at constant voltage (100v). The gel was transferred onto a PVDF membrane using a wet transfer system (Bio-Rad, Hercules, CA) that was run at room temperature for 90 minutes at 100 V. The membranes were blocked for 1 hour at room temperature with a TBS-T solution containing 5% Bovine Serum Albumin (BSA). The primary antibody was suspended at the same concentration as previously [14 ] used and incubated overnight at 4°C. The membrane was washed in TBST in triplicate for five minutes, then secondary antibody was applied at a concentration of 1:5000 in TBST containing 2.5% BSA for an hour at room temperature. The membrane was then washed again in TBST in triplicate for five minutes. The membrane was developed using the LiCor (Li-Cor, Lincoln, NE) imaging system.
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5

Protein Adsorption on 3D Scaffolds

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Since the bone marrow express proteins help in the adhesion of HSCs and leukemic stem cells (LSCs), it was important to coat the 3-D scaffolds with proteins. Protein adsorption was performed by incubating different blends of scaffolds overnight with 20% FBS or with 20 μg/mL FN in PBS. The scaffolds were wetted before protein coating by incubating the scaffolds in 70% ethanol for 1 minute, followed by washing with PBS three times. Subsequently, the scaffolds were incubated in a protein solution for 12 hours and washed twice with PBS by gentle agitation to remove non-adsorbed or weakly adsorbed proteins. The protein-coated scaffolds were then incubated in elution buffer (0.025% SDS and 0.0025% CHAPS) to extract the proteins adsorbed on these scaffolds. To estimate the concentration of total protein adsorbed on the scaffolds, one volume of eluted solution was incubated with eight volumes of BCA reagent for 30 minutes at 37°C. In order to estimate the FN concentration in the extract, the scaffolds were incubated with an equal volume of micro BCA reagent for 2 hours at 37°C. Optical density was recorded at 562 nm using a BioTek PowerWave™ XS plate reader (BioTek Instruments Inc, Winooski, VT, USA).28 (link)
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6

Cell Viability Assay with Crystal Violet

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After cell treatments, culture medium was discarded from plates, and the remaining viable adherent cells were fixed with 10% of glutaraldehyde in PBS. Then, cells were stained with crystal violet (0.1% w/v in water) for 20 min, rinsed with tap water and allowed to dry. After that, 10% of acetic acid in water was added to solubilize them. The absorbance of each plate was read spectrophotometrically at 590 nm (Power Wave, Biotek, Torino, Italy).
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7

Folin-Ciocalteu Antioxidant Capacity Assay

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Total antioxidant capacity was evaluated by the Folin–Ciocalteu assay, in which a mixture of phosphomolybdate and phosphotungstate was used for the colorimetric in vitro assay of phenolic and polyphenolic antioxidants.19 The Folin–Ciocalteu’s phenol reagent was added to serial dilutions of the test product and incubated for 5 minutes. To start the chemical reaction, sodium carbonate was added, and the reaction was allowed to continue for 30 minutes at 37°C. Kinetic measurements of the optical absorbance at 765 nm were read in a colorimetric plate reader (BioTek PowerWave, Winooski, VT, USA).
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8

Quantification of Adherent Macrophage Binding

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Adherent PEMs were incubated for 1 h on ice with bS-LPS in FCS-RPMI, as described previously [19 (link)]. Subsequently, the cells were washed 3 times with 0.5% BSA in PBS (BSA-PBS) and incubated for another 1 h with 5 μg/ml horseradish peroxidase-streptavidin conjugate (HRP-SAV, Vector Laboratories) in BSA-PBS. Following extensive washing, the enzymatic reaction for peroxidase was performed with the use of TMB Substrate Reagent Set (BD Biosciences) as the substrate. The absorbance of the product was measured in a plate reader (PowerWave, Bio-Tek Instruments). Alternatively, PEMs were incubated with 5 μg/ml phycoerythrin-SAV conjugate (eBioscience), instead of HRP-SAV, and cell-associated fluorescence was quantified in a fluorescence plate reader (Infinite M200 PRO, Tecan).
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9

Mitochondrial Activity of PBMCs

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The effects of test products on the mitochondrial metabolic activity of PBMCs were tested using the colorimetric MTT assay in which NAD(P)H-dependent cellular oxidoreductase enzymes reduce the tetrazolium dye MTT to formazan, which has a purple color. Briefly, freshly harvested PBMCs were cultured in the presence of test products for 24 hours at 37°C, 5% CO2, where each test product was evaluated at six concentrations tested in triplicate. After this incubation, the cells were treated with the MTT dye for 4 hours to allow the color formation to take place in proportion to mitochondrial function. This incubation allows the PBMC mitochondria to convert the formazan dye to the purple formazan compound. Subsequently, the cells were lysed overnight with SDS. Measurements of the optical absorbance at 570 nm were read in a colorimetric microplate reader (BioTek PowerWave).
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10

Antiradical Activity of Hydrolysates

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The DPPH assay was used to determine the free-radical scavenging activity (EC50) of preliminary study hydrolysates, but not in the RSM-optimized hydrolysates due to the inclusion of citric acid as a buffer [20 (link)]. Briefly, aliquots (100 µL) were added to a 96-well plate followed by the addition of 0.16 mM methanolic DPPH solution (100 µL). The mixture was shaken and incubated in darkness for 30 min at 25 °C. Absorbance was monitored at 517 nm (Powerwave, Biotek, Winooski, VT, USA). The ability to scavenge the DPPH radical was calculated using Equation (4):
Scavenging effect (%)=[1(AsAbAc)]×100
where As is the absorbance of the test sample; Ab is the absorbance of the sample blank; and Ac is the absorbance of the control. Results are expressed as ascorbic acid equivalents (AAE).
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