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609 protocols using synergy h4

1

Caspase Activation Assay for Cell Lines

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Briefly, WM266–4 and M14 cells were plated in 384-well plates in 5 μL of complete media (EMEM and RPMI-1640, respectively). 5 μL of 200 μM 2155–14 and 2155–18 were added to the cells. Plates were incubated at 37 °C, 5% CO2 and 95% relative humidity for various lengths of time. After incubation, 5 μL of caspase 3/7, caspase 8, and caspase 9 Glo® reagent (Promega cat#: G7570) were added to each well, and incubated for 15 min at room temperature. Luminescence was recorded using a Biotek Synergy H4 multimode microplate reader. In the case of caspase 6, 5 μL of 100 μM caspase 6 substrate AFC-VEID in lysis buffer was added and incubated for 1 h at 37 °C, 5% CO2 and 95% relative humidity and fluorescence intensity was measured at λexcitation = 400 nm and λemission = 505 nm using a Biotek Synergy H4 multimode microplate reader.
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2

Optical Density and GFP Quantification

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Optical density of samples was quantified by measuring the absorbance at 600 nm either in a ThermoFisher Genesys 20 spectrophotometer with a 10 mm path length or in a Biotek Synergy H4 plate reader. When necessary, cultures were diluted to ensure that the reading fell within the linear range of the instruments. 1 mL of culture was used for spectrophotometer measurements, and 150 µL of culture in a 96 well plate was used for plate reader measurements. Calibration curves were made for each instrument and used for uniform reporting of optical density. All optical densities reported correspond with those taken in the spectrophotometer.
For GFP quantification, fluorescence at 485 nm excitation and 510 nm emission were measured on a Biotek Synergy H4 plate reader. All reported fluorescence values are background-subtracted and normalized to optical density.
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3

Comprehensive Cell Viability Assessment

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The cell viability was measured by using Cell Counting Kit-8 (CCK-8, Dojindo, Kumamoto, Japan) in accordance with the manufacturer's protocols. In brief, after being treated, 10 μL of CCK-8 solution were added to the required wells for 2 h at 37 °C. Subsequently, the optical density was measured using a microplate reader (SYNERGY H4, BioTek, VT, USA) at the absorbance of 450 nm. Lactate dehydrogenase (LDH) assay was carried out with the aid of a LDH-cytotoxicity assay kit (Beyotime Institute of Biotechnology, Shanghai, China) following the manufacturer's instructions, and the optical density was measured using a microplate reader (SYNERGY H4, BioTek, VT, USA) at the absorbance of 450 nm. For assessment of cell apoptosis, a commercial kit of Click-iT® TUNEL Alexa Fluor® 594 Imaging Assay (Thermo Fisher Scientific Inc, Waltham, MA. USA) was used. According to the manufacturer's protocols, the red or blue fluorescence was measured with Nikon Eclipse 80i fluorescence microscope (Japan). Furthermore, cell apoptosis was also assessed by a flow cytometry (Accuri C6, BD Biosciences) by using Annexin V-FITC/PI apoptosis detection kit as we previously described [42 (link)].
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4

Spectral Properties of Fluorescent Proteins

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Prior to spectral analysis, all proteins were purified using metal chelating Ni-NTA chromatography and dialyzed into PBS. Emission spectra were recorded with a Biotek Synergy H4 plate reader. Absorbance measurements were made on a Varian Cary 50 UV/Vis Spectrophotometer using a 1 cm quartz microcell cuvette. The alkaline chromophore denaturation method was used to determine ε values. mCitrine (Φ = 0.76) was used as the reference for quantum yield determination for ddOFP. pH titrations were performed by incubating purified proteins in buffers of desired pH and acquiring emission spectra with a 96-well Biotek Synergy H4 plate reader. A 1 μM solution of fluorescent protein was prepared in PBS and diluted 1:10 with a universal buffer of desired pH. This universal buffer solution was prepared by mixing equal volumes of 0.04 M H3BO3, 0.04 M CH3COOH, and 0.04 M H3PO4. The pH was adjusted to the desired value by adding 1M NaOH to the prepared stock solution. The pKa was determined by fitting the experimental data to the equation: F=A+B1+10pKapHnH1 , where F is fluorescence, A and B are variables that define the baselines, and nH is the Hill coefficient. Mean integrated emission peak intensities were normalized and plotted as a function of pH.
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5

Spectral Properties of Fluorescent Proteins

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Prior to spectral analysis, all proteins were purified using metal chelating Ni-NTA chromatography and dialyzed into PBS. Emission spectra were recorded with a Biotek Synergy H4 plate reader. Absorbance measurements were made on a Varian Cary 50 UV/Vis Spectrophotometer using a 1 cm quartz microcell cuvette. The alkaline chromophore denaturation method was used to determine ε values. mCitrine (Φ = 0.76) was used as the reference for quantum yield determination for ddOFP. pH titrations were performed by incubating purified proteins in buffers of desired pH and acquiring emission spectra with a 96-well Biotek Synergy H4 plate reader. A 1 μM solution of fluorescent protein was prepared in PBS and diluted 1:10 with a universal buffer of desired pH. This universal buffer solution was prepared by mixing equal volumes of 0.04 M H3BO3, 0.04 M CH3COOH, and 0.04 M H3PO4. The pH was adjusted to the desired value by adding 1M NaOH to the prepared stock solution. The pKa was determined by fitting the experimental data to the equation: F=A+B1+10pKapHnH1 , where F is fluorescence, A and B are variables that define the baselines, and nH is the Hill coefficient. Mean integrated emission peak intensities were normalized and plotted as a function of pH.
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6

β1-Adrenergic Receptor Activation Assay

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HEK293 cells were plated in 96-well dishes in 100 μl of growth medium. When cells reached 70–80% confluence, they were transfected with 50 ng β1AR-WT or β1AR-WT + β1AR-Mut (25 ng:25 ng) plasmids together with 50ng pGloSensor-22F (Promega) which produce rapid and reversible cAMP-dependent activation of luciferase activity. After incubation for an additional 20–24 hours, growth medium was replaced with 100μl equilibration medium (88% CO2-independent medium, 10% FBS, 2% GloSensor cAMP Reagent stock solution (Promega)). Cells were then equilibrated for 2 hours at room temperature. Baseline luminescence was measured every min for 10 min (synergy H4, Bio Tek). 10nM isoproterenol was then added to the medium, and Luminescence was immediately measured every min for 30 min (synergy H4, Bio Tek).
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7

BACE1 Enzyme Inhibition Assay

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A slightly modified protocol
from the commercially available assay (BPS Bioscience) was used. The
BACE1 enzyme was thawed on ice and diluted to 7.5 ng/μL with
assay buffer. Then, 69 μL of the assay buffer was mixed with
1 μL of the FRET substrate, 10 μL of increasing concentrations
of the complex [2% (v/v) DMSO] diluted in inhibitor buffer, and 20
μL of the BACE1 enzyme in the dark. This yields a mixture containing
10 mM NaOAc, HOAc, and BACE1 substrate at pH 7.4. The fluorescence
signal (λex = 320 nm; λem = 405
nm) was recorded with a Synergy H4 (BioTek) microplate reader. The
plate was immediately covered with aluminum foil, kept in the dark,
and incubated for 20 min at 37 °C with slow shaking. The generated
fluorescence signal (λex = 320 nm; λem = 405 nm) was recorded with a Synergy H4 (BioTek) microplate reader.
The difference in fluorescence intensity was correlated to the concentration
of the complex, and the IC50 values were determined. As
a positive control, the known inhibitor verubecestat (IC50 = 37 ± 8 nM) was used.
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8

Optical Density and RFP Quantification

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Optical density of samples was quantified by measuring the absorbance at 600 nm either in a ThermoFisher Genesys 20 spectrophotometer with a 10 mm path length or in a Biotek Synergy H4 plate reader. 1 mL of culture was used for spectrophotometer measurements, and 150 µL of culture in a 96 well plate was used for plate reader measurements. Calibration curves were made for each instrument and used for uniform reporting of optical density. All optical densities reported correspond with those taken in the spectrophotometer.
For RFP quantification, fluorescence at 585 nm excitation and 610 nm emission was measured on a Biotek Synergy H4 plate reader. All reported fluorescence values are background-subtracted and normalized to optical density.
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9

Enzymatic Activity Characterization of CALB

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Purified commercial CALB, free Strep-tag II CALB and immobilized Strep-tag II CALB (prepared as described above using 6 µg/µL of purified enzyme) samples were tested for activity using 0.1–2 mM p-NPB at 37 °C in 10 mM MES buffer (pH 7.0) under constant shaking (Biotek Synergy H4; medium speed). Immobilized Strep-tag II CALB samples were prepared as described above using 6 µg/µL of purified enzyme. Absorbance values were read at 400 nm excitation for 15 min (Biotek Synergy H4). A standard curve of p-nitrophenol (extinction coefficient ∼ 7700 M−1 cm−1) was used to determine substrate conversion and subsequent rates. The Michaelis constant (Km) and maximum velocity (Vmax) were extrapolated from nonlinear regression of a plot of velocity versus substrate concentration using Michaelis–Menten enzyme kinetics (Graph Pad Prism Software, U.S.A.). Vmax was divided by the enzyme concentration to obtain the apparent turnover number (kcat).
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10

Caspase Activation Assay for Cell Lines

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Briefly, WM266–4 and M14 cells were plated in 384-well plates in 5 μL of complete media (EMEM and RPMI-1640, respectively). 5 μL of 200 μM 2155–14 and 2155–18 were added to the cells. Plates were incubated at 37 °C, 5% CO2 and 95% relative humidity for various lengths of time. After incubation, 5 μL of caspase 3/7, caspase 8, and caspase 9 Glo® reagent (Promega cat#: G7570) were added to each well, and incubated for 15 min at room temperature. Luminescence was recorded using a Biotek Synergy H4 multimode microplate reader. In the case of caspase 6, 5 μL of 100 μM caspase 6 substrate AFC-VEID in lysis buffer was added and incubated for 1 h at 37 °C, 5% CO2 and 95% relative humidity and fluorescence intensity was measured at λexcitation = 400 nm and λemission = 505 nm using a Biotek Synergy H4 multimode microplate reader.
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