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7 protocols using tetramethylrhodamine methyl ester perchlorate

1

Synthesis and Characterization of Quinoline Derivatives

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All chemicals and compounds were purchased from Sigma-Aldrich (St. Louis, MO) unless otherwise specified. N-(2-benzylphenyl)-2-oxo-1 H-quinoline-4-carboxamide (ER-000444793; CAS number: 792957-74-5) was purchased from Enamine (Kiev, Ukraine); sanglifehrin A (SfA) was isolated from a fermentation broth; functionalised CsA-NH2 was synthesised in-house. Fluorescent probes (tetramethylrhodamine methyl ester perchlorate, TMRM, Fluo-4FF, Alamar Blue) were purchased from Life Technologies (Eugene, OR).
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2

Mitochondrial Regulation Assays

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ISO, CsA, CGP 20712A (CGP), ICI-118,551 (ICI), PKA inhibitor fragment 14–22 (PKI), RP-8-PIP-CAMPS (8-RP-cAMPs), AIP, (±)-propranolol hydrochloride (Prop), Mdivi-1, atractyloside and mitoTEMPO were purchased from Sigma-Aldrich (St Louis, MO, USA). KN93 and KN92 were purchased from Merck Millipore Corporation (La Jolla, CA, USA). The fluorescent dyes, tetramethylrhodamine methyl ester perchlorate (TMRM), Fluo-4 AM, DCFH-DA, MitoSOX red MitoTracker Red CMXRos and MitoTracker Green FM were purchased from Life Technologies (Eugene, OR, USA).
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3

Apoptosis Quantification by Flow Cytometry and Imaging

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Cell apoptosis was assayed using the Annexin V/Propidium Iodide Apoptosis (AV/PI) Detection Kit (BD Biosciences) and measured by FCM. Furthermore, cells were treated with 7.5 μmol/L of the CellEvent Caspase 3/7 Green Detection Reagent (Invitrogen, United States) and 10 nmol/L tetramethylrhodamine methyl ester perchlorate (Invitrogen), and observed under confocal microscopy to confirm the results obtained from FCM.
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4

Comprehensive Immunofluorescence Staining Protocol

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Immunofluorescence staining was performed as previously described11, 12, 18, 23 and imaging was performed using a Zeiss LSM‐710 model, equipped with an Airyscan module (Carl Zeiss). Antibodies used were alpha smooth muscle actin (Abcam, ab5694), von Willebrand factor (Abcam, ab11713), CD4 (Invitrogen, LS14004182), Ki67 (Abcam, ab16667), nuclear factor of activated T‐cells c2 (Abcam, ab2722), hypoxia inducible factor 1α (Abcam, 51608), and Y705p‐STAT3 (Cell Signaling Technology, 9131). All antibodies used for immunofluorescence were diluted in 1:100 and all secondary antibodies in 1:1000. Apoptosis was measured using the Apoptag Apoptosis Detection Kit for TUNEL (Invitrogen) and the Dead Cell Apoptosis Kit with Annexin V FITC and Propidium iodide (Invitrogen). The mitochondrial membrane potential was measured by staining live PASMCs with 20 nmol/L tetramethyl‐rhodamine methyl‐ester perchlorate (Invitrogen) and 500 nmol/L Hoechst 33342 (Invitrogen) for 30 minutes at 37 °C. The mitochondrial reactive oxygen species were measured by staining live PASMCs with 5 μmol/L MitoSOX (Invitrogen) and 500 nmol/L Hoechst 33342 in nonserum media for 15 minutes at 37 °C, and then cells were washed and replaced with regular media.
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5

Measuring Mitochondrial Membrane Potential

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Mitochondrial membrane potential was measured according to a previously published procedure with minor modifications [48 (link)]. Briefly, mitochondria freshly isolated from pupae were resuspended in respiration buffer (0.5 mg/ml) containing Tetramethylrhodamine methyl ester perchlorate (0.5 μM) (Thermo Fisher). The excitation spectra were scanned from 520 nm to 580 nm using 590 nm emission wavelengths. Mitochondrial membrane potential was estimated from the 573/546 fluorescence ratio. To check for specificity, the scan was repeated in the presence of Carbonyl cyanide m-chlorophenyl hydrazine (CCCP) (0.5 μM) to depolarize the mitochondria.
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6

Mitochondrial Staining for Cell Imaging

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Tetramethylrhodamine Methyl Ester Perchlorate (Thermo) was added to cell culture media. This dye is sequestered by active mitochondria based on their membrane potential. Cells were incubated for 30 min at 37 °C in 5% CO2 and washed two times with HBSS/Ca/Mg before staining for 15 min using CellTracker Deep Red. Finally, cells were imaged in fresh HBSS/Ca/Mg using the Operetta High-Content Imaging System (Perkin Elmer).
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7

Measurement of Mitochondrial Membrane Potential

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Mitochondrial membrane potential was measured according to previously published protocols with minor modifications (46) . Briefly, freshly mitochondria isolated from pupae were resuspended in respiration buffer (0.5 mg/ml) containing Tetramethylrhodamine methyl ester perchlorate (0.5 µM) (Thermo Fisher). The excitation spectra were scanned from 520 nm to 580 nm using 590 nm emission wavelengths. Mitochondrial membrane potential was estimated from was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (which this version posted June 1, 2020. ; https://doi.org/10.1101/2020.05.31.126607 doi: bioRxiv preprint the 573/546 fluorescence ratio. To check for specificity, the scan was repeated in the presence of Carbonyl cyanide m-chlorophenyl hydrazine (CCCP) (0.5 µM) to depolarize the mitochondria.
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