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9 protocols using rhogdi

1

Comprehensive Mitophagy Regulation Assay

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The primary antibodies used were RhoA (#2117, for WB), Parkin (#2132), COX-IV (#11967), VDAC (#4661), lamin A/C (#2032), Rho-GDI (#2564), HA (#3724), PKD (#90039), P-PKD S916 (#2051), GAPDH (#2118), α-actinin (#3134) and LC3B (#3868) from Cell Signaling Technology; PINK1 from Novus Biologicals (#NB600-973); RhoA (SC-418, for IP) and ubiquitin (SC-8017) from Santa Cruz Biotechnology; miniSOG from Kerafast (#EFH004). Horseradish peroxidase (HRP)-conjugated secondary antibodies for WB, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP), cycloheximide (CHX), MG-132, CID755673, Bafilomycin A1, Evans blue and triphenyltetrazolium chloride (TTC) were purchased from MilliporeSigma. Y-27632 was purchased from Cell Signaling Technology. DharmaFECT-1 and LysoTracker Blue were purchased from Thermo Fisher Scientific. C3 exoenzyme was purchased from Cytoskeletton, Inc.
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2

Western Blotting of Protein Extracts

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Western blots of protein extracts prepared from VS or GAN tissue or culture lysates were performed as described previously (Brown and Hansen 2008 (link); Hansen et al. 2006 (link); Yue et al. 2011 (link)). The primary antibodies used were anti-p75NTR (kindly provided by Dr. Moses Chao), phosphorylated JNK (pJNK, Cell Signaling), JNK (Cell Signaling), phosphorylated JUN (pJUN, Cell Signaling), merlin (Santa Cruz), cleaved caspase-3 (Cell Signaling), RIP2 (Enzo Lifesciences, Farmingdale, NY), sortilin (Abcam), β-actin (Sigma), and Rho-GDI (Cell Signaling). Secondary antibodies (dilution,1:5000-50,000; Santa Cruz) were conjugated with horseradish peroxidase. Blots were developed using Super Signal West Femto kit (Thermo Fisher Scientific, Rockford, IL) and exposed to film (Amersham Hyperfilm TM ECL; GE Healthcare). As needed, membranes were stripped and re-probed with other antibody combinations. Densitometry to quantify protein levels was performed as previously described and statistical significance was determined with a student's non paired, two-tailed t- test.
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3

ELISA and Western Blot for IL-10 Quantification

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ELISA kits for measuring human and mouse IL-10 (#88-7106 and #88-7105, respectively; eBioscience; San Diego, CA) were used according to the manufacturer's directions. The mouse-specific neutralizing anti-IL-10 antibody (#16-7102-85) and a corresponding IgG isotype control antibody (#14-4714-82) were also obtained from eBioscience. For western blots, antibodies specific for phospho-STAT3 (#9145S, diluted 1:500), STAT3 (#9139, diluted 1:1000) and RhoGDI (#2564, diluted 1:1000) were obtained from Cell Signaling Technology (Danvers, MO); the anti-tubulin antibody was from Sigma-Aldrich (#T5201, St. Louis, MO, diluted 1:1000). STAT3 Inhibitor VII (#573103) was obtained from EMD Millipore (Billerica, MA), Stattic (#2798) from Tocris (Fisher Scientific; Pittsburgh, PA) and ruxolitinib (#11609) from Cayman Chemical (Ann Arbor, MI).
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4

Western Blot Analysis of Signaling Proteins

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Proteins were extracted in RIPA buffer (50 mM Tris-base, 1.0 mM EDTA, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 1% sodium deoxycholate, 1 mM PMSF) and quantified by the DC protein assay kit (Bio-Rad). Samples were separated by 12% SDS-PAGE and transferred to PVDF membranes (Amersham Biosciences, Piscataway, NJ, USA). After blocking with 5% non-fat milk in Tris-buffered saline, 0.1% Tween 20 for 1 h, the membranes was incubated overnight at 4 °C with respective primary antibodies. The primary antibodies for RhoGDI, JNK, p-JNK, Akt/p-Akt and MAPK/p-MAPK were purchased from Cell Signaling Technology (Beverly, MA, USA). The primary antibodies for c-Jun, p-c-Jun, caspase-3 and GAPDH were acquired from Santa Cruz Biotechnology. After that, the blots were incubated with secondary antibody conjugated to HRP for 2 h at room temperature. Target proteins were detected by enhanced chemiluminescence reagents (Amersham Pharmacia Biotech, Piscataway, NJ, USA).
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5

Western blot analysis of cell signaling

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The western blot was done as previously described [7 (link)]. The primary antibodies for RhoGDI and Akt/p-Akt were purchased from Cell Signaling Technology (Beverly, MA, USA). The primary antibodies for caspase-3 and GAPDH were acquired from Santa Cruz Biotechnology.
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6

Signaling Protein Activation Assay

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Activation of the cells was examined
using SDS-PAGE and Western blotting. The concentration of the proteins
in the supernatant was measured using a BCA assay (Pierce), and 10
μg of total protein for each time point was run on a 10% SDS
polyacrylamide gel and then transferred to a nitrocellulose membrane.
The membrane was probed for phospho-P38 (Thr180/Tyr182, Cell Signaling),
phospho-SAPK/JNK (Thr183/Tyr185, Cell Signaling), phospho-NF-κB
P65 (Ser536, Cell Signaling), and phospho-NF-κB P105 (Ser933,
Cell Signaling) and RhoGDI (Cell Signaling) as a loading control.
These experiments were performed in triplicate.
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7

Western Blot Analysis of Cell Signaling

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Western blot analysis was performed according to protocols as previously described [28 (link)]. The primary antibodies used were Drp1 from BD Transduction Laboratories; phospho-Drp1 (Ser616), phospho-Drp1 (Ser637), RhoGDI, COX-IV, GAPDH, phospho-Akt (Ser473), and Akt from Cell Signaling Technology; RhoA from Santa Cruz; cofilin2, and phospho-cofilin2 (Ser3) from Millipore. Peroxidase-conjugated secondary antibodies (Sigma) were used at a dilution of 1:2000, and enhanced chemiluminescent substrate was from Thermo Scientific.
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8

Legionella Infection Dynamics in RAW 264.7 Cells

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RAW 264.7 cells were plated at a density of 1 × 107 cells per well in 10-cm dishes and then challenged with L. pneumophila-GFP strains at an MOI of 50. When appropriate, cells were incubated for 1 h before Legionella challenge with 50 µg/mL CHX or 10 µM MG132. At 2 hpi, cells were washed with 1× PBS solution and harvested. Cells were fluorescently sorted based on GFP signal by using a BD INFLUX sorter. Postsorted infected cells (GFP+) and bystander cells (GFP) were centrifuged and lysed by using 2× SDS Laemmli sample buffer (0.125 M Tris⋅HCl, pH 6.8, 4% SDS, 20% glycerol, 20% glycerol, 10% β-mercaptoethanol, 0.01% bromophenol blue) and boiled for 10 min. Proteins were transferred to PVDF membranes, blocked in 5% BSA, and probed with antibodies to cyclin D1 (Abcam), cyclin E1 (Cell Signaling), RhoGDI (Cell Signaling), GAPDH (Cell Signaling), or tubulin (Sigma). Immunoblotting with primary antibodies was carried out overnight at 4°. Dylight anti-rabbit IgG 680 and anti-mouse IgG 800 were used as secondary antibodies (1:20,000; Cell Signaling). Capture and analysis of membranes was performed by using an Odyssey scanner and Image Studio software (LI-COR Biosciences).
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9

Mitochondrial Dysfunction and Apoptosis

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Primary antibodies for hexokinase-II, Parkin, COX-IV, VDAC, lamin A/C, Rho-GDI, α-actinin, cleaved-caspase-3, cleaved caspase-9, and LC-3B were from Cell Signaling Technology; PINK1 and BAG2 were from Novus Biologicals; GFP and ubiquitin were from Santa Cruz Biotechnology; and BAG5 was from Abcam. Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP), Bafilomycin A1 (BFA), 3-bromopyruvate (3BP), sodium iodoacetate, Evans blue and triphenyltetrazolium chloride (TTC) were purchased from MilliporeSigma. DharmaFECT 1 and LysoTracker Blue were purchased from Thermo Fisher Scientific.
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