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9 protocols using anti mtor

1

Western Blot Analysis of Autophagy Proteins

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Cells were lysed with RIPA buffer containing protease inhibitor cocktail (Roche, Basel, Switzerland). Protein concentration was assessed with a Bio-Rad Protein Assay Kit (Bio-Rad Laboratories, Hercules, CA, USA). Equal amounts of proteins from each sample (30 μg) were separated by 10 or 12% SDS-PAGE and transferred to polyvinylidene difluoride membrane (Merck Millipore, Billerica, MA, USA). The membrane was blocked for 1 h in PBS containing 5% non-fat milk. For detection with primary antibodies (anti-iASPP: Rockland; anti-GAPDH: Santa Cruz Biotechnology, Dallas, TX, USA; anti-p-mTOR and anti-ATG3: Cell Signaling Technology, Danvers, MA, USA; anti-Beclin1 and anti-ATG7: Abcam; anti-LC3B, anti-GFP, anti- mTOR, anti- p70S6K and anti-p-p70S6K: Sigma), the membranes were incubated with the appropriate antibody at 4 °C overnight, followed by incubation with HRP-conjugated secondary antibodies, and then developed using ECL western blot detection reagents (PerkinElmer, Waltham, MA, USA).
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2

Chloroquine Modulates ESC Autophagy

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ESCs were either treated or not treated with 100 μM Chloroquine (Sigma) for 4 h. After the treatments, the cells were collected and lysed by RIPA buffer with protease inhibitor PMSF (Beyotime). The lysates were resolved by SDS/PAGE, and proteins were transferred onto PVDF membranes. For WB, the following antibodies were used: the anti-actin (1:5000) was purchased from Abcam, anti-LC3B (1:2000) and anti-ULK1 (1:1000) were obtained from Sigma-Aldrich, anti-pULK1 (S555) (1:1000), and anti-pULK1 (S757) (1:1000) were purchased from Sigma, and anti-mTOR (1:1000), anti-mTOR (1:1000), anti-AMPK (1:1000), anti-p-AMPK (1:1000) were purchased from Cell Signaling Technology.
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3

Apoptosis and Autophagy Modulation

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SIN was purchased from AdooQ Bioscience (Nanjing, China). The primary antibody, including anti-Bax, anti-Bcl-2, anti-Be-clin1, anti-p-p62/SQSTM1 (Thr269/Ser272), and anti-p62 were obtained from Abcam (Cambridge, UK). Anti-LC3, anti-pAkt (S473), anti-Akt, anti-pmTOR (S2448), and anti-mTOR antibodies were purchased from Sigma-Aldrich Co., (St Louis, MO, USA). LY294002 and CQ were obtained from Selleck Chemicals (Houston, TX, USA). IGF-1 was purchased from Abcam. Caspase-3 enzyme-linked immunosorbent assay (ELISA) kit was purchased from Sangon Biotech (Shanghai, China).
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4

Immunofluorescence Staining of Tissue Sections

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Every tenth serial section was rinsed in PBS, permeabilized with PBS containing 0.1% (v/v) saponin and 4% (v/v) normal goat serum (NGS) for 15 min and then blocked with PBS containing 0.05% (v/v) saponin and 5% (v/v) NGS for 15 min at room temperature. The sections were incubated overnight at 4℃ with anti-laminin (Sigma Aldrich), anti-human nuclei (Millipore), anti-Tie2 (Santa Cruz Biotechnology, Santa Cruz, CA, USA) anti-FAK (Santa Cruz Biotechnology), anti-AKT (Cell Signaling Technology, Danvers, MA, USA), anti-pp38 (Cell Signaling Technology), anti-pERK1/2 (Cell Signaling Technology), anti-pSAPK/JNK (Cell Signaling Technology), anti-mTOR (Sigma Aldrich), anti-SDF1 (Santa Cruz Biotechnology), anti-FLAG (Sigma Aldrich). Subsequently, the sections were incubated for 1 h at room temperature with a fluorescent-labeled secondary antibody (FITC, Alexa488-labeled, raised in mouse; Jackson Immuno Research Laboratories, West Grove, PA, USA) and mounted with Vectashield medium containing DAPI (Vector Laboratories). Fluorescence staining was evaluated using the aforementioned confocal laser scanning microscope.
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5

Molecular Mechanisms of Bone Homeostasis

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After the soft tissue on the tibia of mice had been removed, tibias were cut by ophthalmic scissors and 80g weighed by electronic scale. The tibia of each sample was placed in the grinding tube, to which had been added grinding beads and lysis buffer, and placed in the tissue homogenizer for grinding. The supernatant and was gotten for examining concentration of total protein by bicinchoninic acid method(BCA). Polyacrylamide gel electrophoresis was performed to separate the target proteins from the samples with the equal amount of total protein. Proteins were transferred to PVDF membrane (Invitrogen) and closed non-specific binding with 5% skimmed milk. The protein was added with primal antibodies of anti-PI3K (1:1000, Abcam), anti-Akt (1:1000, Abcam), anti-pAkt (1:1000, Abcam), anti-mTOR (1:1000, Sigma), anti-Beclin-1 (1:1000, Proteintech), anti-LC3 II (1:1000, Proteintech), anti-p62 (1:1000, Proteintech), anti-NF-κB (1:1000, Proteintech), anti-Runx2 (1:1000, Sigma), anti-beta actin (1:1000, Abcam) and secondary antibodies (Abcam) in turn, and then washed with tris-buffered saline Tween (TBST). The PVDF film was developed and photographed by Alpha gel imaging system. Beta-actin was used as an internal reference, and the data were analyzed by self-contained software.
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6

Western Blot Analysis of Cell Signaling Proteins

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RIPA buffer (MilliporeSigma; Merck KGaA) was used to extract total proteins from cultured 22Rv1 or PC-3 cells. Proteins were quantified with a BCA method and separated by 12% SDS-PAGE, and transferred onto PVDF membranes (GEHealthcare). The membranes were blocked in 5% non-fat dry milk diluted with TBST (Tris–HCl 20 mmol/L, NaCl 150 mmol/L, pH 7.5, 0.1% Tween 20) at room temperature for 1 h and washed with TBST for three times. Subsequently, specific primary antibodies (anti-Vimentin, anti-N-cadherin, anti-a-SMA, anti-E-cadherin, anti-Claudin 1, anti-GAPDH, anti-p-Akt, anti-Akt, anti-p-mTOR, anti-mTOR, anti-PTEN, anti-p-Smad2, anti-Smad2, anti-p-Smad3, anti-Smad3, anti-p-Smad2/3, anti-Smad2/3, and anti-laminB, Sigma, USA) were incubated with the membranes at 4 °C overnight. Next, the membranes were washed with TBST for three times and incubated with the secondary antibodies at room temperature for 2 h. Proteins were visualized using chemiluminescence using ECL luminescence reagent (Absin Bioscience Inc., Shanghai, China). The band intensities were quantified using Image-Pro Plus 6.0 (Media Cybernetics, Inc.). GAPDH was used as a loading control for normalization. The primary antibodies and secondary antibodies used in western blotting are included in Table 1.
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7

Whole-Cell Lysate Preparation and Immunoblotting

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Whole-cell lysates were prepared from cells collected in lysis buffer (50 mM Tris pH7.5, 150 mM NaCl, 1 mM EDTA, 1% NP40, 0.5% sodium deoxycholate, 1.0% SDS, 2 mM NaF, 2 mM Na3VO4, and protease inhibitors (Roche) followed by sonication and centrifugation at 13,000g for 10 minutes. Tumor lysates were prepared by homogenizing tumor tissue in lysis buffer and centrifuging at 13,000g for 10 minutes at 4°C. Proteins were quantified using a BCA assay kit, separated by electrophoresis on SDS PAGE gels, and transferred to PVDF membranes. After one hour in blocking buffer (SuperBlock), membranes were incubated overnight with primary antibodies. The following antibodies were used: anti-p-Akt (Cell Signaling), anti-Akt (Cell Signaling), anti-rpS6 (Abcam), anti-p-rpS6 (Abcam), anti-mTOR (Sigma-Aldrich), anti-p-mTOR (Sigma-Aldrich), anti-ERK (Abcam), anti-p-ERK (Abcam), anti-LC3B-II (Abcam), anti-Atg7 (Santa Cruz Biotechnology), anti-Atg12 (Santa Cruz Biotechnology), anti-Beclin-1 (Abcam), anti-C/EBPα (Abcam), anti-PPARγ (Abcam), anti-FABP4 (Abcam), anti-FAS (Abcam), anti-Tubulin (Abcam), and anti-β-Actin (Santa Cruz Biotechnology). The anti-Tubulin and anti-β-Actin were used as controls. Specific protein bands were imaged using secondary antibody conjugated with horseradish peroxidase and chemiluminescent ECL reagents. Image J was used for quantification.
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8

Western Blot Analysis of Autophagy Markers

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Cells were collected and lysed. The protein contents were determined. Samples were resolved by SDS-PAGE and electroblotted onto a polyvinylidene difluoride membrane. Afterward, membranes were incubated respectively with an anti-Belcin1(1:1000 dilution, Abcam, USA), anti-LC3(1:1000 dilution, Abcam, USA), anti-phosphorylated PI3K (p-PI3K, 1:1000 dilution, Abcam, USA) and total PI3K (t-PI3K, 1:1000 dilution, Abcam, USA), anti-phosphorylated Akt (p-Akt, 1:1000 dilution, Millipore, USA) and total Akt (t-Akt, 1:1000 dilution, Millipore, USA), anti-mTOR (1:1000 dilution, Millipore, USA) and anti-GAPDH antibodies 1:1000 dilution, Millipore, USA) overnight at 4°C, followed by incubation with the horseradish peroxidase-conjugated anti-rabbit IgG for 1 h at room temperature. The signals were enhanced using a chemiluminescence system (Amersham Pharmacia Biotech, Buckinghamshire, England).
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9

Comprehensive Autophagy Signaling Antibody Panel

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The following primary antibodies were used in this study: anti-AMPK antibody (#2532S; Cell Signaling Technology), anti-p-AMPK antibody (#2535S; Cell Signaling Technology), anti-LC3 I/II (#4108S; Cell Signaling Technology), anti-P62/SQSTM1 (#8025S; Cell Signaling Technology), anti-Beclin1 (ab62557; Abcam), anti-NRAGE (sc-136552; Santa Cruz Biotechnology), anti-GAPDH (#5174; Cell Signaling Technology), anti-Ulk1 (#2707773; Millipore), anti-p-Ulk1 (Ser758; #2571270; Millipore), anti-ATG13 (#13468S; Cell Signaling Technology), anti-p-ATG13 (S355; #43533S; Cell Signaling Technology), anti-PI3k (#4263S; Cell Signaling Technology), and anti-mTOR (#2643610; Millipore). Secondary antibodies used for western blotting were as follows: 800CW goat anti-mouse and 800CW goat antirabbit, purchased from LI-COR Biosciences. Hydroxychloroquine (HCQ), purchased from Sigma, was diluted in phosphate-buffered saline (PBS, pH 8.0) at a stock concentration 5 M.
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