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47 protocols using pgc 1α

1

Profiling Acetylation and Phosphorylation of Key Regulatory Proteins

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Whole-lysate western blots were probed for the following antibodies phos-SMAD1/5 (9516, Cell Signaling Technologies), SIRT1 (9475, Cell Signaling Technologies), p21 (4060, Cell Signaling Technologies), PGC-1α (ST1202, EMD Millipore), Total OXPHOS Rodent (ab110413, Abcam), PGC-1α (ST1202, EMD Millipore), lamin B (sc-6217, Santa Cruz Biotechnology), Rho A (sc-418, Santa Cruz Biotechnology), p53 (sc-126, Santa Cruz Biotechnology), K382 acetyl-p53 (2525, Cell Signaling Technologies), and β-actin (sc-47778, Santa Cruz Biotechnology). The NE-PER Nuclear and Cytoplasmic Extraction Reagent Kit (PI-78833, Thermo Scientific) was used according to protocol. To enrich for p53, samples were immunoprecipitated using p53 N-term-Trap (pta-20, Chromotek) according to the manufacter’s protocol with addition of 200 µg/ml of nicotinamide to lysis and wash buffers.
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2

Profiling Acetylated p53 and OXPHOS Proteins

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Whole lysate western blots were probed for the following antibodies phos-SMAD1/5 (9516, Cell Signaling Technologies), SIRT1 (9475, Cell Signaling Technologies), p21 (4060, Cell Signaling Technologies), PGC-1α (ST1202, EMD Millipore), Total OXPHOS Rodent (ab110413,Abcam), PGC-1α (ST1202, EMD Millipore), lamin B (sc-6217, Santa Cruz Biotechnology), Rho A (sc-418, Santa Cruz Biotechnology), p53 (sc-126, Santa Cruz Biotechnology), K382 acetyl-p53 (2525, Cell Signaling Technologies), and β-actin (sc-47778, Santa Cruz Biotechnology). The NE-PER Nuclear and Cytoplasmic Extraction Reagent Kit (PI-78833, Thermo Scientific) was used according to protocol. To enrich for p53, samples were immunoprecipitated using p53 N-term-Trap (pta-20, Chromotek) according to manufacter’s protocol with addition of 200 µg/ml of nicotinamide to lysis and wash buffers.
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3

Protein Extraction and Western Blot Analysis

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Protein was extracted from muscle tissues using a lysis buffer (Sigma, St. Louise, MO). Equal amounts of protein in the lysates were separated by 10% SDS-PAGE, and proteins were then transferred onto nitrocellulose membranes. The blots were incubated with primary antibodies against PGC-1α (Chemicon International, Temecula, CA), cytochrome c (Cell Signaling Technology, MA), and fibronectin type III domain containing 5 (FNDC5) (Phoenix Pharmaceuticals, CA), and reaction products visualized using a horseradish peroxidase (HRP)-conjugated secondary antibody (GE Healthcare, Buckinghamshire, UK) and enhanced chemiluminescence (ECL Prime, GE Healthcare). Band densities were measured using Image J software (NIH, Research Service Branch).
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4

Quantitative Protein Analysis in Muscle Tissue

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Protein was extracted from muscle tissues obtained from sedentary groups using a lysis buffer (Sigma, St. Louise, MO) containing protease inhibitor. Equal amounts of protein in the lysates were separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and proteins were then transferred onto nitrocellulose membrane. The blots were incubated with primary antibodies against PGC-1α (Chemicon International, Temecula, CA) and AMP-activated protein kinase (AMPK) (Cell Signaling Technology, Beverly, MA), and the reaction products were visualized using a horseradish peroxidase-conjugated secondary antibody (Invitrogen, Carlsbad, CA) and enhanced chemiluminescence (Chemi-Lumi One Super, Nakarai Tesque, Kyoto, Japan) (Additional file 1: Figure S1). Band densities were measured using ImageQuant LAS4000 (GE Healthcare, Buckinghamshire, UK).
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5

Autophagy and Mitochondrial Regulation in Cellular Signaling

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The following primary antibodies were used: Ubiquitin (#3933; Cell Signaling Technology (CST) Japan, Tokyo, Japan), p‐Forkhead box O (FOXO) 1Ser256 (#84192; CST), FOXO1 (#2880; CST), p‐FOXO3aSer253 (#9466; CST), FOXO3a (#2497; CST), LC3 (#2775; CST), p62/SQSTM (PM045, Medical & Biological Laboratory, Nagoya, Japan), p‐UNC‐551‐like kinase 1 (ULK1)Ser757 (#14202; CST), p‐ULK1Ser555 (#5869; CST), ULK1 (#8054; CST), p‐AktSer473 (#9271; CST), Akt (#4685; CST), p‐p70S6KThr389 (#9205; CST), p70S6K (#2708; CST), p‐rpS6Ser240/244 (#2215; CST), rpS6 (#2217; CST), p‐4E‐binding protein 1 (4E‐BP1) Thr37/46 (#9459; CST), 4E‐BP1 (#9452; CST), Oxidative phosphorylation (OXPHOS, ab110413; Abcam, Cambridge, UK), Peroxisome proliferator‐activated receptor‐γ coactivator‐1α (PGC‐1α, 516557; Millipore, CA), Parkin (ab77924; Abcam), OPA1 (#612606; BD Transduction Laboratories, Tokyo, Japan), Mitofusion‐2 (MFN2, ab124773; Abcam), FIS1 (ab96764; Abcam), DRP1 (ab56788; Abcam), p‐AMPKThr172 (#2531; CST), AMPK (#2532; CST), 4‐hydroxy‐2‐nonenal (4‐HNE, ab8506; Abcam), p‐Tuberous sclerosis complex 2 (TSC2)Ser1387 (#5584; CST), TSC2 (#4308; CST), and Nuclear factor‐kappa B(NF‐κB, #8242; CST).
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6

Analyzing Mitochondrial Protein Levels

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Western blot analysis was performed as described previously (23 (link)). The following antibodies were used: POLG (Novus Biologicals) and PGC-1α (Millipore). A β-actin antibody was purchased from Sigma-Aldrich. Manganese superoxide dismutase (MnSOD) protein levels were measured on protein extracts from isolated liver mitochondria using a polyclonal antibody (Santa Cruz Biotechnology) and a Ponceau S (Sigma-Aldrich), staining was used as mitochondrial loading control.
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7

Muscle Protein Signaling Analysis

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Muscle samples were lysed and protein concentration was determined as previously described (26 (link)). Immunoblotting was performed using the following primary antibodies: pAkt Ser473, pAkt Thr308, total Akt, pSAPK/JNK Thr183/Tyr185, total JNK, SIRT1 (mouse specific), acetylated Lys, parkin, LC3, ATG12, PKC-α, PKC-δ, and PKC-θ (Cell Signaling); lipoprotein lipase (LPL) (Abcam); CD36 (R&D Systems); p62 (ProGen); PINK1 (Cayman Chemicals); PGC-1α (Millipore); and α-tubulin (Sigma-Aldrich). For protein kinase C (PKC) studies, subcellular fractionation was carried out as previously described (13 (link)).
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8

Western Blot Analysis of Metabolic Proteins

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Western blots were performed on lysates prepared from tissues collected at the end of the experiments. Samples of 30 μg of protein were boiled in Laemmli sample buffer (Bio-Rad, Hercules, CA) for 5 min and electrophoresed on 10 or 12.5% SDS-polyacrylamide gels and blotted onto nitrocellulose membrane. Membranes were blocked with Odyssey blocking buffer (LI-COR, Lincoln, NE) for 2 hours at room temperature and then incubated with primary antibodies overnight at 4°C. Membranes were incubated with either Alex 680 (Molecular Probes) or IRDye 800 (Rockland, Gilbertsville, PA) secondary antibodies for 1 hour at room temperature. Membranes were visualized using an Odyssey infrared imager (Li-COR, Lincoln, NE) which allows for the simultaneous detection of 2 proteins. Densitometry analysis was performed using Odyssey software (LI-COR, Lincoln, NE). Antibodies for Western blots were as follows: HMBG1 (Abcam, Boston, MA), NRF-1 (Rockland, Gilbertsville, PA), PGC1-α (Millipore, Temecula, CA), UCP-1 (Sigma, St. Louis, MO) and β-actin (Abcam, Cambridge, MA). All antibodies were used at a ratio of 1:1000 with blocking buffer, the lone exception being β-actin which was used at a ratio of 1:5000. All blots from tissue samples were run with 3 samples from all groups of mice per gel.
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9

Fatty Acid Metabolism Assay

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Fatty acid‐free bovine serum albumin (BSA) and palmitic acid were obtained from Sigma (St. Louis, MO, USA). Glycogen, amyloglucosidase, hexokinase, and glucose‐6‐phosphate dehydrogenase were obtained from Sigma (St. Louis, MO). [1‐14C] palmitic acid was from American Radiolabeled Chemicals (St. Louis) and D‐[U‐14C] glucose was from GE Healthcare (Little Chalfont, UK). Protease (cOmplete Ultra Tablets) and phosphatase (PhosStop) inhibitors were from Roche Diagnostics GmbH (Mannheim, Germany). The nonesterified fatty acids (NEFAs) kit was from Wako (Mountain View, CA). Glucose was measured by the glucose oxidase method using a OneTouch Ultra Mini Monitor. The rat glucagon and insulin ELISA kits were from R&D Systems (Minneapolis, MN) and Alpco (Salem, NH), respectively. All antibodies were purchased from Cell Signaling (Danvers, MA), except for P‐ACC and PGC‐1α which were purchased from Millipore (Billerica, MA), and the PEPCK antibody that was purchased from Abcam (Cambridge, MA).
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10

Protein Expression Analysis of Cell Signaling Pathways

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Antibodies for cleaved-caspase 3 (Asp175), caspase 3, phospho-AMPK (Thr172), AMPK, cyclin D1, acetylated-lysine, phospho-Akt (Ser473), phospho-GSK-3β (Ser9), phospho-cdc2 (Tyr15), cdc2, c-myc, phospho-Erk1/2 (Thr202/Tyr204) were purchased from Cell Signaling. β-catenin, Sirt-1, Sirt-2 were purchased from Abcam. PGC1α was purchased from Millipore. β-actin was purchased from Sungene. Whole cell lysate was prepared using RIPA lysis buffer in the presence of protease inhibitors. Protein concentrations were determined using the bicinchoninic acid (BCA) method (Biomed, Beijing, China). Total cell lysates were separated using 8%-12% SDS-PAGE, transferred onto PVDF membranes, and then detected using various primary antibodies. The antibody-antigen complexes were detected using the Chemiluminescent HRP Substrate (Millipore, MA, USA).
For immunoprecipitations, cells were lysed in lysis buffer (50 mM Tris-HCl at pH 7.4, 0.2 mM EDTA, 150 mM NaCl, 3% NP-40, 1 mM phenyl methylsulfonyl fluoride (PMSF) and, Protease inhibitor cocktail). Equal amounts of cell extracts were incubated with anti-PGC1α antibodies. Subsequent immunoblots were performed as described above.
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