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404 protocols using p ampk

1

Measuring AMPK and p-AMPK Levels

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Total AMPK and p-AMPK protein levels were measured by Western-blot (8 or 12% polyacrylamide gels) in AMN/C-ALD fibroblasts and in Abcd1 KO glial cells, as described (Supplemental Material), using the following antibodies: AMPKα1/2 (T-AMPK, Cell Signaling, #2532) and p-AMPK (Cell Signaling, #2535).
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2

Immunohistochemical Analysis of PPARγ and p-AMPK in Liver and Adipose Tissues

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For histopathological examination, paraffin sections (4 μM) from dissected liver and adipose tissues were stained with hematoxylin and eosin. Immunohistochemical staining of PPARγ (Novus, Littleton, CO, USA) and p-AMPK (Cell signaling Tech., MA, USA) was performed using the indirect avidin/biotin-enhanced horseradish peroxidase method. Antigen retrieval was performed after dewaxing and dehydration of the tissue sections by microwaving for 10 min in 10 mM citrate buffer. Sections were cooled to room temperature, treated with 3 % hydrogen peroxide in methanol for 10 min, and blocked with 6 % horse serum for 30 min at room temperature in a humidity chamber. The sections were then incubated with primary antibody against PPARγ (diluted 1: 200; Novus, Littleton, CO, USA) or p-AMPK (diluted 1: 150; Cell Signaling) at 4 °C overnight in a humidity chamber. The sections were washed in PBS and incubated with secondary antibody (biotinylated goat anti-rabbit antibody; diluted 1: 150; Vector Laboratories, Burlingame, CA, USA) for 30 min in the humidity chamber. After further washes, the antibodies were detected with the Vector ABC complex/horseradish peroxidase (HRP) kit (Vector Laboratories, Burlingame, CA, USA) and color developed with 3,3′-diaminobenzidine tetrahydrochloride. For semiquantitation, ten photomicrographs (200×) were taken with a CCD camera, avoiding gross necrotic areas.
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3

Cardiac Lipid Metabolism and Angiogenesis

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We analysed the expression of cardiac lipid metabolism proteins by the Western blot method as previously described in detail.28 As severe LV hypertrophy is related to the impaired angiogenesis pathway, we also studied the expression of key proteins that regulate angiogenesis and signal hypoxia. Primary antibodies: HIF1α (ab463, Abcam; 1:500); fatty acid transporter (CD36; ab133625, Abcam; 1:1000); carnitine palmitoyltransferase 1 (CPT1; NBP1‐59576, Novus Biological; 1:1000); fatty acid‐binding protein (FABP3; ab133585, Abcam; 1:1000); acyl‐CoA dehydrogenase (ACADL; ab196655, Abcam; 1:3000); medium‐chain acyl‐CoA dehydrogenase (MCAD; ab110296, Abcam; 1:1000); 2,4‐dienoyl‐CoA reductase (DECR1; ab198848, Abcam; 1:2000). AMP‐activated protein kinase (AMPK; 2532 s, Cell Signaling; 1:1000); phosphorylated AMPK (Thr 172) (pAMPK; 2535 s, Cell Signaling; 1:500); SIRT1 (8469 s, Cell Signaling; 1:1000); PPARα (ab8934, Abcam; 1:1000); retinoid X receptor (RXRα; 3085 s, Cell; 1:1000); peroxisome proliferator‐activated receptor gamma coactivator 1α (PGC1α; 20,658‐1‐AP, Proteintech; 1:1000). Targeted bands were normalized to the expression of cardiac GAPDH (sc‐32,233, Santa Cruz Biotechnology; 1:2000).
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4

Quantifying Hepatic Nuclear Proteins

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Nuclear proteins were extracted from livers with Nuclear Extraction Kit (Abcam, Cambridge, MA). Protein concentration was determined using a Pierce BCA Protein Assay kit (Thermo Fisher Scientific, Inc., Waltham, MA). Western blot was performed as described previously [29] (link) to detect PPARα (peroxisome proliferator-activated receptor-α), CPT1 (Carnitine palmitoyltransferase I), SREBP (Sterol-regulatory element binding protein), ADPN receptor 1, ADPN receptor 2, methyl-PP2A-C(Santa Cruz Biotechnologies, Santa Cruz, CA), FAS (fatty acid synthetase), SCD1 (Stearoyl-CoA desaturase-1), PP2A (protein phosphatase 2A) A, PP2A B, PP2A C, pAMPK, LKB1 (Cell Signaling Technologies, Beverly, MA), and ChREBP (Novus Biologicals, Littleton, CO). Blots were scanned using a Bio-Rad Imaging System (Image Lab™ Upgrade for ChemiDoc™ XRS + System #170-8299). All specific bands were quantified with the Automated Digitizing System (Image Lab 4.1). Results are representative of three independent experiments.
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5

Comprehensive Evaluation of PMF Efficacy

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Chromatographical acetonitrile was bought from Thermo Fisher Scientific (China). Analytical-grade petroleum ether (PE), methanol, and ethyl acetate were bought from Honeywell (USA). Ultrapure water was obtained from a Milli-Q system (Millipore, USA). The other chemicals were analysis-grade chemicals.
RPMI 1640 medium and fetal bovine serum (FBS) were purchased from Gibco (Logan, UT, USA). Cell counting kit 8 (CCK-8) was bought from DOJINDO (Japan). Antibodies (including β-actin, p-AMPK, AMPK, p-S6, S6, p-P70S6K, P70S6K, p-p53, p53, and COX-2) were purchased from Cell Signaling Technology (USA); Compound C (an AMPK inhibitor) was bought from Santa Cruz Biotech (USA). Matrix basement membrane was purchased from Corning Co., Ltd. (USA). The apoptosis-Hoechst Staining Kit was purchased from Beyotime Biotechnology Co., Ltd. (Shanghai, China). Crystal violet reagent was purchased from Damao (Tianjin, China). Ki-67 was purchased from Wuhan Servicebio Technology Co., Ltd. The four PMFs obtained from CRCP were used in DMSO and were stored at −20°C and diluted for use.
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6

Immunofluorescence Assay for Apoptosis Markers

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For immunofluorescence assays, cells were fixed with 4% paraformaldehyde for 30 minutes, followed by permeabilization using 0.5% Triton X-100 for 10 minutes. Next, cells were blocked with 5% bovine serum albumin for 1 hour and incubated with primary antibodies against Runx2 (1 : 200, Cell Signaling Technology), OPA1 (1 : 200, Cell Signaling Technology), cleaved caspase 3 (1 : 200, Cell Signaling Technology), LC3II (1 : 200, Cell Signaling Technology), or p-AMPK (1 : 200, Cell Signaling Technology) overnight at 4°C. The next day, cells were incubated with an appropriate secondary antibody (1 : 200, Cell Signaling Technology) for 1 hour at 37°C. Images were acquired using a fluorescence microscope (Olympus DX51, Tokyo, Japan). Apoptosis was detected using a terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay (Roche, Basel, Switzerland) according to the manufacturer's instructions. The apoptosis index was calculated by calculating the percentage of TUNEL-positive cells to total nucleated cells stained by DAPI.
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7

Molecular Markers in Neurodegeneration

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The following antibodies were used in western blot and immunofluorescence studies: p-AMPK, AMPK p-CREB (Cell Signaling), anti-Nrf-2, anti-PSD-95, anti-Syntaxin, anti-synaptosomal-associated protein 23 (SNAP-23), anti-Caspase 3, anti- PARP-1, anti-Cleaved Caspase-3, Synaptophysin, anti-Bax, anti-Bcl2, anti-TNF-α, anti-IL-1β, anti-p-NF-κB, anti-Iba-1, anti-GFAP, and anti-β-actin, which were all obtained from Santa Cruz Biotechnology (Dallas, TX, USA). Primary antibodies were diluted in 1× TBST (Tris-buffered saline plus Tween) (1:1000), and secondary conjugated anti-mouse horseradish peroxidase (HRP) and conjugated anti-rabbit HRP were diluted 1:10,000 in 1× TBST, all purchased from Promega USA. For confocal microscopic studies, the secondary fluorescent antibodies used were goat anti-mouse and goat anti-rabbit diluted in 1 × 100 phosphate-buffered saline (PBS).
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8

Metformin, Celecoxib, and PGE2 Effects

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T24 or RT4 cells were seeded in 6-well plates 2×105 cells/well, treated with corresponding reagents, including metformin (0, 1 mM, 5 mM, 10 mM, 20 mM), Celecoxib (20 μM YUANYE BioTECH, Shanghai, China) and PGE2(10 μM, Sigma). Cell lysates were separated on SDS-PAGE followed by western blotting assay as described [26 (link)] with the following primary antibodies: Bcl-2 (1:1000 Epitomics), Cyclin D1 (1:1000 Fantibody, China), CK14 (1:400 Abcam), STAT3 (1:2000 Abcam), OCT3/4 (1:400 Santa Cruz Biotech-nology), COX2 (1:2000 Origene), p-STAT3 (Tyr705) (1:2000 Cell Signaling), AMPK (1:700 Proteintech), p-AMPK (1:1000 Cell Signaling) and β-actin (1:5000 Cell Signaling).
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9

Western Blot Analysis of Brain Proteins

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Sagittally cut hemi-brains brains were homogenized in ice-cold RIPA buffer (PBS, 1% Igepal, 0.5% sodium deoxycholate, 0.1% SDS) with freshly added protease inhibitors (Protease Inhibitor Cocktail P8340 and, Phosphatase Inhibitor Cocktail 1&2, Sigma-Aldrich, St. Louis, MO; Phenylmethylsulfonylfluoride (PMSF), Fluka-Biochemica, Switzerland), incubated on ice for 30 min and centrifuged at 14,000 g for 10 min at 4°C. After centrifugation, the supernatant was collected and total protein concentrations were measured using the Bradford method. Tissue lysate was added to electrophoresis sample buffer and separated by SDS/PAGE under reducing conditions on a 12% separation gel. Proteins were transferred to nitrocellulose membranes using the iBlot dry-blotting system (Invitrogen Corp., Carlsbad, CA). Unspecific binding was blocked by incubation in 5% milk blocking buffer (PBS, 5% nonfat milk and 0.1% Tween 20). Membrane bound proteins were immunoblotted with antibodies to BDNF, NGF, NT3, Nrf2 (Santa Cruz Biotech, Santa Cruz, CA), p-AMPK, AMPKα (Cell Signaling, Beverly, MA), p-Nrf2 (BIOSS Antibodies, Woburn, MA) and β-actin (Abcam Inc., Cambridge, MA). Signals were developed using ECL reagent (Amersham Pharmacia Biotech, Buckinghamshire, England). Densities of the bands were evaluated using Image J software.
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10

Antibody Immunoblotting Panel

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Antibodies against CaMKII, pCaMKII, AMPK, pAMPK, mTOR, pmTOR, S6K, pS6K, 4E-BP, ACC, pACC, and Cleaved caspase-3 were obtained from Cell Signaling Technology (Beverly, MA, USA). Antibodies against NQO were purchased from Invitrogen (Carlsbad, CA, USA). Anti-β-actin, anti-rabbit IgG, and anti-mouse IgG antibodies were purchased from Sigma-Aldrich Co. (St. Louis, MO, USA).
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