Publication protocol
Nuclear and cytoplasmic protein extracts were prepared using NE-PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Scientific, Rockford, IL) according to the manufacturer’s instructions. Protein concentrations were measured using a BCA protein assay reagent kit (Thermo Scientific). Primary antibody binding was detected using horseradish peroxidase-conjugated secondary antibodies (1:2000 dilution; Cell Signaling Technology, Beverly, MA) and SuperSignal West Femto Maximum Sensitivity Substrate (Thermo Scientific). Densitometry was performed using a ChemiDoc XRS with Quantity One software (Bio-Rad).
Several bioenergetic pathway proteins were analyzed. Primary antibodies purchased from Cell Signaling Technology included antibodies to phospho-Thr172 AMP-activated protein kinase (AMPK) (1:1000 dilution; #2531), AMPK (1:1000 dilution; #2603), phospho-Ser133 cAMP-response element binding protein (CREB) (1:500 dilution; #9198), p38 mitogen activated protein kinase (p38 MAPK) (1:1000 dilution; #9212), phospho-Thr180/Tyr182-p38 (1:1000 dilution; #4511), Akt (1:1000 dilution; #5373), phosphor-Ser473 Akt (1:1000 dilution; #4060), mammalian target of rapamycin (mTOR) (1:1000 dilution; #2983), phospho-Ser2448 mTOR (1:1000 dilution; #2976), TFAM (1:500 dilution; #7495), forkhead box protein O1 (FOXO1) (1:500 dilution; #2880), and GAPDH (1:2000 dilution; #2118). Primary antibodies purchased from Abcam (Cambridge, MA) included antibodies to PGC-1β (1:500 dilution; #ab61249), and citrate synthase (CS) (1:500 dilution; #ab96600). Primary antibodies purchased from Santa Cruz Biotechnology (Santa Cruz, CA) included antibodies to CREB (1:200 dilution; #sc-25785) and NRF1 (1:200 dilution; #sc-33771). Antibodies to PGC-1α (1:1000 dilution; #PA5-22958) and histone deacetylase 1 (HDAC1) (1:1000 dilution; #PA1-860) were purchased from Thermo Scientific. An antibody to COX4 was purchased from Life Technologies (A21348, 1: 2000). GAPDH and HDAC1 were used as internal loading controls for cytoplasmic and nuclear fractions, respectively.
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