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7 protocols using p ulk

1

Immunoblotting Analysis of Cell Signaling

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Cells were harvested and protein concentration was determined using the Bio-Rad Protein Assay (Bio-Rad, Munich, Germany). We subjected 20 µg acquired protein to SDS page analysis. After washing with tris-buffered saline with Tween20 and blocking in 5% skim milk, the resulting membranes were incubated overnight with antibodies to NDRG1, P-NDRG1 (Thr346), S6RP, P-S6RP (Ser240/44), 4EBP1, P-4EBP1, p62, p-ULK (all from Cell Signaling, Cambridge, UK) and LC-3 (Sigma). Following one hour of incubation with secondary rabbit or goat antibody (Santa Cruz Biotechnology, Dallas, TX, USA), chemiluminescence was used for detection.
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2

Immunoblotting Experimental Protocol

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Immunoblotting experiments were conducted as previously described (15 (link)). Antibodies used for immunoblotting were specific for the following proteins: LC3b, PERK, IRE1α, P-AMPK, AMPK (total), P-ULK (Ser757), P-ULK (Ser317), ULK (total), COXIV, cytochrome c, calnexin, HSP60, mitofusin-1, and Bcl-2 (Cell Signaling Technology); BAP31, ATF6, Tom40, Tom22, prohibitin, and VDAC1 (Santa Cruz Biotechnology); Parkin and FACL-4 (Abcam); and NDUFS4, NDUFB11, α-tubulin, β-actin, and flag (Sigma-Aldrich). Antibodies were diluted to 1:1000, except for NDUFS4 (1:500) or anti–β-actin (1:10,000). Secondary antibodies were purchased from Promega (anti-rabbit and anti-mouse at 1:5000).
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3

Vasicinone's Neuroprotective Effects on Paraquat-Induced Oxidative Stress

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Vasicinone (purity > 98%) was purchased from Cayman Chemical (CAS-486-64-6, Ann Arbor, MI, USA). Paraquat, a Mitochondria Staining Kit (JC-1 stain) and 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyltetrazolium bromide (MTT) were purchased from Sigma-Aldrich (St. Louis, MO, USA). The MitoSOXTM Red kit (M36008) was purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dulbecco’s modified Eagle medium (DMEM:F12) and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Primary antibodies against SOD-1, SOD-2, GST, GPx, TOM-20, VDAC-1, Parkin, PINK-1 and GAPDH were purchased from Santa Cruz Technology (Dallas, TX, USA), antibodies against DJ-1, α-synuclein, p-ULK, ATG7, ATG12 and LC3B were purchased from Cell Signaling Technology (Danvers, MA, USA) and an antibody against Nrf-2 was purchased from Abcam (Cambridge, MA, USA). All fluorescent secondary antibodies were purchased from Thermo Fisher Scientific in the USA.
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4

AMPK Signaling Modulation in Cell Culture

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Cell culture medium, DMEM, RPMI-1640, trypsin, phosphate-buffered saline (PBS), and FBS were purchased from Gibco (CA, United States). DMSO, 3-Methyladenine (3-MA), Compound C (HY-13418), and AMPKinone (HY-12831) were products of MedChem Express (NJ, United States). Antibodies against AMPK, p-AMPK, mTOR, p-mTOR, ULK, p-ULK, Beclin-1, and LC3I/II were obtained from Cell Signaling Technology (Danvers, MA, United States). Horseradish peroxidase-conjugated secondary antibody (IgG goat anti-rabbit or anti-mouse) and beta -tubulin antibody were purchased from CWBIO. BCA protein assay kit was product of Beyotime (Shanghai, China). MTS assay kit was purchased from Promega (Promega, WI, United States). All other chemicals used were the highest purity obtained from commercial sources.
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5

Western Blot Analysis of Protein Expression

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HCT116 and SW620 cells were lysed by cell lysis solution (1× PBS, 1% Nonidet P40, and 1 mM EDTA) containing a protease inhibitor cocktail (Roche, Mannheim, Germany). Equal amounts of protein were diluted in 2× sodium dodecyl sulfate (SDS) loading dye, separated on 8–15% SDS-polyacrylamide (SDS-PAGE) gels, and transferred onto nitro-cellulose membranes (GE Healthcare Life Sciences, Boston, MA, USA). After blocking with 5% skim milk at room temperature for 1 h, the membranes were probed overnight with primary antibodies at 4 °C. Anti-O-GlcNAc antibody was purchased from Sigma-Aldrich. An anti-PARP antibody was purchased from Invitrogen. Anti-cleaved caspase-3, IRE1α, P-eIF2α, eIF2α, CHOP, P-AMPK, AMPK, P-ULK, P-mTOR, mTOR, P-p70 S6K, p70 S6K, ATG5, and LC3B antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA). Anti-ULK, PERK, ATF6, ATF4, P-JNK, JNK, Bax, P-Bcl2, Bcl2, p62, GFAT, caspase-8, and β-actin were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Membranes were washed with TBST and incubated with horseradish peroxidase (HRP)-conjugated anti-mouse or anti-rabbit immunoglobulin G secondary antibodies at room temperature for 30 min. Immunoreactive bands were developed using an ECL Plus Detection System (GE Healthcare Life Sciences) and the bands were quantified using ImageJ software (NIH, USA).
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6

Autophagy Regulation in Cell Signaling

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TRIzol, LPS and phenylmethanesulfonyl fluoride (PMSF) were purchased from Sigma (Saint Louis, MO, USA). Deh was purchased from Shanghai Yuanye Bio-Technology Co. CCK8 was purchased from Saint-Bio Co. (Shanghai, China). Compound C (CC) and 3-methyladenine (3-MA) were purchased from Selleckchem (Shanghai, China). p-Beclin, Beclin, p-ULK, ULK, AMPK, p-AMPK and LC3B were purchased from Cell Signaling Technology (Boston, MA, USA). P62 was purchased from Proteintech (Rosemont, IL, USA). β-Tubulin was purchased from Bosterbio in Dallas (Pleasanton, USA). IgG was purchased from Beyotime (Shanghai, China). HRP-conjugated anti-mouse and anti-rabbit secondary antibodies were purchased from Bosterbio.
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7

Autophagy Regulation by OMT and RAPA

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HSFs were seeded and treated with RAPA, OMT (4.5 mg/mL), or OMT + RAPA for 12 hours, lysed, and collected. Proteins were separated, transferred, and blocked for 1 hour. The primary antibodies against light chain 3 (LC3) (Santa Cruz Biotechnology, Texas, USA) and p‐ULK (Cell Signalling Technology, Danvers, USA) were added and incubated. The secondary antibody was then added and incubated. The expression of the labelled proteins was identified by a chemiluminescence reagent on an Amersham Imager 600 chemical imaging system (GE healthcare Sciences AB, Sweden). The intensity of the band was quantified by densitometry and expressed relative to GAPDH loading controls.
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