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16 protocols using cox 4

1

Immunofluorescence Imaging of Platelet Proteins

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Washed platelets (1 × 106 cells/ml) were allowed to settle on glass‐bottomed dishes for 1 h prior to fixing with 4% paraformaldehyde solution (Santa cruz Biotechnology). The platelets were then washed 2 × 5 min in PBS and permeabilized for 5 min in 0.25% Triton X‐100/PBS. They were blocked for 60 min in 10% bovine serum albumin (BSA)/PBS at 37°C and incubated in 3% BSA/PBS/primary antibody for 2 h at 37°C, or overnight at 4°C, and then washed 6 × 2 min in PBS, followed by an additional incubation for 45 min at 37°C in secondary antibody/3% BSA/PBS. Antibodies for LC3 (Cosmo bio, Japan), Parkin (Abcam, USA), LAMP1 and pp53 (Ser15) (Cell Signal, USA), and CoxIV (Santa Cruz, USA) were used. The stained platelets were observed using a Nikon Eclipse‐Ti confocal microscope with 100× oil immersion lens.
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2

Western Blot Analysis of Oxidative Stress Markers

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Homogenized lung tissue or cell lysates were supplemented with phosphatase and protease inhibitors (both from Gold Biotechnology, Olivette, MO). Western blotting was performed as we previously described26 (link). Briefly, 8–16% polyacrylamide gels (Invitrogen Corp, Carlsbad, CA) were used to separate the proteins. We used GAPDH (Abcam, Cambridge, MA), 4-HNE (Percipio Biosciences, Burlingame, CA), Cys106-oxidized DJ-1 (HCA024, Bio-Rad, Hercules, CA), β-actin (Sigma, St. Louis, MO), lamin-B1, Tom 20, DJ-1, His-tag, VDAC1, IKBα, COX IV and PDI (all were purchased from Santa Cruz Biotechnology, Dallas, TX). Horseradish peroxidase (HRP)-conjugated AffiniPure donkey IgG were obtained from Jackson ImmunoResearch (West Grove, PA). The blots were then developed using an enhanced chemiluminescence western blotting kit according to the manufacturer’s instructions (Amersham Pharmacia Biotech, Piscataway, NJ). Images were quantitated using ImageJ software.
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3

Prostate Cancer Cell Lines and Signaling

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Stable DAB2IP-expressing sublines (i.e., D1, D2) of androgen-independent C4-2 with its empty vector control (i.e., Neo) subline and stable DAB2IP-knockdown subline (i.e., KD) of androgen-responsive LAPC-4 with its empty vector control (i.e., Con) subline were generated previously.12 (link) C4-2 cells were maintained in T-medium (Gibco, San Diego, CA, USA) containing 5% (v/v) FBS (Invitrogen, Carlsbad, CA, USA) and LAPC-4 cells were maintained in Iscove's modified Dulbecco's medium (Gibco) containing 10% FBS at 37 °C with 5% CO2 in a humidified incubator. To deplete androgen, cells were sub-cultured in Phenol Red-free RPMI-1640 with 5% or 10% CS-FBS (Hyclone, Omaha, NE, USA). Antibodies for p-STAT3 (Tyr705), p-STAT3 (Ser727), Bcl-2, Bcl-xL, Mcl-1, Caspase-9, cleaved Caspase-3 and cleaved PARP were purchased form Cell Signaling Biotechnology (Beverly, MA, USA). Antibodies for t-STAT3, survivin, Bax, p53, cytochrome c, Omi/HtrA2, Smac, GAPDH and COX IV were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Antibody for Actin was purchased form Sigma-Aldrich (St. Louis, MO, USA).
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4

Comprehensive Antibody Profiling for Cellular Analysis

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Antibodies including; CBS, CSE, MTHFR, Hcy, DNMT1 and DNMT3a were all obtained from Abcam (Cambridge, MA USA). Additional antibodies SAHH, HSP-60, Calpain-1, p47phox, gp91phox, TRX-2, MnSOD, TIMP-1, TIMP-2, ZO-1,Occludin, LC3, Mfn-2, Drp-1 and COXIV were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). GAPDH was acquired from Boster Biological Technology (Pleasanton, CA, USA).
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5

Mitochondrial Protein Extraction and Western Blot Analysis

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Total proteins were extracted with a RIPA buffer (Sigma Chemical Co., St. Louis, MO, USA). The mitochondria and cytosol fractions were isolated using a Mitochondria Isolation Kit (Abcam, Cambridge, MA, USA) following the manufacturer’s procedure. Western blotting was conducted as describe in our previous report [24 (link)]. Briefly, 25 μg of total extracted proteins were separated via 10–12% SDS-PAGE prior to nitrocellulose membranes transfer by electroblotting, which was then blocked with 5% skimmed milk for 1 h. Blots were then incubated with specific antibodies HO-1 (1:200), Bax (1:200), Bcl-2 (1:200), cytochrom C (1:200), β-actin (1:500), and Cox IV (1:500) (Santa Cruz Biotechnology, Santa Cruz, CA, USA) and caspase-3 (1:500) (Cell Signaling Technology, Beverly, MA, USA) overnight at 4 °C;. The horseradish peroxidase-conjugated antibodies were regarded as the secondary antibody. The bands were detected by chemiluminescence using the ECL Western blotting assay kit (Life Technologies, Seoul, Korea) and visualized by Davinch-Chemi Imager™ (CAS-400SM, Core Bio, Seoul, Korea).
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6

Mitochondrial Pathway Analysis in Laryngeal Cancer

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Human laryngeal carcinoma tissues or cells were washed with ice-cold PBS and lysed with RIPA lysis buffer (Beyotime, Jiangsu, P.R. China) containing protease and phosphatase inhibitors (Roche Applied Science, Indianapolis, IN, USA) at 4°C. Mitochondrial fractions were extracted using the Mitochondria Isolation Kit (Sigma-Aldrich) according to the supplier’s instructions. The protein concentration was determined by Enhanced BCA Protein Assay Kit (Beyotime). An equal amount of protein was separated by 10%–12% SDS-polyacrylamide gels and then transferred to polyvinylidene fluoride (PVDF) membranes (Millipore, Billerica, MA, USA). Five percent nonfat milk was added to membranes to block nonspecific binding at room temperature for 1 h. The membranes were then incubated with the following primary antibodies: TIMP-3 (1:500), Cox-IV, GAPDH, β-actin (1:1,000; Santa Cruz Biotechnology, Santa Cruz, CA, USA); cytochrome c, caspase 9, and caspase 3 (1:1,000; Cell Signaling Technology, Billerica, MA, USA). The immunoreactive proteins were detected with horseradish peroxidase-conjugated secondary antibodies (goat anti-rabbit or rabbit anti-mouse; 1:1,000; Beyotime) and an enhanced chemiluminescence reagent (Pierce Biotech, Rockford, IL, USA). Densitometry of bands was quantified using ImageJ software (NIH, Bethesda, MD, USA).
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7

Apoptosis Induction in Glioma Cells

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The SW used in this study was extracted from Oxytropis kansuensis Bunge and characterized in our laboratory according to the published protocol 22 . Its purity was up to 99%. SW was dissolved in phosphate buffered saline (PBS, 0.01 mol/L, pH 7.2) at 10 mg/mL as stock solution, and stored at -20 oC after sterile filtration.
Antibodies against caspase-8, caspase-9, caspase-3, PARP, Bid, Bcl-2, Bax, cytochrome c, COX IV and β-actin were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Horseradish peroxidase (HRP)-conjugated secondary antibody was purchased from Wuhan Boster Bio-Engineering (Wuhan, China). Caspase-8 inhibitor (z-IETD-fmk), caspase-9 inhibitor (z-LEHD-fmk) and caspase-3 inhibitor (z-DEVD-fmk) were all purchased from Sigma-Aldrich (St. Louis, MO, US). TUNEL BrightRed Apoptosis Detection Kit was purchased from Vazyme (NJ, USA). All of other chemicals and reagents were the highest quality and obtained from standard commercial sources.
Primary GTCs were obtained according to our previous study 23 (link), and cultured in complete DMEM/F12 culture medium supplemented with 10% FBS, 100 U/mL of penicillin and 100 μg/mL of streptomycin, at 37 oC in a 5% CO2 atmosphere incubator. All animal experiments were carried out in accordance with policy and ethical guidelines.
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8

Mitochondrial and Cytosolic Protein Profiling

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Protein (20-60 g cytosol, mitochondrial) was separated on an 8–19% SDS–PAGE, transferred to a nitrocellulose membrane, and blocked with 5% non-fat milk for 1 hour. The membranes were incubated with antibodies against TFAM (Santa Cruz Biotechnology, Santa Cruz-CA) or Hsp70 (Abcam, Cambridge, MA) overnight at 4°C. β-actin (Sigma-Aldrich) was used as a loading control for cytosolic fraction, and Cox IV (Santa Cruz Biotechnology) for the mitochondria fraction.
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9

Andrographolide-Induced Apoptosis Pathway

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Andrographolide was procured from Santa Cruz Biotechnology (Santa Cruz, CA, USA), dissolved in DMSO and kept at 4 °C at a concentration of 50 mM. AnnexinV-FITC Apoptosis Detection Kit was purchased from BD Pharmingen (Pharmingen, USA). Caspases fluoremetric assay kit was purchased from Chemicon International Corporation (USA). Ac-DEVD-CHO (caspase-3 inhibitor), and Ac-LEHD-CHO (caspase-9 inhibitor) were from Calbiochem (La Jolla, USA). Primary antibodies (Bcl-2, Bcl-xL, Bax, Apaf-1, cytochrome c, β-actin and COX IV) and polyclonal secondary antibody were obtained from Santa Cruz Biotechnology Inc. (Santa Cruz, USA). The fetal bovine serum (FBS), Dulbecco’s Modified Eagle’s Medium (DMEM), and antibiotics were purchased from Gibco BRL (Grand Island, USA). Plastic wares for cell culture were procured from NUNC (Roskilde, Denmark). Other chemicals including 4, 6-diamidino-2-phenylindole (DAPI), 3[4-dimethylthiazol-2-71]-2-5-diphenyl tetrazolium bromide (MTT) were from Sigma-Aldrich (St. Louis, USA).
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10

Characterization of Mitochondrial Dynamics

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Common laboratory reagents were purchased from Life Technologies (Grand Island, NY, USA), Sigma (St. Louis, MO, USA) and Thermo Scientific (Waltham, MA, USA), unless otherwise mentioned. PE, Ang II, Iso and LMB were from Sigma. Ionomycin, BAPTA-AM, fluorescent conjugates and other microscopy consumables were from Life Technologies. Mitochondria Isolation Kit and Co-IP Kits were from Pierce Biotechnology (Rockford, IL, USA). PInh was from Calbiochem (La Jolla, CA, USA). JC-1 Staining Kit was from Cayman Chemicals (Ann Arbor, MI, USA). DAPI, Hoechst 33342, propidium podide (PI), Annexin V-Alexa Fluor 488, TMRM, MitoTracker red FM, CellLight Mitochondria-RFP and BacMam 2.0 system were from Life Technologies. Primary antibodies were procured from the following sources: Anxa6 (monoclonal antibody) from BD (Lexington, KY, USA); Anxa6 (polyclonal antibody), COX IV (cytochrome c oxidase subunit IV), Akt, p-AktS473 and α-SkA from Santa Cruz Biotechnology (Santa Cruz, CA, USA); α-tubulin, cleaved caspase-3, cleaved caspase-9, Parp1 and cleaved Parp1 from Cell Signaling Technology (Beverly, MA, USA); pro-ANP from Abcam (Cambridge, MA, USA); anti-COX I monoclonal antibody from Invitrogen (Carlsbad, CA, USA); Living Colors anti-fluorescent protein antibody (JL-8) from Clontech (Mountain View, CA, USA) and pan-actin from Chemicon (Temecula, CA, USA).
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