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76 protocols using caspase 3

1

Quantification of Apoptosis Markers

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Apoptosis was quantitated by measuring the activities of caspase- 3 (Millipore Corporation, Bedford, MA, USA) and cytochrome c. The catalytic activity of caspase-3 was measured independently by using a commercial colorimetric assay according to the manufacturer’s instructions [53 (link)]. The determination is based on the detection of the chromophore p-nitroanilide at 405 nm after its enzymatic cleavage from the labeled substrate DEVD-p-nitroanilide. The specific caspase- 3 inhibitor,0.1 mM Ac-DEVD-CHO, were used as enzymatic activity controls, according to the manufacturer’s instructions. Enzyme activity was calculated as µmol of p-nitroanilide released/minute/mg of protein. Cytochrome c was measured using a Cytochromec Kit ELISA assay (Life Technologies, CA, USA), according to manufacturer’s instructions [53 (link)].
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2

Western Blot Analysis of Cellular Proteins

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Western blot analysis was performed as described previously (Binukumar et al., 2014 (link)). In brief, cells or brain tissues were lysed or homogenized in extraction buffer, respectively, and centrifuged at 10,000 × g for 5 min, and supernatants were collected and protein determined. Equal amounts of total protein (50 μg/lane) were resolved on a 4–20% SDS–polyacrylamide gel and blotted onto a polyvinylidene fluoride membrane. This membrane was incubated in blocking buffer/5% dry milk powder (wt/vol) for 1 h at room temperature, followed by incubation overnight at 4°C in primary antibodies. Primary antibodies used were as follows: Cdk5 (1:500), p35 (1:1000), TH (1:1000), cytochrome c (1:250) Bcl2 (1:200), and Bax (1:200; all Biovision), β-actin (1:10,000; Sigma-Aldrich), caspase-3 (1:250), and tubulin (1:10,000; Sigma-Aldrich). The membranes were then washed four times in Tris-buffered saline/Tween-20 (5 min each), followed by incubation in respective secondary antibody (goat anti-mouse or goat anti-rabbit immunoglobulin (L)–horseradish peroxidase conjugate at a dilution of 1:3000) for 2 h at room temperature. Western blots were analyzed using the Amersham Biosciences ECL kit following the manufacturer’s instructions (GE Healthcare).
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3

Chrysin and Sodium Selenite Cytotoxicity Study

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Chrysin (97% pure) was purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO), sodium selenite (Na2SeO3) was obtained from LOBA Chemie (Mumbai, India), and Dulbecco’s modified Eagle’s medium (DMEM) and the antibiotics streptomycin and penicillin were obtained from HiMedia (Mumbai, India). Antibodies for m-calpain, Lp82, EGR-1, COX-1, caspase-3, caspase-8, caspase-9, and β-actin were purchased from Sigma-Aldrich Chemical Co. and Cell Signaling Technologies (CST; Danvers, MA). Anti-rabbit immunoglobulin (IgG) secondary antibody was obtained from Genei (Bengaluru, India). All other chemicals and reagents were of analytical grade. Milli-Q water (Millipore, Bengaluru, India) was used throughout the experiments.
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4

Western Blot Analysis of Caco-2 Cells

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For western blot analysis, Caco-2 monolayers were grown on 6-well cell-culture plates (corning) until 100% confluency. Monolayers were then incubated with 1 × 108 parasites/mL for 6 and 12 h, respectively, washed with PBS twice, and then scraped and collected. Monolayers were then incubated with RIPA lysis buffer supplemented with protease and phosphatase inhibitors (Pierce). Lysed samples were centrifuged at 21,000 rpm at 4°C for 30 minutes. Protein concentration of the supernatant was determined with the DC Protein Assay (Bio-Rad Laboratories). SDS-PAGE gels (12% and 15% Tris-HCL Ready-Gels; Bio-Rad Laboratories) were used to separate total proteins. Proteins were then transferred using a polyvinylidene difluoride (PVDF) membrane (Immobilon-P; Millipore). 5% of nonfat dry milk in % TBS-T was then used to block the membranes. After blocking, membranes were incubated with primary antibodies against, caspase 3, caspase 8, caspase 9, or ZO-1 (1 : 1000; Sigma) overnight at 4°C. After incubation with primary antibodies, membranes were washed and incubated with HRP-tagged secondary antibodies. Bands were detected using Amersham ECL Plus western blotting detection system (GE Healthcare). Autoradiographic films (Kodak) were then exposed to the membranes and developed on X-ray film processor SRX-101A (Konica Minolta).
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5

Immunoblotting for Apoptosis Markers

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Immunoblotting was performed as previously described20 (link) using the LiCOR imaging system (Lincoln, Nebraska USA). The following primary antibodies from Cell Signalling Technology (London, UK) were used: PARP (#9542), cleaved PARP (#5625), Caspase 3 (#9662), cleaved Caspase 3 (#9664), pH2A.X (#9718), as well as CLIC5 (AV35262, Sigma-Aldrich, Gillingham, UK) and Beta-Actin (Clone C4, MP Biomedicals, Loughborough UK).
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6

Molecular Mechanisms of Cytotoxicity

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All RPMI 1640 culture media, glutamine, FBS, penicillin, streptomycin, trypsin, primers for p53, caspase-3, Bcl-2, Bax, GAPDH, solvents, dyes, and chemicals were purchased from Sigma-Aldrich, St. Louis, MO, USA. Primary antibodies included TNF-α, 8-OHDG, Cas-3, GAPDH, IKK-α, and IKK-β, and horseradish peroxidase-conjugated secondary antibodies were obtained from Santa Cruz Biotechnology, (Dallas, TX, USA). Western blot kits were purchased from Amersham, Buckinghamshire, UK.
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7

Immunoprecipitation and Western Blot Analysis

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MCF-7 and SKBR-3 cells were washed with cold phosphate-buffered saline (PBS), and then total proteins were extracted with 100 uL of radioimmunoprecipitation assay (RIPA) buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM Na2EDTA, 1 mM EGTA, 1% NP-40, 1% sodium deoxycholate) containing 1X protease inhibitors cocktail from Sigma (cat.# P8340; (St. Louis, MO, USA). Immunoprecipitation by specific antibodies was performed as previously reported [19 (link)]. Immunoprecipitated proteins were subjected to Western blotting (WB) following standard protocols (Amersham BioSciences, Piscataway, NJ, USA), and the membranes were probed for FASN, AKT1, p-AKT1, small ubiquitin-like modifier (SUMO)1, SUMO2/3, ubiquitin-conjugating enzyme 9 (UBC9) (Santa Cruz Biotechnology, Dallas, TX, USA), Ubiquitin (UBC) (Proteintech, Rosemont, IL, USA), caspase-3 (CASP-3), caspase-9 (CASP-9), and β-actin (Sigma-Aldrich). Bands were detected using an enhanced chemiluminescence detection system (Millipore Corporation, Billerica, MA, USA). Quantification of relative band intensity was performed using Quantity One version 4.6.6. basic (Bio-Rad, Hercules, USA), and β-actin was used as a normalizing factor.
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8

Western Blot Analysis of Apoptosis and Autophagy

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Cells were harvested and lysed in a lysis buffer (62.5 mM Tris at pH 6.8, 20% glycerol, 2% SDS, phosphatase inhibitor), proteins were separated on SDS polyacrylamide gels and transferred to PVDF membranes (Millipore, Billerica, MA, USA). The membranes were blocked with 5% nonfat milk, and immunoblotted with primary antibodies at 4 °C overnight. After washed three times with TBST, membranes were incubated for 1 h with appropriate secondary antibodies at room temperature. The follow antibodies were used in our experiments: Caspase-3 (CST, 9662), Cleaved-Caspase-3 (CST, 9661), Caspase-9 (CST, 9502), PARP (CST, 9542), LC3 (Sigma, L7543), P62 (BML, PM045), PINK1 (CST, 6946), Tim23 (BD, 611222), Tom20 (sc-17764), E-cadherin (CST, 3195), Vimentin (CST, 5741), pAKT (Ser473, CST, 9171), AKT (CST, 9272), Cofilin (CST, 5175) and GAPDH (CST, 5174). GAPDH was used as the loading control. Membranes were visualized with Image Quant LAS 4000 (General Electric Company).
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9

Nanocarrier-Mediated Doxorubicin Delivery

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Doxorubicin (DOX), GO-201 trifluoroacetate salt (MUC1 inhibitor), Rhodamine 123 (Rh 123), Rhodamine B (RhoB), 4,6-diamidino-2-phenylindole (DAPI), Fluorescein isothiocyanate (FITC), Coumarin-6, poly ethylene glycol-5000 (PEG-5000), caprolactone, Tin (II) 2-ethylhexanoate, 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT), Dimethylsulfoxide (DMSO), Bradford reagent, chemiluminescence reagent purchased from Sigma aldrich (Merck, USA). Amicon ultracentrifugal filters (10 kDa), Protein estimation kit by BCA (Bicinchoninic acid) method (GeNei) were obtained from Merck Millipore (Billerica, MA, USA.) Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum (FBS), Trypsin, Dulbecco Phosphate Buffered Saline (PBS) and penicillin–streptomycin antibiotic solution were purchased from Gibco (Life Technologies), USA. Acridine Orange (Thermo scientific), 4% Paraformaldehyde, Crystal Violet, Radio-immunoprecipitation assay (RIPA) lysis buffer, Tris-buffered saline (TBST) were obtained from Hi Media (India). Annexin V-FITC assay kit was obtained from BD Biosciences (San Jose, USA). Primary antibodies i.e. caspase-3 and Bcl-2 were procured from Sigma Aldrich (USA), β-actin and secondary antibodies were purchased from (Santa Cruz Biotechnology, USA). X-ray films were purchased from Amersham Biosciences, UK.
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10

Colorimetric Assay for Caspase Activity

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The activities of caspases were assayed using caspase-3 (Sigma, St. Louis MO, USA) and caspase-9 (Calbiochem, USA) colorimetric assay kits according to the manufacturer’s instructions. Cytosolic extracts were prepared by homogenizing tissues in lysis buffer containing 50 mM HEPES (pH 7.4), 5 mM 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate (CHAPS) and 5 mM DTT. The supernatant was collected as an enzyme source. The assays are based on the hydrolysis of the peptide substrate acetyl-Asp-Glu-Val-Asp-nitroanilide (Ac-DEVD-pNA) by caspase-3, and Leu-Glu-His-Asp-nitroanilide (LEHD-pNA) by caspase-9 and subsequent release of the chromophore p-nitroaniline (pNA). The concentration of pNA released from the substrate was calculated from the absorbance values at 405 nm.
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