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19 protocols using q vd oph

1

Caspase Inhibition in Chick Embryo Development

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Fertilized white Leghorn chicken eggs were incubated at 38°C to reach Hamburger-Hamilton stages 11–17 (HH11–17, 40–64 hours) (Hamburger and Hamilton, 1951 (link)). Embryos were removed from eggs using a ring of filter paper adhered to the vitelline membrane and placed ventral side up into 35 mm Petri dishes, as described previously (Voronov and Taber, 2002 (link)). To eliminate artifacts due to surface tension, a second filter paper ring and a stainless steel ring were placed on the embryo to keep it submerged under approximately 1 ml of culture media. Embryos were cultured in a plastic bag with supplemented oxygen (Voronov and Taber, 2002 (link)).
To inhibit apoptosis, the irreversible caspase inhibitor Q-VD-OPh (ApexBio, A1901) or Z-VAD-fmk (ApexBio, A1902) was added to the media at stages HH11 to HH14-, before significant invagination occurred, for a concentration of 100, 150, or 200 μM. Q-VD-OPh is a pan-caspase inhibitor with very little toxicity to cells (Caserta et al., 2003 (link)), while Z-VAD-fmk preferentially inhibits caspase 3 at low concentrations (Caserta et al., 2003 (link)). Embryos were cultured overnight (16 to 23 hours), then imaged as described below.
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2

Subcutaneous Q-VD-OPh Administration

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Q-VD-OPh (APExBio, Cat.No.: A1901) was dissolved first in DMSO and then diluted to the final concentration (2 mg/mL, 50% DMSO) with saline. Animals received injections of 10 mg/kg s.c., twice daily, with an injection volume of 5 mL/kg body weight.
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3

Combinatorial Inhibitor Treatment Protocol

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The HDI romidepsin (Cat #S3020) and the ERK inhibitor ulixertinib (Cat #S7854) were purchased from Selleck Chemicals (Houston, TX, USA). The PI3K inhibitor GDC-0941 (Cat #CT-G0941) and mTOR inhibitors AZD-8055 (Cat #CT-A8055) and NVP-BEZ235 (Cat #CT-BEZ) were from ChemieTek (Indianapolis, IN, USA). The mTOR inhibitor rapamycin (Cat #1292) was obtained from Tocris/R&D Systems (Minneapolis, MN, USA). The BRD inhibitor OTX-015 (Cat #15947) was purchased from Cayman Chemicals (Ann Arbor, MI, USA). The pan-caspase inhibitor Q-VD-OPh (Cat #A1901) was obtained from ApexBio Technology (Houston, TX, USA).
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4

Neutrophil Death Kinetics Assay

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In cell death induction assays, leukocytes (1×106 cells/ml) were incubated at indicated concentrations with L-leucyl-L-leucine methyl ester (LLME) (G-2550; Bachem), Q-VD-OPh (ApexBio), necrostatin-1 (Enzo LifeScience), TNF-α (Promokine) and actinomycin (PeproTech). MitoQ was a gift from Michael Murphy. Viability was assessed by flow cytometry as described above. Live cell images were acquired on a Zeiss Axio Observer of total bone marrow cells of female and male 6–12 week-old mice stained for 30–40 min on ice with fluorescently labeled antibody for neutrophils (Ly6G+) and DAPI to visualize dead cells. Cells were kept at 37°C following administration of 100μM LLME. Life cell images were taken every 30sec over a time frame of 120min. Live cell images over time were analysed using dot quantification feature of IMARIS quantifying the number of Ly-6G+ neutrophils and DAPI+ dead cells over time.
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5

Protease-Mediated Protein Cleavage Analysis

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HEK and THP-1 cells were lysed in 0.1% Triton X-100 lysis buffer without protease inhibitors followed by 2× 30sec sonication (Soniprep 150 plus, MSE). Lysates were clarified at 10’000g for 10min at 4°C and supernatant was collected. Total protein concentration in lysates was determined by the BCA assay (ThermoFisher Scientific). Cell lysates (12.5 μg HEK; 25μg THP-1) were incubated for 1h at 37°C with recombinant caspase-11 (175nM final concentration) (Enzo LifeScience, BML-SE155–5000) or with purified human CatG, NE or PR3 (Athens Research Technologies) at indicated concentrations ranging from 4–136nM. Where indicated, Q-VD-OPh (1mM)(ApexBio) or cathepsin G inhibitor I (CatGInh)(1mM)(Calbiochem, 429676–93-7) were preincubated for 5 min at 37°C before the protease treatment. Proteolysis was stopped by adding final concentration of 1x Laemmli Buffer with DTT (25mM) to the reaction and incubated for 5 min at 95°C prior to loading on SDS-PAGE.
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6

GFP-Bax Expression and Apoptosis Imaging

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hBax-C3-EGFP (Addgene plasmid 19741) (Nechushtan et al., 1999 (link)) was used for transient GFP-Bax expression in HeLa cells. Transient transfection was performed using X-tremeGENE 9 (Roche 06365787001) at a ratio of 3 µL of transfection reagent to 1 µg DNA. MitoTracker Deep Red (Thermo 22426) was used for cellular staining at 20 nM. Drug treatments used were ABT-737 at 10 µM (Cayman 11501) and Q-VD-OPh at 10 µM (APExBIO A1901).
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7

Cell Viability Assay for MCL-1 Inhibitors

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Human cell lines were originally sourced from the American Type Culture Collection (ATCC) and were authenticated by Promega GenePrint 10 System (Promega WI, USA). Cells were maintained at 37 °C with 5% CO2 with 10% fetal bovine serum (FBS), except for in vitro experiments using A1210477 where FBS level was reduced to 3% during drug treatment and also in the relevant control samples. Cell viability was determined by CellTiter 96 MTS assay (Promega) after 48 h incubation with the indicated concentration of MCL-1 inhibitor UMI-77 (Selleck, UK), S63845 (Apexbio, UK) or A1210477 (Apexbio, UK). SYTOX Green (Invitrogen, UK) was used to identify dead cells and cell confluence measured using the Incucyte Live Cell Analysis System (Essen Bioscience, UK). 10 μM etoposide (Sigma, UK) was used to induce apoptosis and 10 μM Q-VD-OPh (Apexbio, UK) was used to block caspase activity. CRISPR/Cas9 gene editing using the LentiCRISPRv2 system (Addgene, MA, USA) was performed for BAX and BAK as described previously2 (link).
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8

Lung Cancer Cell Line Authentication

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All human non-small cell lung cancer cell lines, (A549, H460, H358, H23, H727, H23, Calu-1, Calu-6, PC-9, H1975, H3255, Hcc827, H1650, H1437, H596, H1648, and H1993) and embryonic kidney cell line HEK 293T were obtained from the American Type Culture Collection (ATCC) and grown in media as recommended by ATCC. Cell lines were authenticated using a short tandem repeat (STR) DNA profiling from the cell bank from which they were acquired. Cell lines were authenticated when initially acquired and every six months using a commercial vendor. Cell lines were tested for mycoplasma every six months using MycoAlert Detection Kit (Lonza). Harmine (286044-1G) and cyclohexamide (C4859) was purchased from Sigma-Aldrich and Q-VD-oPH (A1901) was purchased from ApexBio Technology.
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9

Cytotoxicity Assay of CLL Cells

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Cell-lines or primary CLL samples were labeled with cell trace violet (CTV) (Thermo Fisher Scientific) according to manufacturer’s instructions and cocultured with HD PBMCs or CLL derived (autologous) T cells in different effector to target (E:T) ratios. Where indicated, T cells were pretreated for 2 hours with 1 µM concanamycin A (CMA) or dimethyl sulfoxide (DMSO) as a control. The treated T cells were thoroughly washed before using in the coculture. 10 or 20 µM of the pan-caspase inhibitor QVD-OPh (APExBIO) was added to the cocultures where indicated. Viability of the target cells was assessed using TO-PRO-3 (Invitrogen) and MitoTracker Orange (Invitrogen) using Flow Cytometry. Specific lysis of target cells was calculated as (% target cell death in treated sample - % cell death target cells in medium control)/(100 – % cell death target cells in medium control) * 100%. Samples were excluded when cell death in medium controls exceeded 50%.
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10

Cytokine-Driven Cellular Signaling Assay

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Recombinant human proteins were obtained from the following the manufacturers: basic fibroblast growth factor, platelet-derived growth factor, Fms-related tyrosine kinase 3 ligand and vascular endothelial growth factor (all R&D Systems), Epidermal growth factor (Sigma), stem cell factor (Peprotech, Rocky Hill, NJ, USA), CCL3 (R&D Systems), CCL5 (R&D Systems) and CCL23 (BioLegend, San Diego, CA, USA).
The following inhibitors were used: mTOR inhibitors AZD8055 (Selleckchem, Houston, TX, USA) and rapamycin (Cell Signaling, Boston, MA, USA), PI3K inhibitor CAL101 (Selleckchem), caspase inhibitor Q-VD-OPh (Apexbio, Houston, TX, USA), GSK3 inhibitor CHIR99021 (Sigma), CCR1 inhibitor BX471 (Sigma), CCR2 inhibitor INCB3284 (Tocris Bioscience, Bristol, UK) and CCR5 inhibitor Maraviroc (Apexbio).
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