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13 protocols using sirolimus

1

Cell Viability Assessment of Sirolimus and Rapamycin

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The MTT (3-[4,5-dimethylthiazole-2-yl]-2,5-diphenyltetrazolium bromide) assay was used to examine cell viability. SMM103 cells (1500/well) were seeded into 96-well plate with 50ul of medium and maintained in an incubator at 37 °C in a humidified, 5% CO2 atmosphere. After culturing for 24 h, cells were treated with 50ul of culture medium containing various concentrations of sirolimus (a kindly gift from Hangzhou Zhong Mei Hua Dong Pharmaceutical CO., LTD) (0, 0.01, 0.1, 1, 10, 100 nM) or rapamycin (Selleck, S1039) (0, 0.01, 0.1, 1, 10, 100 nM) for 72 h or treated with 50ul of culture medium captaining 100nM sirolimus or rapamycin at various timepoints (0, 3, 6, 24, 48, 72 h). Five multiple wells were set for each sample. Subsequently, 15ul of dye solution was added to each well and incubated for 4 h. The 96-well plate was read at 570nm absorbance by a microplate reader.
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2

Solubilization of mTORC1/2 Inhibitors

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The dual mTORC1/2 inhibitor, AZD8055 (AstraZeneca, London, UK), was prepared for in vitro assays by dissolution in DMSO to 10 mM (4.65 mg/mL), per manufacturer instructions. The selective mTORC1 inhibitor, sirolimus (Selleckchem, Houston, TX), was prepared for in vitro assays by dissolution in 100% ethanol to 10.9 mM (10 mg/mL). For in vivo assays, AZD8055 was dissolved by sonication in 30% Captisol (CyDex Pharmaceuticals, Lenexa, KS) to a working concentration of 2 mg/ml and pH of 5.0 per manufacturer instructions. For in vivo assays, sirolimus was dissolved in 5% Tween-80 (Sigma Aldrich) and 5% PEG-400 (Hampton Research, Aliso Viejo, CA) to a working concentration of 0.4 mg/ml. Doses of ~ 200 μl drugs were administered to each animal.
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3

Standardized Vehicle Preparation for Pharmacological Studies

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Tacrolimus (Selleckchem, Houston, TX) and sirolimus (Selleckchem) were mixed into
1.5% Tween-80 in 0.9% saline, which served as the vehicle for both drugs. PEA
(Selleckchem), was dissolved in sterile corn oil (Sigma-Aldrich, Saint Louis,
MO), which also served as the vehicle for that experiment. Secukinumab (VA
Inpatient Pharmacy, Portland, OR) was made in a in a vehicle of 1.75% Tween-80
in 0.9% saline. Tacrolimus and sirolimus were administered by intraperitoneal
(i.p.) injection at a volume of 10 mL/kg body weight. PEA and secukinumab were
administered subcutaneously (s.c.) at a volume of 10 mL/kg body weight. Ethanol
(200 proof, Decon Labs, King of Prussia, PA) was dissolved in tap water to a 20%
v/v Ethanol solution. Saccharin sodium salt hydrate (Sigma) was dissolved in tap
water to a concentration of 8.5 mM.
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4

Cell Line Characterization and Compound Screening

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T47D, MCF7 cells were purchased from American Type Culture Collection (ATCC) in 2012 - 2015. They were authenticated using STR testing and tested negative for Mycoplasma contamination. EFM19, BT474, MDAMB453, HCC202, MDAMB361, HCC1419, MDAMB415, HCC1937, CAL51, BT20, HCC1954, and JIMT1 cells were purchased from Cancer Cell Line Encyclopedia (CCLE) at the Broad Institute in 2015-2016, and were authenticated using SpectroCHIPII-G384 by Sequenom's MassARRAY Analyzer Compact. All the cells were maintained in RPMI-1640 with 10% fetal bovine serum. BYL719, GDC0941, BKM120, AZD1208, GDC0032, PI-103, BX795, BX912, MK2204, GDC0068, sirolimus, everolimus, PP242 and WYE were purchased from Selleck Chemicals (Supplementary Material and Methods). Blasticidine was purchased from Life Technologies. LGH447 was obtained from Novartis.
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5

Evaluation of mTOR Inhibitors

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The following drugs were used in this study: PP242 (Selleckchem; S2218), sirolimus (Selleckchem; S1039), torin 1 (MilliporeSigma; 475991), cycloheximide (CHX) (MilliporeSigma; 239763), tacrolimus (FK506; MilliporeSigma, F4679). Treatment with different compounds was carried out for 18 hours unless stated otherwise in the figure legends.
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6

Seizure Behavior Monitoring in cKO Mice

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cKO mice and littermates (n = 5 mice/goup) were tested for seizure behavior during the night, because mice are nocturnal animals and more active at night. Spontaneous seizure and seizures induced by the ringing of a clock every 1 hour were video-recorded for 5 days. The behaviors of the mice were scored by two independent observers, who were blinded to their genotype. In the rapamycin treatment experiments, behavior analysis was performed after 3 weeks of oral sirolimus (Selleck) in distilled water.
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7

Cilia Imaging Protocol for CFPAC-1 Cells

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CFPAC-1 cells were seeded on glass coverslips in 12-well plates containing 1 ml of culture medium per well. At 30% confluency, cell media was replaced by low serum medium containing 2% FBS. After 8 days of compound treatment, cells were fixed with 4% Formaldehyde (Merck), permeabilized with 0.1% Triton X100 (Merck) in DPBS, blocked with 1% BSA (Applichem) in DPBS, and incubated with 1:1000 dilution of anti-acetylated tubulin antibody or 1:500 dilution of anti-IFT88 antibody (Cat. No. 13967–1-AP, Proteintech) for 1 h, followed by incubation with 1:1000 dilution of fluorescent secondary antibody for 1 h. Nuclei were counterstained with DAPI (Vector Laboratories, Vectashield (Cat. No. H-1500). Images of primary cilia were captured by acquiring Z-stacks using either a Bio-Rad Radiance or Nikon C2 Eclipse Ti-E confocal laser scanning microscope by 40X or 60X oil immersion lenses. All drugs selected for confocal reconfirmation experiments were purchased from Sigma, except for Almotriptan Malate and Sirolimus which were obtained from Selleckchem. Gefitinib was from Invivogen, Cefprozil Monohydrate from Abcam and Imexon from MicroSource Discovery Systems Inc.
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8

Antibody Screening for Cell Signaling

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Antibodies used in these experiments included the following: anti-RND2 (13844–1-AP, Proteintech, USA), anti-Rho7/Rnd2 (GXT56070, GeneTex, USA), anti-p-p38 (#4511, Cell Signaling Technology, USA), anti-p38 (#9212, Cell Signaling Technology, USA), anti-cleaved-caspase3 (ab32042, Abcam, UK), anti-caspase3 (NB100-56708SS, Novus, USA), anti-BAX (50599–2-Ig, Proteintech, USA), anti-GAPDH (#5174, Cell Signaling Technology), anti-P62 (M162–3, Medical Biological Laboratories, Japan), anti-Beclin1 (11306–1-AP, Proteintech, USA), anti-LC3B (GB11124, Servicebio, China), anti-DYKDDDK/Flag-tag (ANT102, Antgene, China), and anti-His-tag (D291–3, Medical Biological Laboratories, Japan). The autophagy inhibitor wortmannin (3-MA) and the autophagy activator rapamycin (Sirolimus) (S1039, USA) were purchased from Selleck (S2758, USA).
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9

VZV Glycoprotein Fusion Assay

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Tacrolimus (FK506) (Selleckchem), pimecrolimus (Selleckchem), sirolimus (Selleckchem), and ionomycin (Alomone labs) were all dissolved in DMSO (Sigma Aldrich). Activity of the compounds on VZV gB/gH-gL mediated cell fusion were evaluated by stable reporter fusion assay as described previously [28 (link)]. Briefly, CHO-DSP1 or MeWo-DSP1 cells transfected with equal quantities of pCAGGS-gB, pME18S-gH[TL], and pcDNA3.1-gL plasmids using Lipofectamine 2000 were harvested at 6 hrs post-transfection, and mixed with MeWo-DSP2 cells in the presence of various concentrations of the compounds prepared in two-fold serial dilutions, ranging from 10 μM to 1.25 μM. Co-culture of cells were seeded into Nunc MicroWell 96-well Optical-Bottom Plates (ThermoFisher) and incubated for 48 hrs. The activity of Renilla luciferase was read immediately after adding substrate h-Coelenterazine (Nanolight Technology). Transfection with only vehicle plasmids pcDNA3.1 (+) and pME18S, or pcDNA3.1 (+), pME18S and pCAGGS-gB served as negative control. Cell viability was measured using CellTiter-Glo Luminescent substrate (Promega). Luminescence signal was recorded using Synergy H1 Hybrid Multi-Mode Reader (BioTek). Experiments were performed at least in triplicate.
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10

Melanocyte-specific Tsc2 Knockout Mice

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Tsc2flox/flox mice and Mitf-M-Cre mice were generated as described previously[9 (link)]. Melanocyte-specific Tsc2 knockout mice were generated by breeding Tsc2flox/flox mice with Mitf-M-Cre mice. Both lines maintained a C57BL/6 inbred background. The controls were littermates, either without cre or in a few cases, Mitf-M-cre;Tsc2flox/-. For rapamycin treatment, sirolimus was purchased from Selleck (Osaka, Japan) and dissolved in distilled water for oral administration at 2.285 mg/kg/day for 3 weeks (n = 5 mice/goup). All animal experiments were conducted in accordance with the Guiding Principles for the Care and Use of Laboratory Animals, and the experimental protocol used in this study was approved by the Committee for Animal Experiments at Osaka University (Osaka, Japan).
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