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16 protocols using scintiverse

1

Steady-State Methylation Kinetics of DNMT1

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The hemiDNA 36-mer DNA duplex described above was used as substrate for measuring the steady-state methylation kinetics of DNMT1, where the Apt. #9 was used for inhibition. The 20-μL reaction contains 50 nM DNMT1, 5–400 nM hemiDNA, 0 or 0.1 μM Apt. #9, 0.5 μM S-adenosyl-l-[methyl-3H] methionine (specific activity 18 Ci/mmol, PerkinElmer), 2 μM AdoMet in 50 mM Tris–HCl, pH 8.0, 0.05% β-mercaptoethanol, 5% glycerol and 200 μg/ml BSA. The reactions were carried out in triplicate at 37°C for 0 min or 60 min, which falls into the linear range of the progression curve (Supplementary Figure S13), and quenched by addition of 5 μL of 10 mM AdoMet. For detection, 10 μL of reaction mixture was spot on Amersham Hybond™-XL membrane (GE Healthcare) and dried out. The membrane was then washed 3 times with 5 mL of 0.2 M cold ammonium bicarbonate (pH 8.2), 5 mL of Milli Q water and 5 mL of EtOH. Subsequently, the membrane was air dried, transferred to scintillation vials filled with 5 mL of ScintiVerse (Fisher) and subject to radioactivity measurement by a Beckman LS6500 counter. The data were analyzed by Michaelis–Menten enzymatic kinetics nonlinear regression fitting (Y = Vmax*X/(KM + X)) using GraphPad Prism7 software.
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2

AMPK Activity Measurement Protocol

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AMPK activity measurements were based on AMPK-specific phosphorylation of a SAMS peptide [22 (link)]. Briefly, SAMS peptide substrate (His-Met-Arg-Ser-Ala-Met-Ser-Gly-Leu-His-Leu-Val-Lys-Arg-Arg, obtained from Invitrogen, Carlsbad, CA, USA) was used for the assay. As-obtained muscle homogenate was centrifuged at 1,3000g at 4 °C for 5 min. Ten microlitres of supernatant was incubated for 10 min at 37 °C at pH 7.0. Its final volume was 50 µL, and it contained 0.2 mM of ATP + 2 µCi [32P] ATP, 0.2 of mM AMP, 5 mM of MgCl2, 0.2 of mM SAMS peptide, 80 of mM NaCl, 0.8 mM of dithiothreitol, 0.8 mM of EDTA, 8% (w/v) of glycerol, and 40 mM of 4-2-hydroxyethyl-1-piperazineethanesulfonic acid. Twenty microliters of this mixtures was removed and placed on Whatman P81 filter paper (Whatman, Maidstone, UK) that had been cut into 2 cm × 2 cm pieces. Six washes of 1% phosphoric acid were conducted to remove the ATP. Finally, the filter paper was immersed in 3 mL of Scinti Verse (obtained from Fisher Scientific, Waltham, MA, USA). AMPK nanomolar peptide activity phosphorylation was expressed per minute per gram of muscle.
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3

Plasma Sample Analysis for Tritium and Retinol

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An aliquot of each plasma sample (10–60 μl) was transferred into a vial containing 4 ml Scintiverse (Fisher Chemical) and analyzed for tritium content by liquid scintillation spectrometry; counting was done to a 1% counting error (38 (link)). Another aliquot of plasma (25–100 μl) was analyzed for total retinol concentration by ultra performance liquid chromatography (UPLC) as previously reported (30 (link), 42 (link)).
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4

Neurotransmitter Uptake Assay Protocol

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Neurotransmitter uptake
assays were performed as previously reported.59 (link),94 (link) Briefly, cells were washed with room temperature phosphate buffer
PBS-CM (2.7 mM KCl; 1.2 mM KH2PO4, 138 mM NaCl;
8.1 mM Na2HPO4, added 0.1 mM CaCl2 and 1 mM MgCl2, pH 7.4) and incubated for 10 min at 37
°C with compounds (R)-7 [(R)-AS-1] and (R)-8 [(R)-AS-7] at 0.01–100 μM final concentration. Uptake reactions
were initiated by the addition of an appropriate radiolabeled substrate
([3H]-l-glutamate or [3H]-GABA) at
a final concentration of 50 nM. After 10 min, reactions were terminated
in two washes with buffer and lysis with 1% sodium dodecyl sulfate
(SDS)/0.1 M NaOH. The lysate was transferred to scintillation vials
containing 3 mL of scintillation fluid (ScintiVerse, Fisher Scientific,
Pittsburgh, PA) and radioactivity was quantified in a scintillation
counter LS 6500 (Beckman Coulter, Brea, CA).
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5

Caco-2 Cell Gly-Sar Uptake Inhibition

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Caco-2 cells at 10 days postseeding were incubated with 10 µmol/L Gly-Sar (9.98 µmol/L Gly-Sar and 0.02 µmol/L [3H]Gly-Sar (Moravek Biochemicals, Brea, CA, USA)), along with various concentrations (5–0.05 mmol/L) of Gem and Gem prodrugs for 30 min. After the incubation, the drug solution was removed. The cells were gently washed three times with ice-cold PBS and solubilized with 2 mL of scintillation cocktail (ScintiVerse, Fisher Scientific, St. Louis, MO, USA), and the radioactivity was determined by scintillation counting (Beckman LS-9000, Beckman Instruments, Fullerton, CA, USA). Inhibitory concentration 50 (IC50) values were determined using nonlinear data fitting (GraphPad Prism version 6, GraphPad Software, Inc., La Jolla, CA, USA).
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6

Caco-2 Cell Gly-Sar Uptake Inhibition

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Caco-2 cells at 10 days postseeding were incubated with 10 µmol/L Gly-Sar (9.98 µmol/L Gly-Sar and 0.02 µmol/L [3H]Gly-Sar (Moravek Biochemicals, Brea, CA, USA)), along with various concentrations (5–0.05 mmol/L) of Gem and Gem prodrugs for 30 min. After the incubation, the drug solution was removed. The cells were gently washed three times with ice-cold PBS and solubilized with 2 mL of scintillation cocktail (ScintiVerse, Fisher Scientific, St. Louis, MO, USA), and the radioactivity was determined by scintillation counting (Beckman LS-9000, Beckman Instruments, Fullerton, CA, USA). Inhibitory concentration 50 (IC50) values were determined using nonlinear data fitting (GraphPad Prism version 6, GraphPad Software, Inc., La Jolla, CA, USA).
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7

Cell Proliferation Assay with Thymidine

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[3H]-thymidine incorporation was evaluated after plating in 2.5 × 105 cells/well in 6-well culture plates. Twenty-four hours after plating, cells were incubated in a growth arrest medium (0.5% FBS-MEM, L-Glu, Pen-Strep) for 24 hours. Then, cells were incubated an additional 24 hours either in the presence of serum. When indicated, the furin inhibitor, CMK, 50 or 100 μmol/L was included in the incubation mixture. For the last 4 hours of incubation, 3 μCi/well [H3]methylthymidine (Moravek, Biochemicals, Brea, CA) was added. After this period of time, cells were washed three times with phosphate-buffered saline (PBS) and treated with 10% trichloroacetic acid at 4°C for 30 minutes and washed three times with water. Cells were then rinsed with 70% ethanol and air-dried. Labeled DNA was dissolved with 200 μl 10 mmol/L NaOH, 1% SDS and counted with Scintiverse (Fisher, Pittsburgh, PA).
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8

Quantifying VA Fractions in Intestine

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A 0.5 mL aliquot of the above-described hexane extract was evaporated to dryness in a water bath under a gentle flow of nitrogen, then used for determination of 3H tracer by liquid scintillation spectrometry (Beckman Coulter, Brea, CA, USA) using Scintiverse (Fisher Chemical, Waltham, MA, USA) as scintillation fluid, as described earlier [35 (link)]. Samples were counted to a 2-sigma error of 1% or for a maximum of 60 min.
To further identify the form of VA in intestine, we separated retinyl esters (RE) and retinol from the hexane extract using alumina column chromatography [36 (link)]. Briefly, the hexane extract was loaded onto the column, and then the column was sequentially eluted with 3% diethyl ether and 50% diethyl ether to obtain the retinyl ester- and retinol fractions, respectively. Then, 3H content in these fractions was determined as mentioned above.
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9

Quantifying Antigen-Specific Lymphocytes

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HSV-1- or EIV-specific responder cells were quantified by a modified limiting dilution lymphoproliferation assay (55 (link)), using either cell-free HSV-1 or EIV Prague/56 HA protein lysate and control antigen lysate. Briefly, wells of 96-well plates were coated with 20 μl/well of antigen extract (HSV-1 or RS cell control lysate, or EIV Prague/56 HA or Vero cell control lysate) and were allowed to air dry in a laminar flow hood. Dilutions of mouse PBMCs in DMEM were added to each well so that each well contained a minimum of 1 and a maximum of 10 lymphocytes per well in a volume of 100 μl complete medium (with serum). The plates were then incubated at 37°C. After 24 h, medium containing 10 μCi of [3H]thymidine was added to each plate for 12 h, the medium was replaced, and the plates were incubated for an additional 72 h. The wells were harvested, and the DNA was precipitated in 20 volumes of cold 10% trichloroacetic acid, transferred onto glass fiber discs (Whatman; GF/C) by filtration, rinsed with 95% ethanol, and dried using a heat lamp. The filters were then transferred to scintillation vials with Scintiverse (Fisher Scientific) and counted. The counts per minute (cpm) of [3H]thymidine were converted to RCF using the maximum-likelihood estimate method of Levin et al. (56 (link)).
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10

DNA Methylation Assay for CG, CA, and CT Substrates

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Synthesized (GAC)12, (AAC)12 and (TAC)12 DNA duplexes were used as CG-, CA- and CT-containing substrates, respectively. The DNA methylation assays were carried out in triplicate at 37 °C for 1 hr., unless otherwise indicated. Briefly, a 20-μL reaction mixture contained 2.5 μM S-adenosyl-L-[methyl-3H]methionine (AdoMet) (specific activity 18 Ci/mmol, PerkinElmer), 0.3 μM DNMT3A-DNMT3L, 0.75 μM DNA in 59 mM Tris-HCl, pH 8.0, 0.05% β-mercaptoethanol, 5% glycerol and 200 μg/mL BSA. The methylation reactions were stopped by flash freezing in liquid nitrogen, followed by precipitation and incubation on ice for 1 hr. in 1 ml of 15% trichloroacetic acid (TCA) solution plus 40 μg/ml BSA. The TCA-precipitated samples were then passed through a GF/C filter (GE Healthcare) using a vacuum-filtration apparatus. After sequential washing with 2 × 5 ml of cold 10% TCA and 5 ml of ethanol, the filters were dried and transferred to scintillation vials filled with 5 ml of ScintiVerse (Fisher), followed by measurement of tritium scintillation with a Beckman LS6500 counter.
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