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66 protocols using dl dithiothreitol dtt

1

Postmortem Brain Tissue Sectioning

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Whole postmortem brain specimens were transported to the Allen Institute on ice. Standard processing of whole brain specimens involved bisecting the brain through the midline and embedding of individual hemispheres in Cavex Impressional Alginate for slabbing. Coronal brain slabs were cut at 1cm intervals through each hemisphere and individual slabs were frozen in a slurry of dry ice and isopentane. Slabs were then vacuum sealed and stored at −80°C until the time of further use.
Middle temporal gyrus (MTG) was identified on and removed from frozen slabs of interest, and subdivided into smaller blocks for further sectioning. Individual tissue blocks were processed by thawing in PBS supplemented with 10mM DL-Dithiothreitol (DTT, Sigma Aldrich), mounting on a vibratome (Leica), and sectioning at 500μm in the coronal plane. Sections were placed in fluorescent Nissl staining solution (Neurotrace 500/525, ThermoFisher Scientific) prepared in PBS with 10mM DTT and 0.5% RNasin Plus RNase inhibitor (Promega) and stained for 5 min on ice. After staining, sections were visualized on a fluorescence dissecting microscope (Leica) and cortical layers were individually microdissected using a needle blade micro-knife (Fine Science Tools).
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2

Pectin-based Drug Delivery System

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Low methoxy pectin (type CU701, lot number 00412079) with DE of 38% and high methoxy pectin (type CU201, lot number 00501087) with DE of 70% were obtained from Herbstreith & Fox AG, Germany. Cystamine dihydrochloride (lot number BCBL6131V) was purchased from Fluka Analytical, Switzerland. Thioglycolic acid (98%) for synthesis (lot number S5678863411) and N-hydroxysuccinamide (NHS) (lot number A0266926) were from Merck KGaA (Germany) and ACROS Organic (USA), respectively. l-Cysteine hydrochloride (lot number BCBM8363V), 3,3′-dithiopropionic acid (lot number MKBL7043V), 5,5′-dithio-bis-(2-nitrobenzoic acid) (lot number MCFD00007140), N-(3-dimethylaminopropyl)-N-ethylcarbodiimide hydrochloride (EDC) (lot number 037K0753), dl-dithiothreitol (DTT) (lot number SLBK 4951V), and DOX (hydrochloride salt) (lot number SLB 1340V) were purchased from Sigma-Aldrich Co., Ltd. (MO, USA). Ethylene diamine tetraacetic acid disodium salt dehydrate (EDTA) (lot number J069H11) and zinc acetate (lot number 1501186173) were purchased from Rankem, Ltd. (India) and Ajax Finechem (Australia), respectively. All other chemicals used were of reagent grade or analytical grade.
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3

Isotopically Labeled Metabolite Analysis

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Isotopically labeled MMA and Hcys (MMA-d3 and Hcys-d8, respectively) were purchased from Cambridge Isotope Laboratories (Tewksbury, MA, USA). MCA and MCA-d3 were provided by CDN Isotopes (Pointe-Claire, Quebec, Canada). MMA, Hcys, formic acid and DL-dithiothreitol (DTT) were obtained from Sigma-Aldrich (Saint Louis, USA). Methanol and acetonitrile (LC/MS PAI grade) were obtained from EMD Millipore Corporation (Madrid, Spain). Milli-Q system (Millipore) purified water was used.
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4

Isolation and Culture of Porcine Coronary Artery Smooth Muscle Cells

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PCASMCs were cultured after isolation by enzymatic digestion from porcine small coronary arteries [41 (link)]. In brief, small coronary arteries were cut open longitudinally and the endothelium was gently scraped off with a microsurgical blade. The tissue strip was then washed with cold Krebs and dissected into 1×1 mm2 strips, followed by 30-min digestion at 37°C in 2 ml of phosphate-buffered saline solution (PBS), containing 2 mg/ml of collagenase (type 2; Worthington Biochemicals, USA), 0.5 mg/ml of papain (Worthington Biochemicals, USA), 1.75 mg/ml of DL-Dithiothreitol (DTT, Sigma, USA), and 5 mg/ml albumin bovine (BSA, Amresco, USA). The enzymatic activity was stopped by Dulbecco's Modified Eagle Medium (DMEM, Thermo Fisher Scientific, USA) containing 10% fetal bovine serum (FBS, Thermo Fisher Scientific, USA). The suspension was centrifuged at 1600 rpm for 5 min. Cells were then resuspended in 12 ml DMEM containing 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin (Thermo Fisher Scientific, USA). After 1-h incubation at 37°C, the medium was replaced once to remove unattached cells. Attached PCASMCs were cultured in a humidified incubator with 5%CO2 at 37°C. For maintaining electrophysiological properties of isolated PCASMCs, only primary cultured cells were used for experiments.
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5

Mass Spectrometry Protein Analysis

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The chemicals and reagents used in this work are the following: water (LC-MS grade-LiChrosolv®) (Merck KGaA, Darmstadt, Germany), acetonitrile (LC-MS grade-LiChrosolv®) (Merck KGaA, Darmstadt, Germany), 2-propanol (LC-MS grade-LiChrosolv®) (Merck KGaA, Darmstadt, Germany), ammonium bicarbonate (NH4HCO3) (Sigma-Aldrich, Buchs, Switzerland), RapiGestTM SF surfactant (Waters, Milford (MA), USA), DL-dithiothreitol (DTT) (Sigma-Aldrich, Buchs, Switzerland), iodoacetamide (IAA) (Sigma-Aldrich, Buchs, Switzerland), trypsin (porcine pancreas) (Sigma-Aldrich, Buchs, Switzerland), trifluoroacetic acid (TFA) (Honeywell SC, Seeelze, Germany), formic acid (FA) LiChropur® (Merck KGaA, Darmstadt, Germany), PierceTM HeLa protein digest standard (Thermo ScientificTM, Waltham, MA, USA) and MMI-L low concentration tuning mix (Agilent Technologies, Santa Clara, CA, USA).
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6

Plasma Membrane LMTK2 Detection Protocol

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Detection of plasma membrane LMTK2 was performed by domain selective plasma membrane biotinylation, as previously described (Swiatecka-Urban et al., 2002 (link)). CFBE41o- cells were treated with TGF-β1 or vehicle for 1 h. Apical or basolateral plasma membrane proteins of ALI cultures of HBE or CFBE41o- cells were selectively biotinylated using cell membrane impermeable EZ-LinkTM Sulfo-NHS-LC-Biotin (Pierce Chemical Co., Dallas, TX, United States), followed by cell lysis in buffer containing 25 mM HEPES, 10% v/v glycerol, 1% v/v Triton X-100, and Complete Protease Inhibitor Mixture (Roche Applied Sciences, Indianapolis, IN, United States). Lysates were centrifuged at 14,000 x g and biotinylated proteins were isolated from the supernatants, considered as whole cell lysates (WCL), by incubation with streptavidin-agarose beads, eluted into 2x Laemmli sample buffer (Bio-Rad Laboratories) containing DL-dithiothreitol (DTT; Sigma-Aldrich), and separated by 7.5% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE; Bio-Rad Laboratories). The immunoreactive bands were visualized by western blotting (WB) with Western Lightning Chemiluminescence Reagent Plus (PerkinElmer LAS Inc., Boston, MA, United States). Protein abundance was quantified by densitometry using exposures within the linear dynamic range of the film.
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7

Isolation of Colonic Lamina Propria Cells

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Colonic lamina propria cells were isolated as detailed.35 Briefly, animals were euthanised as previously described, and the large intestine was dissected, longitudinally opened, washed with PBS and cut into small pieces. Tissue fragments were placed in Petri dishes and washed three times in calcium- and magnesium-free HBSS containing 1 mM dl-dithiothreitol (DTT, Sigma-Aldrich, Irvine, UK) for 30 min. Supernatants were discarded. After that, tissue fragments were incubated with 100 µl/mL of collagenase II (Sigma-Aldrich) for 60 min at 37 °C on a shaker. Supernatants were passed through a 70-µm cell strainer (Falcon, Corning, NY, USA), and then resuspended in R-10 medium (RPMI with 10% FBS, 2 mM L-glutamine (Thermo Fisher), 1 mM sodium pyruvate (Thermo Fisher), 1% non-essential amino acids (Thermo Fisher), 1% Pen/Strep, 1% vitamin solution (Thermo Fisher) and 5 × 10−5 M 2β-mercaptoetanol) for further analysis.
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8

Proteomic Sample Preparation Procedure

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DSSO, Dulbecco’s modified Eagle’s medium (DMEM), foetal bovine serum (FBS), l-glutamine, penicillin, streptomycin and phosphate-buffered saline (PBS) were obtained from Thermo Fisher Scientific (Les Ulis, France). Formic acid (FA), HPLC grade water, trifluoroacetic acid (TFA), acetonitrile (ACN), methanol, ethanol, acetone and trichloroacetic acid were all purchased from Biosolve (Dieuze, France). dl-Dithiothreitol (DTT), iodoacetamide (IAA), chloroform, dimethyl sulfoxide (DMSO), ammonium bicarbonate (AB), 4-(2-hydroxyethyl)piperazine-1-ethane sulfonic acid, N-(2-hydroxyethyl)piperazine-N-(2-ethane sulfonic acid) (HEPES), sodium chloride (NaCl) and magnesium chloride (MgCl2) were obtained from Sigma-Aldrich. Tris was purchased from Bio-Rad (Steenvoorde, France). Extraction Illustra triplePrep Kit was from GE Healthcare. LysC/trypsin was obtained from Promega (Charbonnières-les-Bains, France). Amicon centrifugal filters and C18 ZipTip pipette tips were from Merck Millipore (Merck KGaA, Darmstadt, Germany).
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9

Fertilization and Vitelline Layer Removal in Sea Urchin Eggs

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The P. lividus were collected from October to May in the Gulf of Naples and maintained at 16 °C in circulating seawater. The eggs were spawned by injecting 0.5 M of KCl into the body cavity. The released eggs were collected in natural seawater (NSW, pH 8.1) filtered with a Millipore membrane of 0.2 µm pore size (Nalgene vacuum filtration system, Rochester, NY, USA) and used for the experiments in the next 3 hr. The dry sperm were collected by pipetting from the male animal’s body and kept at 4 °C. A few minutes before insemination, the sperm were diluted in NSW at a final concentration of 1.84 × 106 units/mL. In the experiments where dejellied eggs were used, the egg jelly was removed by placing the eggs in seawater titrated with HCl to pH 5.5 for 5 min. The eggs incubated in 1 mL of seawater at pH 5.5 or after washing with NSW were fertilized with 10 µL of sperm diluted in NSW. The removal of the VL was performed by incubating the eggs for 20 min in NSW containing a final concentration of 10 mM of DL-Dithiothreitol (DTT) (Sigma-Aldrich, St. Louis, MO, USA) at pH 9 adjusted with 1 mM of NaOH [26 (link)]. When needed, the eggs suspended in acidic seawater or after the removal of the VL were transferred to NSW for the fertilization experiments.
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10

Caspase-1 CARD Oligomerization Assay

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Sandwich-tagged caspase-1 CARD was incubated with SUMO-SERPINB1 at a molar ratio of 1:1 at 4 °C for 12 h, and nucleation of caspase-1 CARD was initiated by removal of the MBP tag by TEV (Sigma, His- and GST-tagged) in buffer containing 1 mM DL-dithiothreitol (DTT, Sigma) at 4 °C for 12 h. The TEV enzyme was removed by incubation with glutathione-conjugated Sepharose beads at 4 °C for 1 h. The protein mixtures were passed through a pre-equilibrated Superose 6 10/300 GL size-exclusion column (GE) with a Biologic Duo Flow system (Bio-Rad). Size-exclusion chromatography buffer contains 20 mM Tris-HCl, pH 8.0, 150 mM NaCl and 1 mM DTT. Chromatography was operated with 0.2 ml min−1 flow rate, 217 psi max pressure and 250 μl fractionation volume. Each fraction (20 μl) was separated by SDS-PAGE, followed by Coomassie Brilliant Blue staining (Brilliant blue R, Sigma). The molecular mass of eluted proteins was estimated by pre-running of standard markers (MWGF1000, Sigma).
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