The largest database of trusted experimental protocols

14 protocols using complete tablets edta free

1

Affinity Purification and UPF1 Kinase Assay

Check if the same lab product or an alternative is used in the 5 most similar protocols
Five microgram of pSG5-FLAG GFP (generously donated by Dr Samuel Buchsbaum) or 5 μg of pcDNA-FLAG-SMG5 and 5 μg of pcDNA-FLAG-SMG7 or 5 μg of pcDNA-FLAG-SMG6 and 10 nM UPF1 siRNA were transfected in 10 cm dishes using jetPRIME (Polyplus) according to the manufacturer's protocol. Forty-eight hours later, cells were collected in PBS and lysed in 800 μl of hypotonic gentle lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 2 mM EDTA, 0.5% Triton X-100, 1 × protease inhibitor cocktail (cOmplete Tablets EDTA-free, Roche) for 5 min on ice. NaCl concentration was brought to 150 mM and RNase A was added at 125 μg ml−1. Lysates were incubated for 2 h with 100 μl of anti-FLAG M2 affinity gel (Sigma-Aldrich). Beads were then washed seven times with NET2 (50 mM Tris-HCl pH 7.5, 150 mM NaCl and 0.05% Triton X-100) and resuspended in 400 μl of NET2 containing 1 × protease inhibitor cocktail (cOmplete Tablets EDTA-free, Roche), 20 mM β-glycerophosphate and UPF1-HD-SQ in vitro kinase reactions. After 2 h incubation at 4 °C, beads were washed five times in NET2 and resuspended in 30 μl of 2 × SDS loading buffer (100 mM Tris-HCl pH 6.8, 4% SDS, 12% β-mercaptoethanol, 20% glycerol and 0.1% bromophenol blue). Immunoprecipitates were separated by sSDS–PAGE followed by western blotting.
+ Open protocol
+ Expand
2

Purification and Spin-Labeling Optimization

Check if the same lab product or an alternative is used in the 5 most similar protocols
Luria Bertani (LB) medium (CAPSULES) was purchased from MP Biomedicals (Solon, OH, USA) and LB agar plates with 100 μg/ml ampicilin from IPMscientific (MD, USA). Ampicillin sodium salt, isopropyl β-D-1-thiogalactopyranoside (IPTG) (OmniPur, Calbiochem), DL-dithiothreitol (DTT), tris(2-carboxyethyl)phosphine (TCEP), sodium chloride (NaCl), albumin from bovine serum (BSA), adenosine 5’ diphosphate disodium salt (ADP), adenosine 5’ triphosphate disodium salt (ATP), ammonium sulfate ((NH4)2SO4) for molecular biology, and streptomycin sulfate salt were obtained from Millipore Sigma (St. Louis, MO, USA). cOmplete tablets EDTA-free (Roche, Germany) were used as a protease inhibitor. 1M Tris-HCl at pH 7.4 or 8, and ethylenediaminetetraacetic acid (EDTA) were purchased from K-D Medicals (Columbia, MD, USA). Molecular biology grade magnesium chloride (MgCl2) was obtained from Quality Biological (MD, USA), and Urea (UltraPure™) and guanidinium hydrochloride (GuHCl) from Invitrogen (ThermoFisher Scientific, NY, USA). Nitroxide spin-labels (MTSL, S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl) methyl methanesulfonothioate, and the diamagnetic control MTS (1-acetoxy-2,2,5,5-tetramethyl-δ-3-pyrroline-3-methyl) methanethiosulfonate) were obtained from Toronto Research Chemicals (Canada).
+ Open protocol
+ Expand
3

Western Blot Analysis of AQP1 Protein

Check if the same lab product or an alternative is used in the 5 most similar protocols
Cell lysates were lysed in 40 mM Hepes pH 7.5, 120 mM NaCl, 5 mM MgCl2, 1 mM EGTA, 0.5 mM EDTA, 1% Triton X-100 containing protease (Complete Tablets-EDTA free, Roche, Basel, Switzerland) and phosphatase inhibitors (20 mM a-glycerol-3-phosphate, 2.5 mM Na-pyrophosphate) according to the method previously described [39 (link)]. After homogenization and centrifugation for 15 min at 13,000× g at 4 °C the protein suspension was collected and the protein content was determined using a BCA protein assay kit (Thermo, Waltham, MA, USA). Equal proteins samples (50 µg) were loaded and separated by SDS-PAGE under reducing conditions. The next step was to transfer the separated proteins to PVDF membranes. After blocking in 5% milk, primary antibodies were added. After being washed in TTBS buffer, the membranes were incubated with horseradish peroxidase-labeled antimouse or antirabbit Ig antibodies for 1 h and then protein detection was performed by ECL system (Menlo Park, CA, USA). Each band of western blot was quantified by densitometric analysis using Image J. Anti-AQP1 (sc-20810, Santa Cruz, CA, USA) and anti-β-actin (A4700, Sigma-Aldrich) were used in the experiment.
+ Open protocol
+ Expand
4

CFBE41o- Cell Culture and Protein Extraction

Check if the same lab product or an alternative is used in the 5 most similar protocols
The native CFBE41o-cells and the transduced CFBE41o-cell lines (CFBE41o-/corrected (corr) and CFBE41o-/F508del) were cultured, as previously described [34 (link)]. These cells are human bronchial epithelial cells, derived from a CF patient homozygous for the p.Phe508del mutation and immortalized with an SV40 plasmid (pSVori-) [34 (link),35 (link)]. Cells were obtained from the Cystic Fibrosis Foundation (Bethesda, MD, USA). In some experiments, cells were treated with PF-429242 (PF) that specifically inhibits MBTP1 [36 (link)] (10 µM for 48 h; SML0667, Sigma-Aldrich, Saint-Quentin Fallavier, France); and/or with thapsigargin (0.5 µM for 4 h; #10798352, ThermoFischer, Saint Rémy les Chevreuses, France) to induce UPR; and/or with VX-809 (3 µM for 48 h; S1565, Selleckchem, Cologne, Germany).
For protein extraction, cells were washed with cold PBS ×1 and lyzed in RIPA buffer (25 mM Tris, 150 mM NaCl, 1% Triton ×-100, 1% Na-Deoxycholate, 0.1% SDS, 10 mM iodoacetamide, 100 mM PMSF; pH = 7.5) in the presence of the Complete Protease Inhibitor Cocktail (PI; 40 µL/mL, Complete tablets EDTA free, Roche, Mannheim, Germany).
For Ussing chamber experiments, human-airway epithelial cells were obtained from the department of thoracic surgery and lung transplantation of Foch hospital (Suresnes, France).
+ Open protocol
+ Expand
5

Protein Expression Analysis from Cell Lysates

Check if the same lab product or an alternative is used in the 5 most similar protocols
For the analysis of protein expression, the cells were homogenized in lysis buffer (40 mM Hepes pH 7.5, 120 mM NaCl, 5 mM MgCl2, 1 mM EGTA, 0.5 mM EDTA, 1% Triton X-100) containing protease (Complete Tablets-EDTA-free, Roche) and phosphatase (20 mM a-glycerolphosphate, 2.5 mM Na-pyrophosphate) inhibitors. Twenty-five micrograms of cell lysates were analyzed on 12%-10% SDS-PAGE and the following primary antibodies were used: anti-CXCR4 (Abcam, ab2074), anti-CD133 (Abcam, ab19898), anti-tubulin (Santa Cruz Biotech, CA). Anti-mouse and anti-rabbit IgG coupled to peroxidase were used as secondary antibodies (Santa Cruz Biotech, CA) and the signal was revealed through chemo luminescent detection kit (ECL detection kit, Amersham Biosciences, Freiburg, Germany).
+ Open protocol
+ Expand
6

Quantifying Bacterial Load and Inflammatory Markers

Check if the same lab product or an alternative is used in the 5 most similar protocols
Lung, liver and spleen were collected and homogenized in 1 ml PBS containing protease inhibitors (Complete tablets EDTA-free, Roche Diagnostic) and 1 mM PMSF (Sigma) and used for CFU count. The homogenates were then centrifuged at 13000 rpm for 20 minutes at 4°C and the supernatants were stored at -80°C. Blood was drawn either from the cava vein or the retro-orbital plexus, collected in an appropriate anti-coagulant (heparin, EDTA or citrate) vacutainer tube.
Lung, liver and spleen homogenates and blood were serially diluted 1:10 in PBS, plated in Tryptic Soy Broth (TSB) agar (BD) and incubated overnight at 37°C for CFU count. EDTA-blood samples from retro-orbital plexus were analyzed by the laser automated counter ADVIA 120 (Siemens).
Citrate-blood from cava vein was used to measure fibrinogen by converting the clotting time under bovine thrombin activation (Futurlab srl, Limena, PD Italy). ELISA assays were used to measure murine cytokines, MPO, PTX3 (R&D DuoSet ELISA Development System, USA) and TAT (Thrombin-Antithrombin Complexes- Abcam, Cambridge, UK) according to manufacturer’s instructions. Magnetic beads multiplex immunoassay (ProcartaPlex- Invitrogen) was used to measure cytokines in the blood. Protein quantitation was performed on the Luminex instrument platform (Bio-plex 200 system- Bio-Rad).
+ Open protocol
+ Expand
7

Biotinylation and Protein Purification

Check if the same lab product or an alternative is used in the 5 most similar protocols
Confluent cells were placed on ice and washed with cold PBS 2+ (PBS pH8 containing 1 mM MgCl 2 , and 0.1 mM CaCl 2 ). Cells were then incubated at 4 °C for 1 h in PBS 2+ containing 1 mg/ml EZ-Link Sulfo-NHS-LC-biotin. Biotinylation was stopped by washing with PBS 2+ supplemented with 100 mM glycine. Then they were washed with cold PBS 2+ and lysed for 20 to 30 min in 0.2 ml of lysis buffer (100 mM NaCl, 1 mM EDTA, 50 mM Tris, pH 7.4; 1% (vol/vol) Triton X-100; 0.1% SDS) containing protease inhibitors (Complete Tablets, EDTA-free, Roche Diagnostics). Samples were harvested and centrifuged at 10,000g for 10 min at 4 °C. Protein content was measured with protein assay quantification kit (BCA Protein Kit Assay, Pierce, Villebon-sur-Yvette, France). After normalization, aliquots of equal amounts of proteins were taken for total protein fraction, and the rest of proteins were precipitated at 4 °C overnight using Neutravidin-Agarose Resin (Pierce). After overnight incubation, supernatant was removed centrifugation (11,000g for 5 min at 4 °C). Then resins containing biotinylated proteins were washed seven times with cold lysis buffer and centrifuged for 5 min at 11,000g. After last wash, resins were incubated in a solution containing lysis buffer and Laemmli buffer for 5 min at 95 °C.
+ Open protocol
+ Expand
8

Simultaneous Monitoring of Mitochondrial Calcium and Membrane Potential

Check if the same lab product or an alternative is used in the 5 most similar protocols
Mitochondrial Ca2+ uptake and ΔΨm were determined by simultaneous monitoring of cytosolic Ca2+ with Fura-2FF (0.5 μM; Life Technologies) and ΔΨm with the lipophilic cationic dye 5,5′,6,6′-tetrachloro-3,3′-tetraethylbenzimidazolcarbocyanine (JC-1; 800 nM; Life Technologies). After trypsinization and neutralization, cells were pelleted at 200 × g for 5 min, resuspended in 20 mL of phosphate-buffered saline, and pelleted at 150 × g for 2 min. 8 × 106 cells were resuspended in 1.5 mL ICM buffer containing 40 μg/ml digitonin to permeabilize the cells, protease inhibitors (EDTA-free complete tablets; Roche Applied Science, Indianapolis, IN), 2 μM thapsigargin to block the SERCA pump, and 2 mM succinate to energize mitochondria (67 (link)). Fura-2FF (1 μM) was used as a cytosolic Ca2+ indicator. After 20 s of data recording, JC-1 was added. At 1200 s or 400 s CCCP, 10 μM, was added. Fluorescence was measured using a dual-wavelength spectrofluorometer (PTI) with 490-nm excitation and 535-nm emission for monomeric JC-1 and 570/595 nm for the J-aggregate. ΔΨm was calculated as the ratio of J-aggregate and the monomer (68 (link)).
+ Open protocol
+ Expand
9

Western Blot Analysis of Ubiquitin Chains

Check if the same lab product or an alternative is used in the 5 most similar protocols
We employed the following antibodies: rabbit anti-UbK63 chains (Millipore), mouse anti-ubiquitin (Chemicon), mouse anti-γH2AX (clone JBW301, Upstate), rabbit anti-γH2AX (Epitomics), rabbit anti-53BP1 (Alexis). Following the indicated treatments whole cell lysates were prepared using lysis buffer containing: 50 mM Tris-HCl [pH 7.4], 150 mM NaCl, 1% NP-40, 0.5% Sodium Deoxycholate, 1 mM EDTA, 0.1% SDS, supplemented with protease- (EDTA-free Complete tablets, Roche) and phosphatase inhibitors (PhosSTOP tablets, Roche). Supernatants were boiled in Laemmli buffer and proteins were resolved by SDS-PAGE. Proteins were transferred onto PVDF membranes and blocked for 1 hour in 5% skim milk in TBS, 0.05% Tween-20 (TBS-T). Membranes were probed overnight at 4°C with antibodies directed against K63 chains (1∶1000) or ubiquitin (1∶500). Bound antibodies were visualized using HRP-linked secondary antibodies (anti-rabbit (GE Healthcare) and anti-mouse (GE Healthcare)) and ECL luminescence (Pierce).
+ Open protocol
+ Expand
10

Simultaneous Measurement of Mitochondrial Membrane Potential and Cytosolic Calcium Dynamics

Check if the same lab product or an alternative is used in the 5 most similar protocols
Freshly isolated LV myocytes from WT and Tg26 mice were subjected to 2h of either normoxia or H/R. After gentle centrifugation, myocytes were transferred to an intracellular-like medium containing (in mM): 120 KCl, 10 NaCl, 1 KH2PO4, 20 4-(2-hydroxyethyl)-1-piperazine-ethanesulfonic acid (HEPES)-Tris, 10 succinate, thapsigargin (2 ¼g/ml), digitonin (80 ¼g/ml), pH 7.2, and protease inhibitors (EDTA-free complete tablets, Roche Applied Science). Fura-FF (0.5 ¼M) was added at 0 s, and JC-1 (800 nM)(both from Molecular Probes) was added at 20s to measure extra-mitochondrial Ca2+ and ΔΨm, respectively. Fluorescence signals were monitored in a temperature-controlled (37°C) multi-wavelength excitation (ex) and dual wavelength emission (em) spectrofluorometer (Delta RAM, Photon Technology Int.) using 490-nm ex/535-nm em for the monomer, 570-nm ex/595-nm em for the J-aggregate of JC-1, and 340- and 380-nm ex/510-nm em for Fura-FF. The ratiometric dye Fura-FF was calibrated as previously described (Mallilankaraman et al. 2012 (link), Miller et al. 2014 (link)). At 450 s, 10 ¼M Ca2+ pulse was added, and ΔΨm and extra-mitochondrial Ca2+ were monitored simultaneously. ΔΨm was calculated as the ratio of the fluorescence of the JC-1 oligomeric to monomeric forms. Cytosolic Ca2+ clearance rate was taken to represent mitochondrial Ca2+ uptake.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!