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142 protocols using complete ultra tablet

1

Hippocampus and Cortex Tissue Fractionation

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Western blotting was performed as we previously described46 ,51 ,53 , 54 . The hippocampus and cortex from control and knockout mice were isolated from 5–7 week-old mice. Tissue was homogenized in cold lysis buffer [200 mM HEPES, 50 mM NaCl, 10% Glycerol, 1% Triton X-100, 1 mM EDTA, 50 mM NaF, 2 mM Na3VO4, 25 mM β-glycerophosphate, and EDTA-free complete ULTRA tablets (Roche, Indianapolis, IN)], and centrifuged at 13,000 × g for 10 min. The supernatants were collected and resolved on SDS–PAGE (6–10%) and transferred onto nitrocellulose membranes (Pall, Port Washington, NY).
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2

Caspase-3 Activity Assay in C6 Cells

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To measure caspase activity in C6 cells, cells were detached enzymatically and collected 12 h after treatment and subjected to centrifugation at 2000× g. The pellets were resuspended in caspase buffer (20 mM HEPES, pH 7.5, 50 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM EGTA, 1 mM DTT supplemented with protease inhibitor cocktail (Complete ULTRA Tablets, Roche Diagnostics, Indianapolis, IN, USA), and lysed with three freeze/thaw cycles. The lysates were then incubated for one hour at 37 °C with 0.2 μM fluorogenic caspase-3 substrate, Ac-DEVD-AFC (Ac-Asp-Glu-Val-Asp-7-Amino-4-trifluoromethylcoumarin, Santa Cruz Biotechnology, Dallas, TX, USA; product number, sc-311274). The amount of the fluorescent product resulting from caspase-3 activity was determined fluorometrically (excitation 405 nm, emission 535 nm) and activity was expressed in relative arbitrary fluorescence units as described by us previously [11 (link)].
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3

Purification of His-tagged Pfnek-2 Protein

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Full-length Pfnek-2 as a 6-HIS-tagged protein was expressed in E. coli BL21-Codon Plus(DE3)-RIPL strain (Agilent Technologies). Cells were treated with 1 mM IPTG when the optical density of the cell culture at 600 nm reached 0.6, and protein expression was induced overnight at 18 °C. For purification, cells were lysed in buffer [50 mM bicine, pH 8.0, 150 mM NaCl, 20 mM Imidazole, 1% glycerol, 1 mM DTT, Protease Inhibitor Cocktail (Roche)] [1 tablet per 10 ml (cOmplete™ ULTRA Tablets by Roche)] by sonication for 10 cycles of 10 s bursts at 10 mA with a 30 s rest between each cycle. During sonication the cells were kept on ice. Lysates were then centrifuged at 20,000g for 30 min. The resulting supernatants were loaded onto a 0.5 ml pre-equilibrated Ni–NTA Superflow resin (Qiagen) column, washed with buffer (50 mM bicine, pH 8.0, 150 mM NaCl, 20 mM Imidazole, 1% glycerol and 1 mM DTT) and proteins were eluted with the same buffer containing 400 mM Imidazole. Eluted proteins were dialysed against 50 mM bicine, pH 8.0, 150 mM NaCl, 1% glycerol and 1 mM DTT at 4 °C overnight. Dialysed Pfnek-2 protein was aliquoted and stored at −80 °C.
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4

NIH 3T3 Cell Transfection and Protein Isolation

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NIH 3T3 mouse fibroblast cells (ATCCRCRL-1658) were maintained in Dulbecco’s modification of Eagle’s medium (DMEM, with 4.5 g/l glucose, L-glutamine & sodium pyruvate, Corning) with fetal bovine serum (FBS, 10% v/v, Biowest) and Penicillin/Streptomycin (100 U/mL, Roche Diagnostics GmbH). Cells were cultured on 10 cm sterile plates in 37°C, in humidified a chamber with 5% CO2. Lipofectamine 2000 (Invitrogen) was used to transfect cells (at 70% confluence, one day after seeding) according to manufacturer’s protocol. 10 μg of plasmid DNA (4 variants of shRNA carrying plasmids, OriGene TL501619) DNA was used to transfect one plate. The medium was replaced 6 hours after transfection with a standard one. 3 days after transfection cells were washed twice with cold PBS (137 mM NaCl, 7.97 mM Na2HPO4 × 12 H2O, 2.68 mM KCl, 1.47 mM KH2PO4), detached in PBS and moved to a 1.5 ml tube. After centrifugation the cell pellet was lysed in 1 ml of cold RIPA buffer (50 mM Tris-HCl pH7.4, 1% NP-40, 0.5% Na-deoxycholate, 0.1% SDS, 150 mM NaCl, 2 mM EDTA, 50 mM NaF) with freshly added protease (cOmplete ULTRA tablets, EDTA-free, Roche Diagnostics GmbH) and phosphatase inhibitors (PMSF 1mM, Na3VO4 0.2mM). The protein isolate was separated from cell debris by centrifugation (15 min, 14000g, 4°C) and stored at -20°C.
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5

Cultivation and Lysis of Helicobacter hepaticus

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The Helicobacter hepaticus strain Hh-2 (ATCC 51448)59 (link) was purchased from the Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures (DSM No.22909) and cultivated at the Max von Pettenkofer-Institute, LMU Munich. Bacteria from cryo stock were resuspended in Brain Heart Infusion (BHI) medium and put on blood agar plates (Columbia agar with 5% sheep blood, BD, Cat: 4354005). Plates were incubated in a chamber with anaerobic conditions (83% N2, 10% CO2, 7% H2) for 4 days at 37°C. A subculture was cultivated further on in BHI medium with 3% sheep serum in a culture flask in the chamber with anaerobic conditions for additional 4 days at 37°C.
For Hh lysate (HhL) preparation, bacterial cells were harvested and washed 2–3 times with PBS. Cell pellets were resuspended in PBS and lyzed by sonification with the Sonifier 150 Cell Disruptor (Branson) 6 times for 3 min at level 3 on ice. Lyzed cells were centrifuged at 20,000 x g for 30 min at 4°C and the supernatant was mixed with a protease inhibitor (cOmplete ULTRA Tablets, Roche, Sigma-Aldrich, Cat: 05892953001). Protein concentration was determined using the Qubit Protein Assay Kit and Fluorometer (Invitrogen), according to the manufacturer’s instructions and the lysate was stored at −20°C until use for immunoblot or ELISA.
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6

Meiotic Protein Phosphorylation Analysis

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Total cell extracts were prepared by trichloroacetic acid (TCA) precipitation from 5-ml aliquots of sporulation cultures as previously described (13 (link)). Analysis of Mek1 phosphorylation using Phos-tag gels was performed as reported (8 (link)). The antibodies used are listed in Supplementary Table S3. The ECL or ECL2 reagents (ThermoFisher Scientific) were used for detection. The signal was captured on films and/or with a ChemiDoc XRS system (Bio-Rad) and quantified with the Quantity One software (Bio-Rad).
For immunoprecipitation of Pch2, 5-ml aliquots from 16 h meiotic cultures were crosslinked with 1% formaldehyde for 10 min at 30°C. The reaction was quenched by adding glycine to 250 mM and incubating for 5 min on ice. Cells were collected, washed and broken with glass beads in lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM Tris HCl pH 8.0) containing protease inhibitors (Complete Ultra Tablets, Roche). Clarified extracts were immunoprecipitated with anti-HA antibodies conjugated with magnetic MicroBeads using the μMACS Epitope Tag Protein Isolation Kit (Miltenyi Biotec) following the manufacturer's protocol.
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7

VEGFR2 Phosphorylation Analysis by Western Blot

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Western blot analysis was performed with 8% SDS/PAGE using standard methods. In brief, fresh nitrogen-frozen tumor tissues were placed directly into RIPA lysis buffer (Boston BioProducts Inc, MA Cat# BP-115) contained Complete ULTRA tablets, Mini EDTA-free (Roche Diagnostics, IN Cat# 05892791001), and PhosStop (Roche Diagnostics, IN Cat# 04906837001), incubated at 4 °C for 15 min, and then centrifuged at 14,000 rpm (~ 18,000×g), 4 °C, for 10 min for protein extraction. Approximately 20 μg of denatured protein per sample lysates were loaded on SDS/PAGE, separated by electrophoresis and transferred onto a polyvinylidene difluoride membrane (PVDF) using wet electroblotting transfer at 200 mA for 2.5 h. Non-specific binding was blocked with 5% non-fat milk for 1 h. Membranes were incubated overnight at 4 °C with the specific primary antibodies, followed by peroxidase-conjugated anti-rabbit HRP secondary antibodies. The following antibodies were used: Phospho-VEGF Receptor 2 Tyr1175 (1:200, Cell Signaling Technology, MA Cat# 2478), VEGF Receptor 2 (1:1000, Cell Signaling Technology, MA Cat# 2479), and β-Actin (1:5000, Sigma, MO Cat# A5441). Image J software was used for densitometric analysis. The ratio area pixels of the phosphor-VEGFR2 to total VEGFR2 was calculated.
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8

In Vitro Digestion of Insect Powders

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Buffalo worm (A. diaperinus larvae powder) was provided by Protifarm NV (Ermelo, Netherlands). Tenebrio molitor flour of subadult insects was obtained from Iberinsect, S.L. (Tarragona, Spain), and processed by FoodIE Research Group, University Rovira i Virgili, Spain. The nutritional composition of these samples is shown in Supporting Information Table S1.
Chemicals, porcine digestive enzymes (α‐amylase, pepsin, and pancreatin), bile salts, bovine serum albumin (fatty acid free), d‐glucose, d‐mannitol, amino acids, aprotinin, protease inhibitor cocktail (cOmplete™ ULTRA Tablets; Roche), and foetal bovine serum were purchased from Sigma‐Aldrich (Madrid, Spain). Amastatin was from Enzo Life Sciences (Madrid, Spain). Glutamine, penicillin, streptomycin, and Matrigel from Lonza (O Porriño, Spain).
The enzyme‐linked immunosorbent assay kits for total ghrelin (catalogue no. EZGRT‐91K) and total GLP‐1 (catalogue no. EZGLPT1‐36K) were purchased from Millipore (Billerica, MA, USA). Plasmatic parameters were measured with commercial kits according to manufacturer's instructions: insulin with an insulin enzyme‐linked immunosorbent assay kit (catalogue no. EZRMI‐13K) from Millipore (Madrid, Spain), and glucose triglycerides and cholesterol from QCA (Amposta, Spain). The Pierce BCA Protein Assay kit was from ThermoFisher (Waltham, MA, USA).
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9

Mitochondrial Respiration Assays

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Florets were detached from the spadices and used for the preparation of mitochondria. Purification was performed as previously reported23 (link), with the exception that protease inhibitors (cOmplete ULTRA tablets (Roche), or 10 μM E-64 and 0.5 mM 4-(2-Aminoethyl) benzenesulfonyl fluoride hydrochloride) were added upon initiation of the grinding of the florets.
Oxygen consumption rates were determined using freshly prepared mitochondria as described previously20 21 (link). Mitochondrial respiration with citrate as a substrate was measured in an assay buffer21 (link) containing 10 mM citrate, 0.5 mM ADP, 10 mM malonate and 0.1 mM rotenone at 8°C, 15 °C, 23 °C and 30 °C. For respiration assays with NADH as a substrate, 1 mM NADH, 0.5 mM ADP and 0.1 mM rotenone were added to the assay buffer21 (link) at 15 °C, 23 °C, 30 °C and 37 °C. Capacities for AOX-mediated pathway were determined as KCN-insensitive (0.5 mM) and n-propyl gallate-sensitive (0.1 mM) respiration. Pyruvate (10 mM) was added where indicated. COX capacities were also determined as KCN-sensitive (0.5 mM) and n-propyl gallate-insensitive (0.1 mM) respiration. Protein concentrations of purified mitochondria were determined as in our previous report24 (link). Mitochondria were stored at −80 °C and used for enzyme assays.
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10

Western Blot Protein Detection Protocol

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Samples were lysed in RIPA buffer (RIPA Lysis and Extraction Buffer, cat. 89900, Thermo Fisher Scientific) (25 mM Tris-HCl pH 7.6, 150 mM NaCl, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) supplemented with protease inhibitor cocktail (cOmplete™ ULTRA Tablets, Roche). Proteins were separated by SDS-PAGE (Tris-glycine gels with Tris/glycine/SDS buffer) and transferred onto nitrocellulose membranes (Whatman, Dassel, Germany), using the Mini Trans-Blot® Cell (Bio-Rad). Membranes were probed over night with antibodies directed against P2Y10 (Life Technologies GmbH, #PA570914, 1:1000) or GAPDH (Cell Signalling Technology, #2118, 1:1000). After washing, membranes were probed with horseradish peroxidase-conjugated antibodies directed against rabbit or mouse IgG (1:3000, Cell Signalling Technology Europe). The target proteins were visualized by enhanced chemiluminescence reagent (Millipore, Billerica, MA, USA) and a ChemiDoc MP Imaging System (Bio-Rad).
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