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5 protocols using phosphatase inhibitor cocktail edta free

1

TRPV1 Expression in Neuropathic Pain

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The rats were deeply anesthetized with pentobarbital (60 mg/kg, i.p.) on days 0, 7, or 14 after the start of PTX (4 mg/kg) treatment, and spinal cords were removed for Western blot analysis. Spinal cords were homogenized in cold 1× RIPA lysis buffer (Santa Cruz Biotechnology, Santa Cruz, CA, USA) containing phosphatase inhibitor cocktail (EDTA free) (Nacalai Tesque, Inc. Tokyo. Japan) and protease inhibitor cocktail (Nacalai Tesque). The homogenates were centrifuged at 4 °C for 30 min at 15,000× g, and the supernatants were collected. Spinal cord protein (30 μg) was separated by an SDS-polyacrylamide gel (7.5%) and transferred onto polyvinylidene difluoride membranes. Anti-TRPV1 antibody (1:200, Alomone Labs, Jerusalem, Israel) was used for Western blotting, with anti-β-actin (Sigma-Aldrich, 1:1000) used as the internal control. Horseradish peroxidase-labeled goat anti-rabbit immunoglobulin G (IgG) (Santa Cruz Biotechnology, 1:5000) was used as the secondary antibody. Specific bands were detected by enhanced chemiluminescence (ECL) with the ECLTM Prime Western Blotting Detection kit (GE Healthcare, Wauwatosa, WI, USA) using a luminescent image analyzer LAS4000 (Fuji Film, Japan). The intensities of immunoreactive bands were quantified using MultiGage Ver.3 software (Fuji Film, Tokyo, Japan).
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2

Fucoxanthinol Extraction and Inhibition

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Fucoxanthinol was purchased from FUJIFILM Wako Pure Chemical Corporation (Osaka, Japan). Cycloheximide and Phosphatase Inhibitor Cocktail (EDTA free) were purchased from Nacalai Tesque (Kyoto, Japan). MG-132 was purchased from Peptide Institute (Osaka, Japan).
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3

Smad Signaling Pathway Protein Analysis

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hAECs were lysed with PROPREP (iNtRON Biotechnology, MA, USA) supplemented with Phosphatase Inhibitor Cocktail (EDTA free) (Nakarai tesque, Japan). Protein extracts were analyzed by sodium dodecyl sulfate polyacrylamide electrophoresis (SDS–PAGE; Bio-Rad Laboratories, CA, USA) followed by a Western blot assay. EzBlockChemi (ATTO, Japan) was used for blocking, and Western BLoT Immuno Booster (Takara, Japan) was used for the reaction. The primary antibodies were as follows: Smad1, Smad2/3, phospho-Smad1 (Ser463/465)/5 (Ser463/465)/9 (Ser465/467), and phospho-Smad2 (Ser465/467)/3 (Ser423/425) (Cell Signaling Technology, MA, USA) at a 1:1,000 concentration, and GAPDH (GeneTex, CA, USA) at a 1:10,000 concentration. The secondary antibodies were peroxidase AffiniPure goat anti-mouse IgG and anti-rabbit IgG (Jackson ImmunoResearch Laboratory, PA, USA) at a 1:20,000 concentration. Western blot images were developed with Western BLoT Hyper HRP Substrate (Takara, Japan) and taken with a LumiCube System (Liponics, Japan).
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4

Immunoblotting Quantification Protocol

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Immunoblotting was previously described [53 (link), 54 (link)]. Cells were lysed in radio-immunoprecipitation assay buffer (50 mm Tris-HCl (pH 8.0), 150 mm NaCl, 1% Nonidet P-40, 0.1% SDS, and 0.5% sodium deoxycholate) with the Complete Protease Inhibitor Cocktail (Roche Diagnostics, Tokyo, Japan) and an EDTA-free phosphatase inhibitor cocktail (Nacalai Tesque). Protein concentrations were quantified with the BCA Protein Assay (ThermoFisher Scientific, Yokohama, Japan). Equal amounts of total protein were applied to SDS-polyaclylamide gel electrophoresis, and transferred to Fluoro Trans W membrane (Pall, East Hills, NY, USA). Chemiluminescence images were captured on ImageQuant LAS4000 (Fujifilm, Tokyo, Japan). Image J software (NIH) was used to quantify blot band intensities in Figure 3c. See also Supplementary Information.
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5

Immunoprecipitation and Mass Spectrometry

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Cells expressing Mmr1-HA were grown to log phase at 25 °C, further cultured for 2 h at 37 °C, and harvested. Cells were broken by vigorously mixing with glass beads in a solution containing 40 mM Tris–HCl (pH 7.5), 150 mM NaCl, 1 mM dithiothreitol, 0.5% Triton X-100, EDTA-free protease inhibitor cocktail (Complete, Roche, 11836170001), and EDTA-free Phosphatase Inhibitor Cocktail (Nacalai Tesque, 07575-51). After removing the debris and glass beads by centrifugation at 20,000 × g for 5 min, lysates were incubated with anti-HA (1:200 dilution; 12CA5; Sigma, 11666606001) antibody and Dynabeads Protein G (Invitrogen, 100-03D) for 30 min at 4 °C. The beads were then washed thrice with a solution containing 40 mM Tris–HCl (pH 7.5), 150 mM NaCl, 1 mM dithiothreitol, and 0.5% Triton X-100. Immunoprecipitated proteins were partially separated (~1 cm) via SDS-PAGE. The gel lane for each condition was cut horizontally into several pieces (~0.2 cm3 for each piece) and subjected to protein mass spectrometric analysis.
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