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121 protocols using nf κb

1

Quantitative Protein Expression Analysis

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Frozen brain cortical tissues were homogenized in ice-cold lysis buffer [31 (link)], and clarified lysates were processed for SDS-polyacrylamide gel electrophoresis under reducing conditions with proteins transferred to nitrocellulose membranes. The membranes were routinely stained with the Ponceau S dye (Sigma-Aldrich, St-Louis, MO, USA) for the rapid and reversible detection of protein bands. Protein expression was detected using specific primary antibodies. Antibodies raised against Bcl2, cleaved caspase 3, FOXO3a, pVHL, acetyl-α-tubulin and phospho-p65Rel (Ser 536) were purchased from Cell Signaling Technology. (Danvers, MA, USA); NF-κB from Epitomics (Burlingame, CA, USA); eNOS from BD Biosciences (Franklin Lakes, NJ, USA); VEGF, ALDH2, SIRT2, β-actin, GAPDH and α-tubulin from Abcam; and HIF-1α from Cayman Chemicals (Ann Arbor, MI, USA). All antibodies were detected with horseradish peroxidase-conjugated secondary antibodies (Santa Cruz Biotechnology, Dallas, TX, USA) and visualized by enhanced chemiluminescence (GE Healthcare, Piscataway, NJ, USA). Quantitation of the protein bands was performed by volume densitometry using ImageJ software.
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2

Western Blot Analysis of Cellular Proteins

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The protein was separated with 10% SDS-PAGE and transferred to a membrane. Western blot analysis was performed as described previously, using COMT, GRP75, GRP78, CAHIII, Nrf2, PPAR, CYPOR, Cystathionine gamma-lyase, ubiquitin (Santa Cruz), Catalase, c-Myc, NF-κB, HIF-1, HO-1 (Epitomics), GSTP (Bethyl Lab), Endoplasmin, p53, AKT (Cell Signal), NQO1 (Proteintech), α-SMA, β-actin and anti-DNP (Sigma) overnight at 4°C., followed by incubated with HRP-labeled secondary antibody. Enhanced chemiluminescence was used for signal detection. Expression of β-actin was used to control for equal gel loading [54 (link)].
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3

Comprehensive Hepatoprotective Mechanism Study

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DHM (purity ≥99.0%) and TAA (purity ≥99.0%) were purchased from Sigma. Hematoxylin-eosin (H and E), TUNEL and Masson stain kits, and commercial assay kits for ALT and AST, SOD, GSH, MDA were obtained from the Nanjing Jiancheng Bioengineering Research Institute (Nanjing, China). The immunofluorescent staining kits and the enhanced chemiluminescence (ECL) kit were purchased from Beyotime science and technology Co., Ltd. (Beijing, China). The antibody of rabbit monoclonal α-SMA, TGF-β1, CYP2E1, Cleaved Caspase-3, Caspase3, Cleaved Caspase-9, Caspase-9, IκB kinase α (IKK-α), IκB kinase β (IKK-β), p-IKKα, p-IKKβ, inhibitor of IκBα (IκBα), p-IκBα, NF-κB, p-NF-κB, PI3K, p-PI3K, Akt, p-Akt, B-associated X (Bax), Bcl-2, β-actin and secondary antibodies for western blot were all obtained from Abcam (Cambridge, United Kingdom).
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4

Comprehensive Molecular Profiling of CCN3

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Immunohistochemistry, Immunofluorescence, Immunoblotting and ELISA were performed as previously described [7 (link)]. The BCA Protein Assay Kit (Beyotime, Shanghai, China) was used to determine the concentration of extracted protein. Levels of CCN3 in the cultured supernatants were quantified by ELISA kits (R&D Lab Inc., Minneapolis, MN, USA). MEK1/2 inhibitor U0126, NFκB inhibitor EVP4593, and Sorafenib were obtained from Selleckchem (Houston, TX, USA). Primary antibodies used for immunofluorescence, immunoblotting and/or, immunohistochemistry were as follows: CCN3, α-SMA, p-C-RAF, ERK1/2, NFκB, TIMP-2, TGF-β, and p-ERK1/2 (Abcam, Cambridge, MA, USA), RANTES and C-RAF (Cell Signaling, Beverly, MA, USA), p-MEK (Epitomics, Burlingame, CA, USA), Actin (Jackson Labs, Bar Harbor, ME, USA).
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5

Western Blot Analysis of NF-κB, Snail, and GAPDH

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The treated or untreated cells were placed on ice and treated with RIPA lysate for 20 minutes. And the cells were collected in EP tubes and centrifuged to obtain protein samples. All protein samples were adjusted to the same concentration, and the polyacrylamide gel electrophoresis step was performed to separate the proteins with different molecular weights. Then, the protein on the gel was transferred to the nitrocellulose (NC) film. The hydrophobic binding sites on the nitrocellulose film were blocked with 5% BSA. After blocking, the membrane was added with primary antibody NF-κB (Abcam, 1: 1000), snail (Abcam, 1: 500), and GAPDH (Abcam, 1: 2000) and incubate at 4°C overnight. Then, added the corresponding horseradish peroxidase labeled secondary antibody to react in the dark for 1 hour. Finally, the protein was detected and photographed according to the operation of the BeyoECL Plus chemiluminescence kit (Beyotime).
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6

NLRP3 Inflammasome Activation Pathway

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DEX and LPS were purchased from Beyotime Biotech. (Nanjing, China). qPCR Kit (SYBR Premix Ex Taq) and RIPA lysis buffer were supplied by TaKaRa (Dalian, China). A reverse transcription kit was purchased from TransGen (Beijing, China). Enzyme-linked immunosorbent assay (ELISA) kits of tumor necrosis factor-alpha (TNF-α), interleukin IL-1β, and NLR family pyrin domain-containing 3 (NLRP3) were supplied by Elabscience Biotech. (Wuhan, Hubei, China). All antibodies, including caspase-11; Gasdermin D (GSDMD); HMGB1; RAGE; NF-κB; PYD; and CARD domain-containing ASC, NLRP3, caspase-1, GSDMD-N, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were purchased from Abcam Inc. (Cambridge, UK).
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7

Protein Expression Analysis Protocol

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The RIPA buffer (Beyotime, China) was utilized to extract protein samples. Then, the concentration of these protein samples was determined with the BCA kits (Beyotime, China). Next, these proteins underwent the separating procedure in 10% SDS-PAGE gel. After that, these proteins were transferred to the polyvinylidene fluoride (PVDF) membranes (Millipore, USA). The PVDF membranes were blocked with 5% skimmed milk at room temperature for 2 h and incubated with primary antibodies at 4°C overnight. The primary antibodies used were Ki-67 (Abcam, ab16667), HMGB1 (Abcam, ab18256), RAGE (Abcam, ab216329), Bcl-2 (Abcam, ab32124), Bax (Abcam, ab32503), Cleaved caspase3 (Abcam, ab32351), cyclin D1 (Abcam, ab16663), TLR4 (Abcam, ab13556), NF-κB p65 (Abcam, ab207297), NF-κB (Abcam, ab281518), caspase4 (Abcam, ab25898), NLRP3 (Abcam, ab263899) and GAPDH (Abcam, ab8245). On the following day, the membranes were incubated with peroxidase-conjugated secondary antibody. Finally, the immunoreactive signals were detected with the Pierce ECL Western Blotting Substrate (Thermo Fisher Scientific, USA).
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8

Investigating Anti-inflammatory Mechanisms

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As-IV (purity: 98%) was provided by Jingzhu Biotechnology Co., Ltd. (Nanjing, China). LPS, BAY, adenosine triphosphate (ATP) and adenosine monophosphate (AMP) standards were provided by Sigma-Aldrich (St. Louis, MO, USA). ELISA kits for determination of free fatty acid (FFA), tumor necrosis factor alpha (TNF-α), interleukin-1β (IL-1β) and interleukin-6 (IL-6) levels were provided by R&D Systems (Minneapolis, MN, USA). TLR4, NF-κB, p65, PPARα, ATP5D and GAPDH antibodies were purchased from Abcam (Cambridge, MA, USA). All other reagents are analytically pure reagents.
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9

Immunodetection of Key Signaling Proteins

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The following antibodies were used: RNF8 (Proteintech, # 14112-1-AP), β-tubulin (Affinity, # T0023), CD3 (Affinity, # DF6594), IL-12 (Affinity, # AF5133), IFN-γ (Affinity, # DF6045), CXCL-9 (Affinity, # DF9920), CXCL-10 (Affinity, # DF6417), galectin-3 (Proteintech, # 14979-1-AP), HIF-1α (Proteintech, # 66730-1-Ig), p-IκBα (Abcam, # ab133462), NF-κB (Abcam, # ab16502), P-NF-κB (Santacruze, # sc-101752), PCNA (Proteintech, # 60097-1-Ig), Flag (Proteintech, # 20543-1-AP), HA (Proteintech, # 66006-2-Ig), His (Proteintech, # 66005-1-Ig), ubiquitin (CST, # 91112 S), K48 (CST, # 12805), K63 (CST, # 5621S). Secondary anti-mouse (# SA00001-1), and anti-rabbit (# SA00001-2) horseradish-coupled antibodies were from Proteintech.
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10

Protein Isolation and Western Blot Analysis

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Protein was isolated from samples using Trizol (Invitrogen). Protein concentration was measured using the BCA kit (Thermo Scientific) and 40 μg of protein/lane loaded in a 10% SDS PAGE precast gel (Invitrogen). Gel was transferred using the iBlot transfer system (Invitrogen). Nitrocellulose membrane was blocked in 2% I-Block (Applied Biosystems) in 1×TBS-T for one hour, and then either b-actin (Abcam, 1:10,000), Histone H3 (Cell Signaling, 1:1000), RAGE (R&D Biosystems, 1:500), TLR4 (Santa Cruz, 1:500), or NFκB (Abcam, 1:1,000) was used. Secondary antibodies (anti-mouse, Jackson ImmunoResearch) were added at 1:1,000 dilution in 2% I-Block in 1×TBS-T on a room temperature. The membranes were washed with 1×TBS-T, and then Luminol Reagent (Santa Cruz) was added. The membranes were then developed using a FluorChem E Imager system (ProteinSimple).
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