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43 protocols using ikkα β

1

Protein Expression Analysis of Immune Cells

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After 12 or 24 h of treatment, RSC-364 cells and lymphocytes were harvested. Cells were lysed using RIPA Lysis Buffer containing protease inhibitor cocktail (Sigma, St. Louis, MO, USA). Protein samples (2 mg/ml) were separated by 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and electrotransferred onto the polyvinylidene difluoride membranes (Sigma, St. Louis, MO, USA). The membranes were blocked with 5% skim milk and incubated overnight with the following primary antibodies at 4°C: T-bet, GATA-3, RORγt, TRAF2, IKKα/β, phospho-IKKα/β, and NF-κB p50 for lymphocytes; TRAF2, MyD88, IKKα/β, phospho-IKKα/β, NF-κB p50, JAK1, STAT3, and phospho-STAT3 for RSC-364 cells (1 : 1000, Cell Signaling Technology, MA, USA). The membranes were then incubated with horseradish peroxidase- (HRP-) conjugated IgG secondary antibody (1 : 3000, Abcam, Cambridge, MA, USA) at room temperature for 2 h. All immunoreactive proteins were visualized using SuperSignal West Pico Chemiluminescent Substrate (Thermo Scientific, Rockford, IL, USA). Three replicates of each experiment were performed. The densitometry values were normalized to GAPDH and quantified using Image-Pro Plus version 4.0 (Media Cybernetics Inc., Rockville, MD, USA).
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2

Western Blot Analysis of Inflammatory Signaling

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RAW264.7 cells and colon tissues were homogenized, and protein levels were quantified using BCA reagent (Beyotime, Shanghai, China). Nuclear and cytoplasmic extractions were performed as instructed by the manufacturer (Beyotime, Shanghai, China). Samples were loaded and electrophoresed in 10–12% SDS-PAGE and then transferred to nitrocellulose membranes. Membranes were blocked in 5% nonfat milk diluted in TBS-T for 2 h followed by incubation with primary antibodies. The following primary antibodies were used in this experiment: iNOS, COX-2, phospho-IKKα/β, IKKα/β, phospho-IκBα, IκBα, phospho-ERK ½, ERK ½, phospho-p38, p38, p65, phospho-c-Jun, c-Jun, c-Fos, β-tubulin, Lamin A/C, phospho-JNK, JNK, IRAK4, and β-actin at 1:1,000 dilution (Cell Signaling Technology, Danvers, MA, USA). Secondary antibodies included horseradish peroxidase (HRP)-conjugated goat anti-rabbit and anti-mouse IgG at 1:2,500 dilution.
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3

Methanol Extraction of P. attenuatum and Anti-inflammatory Effects

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Methanol extraction of P. attenuatum (Pa-ME) was purchased from the Plant Extract Bank in the Plant Diversity Research Center (Daejeon, Republic of Korea; http://extract.kribb.re.kr, e-mail: mplantext@kribb.re.kr). RAW264.7 cells, a transformed macrophage cell line derived from the BALB/c mouse (ATCC number TIB-71), were purchased from ATCC (Rockville, MD, USA). Dimethyl sulfoxide (DMSO), L-NG-nitroarginine methyl ester (L-NAME), indomethacin, lipopolysaccharide (LPS, Escherichia coli 0111:B4), pam3CSK, and (3-4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) were purchased from Sigma Chemical Co. (St Louis, MO, USA). Poly I:C was obtained from Calbiochem (La Jolla, CA). The enzyme immune assay (EIA) kits used to quantitate the levels of PGE2 were purchased from Amersham (Little Chalfont, Buckinghamshire, UK). Specific PCR primers for iNOS, TNF-α, COX-2, and GAPDH were synthesized from Bioneer Inc. (Daejeon, Republic of Korea). Antibodies that specify phosphorylated and total forms of p65, p50, c-Jun, c-Fos, Lamin A/C, IκBα, IKKα/β, AKT, Src, Syk, ERK, p38, JNK, IRAK1, IRAK4, TAK1, MKK3/6, and β-actin were obtained from Cell Signaling (Beverly, MA, USA).
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4

Malus baccata Extract Macrophage Modulation

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The methanol extract of Malus baccata (L.) Borkh (Mb-ME) was obtained from the Plant Extract Bank in the Plant Diversity Research Center (Daejeon, Korea). The RAW264.7 (murine macrophages) cells and HEK293 (human embryonic kidney) cells were purchased from ATCC (Rockville, MD, USA). The reagents used for culturing cells were purchased from Gibco (Grand Island, NY, USA). Lipopolysaccharide (LPS), polyethylenimine (PEI), ranitidine, sodium carboxymethyl cellulose (Na-CMC), and other chemicals were obtained from Sigma Chemical Co. (St. Louis, MO, USA). Phospho-specific and total antibodies recognizing β-actin, IκBα, p50, IKKα/β, HA, Src, p65, Syk, p85, Lamin A/C, Akt, p85, IκBα, and Myc were purchased from Cell Signaling (Beverly, MA, USA).
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5

Investigating Anti-Inflammatory Mechanisms

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Dulbecco's modified Eagle's medium (DMEM; Welgene Co., Gyeongsangbuk-do, Korea), fetal bovine serum (FBS; Welgene Co.), streptomycin and penicillin (Lonza, Walkersville, MD, USA), TRIzol reagent (Invitrogen, Carlsbad, CA, USA), oligo-dT (Bioneer Co., Daejeon, Korea), inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and IL-1β primers were obtained from Bioneer Co. Lipopolysaccharide (LPS; Escherichia coli 055:B5) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) were purchased from Sigma (St. Louis, MO, USA). Specific antibodies used against phosphorylated extracellular signal-regulated kinase (ERK) and/or total form of ERK, Jun amino-terminal kinases (JNK), p38, IκB kinase (IKK) α/β, IκB, NF-κB p65, iNOS, COX-2, β-actin, and secondary antibody rabbit horseradish peroxidase-linked antibody were purchased from Cell Signaling Technology (Beverly, MA, USA). All other reagents and chemicals were obtained from Sigma Aldrich.
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6

RAW264.7 Cell Inflammatory Response Assay

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RAW264.7 cells from mice (BLAB/c, ATCC number TIB-71) were purchased from ATCC (Rockville, MD, USA). Dimethyl Sulfoxide (DMSO), L-NG–nitroarginine methyl ester (L-NAME), lipopolysaccharide (LPS, Escherichia coli 0111:B4), and (3-4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) were purchased from Sigma Chemical Co. (St Louis, MO, USA). Gene specific PCR primers for iNOS, TNF-α, COX-2, and GAPDH were synthesized from Bioneer Inc. (Daejeon, Republic of Korea). Antibodies to phosphorylated and total protein (p65, p50, IκBα, IKKα/β, Syc, Syk, STAT3, JAK, and β-actin) were obtained from Cell Signaling (Beverly, MA, USA).
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7

Inflammatory Signaling Pathway Analysis

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Fetal bovine serum (FBS), DMEM, and RPMI 1640 were obtained from Thermo Fisher Scientific (Waltham, MA, USA). RAW264.7 cells and HEK293 cells were purchased from ATCC (Rockville, MD, USA). MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, a tetrazole), lipopolysaccharide (LPS), dimethyl sulfoxide (DMSO), and sodium dodecyl sulfate (SDS) were purchased from Sigma Chemical Co. (St. Louis, MO, USA). The total or phospho-specific antibodies against p50, p65, IκBα, IKKα/β, p85/PI3K, Src, Syk, AKT, HA, and β-actin were obtained from Cell Signaling Technology (Beverly, MA, USA) and Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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8

Signaling Pathway Analysis in Cancer Cells

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Cell culture medium was purchased from Invitrogen (Grand Island, NY). Fetal bovine serum (FBS) was purchased from Atlas Biologicals (Fort Collins, CO). Primary antibodies targeting the following were as detailed: Actin, EGFR, pEGFRTyr1069, pEGFRTyr1173, pEGFRTyr1110, ERK1/2, pERK1/2Thr202/204, mTOR, pmTORSer2441, pFAKTyr397, pFAKTyr527, pFAKTyr925, FAK, pMEKSer221, MEK, IKKα/β, pIKK α/βSer180/181, pSRCTyr418, SRC, pAKTSer473, AKT, pSTAT1Ser727, STAT1, Hsp70 and PLCγ were from Cell Signalling (Danvers, MA). Antibodies specific for BAG3 were from Abcam (Cambridge, UK). Secondary HRP-conjugated antibodies, including anti-rabbit Gig and anti-mouse IgG were from Cell Signalling (Danvers, MA). YM-1 was obtained from Sigma Aldrich and the compounds 5-carbamimidamido-2-[2-(phenylformamido) acetamido pentanoic acid (ZINC02516109) and 2-(quinoline-3-carbonyl)-2,8-diazaspiro[4.5]decane-3-carboxylic acid (ZINC72169376) sourced from MolPort (Europe).
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9

Isolation and Characterization of Melianodiol

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Melianodiol (MN) was isolated from the fruits of M. azedarach by our research group. The structure of MN is shown in Fig. 1A (Xu et al., 2008 (link)). NO, IL-6, IL-10, and TNF-α ELISA kits were provided by Shanghai MLBIO Biotechnology Co. Ltd. (Shanghai, China). LPS was obtained from Sigma (Sigma Aldrich, St. Louis, MO, USA). 5-Aminosalicylic acid was provided by Shanghai Aladdin Biochemical Co. Ltd. (Shanghai, China). DSS was provided by MP Biomedicals (USA) and indomethacin by Aladdin (USA). Antibodies against β-actin, JAK2, STAT3, IKKα/β, NF-κBP65, IKBα, p-IKKα/β, p-IκBα, p-P65, iNOS, eNOS, Nrf-2, HO-1, and Keap1 were provided by Cell Signaling Technology (Danvers, MA, USA). SOD, NO, GSH, and malondialdehyde (MDA) were obtained from the Nanjing Jian-Cheng Bioengineering Institute (Jiangsu, China).
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10

Signaling Pathway Protein Analysis

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Antibodies against pIκBαS32/36, IκBα, pIKKα/βS176/180, IKKα/β, pSmad3S423/425, and Smad3 were obtained from Cell Signaling Technology (Beverly, MA). Anti-collagen I, anti-fibronectin, and anti-tubulin antibodies were purchased from abcam (Cambridge, UK), Santa Cruz Biotechnology (Santa Cruz, CA), and Sigma-Aldrich, respectively. The crude extracts were resolved in 6–10% SDS-PAGE gels and probed with the indicated antibodies. The data shown are representative of at least three independent experiments. Quantification for Western blots is shown in Supplementary Figure 3.
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