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15 protocols using traf6

1

Tetrandrine Modulates Osteoclastogenesis

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Tetrandrine (purity >98%) was purchased from MedChemExpress (New Jersey, USA) and was dissolved in DMSO at a 10 mmol/L stock solution and stored -20℃. Further dilution was carried out in culture medium for cells and PBS medium for animals. Primary antibodies against CTSK, CTR, MMP-9, TRAF6, TRAP, GAPDH, and β-actin were purchased from Proteintech (Wuhan, Hubei, China). Primary antibodies against NFATc1, P-PI3K, AKT, P-AKT, P50, P-P50, P65, P-P65, IκBα, P-IκBα, ERK1/2, P-ERK1/2, JNK, P-JNK, P38, and P-P38 were obtained from Cell Signaling Technologies (Beverly, MA, USA). Primary antibodies against RANKL, OPG, and the ELISA kit of RANKL were obtained from ABclonal (Wuhan, Hubei, China). The ELISA kits of OPG, IL-6, TNF-α, TRAcp5B, and CTX-I were purchased from Sangon (Shanghai, China). A CCK-8 assay kit was purchased from Dojindo (Tokyo, Japan). A leukocyte acid phosphatase staining kit was obtained from Sigma‐Aldrich (MO, USA). Recombinant M‐CSF and Recombinant m-RANKL were obtained from R&D Systems (Minneapolis, MN, USA). The cell culture medium that alpha‐modified minimal essential medium (α‐MEM), fetal bovine serum (FBS), and penicillin-streptomycin were purchased from Thermo Fisher Scientific (Scoresby, Vic., Australia).
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2

Analyzing Protein Interactions in Colon Cancer Cells

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Protein lysates were subjected to SDS-PAGE, and the resolved proteins were then transferred to PVDF membranes. The membranes were blocked in 5% non-fat dry milk or bovine serum albumin/fraction V (BSA, Sigma, USA) and then incubated overnight at 4 °C with the following primary antibodies: STX2 (Proteintech, USA), TRAF6 (Proteintech, USA), IKKβ (CST, USA), pIKKα/β (CST, USA), IκBα (CST, USA), pIκBα (CST, USA), P65 (CST, USA), pP65 (CST, USA) and α-Tubulin (Sigma, USA). Finally, the appropriate secondary antibodies (HRP-conjugated anti-rabbit IgG (CST, USA) and HRP-conjugated anti-mouse IgG (CST, USA) were applied. Chemiluminescent signals were detected with SuperSignal West Pico and exposed to autoradiography (HyBlot CL). α-Tubulin was used as the internal control to confirm the equal loading of the proteins.
Cell lysates for Co-IP were prepared from SW480-STX2-Flag and LOVO. The cell lysates were pre-cleared by incubating with protein A + G Sepharose beads (Sigma, USA). Then, the individual antibodies for STX2, TRAF6, and IgG were added to the lysates, and the samples were incubated overnight at 4 °C, after which the complexes were collected with protein A + G Sepharose beads and brief centrifugation. Finally, the bound proteins were separated by SDS-PAGE.
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3

Western Blot Analysis of Inflammatory Mediators

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Cells were lysed in radio immunoprecipitation assay (RIPA) lysis buffer (Beyotime Institute of Biotechnology, Shanghai, China) containing proteinase and phosphatase inhibitors. A BCA assay kit (Beyotime) was used to measure the concentration of protein. The supernatant proteins were precipitated. The protein of lytic samples was transferred to polyvinylidene fluoride (PVDF) membranes (Beyotime, China) after separating by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) (Beyotime). Membranes were incubated with antibodies against gasdermin D (GSDMD, Abcam, Cambridge, UK), IL-1β (Abcam), nuclear factor of activated T-cells, cytoplasmic 1 (NFATc-1, Abcam), TRAP (Abcam), pro caspase-1 (Cell Signaling Technology, Danvers, MA, USA), cleaved caspase-1 (Cell Signaling Technology), ASC (Cell Signaling Technology), TNF receptor-associated factor (TRAF) 2 (Proteintech, Rosemont, IL, USA), TRAF6 (Proteintech), c-Fos (Proteintech), cathepsin K (CTSK, Proteintech), matrix metalloprotein 9 (MMP9, Proteintech), and anti-actin (Beyotime) overnight at 4 °C after blocking with quick block buffer (Beyotime) for 30 min. Then, membranes were washed three times with TBS-Tween and incubated with the appropriate secondary antibody for 1 h at room temperature. The results were visualised via chemiluminescent peroxidase substrate (Proteintech).
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4

DMSO, L-THP, and ConA Hepatoprotective Protocol

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Dimethyl sulfoxide (DMSO), L-THP, and ConA were purchased from Sigma-Aldrich (St. Louis, MO, USA). ALT and AST microplate test kits were purchased from Jiancheng Bioengineering Institute (Nanjing, China). Enzyme-linked immunosorbent assay (ELISA) kits for TNF-α and IL-6 were purchased from Anogen-Yes Biotech (Mississauga, Canada). The antibodies used in the study were from Cell Signaling Technology (Danvers, MA, USA) and included anti-IL-6, -LC3, -p-JNK, -TNF-α, -β-actin, -Bax, -Bcl-2, -cleaved caspase 3, -cleaved caspase 9, -Beclin-1, -TRAF6, and -JNK from Proteintech (Chicago, IL, USA). PCR kits were purchased from Takara (Dalian, China). RPMI-1640 medium was purchased from Thermo (Shanghai, China). The Pan T cell isolation kit was purchased from Miltenyi Biotec (Bergisch Gladbach, Germany).
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5

Western Blot Analysis of Viral and Cellular Proteins

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Western blot assay was carried out as follow: cells were lysed with RIPA buffer (Santa Cruz, USA) and cleared lysate was collected by centrifugation for protein separation on 10% SDS-polyacrylamide gel. The proteins were transferred onto PVDF membranes (Millipore) and detected with respective antibodies at 4°C overnight, followed by incubation with either IRDye Fluor 680-labeled IgG or IRDye Fluor 800-labeled IgG secondary antibody (Li-Cor Bioscience). The images were scanned and quantified by densitometric analysis by Li-COR Odyssey Infrared Imager. Primary antibodies against VP1 (Millipore), CD81 (Cell Signaling Technology), IRAK1 (Santa Cruz), CD63 (Abcam), ISG15 (Abcam) and Rab27a, TRAF6, STAT1, TSG101, BST-2/Tetherin, and GAPDH (all from Proteintech), VP2, 3AB, 3C and 3D (all from Genetex) were used.
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6

Antibody Panel for Signaling Pathway Analysis

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The following antibodies used in this study for western blotting (WB), Immunohistochemistry (IHC) and immunofluorescence (IF) were: PI3K (4292S, Cell Signaling), p-PI3K (Tyr458) (11508-2, Singalway Antibody), AKT (4691, Cell Signaling), p-AKT (Ser473) (4060S, Cell Signaling), MAP2K4 (17340-1-AP, ProteinTech), c-Jun (9165S,Cell Signaling), MYH9 (60233-1-IG, ProteinTech), GSK3β (22104-1-AP, ProteinTech), p-GSK3β (5558S, Cell Signaling), c-Myc (AB32072, Abcam), E-cadherin (60335-1-IG, ProteinTech), N-cadherin (66219-1-IG, ProteinTech), β-catenin (51067-2-AP, ProteinTech), Vimentin (10366-1-AP, ProteinTech), Nanog (14295-1-AP, ProteinTech), OCT-4 (60242-1-IG, ProteinTech), Sox2 (11064-1-AP, ProteinTech), TRAF6 (66498-1-IG, ProteinTech), ubiquitin (10201-2-AP, ProteinTech), β-actin (CW0264M), GAPDH (CW0100M) and Histone (#5748, Cell Signaling), CD133(#64326, Cell Signaling), CD44(#3570, Cell Signaling).
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7

Protein Expression Analysis in BMDMs

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BMDMs were lysed by a cold buffer containing RIPA buffer (beyotime biotechnology, China), phosphatase, and proteinase inhibitors for 15 min. Then, the samples were centrifuged at 12,000g 5 min. The supernatants were subjected to a BCA assay (Beyotime Biotechnology, China) to determine the concentration of protein. The supernatant proteins were precipitated. The Western blot analysis was performed as previously described. The primary antibody of Caspase-1 (Cell Signaling Technology), IL-1β (Santa Cruz Biotechnology), Actin (Beyotime biotechnology), GSDMD (Abcam), TRAF6 (Proteintech), NFATc-1 (Abcam), TRAP (Abcam), CTSK (Santa Cruz Biotechnology), MMP9 (proteintech), c-Fos (proteintech). The quantification analysis was performed by ImageJ.
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8

Quantifying Protein Expression Profiles

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Tissues and cells were lysed on ice using radioimmunoprecipitation assay (RIPA; Biosharp, China) buffer supplemented with phenylmethanesulfonyl fluoride (PMSF; Biosharp, China), protease inhibitors (TargetMol, USA) and phosphatase inhibitors (TargetMol, USA). The total protein concentration in the supernatant of each sample was quantified using a BCA protein assay according to the manufacturer’s protocol (BCA Protein Quantification Kit, Thermo Scientific, USA). The detailed western blotting procedure was previously described [21 (link)]. Primary antibodies against the following proteins were used in the experiments: DPP4 (1:1000, Abcam), CD68 (1:1000, Abcam), ITGAX (1:1000, Proteintech), NF-κB p65 (1:1000, Cell Signaling Technology, USA), MyD88 (1:1000, Proteintech), TRAF6 (1:3000, Proteintech) and NF-κB phosphorylated p65 (p-p65; 1:1000, Cell Signaling Technology, USA). Protein expression is presented relative to the levels of β-actin (1:10000, Abcam).
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9

Western Blot Analysis of Intestinal Inflammation

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According to our previous methods (22 (link), 23 (link)), the total proteins in liver and ileum tissues were extracted, and proteins were quantified using a bicinchoninic acid (BCA) Protein Assay Kit (Nanjing Jiancheng Bioengineering Institute, Nanjing, China). The same amounts of proteins were dissolved on polyacrylamide gels (8–10%) and transferred onto PVDF membranes (Millipore, Bedford, MA, USA). The membranes were blocked with 10% non-fat milk in Tris-buffered saline/Tween (TBST) and then incubated with primary antibodies against TLR4, MyD88, IRAK1, TRAF6 (Proteintech Group, Chicago, USA), IκBα, phospho-IκBα (Santa Cruz, CA, USA), NF-κB, ZO-1, claudin 1, occludin, and β-actin (Cell Signaling Technology, Danvers, MA, USA) at 4°C overnight. After washing with TBST, the membranes were incubated with the corresponding secondary antibodies (Bioeasy, Beijing, China) for 2 h at 37°C. In the end, the bands of proteins were visualized by the Odyssey Infrared Imaging System (Li-Cor Biosciences, Lincoln, NE, USA). β-actin served as an internal control.
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10

PM2.5-Induced Inflammatory Pathways

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PHBA (≥99%) and PHPPA (98%) were provided by Sigma Chemical Co. (St. Louis, MO, United States). PM2.5 particles were provided by Hong-Hai Yu, senior engineer of Huadian Electric Power Research Institute Co., Ltd. Northeast Branch. Mouse tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and interleukin-1β (IL-1β) ELISA kits were purchased from Biyuntian Biotechnology Research Institute. TLR4, TLR2, TRAF6, NF-κB, MyD88, IRAK1, TAK1, and IKKβ polyclonal antibody IgG were obtained from Proteintech Group Inc (Chicago, IL, United States).
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