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4 protocols using anti denv ns3

1

Antiviral Effects of Kinase Inhibitors

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To investigate the antiviral effects of afatinib, erlotinib, sunitinib, and compounds 10b, L1, and L3, HEK-293 or MCF-7 cells were infected with DENV-1, -2, or ZIKV with or without (i.e., only solvent) the compounds. At the indicated time points after infection, the cell lysates were analyzed by Western blot with the antibodies anti-DENV NS3 (GeneTex, Irvine, CA, USA), anti-ZIKV E (GeneTex), anti-HER2 (Cell Signaling Technology, Danvers, MA, USA), anti-HER2 phospho Y877 (Cell signaling), anti-Src (GeneTex), anti-Src phospho Tyr418 (GeneTex), anti-ERK1/2 (Cell Signaling), anti-ERK1/2 phospho Thr/Tyr204 (Cell Signaling), anti-GAPDH (Millipore Corporation. Billerica, MA, USA), and anti-actin (Millipore). Then, the membranes were probed with horseradish peroxidase-conjugated goat anti-mouse IgG secondary antibodies (Jackson ImmunoResearch, Suffolk, UK). The signals were developed by enhanced chemiluminescence (Millipore) and photographed using a Luminescent Image Analyzer (LAS-3000; Fujifilm Corporation, Tokyo, Japan).
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2

Western Blot Analysis of Cellular Proteins

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Cells were lysed in RIPA buffer (Cell Signaling Technologies). Proteins were fractionated on 4–12% acrylamide gels (Novex, Thermo Fisher Scientific) under denaturing conditions. Antibodies used were anti-RPLP1 (Ab121190; Abcam), anti-RPLP2 (Ab154958; Abcam), anti-mouse β-actin (sc-47778; Santa Cruz Biotechnology), anti-DENV NS3 (GTX124252; GeneTex), anti-FLAG (F7425; Sigma-Aldrich), anti-HA (ab18181; Abcam), anti-TSPAN12 (A05472–1; Boster-Bio); anti-MUC16 (sc-365002; Santa Cruz Biotechnology); anti-XRN1 (sc- 165985; Santa Cruz Biotechnology); anti-SEMA7A (sc-374432; Santa Cruz Biotechnology); anti-MIB1 (sc-393551; Santa Cruz Biotechnology); anti-PTPRO (sc-365354; Santa Cruz Biotechnology); anti-PARD6B (sc-166405; Santa Cruz Biotechnology); anti-eEF2K (sc-390710; Santa Cruz Biotechnology); anti-XRN1(ab70259; Abcam); anti-eEF2 (2332; Cell Signaling Technology); anti-EMC4 (ab184544; Abcam). For quantification, protein from triplicate wells were measured and averaged.
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3

Western Blotting of Dengue Virus Proteins

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Transfection of 293T cells and infection of human dendritic cells was performed as described in the sections ‘Dengue infection of MDDCs’, ‘Virus co-infection of MDDCs’ and ‘IFN-β reporter assay’. Cell lysates were obtained after incubation of cells with RIPA lysis buffer (Sigma Aldrich) supplemented with complete protease inhibitor (Roche) and resuspended in a total of 50 μl of Laemmli sample buffer (Bio-Rad). Crude lysates were boiled for 5 min and then kept on ice. Each sample was loaded in a polyacrylamide–SDS gel and the proteins were electrophoretically separated by conventional methods. The proteins in the polyacrylamide gel were transferred to nitrocellulose membranes, and blots were incubated with anti-FLAG, anti-haemagglutinin (HA), anti-β-actin (Sigma Aldrich) and rabbit polyclonal or monoclonal antibodies anti-DENV NS3 were validated in refs 10 and 39 (link) anti-DENV NS2B was purchased from GeneTex. Antibodies against cGAS and STING were purchased from Cell Signalling. Antibody–protein complexes were detected using a Western Lighting chemiluminescence system (Perkin Elmer).
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4

Western Blot Analysis of Apoptosis Regulators

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Cells were lysed in RIPA buffer (150 mM NaCl, 0.5% sodium deoxycholate, 1% NP40, 0.1% SDS, 50 mM Tris-HCl [pH 8.0]) or SDS buffer (2% SDS, 50 mM Tris-HCl [pH 7.5]) containing protease inhibitor and phosphatase inhibitor cocktail (Roche). Harvested extracts were separated by 10% SDS-PAGE and transferred to PVDF membranes. Later, the membranes were incubated with primary antibody, and then with horseradish peroxidase-conjugated secondary antibody (Jackson ImmunoResearch Laboratory, West Grove, PA) and were finally visualized using enhanced chemiluminescence (Thermo Fisher Scientific). Image acquisition and signal density measurements were carried out using the BioSpectrum Image System (UVP, Upland, CA). The following primary antibodies were used: anti-caspase 1 (GTX111630, GeneTex, Irvine, CA), anti-caspase 3 (#9665, Cell Signaling Technology, Danvers, MA), anti-caspase 7 (GTX1002337, GeneTex), anti-caspase 8 (#4790, Cell Signaling Technology), anti-bone morphogenetic protein 4 (BMP-4; GTX100875, GeneTex), anti-phospho-STAT1 (phospho-Tyr701, #9167 Cell signaling), anti-STAT1 (#14994, Cell Signaling), anti-phospho-STAT2 (phospho-Tyr690, GTX50721, GeneTex), anti-STAT2 (#14994, Cell Signaling), anti-DENV NS3 (GTX124252, GeneTex), and anti-GAPDH (#60004-1-Ig, Proteintech Group, Rosemont, IL).
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