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20 protocols using anti p50

1

Western Blotting and Immunoprecipitation Analysis

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Western blotting analysis was performed as previously described [48 (link)]. The blot was probed with antibodies specific for iNOS (BD Biosciences), STAT1 (BD Biosciences), pSTAT1 (BD Biosciences), and β-actin (Sigma-Aldrich). Immunoprecipitation was done with anti-p65 and anti-p50 (Santa Cruz Biotech), as previously described [49 (link), 50 (link)]. The immunoprecipitated proteins were analyzed by Western blot analysis with anti-p65 (Santa Cruz Biotech).
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2

Comprehensive Cell Culture Reagents

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Cell culture reagents were obtained from Invitrogen (San Diego, CA, USA), unless otherwise specified. Fetal bovine serum (FBS) was from Biological Industries (Haemek, Israel) and oligofectamine and G418 from Invitrogen. NGF and BDNF from Peprothec (Rocky Hill, NJ). ProNGF from Scil Proteins GmbH (Halle, Germany) and ammonium pyrrolidinedithiocarbamate (PDTC) from Sigma-Aldrich (St. Louis, MO USA). Antibodies used in this study were the following: mouse anti-α-smooth muscle actin (α-SMA, 1∶500; Dako, Dakopatts, Denmark), anti-smooth muscle myosin (1∶400; NeoMarkers, Fremont, CA USA), anti-CD68 (Dako, 1∶250), anti-α-tubulin and anti-Chromosome Region Maintenance 1 (CRM1, 1∶1000; Sigma-Aldrich), rabbit anti-sortilin (1∶200, Abcam, Cambridge, UK; Chemicon Intern, Temecula, CA USA), anti-proNGF (Sigma-Aldrich), anti-bax protein (1∶200), anti-NF-κB p65 (1∶200), anti-p50 (1∶100), anti-IκB-α (1∶50), goat anti-p75NTR (1∶200), anti-bcl-2 (1∶100, Santa Cruz Biotechnology, CA, USA) and anti-hypoxanthine-guanine phosphoribosyltransferase (HPRT; Abcam). Fluorocrome conjugated secondary antibodies were purchased from Jackson (Suffork, UK) and Invitrogen. Horseradish peroxidase-conjugated secondary antibodies were from Nordic (Tilburg, The Netherlands).
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3

Inflammatory Pathway Modulation in Cell Lines

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Dulbecco’s modified Eagle’s medium (DMEM), foetal bovine serum (FBS), and other tissue culture reagents were purchased from Gibco BRL Co. (Grand Island, NY). All other chemicals, including lipopolysaccharide (LPS), cobalt protoporphyrin IX chloride (CoPP) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), were obtained from Sigma-Aldrich (St. Louis, MO). Primary antibodies such as anti-iNOS, anti-COX-2, anti-inhibitor kappa B (IкB)-α, anti-p-IкB-α, anti-p50, anti-p65, anti-actin and anti-proliferating cell nuclear antigen (PCNA) antibodies were purchased from Santa Cruz Biotechnology (Dallas, TX). Anti-p-extracellular signal-regulated kinase (ERK), anti-ERK, anti-p-c-Jun N-terminal kinase (JNK), anti-JNK, anti-p-p38, anti-p38, anti-p-protein kinase B (Akt) and anti-Akt were obtained from Cell Signaling Technology (Danvers, MA). Anti-HO-1 antibody was gained from Merck Millipore (Darmstadt, Germany), and anti-Nrf2 antibody was purchased from Abcam (Cambridge, MA). Anti-mouse, anti-goat and anti-rabbit secondary antibodies were supplied by Merck Millipore (Darmstadt, Germany). Tin protoporphyrin IX (SnPP IX), an inhibitor of HO activity, was obtained from Porphyrin Products (Logan, UT). The enzyme-linked immunosorbent assay (ELISA) kit for PGE2 was purchased from R&D Systems, Inc. (Minneapolis, MN).
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4

Immuno-cytochemical Analysis of NF-κB Subunits

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HuF and UIII cells were grown for 24 hr in RPMI and M199 medium supplemented with 4% CDT-FBS on Lab-Tek chamber slides (Nalge Nunc International, Rochester, NY). The cells were cultured with IL-1β, IL-1β+curcumin, or vehicle for 24 hr and processed for immuno-cytochemistry as described previously [30 (link)]. Primary antibodies used were rabbit polyclonal anti-p50 and goat polyclonal anti- p65 NF-κB (Santa Cruz Biotechnology, Inc., Dallas, Tx), whereas Cy3-conjugated or Cy2 conjugated donkey anti-rabbit IgG (Jackson ImmunoResearch Laboratories, West Grove, PA) were used as secondary antibodies. The slides were mounted in Vectashield medium (Vector Laboratories, Inc., Burlingame, CA) containing a counterstain for DAPI and were observed with a Nikon Eclipse Ni microscope equipped with Nikon DS-Qi1Mc and DS-Fi2 digital cameras.
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5

Western Blot Analysis of Microglial Signaling Pathways

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The method used for western blot analysis has been described in detail previously [26 (link),27 (link)]. Total proteins were extracted from the microglial cells with Protein Extraction Reagent (Pierce, Rockford, IL) according to the manufacturer’s instructions. Equal amounts of each protein extract (50 μg) were incubated at 4 °C overnight with primary antibodies, namely anti-phospho-extracellular signal–regulated kinase (ERK1/2) (1:2,000), anti-ERK1/2 (1:1,000), anti-phospho-p38 (1:1,000), anti-p38 (1:1,000), anti-phospho-c-Jun N-terminal kinase (JNK; 1:1,000), anti-JNK (1:2,000; all were from Cell Signaling Technology, Beverly, MA), anti-p65 (1:1,000, Santa Cruz Biotechnology, Santa Cruz, CA), and anti-p50 (1:1,000, Santa Cruz Biotechnology). After washing, the membranes were incubated with a peroxidase-conjugated secondary antibody and visualized with a chemiluminescence detection system (Immobilon P, Millipore, Denmark). Images were obtained using a densitometer (Bio-Rad, Hercules, CA) and analyzed quantitatively with Multi-Analyst Macintosh Software. The band densities were normalized relative to the level of β-actin in each sample, which was detected as an internal control.
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6

Immunoblotting and EMSA to Characterize NF-κB Pathway

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Immunoblotting was performed using whole cell lysate as previously described37 (link). Primary antibodies used include: anti-p50 (sc7178, Santa Cruz Biotechnology), anti-GAPDH (sc-137179,), anti-CDK1 (sc-54), anti-HA (sc-7392), anti-actin (sc-1616). Unedited, full-length immunoblots are provided in Supplementary Information (Supplementary Figs. S7–Fig. S15). Several immunoblots were cut prior to antibody hybridization for reagent conservation. To identify the κB-site, the program TFSEARCH was used and a sequence with 86% homology with the canonical κB binding site was identified. For EMSA, nuclear fraction was isolated, a double-stranded oligonucleotide (5′-CGCTGAAGAGAATTCCCAAGGC-3′) (IDT) containing the decameric κB-consensus sequence was end labeled with [ɣ-32P] ATP and used as a probe, and the assay performed as previously described13 (link). Supershift assays were performed using antibodies specific to p50 or BCL-3. Competition was performed by pre-incubating the mixture with cold specific and non-specific DNA probe.
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7

Protein Expression Analysis by Western Blot

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SDS sample buffer was added to cell lysates. Proteins were separated in 10% SDS-polyacrylamide gel and transferred to PVDF membranes. Immunoblotting was performed with the following primary antibodies: anti-beta tubulin (Sigma Aldrich), anti-Hdac1, anti-p65, anti-p50 (Santa Cruz Biotechnology), anti IκBα (Thermo Scientific). Signals were detected using Pierce ECL Western Blotting Substrate (Thermo Scientific).
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8

Immunoprecipitation and Western Blot Analysis

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TH0 and Treg cells were generated and expanded as described above and 1 × 108 cells were lysed in 4 ml Meister Lysis Buffer (20 mM Tris/HCl pH 7.5, 0.25% NP40, 150 mM NaCl, 1,5 mM MgCl2 and Protease Inhibitors (Roche, catalogue number: 04693132001) und 1 mM DTT). 60 μl Protein-G beads (Dynabeads Protein G, catalogue number: 10004D) were pre-coupled with 10 μg antibodies (anti-Bcl-3: Santa-Cruz, catalogue number: sc-185; anti-p50: Abcam, catalogue number: ab7971) in PBS and 0.05% Tween and then equilibrated in Meister Lysis Buffer and added to lysed cells and incubated for 4 h. Washing was performed with Lysis Buffer. Proteins were eluted with 80 μl 1 × SDS Lämmli loading dye, one-fourth was used for western blot analysis. Blottings were incubated with anti-p50 (Santa-Cruz, catalogue number: sc-8414) and anti-Bcl-3 antibodies (Santa-Cruz, catalogue number: sc-185).
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9

Nuclear Protein Extraction Protocol

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Cells were trypsinized with trypsin-EDTA (Sigma), washed with PBS, and the cell pellet was resuspended in 1 ml of cold buffer A (10 mM HEPES, 1.5 mM MgCl2, 10 mM KCl, 1 mM DTT). Nuclear pellets were isolated from the whole cell protein by centrifugation at 14,000 rpm for 1 min at 4°C and resuspended in two-thirds packed cell volume of cold buffer B (20 mM HEPES, 1.5 mM MgCl2, 25% glycerol, 420 mM NaCl, 0.2 mM EDTA, 1 mM DTT) with vigorous agitation in the cold room for 30 min. The supernatant containing nuclear proteins was collected for Western blot. The following antibodies were used for blotting: anti-RelA (Santa Cruz), anti-IκBα (Cell Signaling), anti-PARP (Cell Signaling), anti-Actin (Sigma-Aldrich), and anti-p50 (Santa Cruz).
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10

Immunoblotting and EMSA for NF-kB and p53

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Immunoblotting was performed using whole cell lysate as previously described (7 ). Primary antibodies used include: anti-p50 (sc7178, Santa Cruz Biotechnology), anti-p65 (#8242, Cell Signaling, Beverly, MA, USA), anti-gapdh (sc-137179,), anti-p53 (sc71818,). Alexa-Fluor 680 and Alexa-Fluor 800 fluorescent dye-conjugated secondary antibodies (Invitrogen) were used for visualization with Odyssey Infrared system (LI-COR, Lincoln, NB, USA). For EMSA, nuclear fraction was isolated, or pure protein obtained, and assay performed as described (3 ). Supershift assays were performed using antibody cocktails specific to the indicated NF-кB subunit or p53. Competition was performed by pre-incubating the mixture with cold specific and non-specific DNA probe.
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