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314 protocols using proliferating cell nuclear antigen (pcna)

1

Quantitative Analysis of DNA Damage Response Proteins

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Protein-matched aliquots of whole cell lysates were subjected to SDS-PAGE and immunoblot analysis of RAD6 (17), PCNA (Dako, CA), FANCD2, KU86, KU70 (Santa Cruz Biotechnology Inc., TX), POL η (Abcam, MA), γH2AX (BioLegend, CA), RAD18 (Imgenex Corp., CA), RAD51 (Calbiochem, MA), and β-actin (Sigma-Aldrich Chemicals, MO). Since the peptide we used for generating RAD6B antibody is 91% conserved in human RAD6A, the RAD6 proteins detected by our antibody will not distinguish RAD6A and RAD6B proteins, and hence is referred as RAD6 rather than RAD6A or RAD6B [17 (link)]. For PCNA or H2AX ubiquitination analysis, lysates were immunoprecipitated with anti-PCNA, rabbit anti-H2AX (Abcam) or the corresponding normal IgG, and the captured immune complexes subjected to immunoblotting with anti-ubiquitin antibody (Santa Cruz, TX). Stripped membranes were reprobed with PCNA or mouse anti-H2AX antibody (Santa Cruz) to verify PCNA or H2AX pull-down, respectively. H2AX-depleted supernatants were immunoblotted with anti-γH2AX antibody. The relative levels of monoubiquitinated-PCNA, γH2AX and monoubiquitinated-γH2AX were quantified by Image J.
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2

Immunohistochemical Profiling of Stem Cell Markers

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5 μm fixed sections were incubated with primary antibodies in a hybridization chamber for 1 h at room temperature or overnight at 4°C. The primary antibodies used were DclK1, COX-2, 5-LOX, Ki67, proliferating cell nuclear antigen (PCNA), CD133, CD44, Lgr5, Annexin V and β-catenin procured from Santa Cruz/Abgent/Abcam/Abcam/Cell Signaling. Following primary antibody, sections were incubated for 1 h with anti-mouse/anti-rabbit/anti-goat secondary antibody, then visualized with diaminobenzidine (DAB) and counterstained with H&E for IHC or with DAPI for immunohistofluorescence (IHF). Slides were observed under an Olympus microscope 1X701 and digital computer images were recorded with an Olympus DP70 camera.
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3

Antibody Identification in Protein Analysis

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The rabbit anti-APAP-AD antibody was a kind gift from Dr. Lance Pohl (National Heart, Lung and Blood Institute, USA).13 (link) The other antibodies were: CYP2E1 (#ab28146) from Abcam (Cambridge, UK), p62 (#H00008878-M01) from Abnova (Taipei, China), phospho-S6 (#4858), total S6 (#2217), phospho-JNK (#4668), and GAPDH (#2118) from Cell Signaling Technology (Danvers, MA, USA); β-actin (#a5441) from Sigma-Aldrich (St. Louis, MO, USA), total JNK (#554285) from BD Pharmingen (Franklin Lakes, NJ, USA); proliferating cell nuclear antigen (PCNA) (#SC-56) from Santa Cruz Biotechnology (Dallas, TX, USA). The rabbit anti-microtubule-associated protein 1 light chain 3 (LC3) antibody was described previously.22 (link) The secondary antibodies were HRP-conjugated goat-anti-rabbit (#111-035-045), and HRP-conjugated goat-anti-mouse (#115-035-062) were from Jackson ImmunoResearch (West Glove, PA, USA). All other reagents were either from Sigma (USA) or Thermo Fisher Scientific (USA).
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4

Curcumin-mediated NF-κB Pathway Regulation

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Curcumin and propidium iodide (PI) were purchased from Sigma-Aldrich (Germany). All antibodies (PARP, lamin B, caspase-3, pCREB, catalytic PKA subunits, Ras GAP, pRaf, pErk, NF-κB subunits p50 and p65, RelB, IκBα, actin, and proliferating cell nuclear antigen (PCNA) were obtained from Santa Cruz Biotechnology (USA) and Cell Signaling (USA). Electrophoresis reagents and Bio-Rad protein assay kit were purchased from Bio-Rad Laboratories (USA). The 22-mer double-stranded NF-κB oligonucleotides were obtained from Promega (USA). Dichlorofluorescein diacetate (DCFHDA) was obtained from Molecular Probes (USA). PGE2, hydroxy PGE2, and butaprost were purchased from Cayman Chemicals (USA). H89 and PD98059 were obtained from Sigma Aldrich and Cell Signaling. Nitrocellulose membrane and X-ray reagents were purchased from (Amersham Pharmacia Biotech, UK). These chemicals were used according to the manufacturer’s instructions.
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5

Protein Expression Profiling of TPA-Induced Cells

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The cells were incubated for 24 hours with TPA, which was followed by treatment with 10 or 30 µg/mL CFE for 1 hour. The cells were lysed with ice-cold radioimmunoprecipitation assay (RIPA) buffer (Thermo, Rockford, USA), and the protein lysates (20 µg) were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The separated proteins were transferred to polyvinylidene difluoride (PVDF) membranes using Western blotting apparatus. The membranes were blocked for 2 hours with 2% bovine serum albumin or 5% skim milk and then incubated with 1 µg/mL primary antibody overnight at 4℃. The primary antibodies used for detection were: protein kinase C (PKC)α, PKCβ, PKCδ, p38, phosphorylated p38 (p-p38), c-Jun N-terminal kinase (JNK), p-JNK, extracellular signal-regulated kinase (ERK), p-ERK, p-c-Jun (Cell Signaling Technology, Beverly, USA), sodium potassium ATPase (Na-K ATPase) (Abcam, Cambridge, UK), MMP-9, p50, p65, and proliferating cell nuclear antigen (PCNA) (Santa Cruz Biotechnology, Dallas, USA). Horseradish peroxidase conjugated IgG was used as a secondary antibody and the protein expression levels were evaluated by signal analysis using a MINI HD6 image analyzer (Uvitec, Cambridge, UK).
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6

Butein Modulates Adipocyte Differentiation

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Butein was purchased from Sigma-Aldrich Co. (St. Louis, MO, USA). Dulbecco’s modified Eagle’s medium (DMEM) and phosphate-buffered saline (PBS) were purchased from HyClone (Logan, UT, USA). Bovine calf serum (BS), fetal bovine serum (FBS), and penicillin-streptomycin were obtained from GIBCO (BRL Life Technologies, Grand Island, NY, USA). Insulin (INS), isobutyl methylxanthine (IBMX), dexamethasone (DEX), and dimethyl sulfoxide were purchased from Sigma-Aldrich Co.. Primary antibodies against β-actin, C/EBPα, PPARγ, Nrf2, HO-1, and proliferating cell nuclear antigen (PCNA) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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7

Protein Expression Analysis in Liver Tissues

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Liver tissues were homogenized in 10 volumes (w:v) of ice-cold protein lysis buffer using the Tissue Lyser system (Qiagen, Valencia, CA, USA) with 5 mm sterile stainless steel beads. Thirty micrograms of protein were loaded into the lanes of a SDS-PAGE gel, separated, and blotted onto a PVDF membrane. After blocking with 5% nonfat milk or bovine serum albumin in TTBS, membranes were probed with a specific primary antibody, including proliferating cell nuclear antigen (PCNA; Santa Cruz Biotechnology, Santa Cruz, CA, USA), β-catenin (Santa Cruz Biotechnology, Santa Cruz, CA, USA), cleaved form of caspase-3 (Cell signaling Technology, Danvers, MA, USA) or anti-70-kDa heat shock cognate protein (HSC70; Cell signaling Technology, Danvers, MA, USA). The membranes were then incubated with an IgG-peroxidase-conjugated secondary antibody for chemiluminescent detection. The band intensities were quantified using Quantity One software (Bio-Rad, Hercules, CA, USA).
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8

Protein Expression Analysis in Cancer Cells

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HeLa and A2058 cells were lysed in RIPA buffer (100 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.1% SDS, and 1% Triton 100) at 4 °C. The protein concentration was measured using a DC Protein Assay Kit (Bio-Rad Laboratories, USA). Proteins in the resultant lysate were separated by SDS-PAGE and then electrotransferred to PVDF membranes (Immobilon-P; Millipore, Bedford, MA, USA) using a Bio-Rad Semi-dry Transfer Cell. The blots were then incubated with primary antibodies against α-actinin (ACTN), Ac-H3 (acetylated form of histone H3 at lysine 9/14), fatty acid synthase (FASN), p21, p53, proliferating cell nuclear antigen (PCNA) (Santa Cruz Biotechnology, USA), acetyl-CoA carboxylase (ACC), p-ACC (phosphorylation at Ser 79), AMPK, p-AMPK (phosphorylated at Thr 172), cleaved poly-ADP-ribose polymerase (cPARP) (Cell Signaling, USA), and DEC1 (Bethyl Laboratory, USA). Thereafter, the blots were incubated with horseradish peroxidase-conjugated secondary antibody (Santa Cruz Biotechnology). The immunoreactive proteins were then detected using ECLTM Western Blotting Detection Reagents and Amersham HyperfilmTM ECL (GE Healthcare, USA).
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9

Geniposide Modulates Cellular Signaling

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Geniposide was purchased from Shanghai Winherb Medical Science Co. (Shanghai, China). The purity of geniposide was above 98% as determined by HPLC analysis. Antibodies against p-NF-κB (1 : 1000 dilution), NF-κB (1 : 1000 dilution), β-actin (1 : 1000 dilution), Bax (1 : 1000 dilution), Bcl-2 (1 : 1000 dilution), cleaved caspase 3 (1 : 1000 dilution), acetyl-CoA carboxylase (ACC, 1 : 1000 dilution), p-ACC (1 : 1000 dilution), extracellular regulated protein kinases (ERK, 1 : 1000 dilution), and p-ERK (1 : 1000 dilution) were purchased from Cell Signaling Technology (Danvers, Massachusetts, USA). Proliferating cell nuclear antigen (PCNA, 1 : 200 dilution) was obtained from Santa Cruz (Dallas, TX, USA). Sirt1 (1 : 1000 dilution) and GLP-1R (1 : 1000 dilution) were obtained from Abcam (Cambridge, UK). We used the BCA protein assay kit from Pierce (Rockford, IL, USA) to determine protein concentrations. Palmitic acid (PA) was also obtained from Sigma-Aldrich (St. Louis, MO, USA).
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10

Hepatic Fibrosis Pathway Analysis

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Western blot was performed on samples from untreated and fibrotic wt and KCa3.1−/− mice (12 weeks CCl4 exposure) for Proliferating Cell Nuclear Antigen (PCNA; Santa Cruz-Biotechnology, Santa Cruz, USA). Proto-oncogene tyrosine-protein kinase Src (c-Src) activity was analysed by phosphorylation either at Thr418 or at Thr530 (both Santa Cruz-Biotechnology, Santa Cruz, USA). Activation of c-Jun N-terminal kinases 1 and 2 (pJNK1&2; Life technologies, Darmstadt, Germany) and total JNK (Santa Cruz-Biotechnology, Santa Cruz, USA) was assessed by their phosphorylation at Thr183, respectively Tyr185. GAPDH served as endogenous control.
Snap frozen liver samples were processed as previously described using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)20 (link)21 (link)26 (link). Ponceau S staining was used to confirm equal protein loading. Membranes were blocked and incubated with respective antibodies. Thereafter, membranes were incubated with the corresponding secondary peroxidase-coupled antibodies (Santa Cruz-Biotechnology, Santa Cruz, USA).
After enhanced chemiluminescence (ECL; Amersham, Bucks, UK), digital detection was evaluated using Chemi-Smart (PeqLab Biotechnologies, Erlangen, Germany). Data are expressed as means ± standard error of the mean (SEM) with values of controls normalized to 100%.
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