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160 protocols using sirt1

1

Characterization of c-JUN and SIRT1 Interactions

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AGS cells and stably lentivirus-infected AGS cells were harvested and lysed with NP40 lysis buffer (Beyotime). The proteins were precipitated with antibodies against c-JUN (Cell Signaling), SIRT1 (Abcam), or IgG (Cell Signaling). Next, protein G PLUS-Agarose beads (Santa Cruz Biotechnology, Santa Cruz, CA, USA) were added to the protein antibody mixture. The precipitated materials were collected, boiled, and analyzed by western blot as described above. The anti-acetylated-lysine antibody was purchased from Cell Signaling.
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2

Immunohistochemical Analysis of ARMS

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The application of bright-field microscopy and immunohistochemistry directed against protein analytes can contribute to the defining of the biology of a disease process and facilitate the integration of genomic, proteomic and pharmacogenomics events into its etiopathogenesis and provide rationale for targeted therapies. To that end, we applied immunohistochemical probes against the following protein analytes to formalin-fixed paraffin-embedded sections of the patient's recurrent ARMS in the right lower quadrant: total insulin-like growth factor −1 receptor (IGF-1R[Tyr1165/1166] (Gen Way Biotech Inc. San Diego, CA); c-Met, phosphorylated on tyrosine 1234/1235 (Cell Signaling Technology, Inc, Danvers, MA); mammalian target of rapamycin (mTOR), phosphorylated on serine 2448 (Cell Signaling Technology, Inc); Akt, phosphorylated on serine 473 (Cell Signaling Technology, Inc); silent mating type information regulation 2 homolog 1 (Sirt1)(Abcam Inc. [E104;ab32441]); glioma-associated oncogene protein 2 (Gli2)(Abcam, Inc[ab26056]); and enhancer of Zeste homolog 2 (EZH2, Cell Signaling Technology, Inc). The details of the morphoproteomic staining procedure have been previously described [49 (link)].
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3

AMPK and Cellular Signaling Quantification

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The protein levels of AMPKα, p-AMPKα, SIRT1, PGC-1α, TGF-β1, and α-SMA (1 : 200, Abcam, USA) were determined in each group by incubating the samples in primary antibodies overnight followed by incubation with secondary antibodies and IHC detection reagent (ZSGB-BIO, Beijing, China) at 37°C for 45 min. The results were detected using DAB (ZSGB-BIO, Beijing, China), and hematoxylin staining was used to label the nuclei. The cells were observed and photographed using an optical microscope (BX61). The number of positively stained cells was counted in five microscopic fields at 400x.
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4

Western Blot Analysis of Sirtuins and NLRP3

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Cells were lysed using a cold lysis buffer containing protease and phosphatase inhibitors (Santa Cruz Biotechnology, Santa Cruz, CA, USA). The lysates were centrifuged, and the supernatants were collected. Western blotting analysis was performed by denaturing 25 mg of protein at 95℃ for 5 min in a Laemmli sample buffer and 2-mercaptoethanol. Proteins were separated by SDS-PAGE and transferred onto PVDF membranes. The membranes were blocked, and incubated with antibodies against Sirt1, Sirt6 (Abcam), NLRP3 (Santa Cruz Biotechnology), and beta-actin (Cell Signaling Technology, Danvers, MA, USA). Membranes were exposed to horseradish peroxidase-conjugated secondary antibody (Santa Cruz Biotechnology). Detection was performed using enhanced chemiluminescence (GE Healthcare, Piscataway, NJ, USA). The bands were scanned with LAS 4000 imager (Fujifilm, Duesseldorf, Germany). Densitometry analysis was performed using ImageJ software (NIH, Bethesda, MD, USA).
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5

Comprehensive Protein Extraction and Analysis

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Cells were lysed by a radioimmunoprecipitation assay (RIPA) lysis buffer (Beyotime) supplemented with phenylmethylsulfonyl fluoride, (PMSF) (Santa Cruz). The protein was extracted using a Total Protein Extraction kit (Beyotime) according to the manufacturer’s instruction. The doses of protein were examined with the bicinchoninic acid (BCA) protein assay kit (Beyotime). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to separate the proteins, which was then transferred to polyvinylidene difluoride (PVDF) membranes.
Primary antibodies used included antibodies to the proteins, SIRT1 (1: 4000)(Abcam)), AMPK (1: 2000) (Cell Signaling Tech), phosphorylated (p-AMPK) (1: 2000) (Cell Signaling Technology), mechanistic target of rapamycin (mTOR) (1: 4000) (Abcam), phosphorylated mTOR (p-mTOR) (1: 4000) (Abcam), cleaved caspase-3 (c-caspase-3) (1: 2500) (AbCam), active matrix metalloproteinase-2 (MMP-2) (1: 4000) (Abcam), active MMP-9 (1: 2000) (Abcam) and GAPDH (1: 5000) (Abcam) for 8 hours at 4°C. After washing, the membranes were further incubated with horseradish-peroxidase (HRP)-conjugated secondary antibodies (Cell Signaling Technology). Luminol enhancer reagent (Millipore) was used to develop the membranes, which were visualized on X-ray films. The intensity of the Western blots was analyzed by ImageJ software.
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6

Western Blot Analysis of Sirtuin Proteins

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Liver homogenates or cell lysates containing 10 μg of whole‐cell lysate were separated by 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred to polyvinylidene fluoride membranes. After blocking with 5% skim milk, blots were probed with primary antibodies to Sirt1, Sirt5 (Abcam, Cambridge Science Park, Cambridge, UK), Sirt2, β‐actin, MKP‐1 (Santa Cruz Biotechnology, Dallas, TX), Sirt4, Sirt7 (Biovision, Milpitas, CA), Sirt3, Sirt6, Bax, Bcl‐2, cleaved caspase 3, c‐Jun N‐terminal kinase, p38, extracellular signal‐regulated kinase, phosphorylated c‐Jun N‐terminal kinase, phosphorylated p38, Ac‐lysine (Cell Signaling Technology, Beverly, MA), phosphorylated extracellular signal‐regulated kinase, and glyceraldehyde 3‐phosphate dehydrogenase (Bioworld Technology, St. Louis Park, MN).
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7

Western Blot Analysis of Mitochondrial Proteins

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Cells after treatment were collected and dissolved in RIPA buffer (Beyotime, Nantong, China) and protein concentration was measured using the BCA protein assay kit. A total of 50 μg protein in each sample was isolated by 15% SDS-PAGE and then imprinted on PVDF membrane (Beyotime, Nantong, China). The membrane was blocked and incubated with primary antibodies overnight at 4 °C. The blots were incubated with HRP-conjugated secondary antibody at room temperature for 1 h on the next day. The ECL assay kit (Beyotime, Nantong, China) was used to reveal the protein bands. The density of each band was normalized to the expression of GADPH (Cat. No: ab8245, Abcam, Cambridge, MA, USA) or VDAC1 (Cat. No. ab15895, Abcam). The other primary antibodies used include Cytochrome c (Cat. No: ab13575, Abcam), SIRT1 (Cat. No. ab110304, Abcam), SIRT3 (Cat. No. ab217319, Abcam), LC3B (Cat. No. ab192890, Abcam), PINK1 (Cat. No. ab23707, Abcam), Parkin (Cat. No: ab77924, Abcam), Nrf2 (Cat. No. ab137550, Abcam), Nrf2 (Acetyl-Lys599) (Cat. No. HW147, Signalway Antibody, Nanjing, China). All experiments were repeated three times, and the gray values were quantified using Image J software (version 1.8.0 for Windows, National Institutes of Health, NY, USA).
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8

Protein Expression Analysis of Keloid Tissues

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Keloid tissues and its surrounding normal skin tissues were homogenized, lysed in RIPA for 30 min, and centrifuged at 12,000 r/min for 5 min. The supernatant was collected and the protein concentration was determined with BCA method. Similarly, proteins were also extracted from cells. After SDS-PAGE electrophoresis, the proteins were transferred to PVDF membranes. The membrane was blocked with 5% skimmed milk for more than 2 h, and washed with TBST for 5 min/time for 3 times. Then, the diluted primary antibodies against RUNX3 (1:2000; Abcam, USA), EZH2 (1:2000; Abcam, USA), AC-EZH2 (1:2000; Abcam, USA), SIRT1 (1:2000; Abcam, USA), CyclinD1 (1:2000; Abcam, USA), CDK2 (1:2000; Abcam, USA), CDK4 (1:2000; Abcam, USA), and β-actin (1:2000; Abcam, USA) were added and incubated overnight at 4° C. After incubation with goat anti-rabbit/goat anti-mouse secondary antibody (1:5000; Abcam, USA) for 70 min at room temperature, the membrane was subjected to ECL luminescence color development.
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9

Placental Biomarker Immunofluorescence Analysis

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Placental section slides were prepared by the Northern Ireland Biobank (38 (link)) using fresh tissue before being subjected to immunofluorescence staining for FKBPL (Cat. no.: 10060-1-AP; Proteintech, UK), SIRT-1 (Cat. no.: ab110304; Abcam, UK), PlGF (Cat. no.: ab180734, Abcam, UK) and VEGF-R1 (Cat. no.: AF321, R&D systems, USA). Tissue slides were imaged using a Leica DMi8 fluorescence inverted microscope using the same magnification (20x) and exposure. Analysis was performed using Image J software (NIH, US) by selecting six random fields of view per section and measuring the intensity, with the assessor blind to patient group. Protein expression was quantified as previously described (39 (link)).
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10

Molecular Mechanisms of DMF in Cellular Stress

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Hydrogen peroxide (H2O2, #MKBK8393V) and paraformaldehyde solution (#SZBC2290V) were purchased from Sigma-Aldrich. 5-Bromo-4-chloro-3-indolyl-β-D-galactosidase (X-gal, 11680293001) was purchased from Roche. Antibodies against the following proteins were used: DRG2 (Proteintech group, 14743-1-AP), acetyl-p53 (ac-p53, Cell Signaling Technology (CST), #2525), p53 (CST, #2524), p21Waf1/Cip1 (Santa Cruz Biotechnology (SCBT), sc-397), cyclin D1 (SCBT, sc-717), p16INK4α (BD Pharmingen, 551163), SIRT1 (Merck Millipore, 07-131), SIRT1 (Abcam, ab110304), acetyl-NF-κB p65 (ac-NF-κB p65, CST, #3045), NF-κB p65 (SCBT, sc-8008), phosho-Histone H2A.X (p-H2A.X, CST, 9718 s), and β-actin (SCBT, sc-1616). Secondary antibodies for immunoblotting were from SCBT (goat anti-mouse IgG-HRP, sc-2005; mouse anti-rabbit IgG-HRP, sc-2357; donkey anti-goat IgG-HRP, sc-2020), and those for immunofluorescent staining were from Invitrogen (goat anti-rabbit Alexa Fluor 568, A-11011; goat anti-mouse Alexa Fluor 488, A-11001; goat anti-mouse Alexa Fluor 568, A-11004). DMF (6,4′-dihydroxy-7-methoxyflavanone) was obtained from the Standardized Material Bank for New Botanical Drugs (no. NNMBP012), Wonkwang University (Republic of Korea). DMF (>98%) was isolated from the heartwood of Dalbergia odorifera [25 (link)] and was dissolved in DMSO (0.05% in final culture concentration).
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