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29 protocols using p62 sqstm1

1

Western Blot Analysis of Cell Signaling

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The cultured cells were solubilized in lysis buffer (150 mmol/L NaCl, 50 mmol/L Tris–HCl, 5 mmol/L EDTA–2Na, 1% Triton X-100, and 1 tablet/10 mL complete mini EDTA-free) and centrifuged at 15,000 × g at 4 °C for 30 min. Samples were separated by SDS-PAGE and then transferred to PVDF membranes. The membranes were first blocked in a buffer containing 25 mmol/L Tris–HCl (pH 7.4), 150 mmol/L NaCl, 0.1% Tween 20, and 4% skim milk for 1 h and then incubated with primary antibodies at 4 °C overnight. This was followed by incubation with horseradish peroxidase-conjugated secondary antibodies for 1 h. Primary antibodies against human p21Waf1/Cip1, p16INK4a, phosphorylated H2AX (Ser139, γ-H2AX), retinoblastoma (Rb), phosphorylated Rb (Ser780, pRb), cyclin D, and caspase-3 were all purchased from Cell Signaling Technology, Inc. (Beverly, MA, USA). Antibodies against human cyclin A (Novocastra Laboratories Ltd., Newcastle, UK), p16INK4a (BD Biosciences, Inc., Farmingdale, NY, USA), Ki-67 (Dako from Agilent, Santa Clara, CA, USA), p62/SQSTM1, and β-actin (Santa Cruz Biotechnology, Santa Cruz, CA, USA) were also used. The immunoreactive proteins were then detected by enhanced chemiluminescence (GE Healthcare, Fairfield, CT, USA). Immunoblots were quantified using the CS Analyzer 3.0 software (ATTO, Tokyo); β-actin expression was used as the internal control.
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2

Immunostaining of Autophagy Markers

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Cells were fixed and permeabilized with 100% methanol at −20°C for 30 minutes. Fixed cells were blocked with 2.5% BSA in 1× PBS at room temperature for at least 30 minutes. Antibodies were diluted in 2.5% BSA in 1× PBS. Cells were incubated in primary antibody overnight at 4°C, washed with 1× PBS, and then incubated with fluorescently labeled secondary antibody overnight at 4°C in the dark. Primary antibodies: LC3B (Novus Biologicals; NB600–1384), p62/SQSTM1 (Santa Cruz Biotechnology; sc-28359). Fluorescently labeled secondary antibodies: Alexafluor 488, goat anti-mouse (Invitrogen; A11001), Alexafluor 568, goat anti-rabbit (Invitrogen; A11061). Immunostained cells were imaged at 10x, 20x, and 100x magnification using a Nikon epifluorescence microscope. Images were analyzed using Nikon NIS Elements. Cell counts were performed for five representative microscopy fields at 10x magnification for each treatment. The cell count average and standard deviation of 3 biological replicates per treatment was calculated.
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3

Vascular Structure Analysis for Neointima Formation

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The vessels were fixed and embedded in paraffin (Sigma-Aldrich, USA) or frozen tissue matrix (OCT, Leica biosystems, Germany) for sections. Histological stainings for H&E, elastin stain (Sigma-Aldrich, USA), and Verhoeff’s Van Gieson stain were performed to assess the changes of vascular structure for neointima formation and failure of vein graft. The TUNEL (Roche, Switzerland), immunohistochemical (IHC), and immunofluorescent (IF) stainings were used to determine cell apoptosis and inflammatory responses using specific antibodies against inflammation markers, such as COX-2 (Abcam, UK). Autophagy formation was measured by puncta formation of LC3 (Santa Cruz, USA) and expression patterns of p62/SQSTM1, Beclin 1, Bcl-2, and Bcl-X(L) (Santa Cruz, USA). The CD31 antibody (R&D system) was used to identify the endothelial cells. The ultrastructure of autophagosome was observed by typical double membrane morphologies using a TEM (JEM-1400, JEOL, Japan).
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4

Immunofluorescence Staining of Endothelial Markers

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Silicone-coated 4-0 monofilament nylon sutures were purchased from Doccol Co. (Redlands, CA, USA). Primary antibodies against lysosomal-associated membrane protein 1 (LAMP-1), and p62/SQSTM1, and horseradish peroxidase (HRP)-conjugated secondary antibodies were purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Primary antibodies against LC3B and β-actin were obtained from Sigma-Aldrich (St. Louis, MO, USA). A primary antibody against CD31 was obtained from R&D Systems (Minneapolis, MN, USA). A primary antibody against occludin and the fluorescently labeled secondary antibodies of Alexa Fluor 488 donkey anti-mouse and Alexa Fluor 555 donkey anti-rabbit were purchased from Thermo Fisher Scientific (Rockford, IL, USA). All other chemicals were purchased from Sigma-Aldrich.
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5

Huh7 Hepatocellular Carcinoma Cell Line Manipulation

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Human hepatocellular carcinoma Huh7 cell line was purchased from the American Type Culture Collection (ATCC). Retroviral pBABE-puro mCherry-EGFP-LC3B was purchased from Addgene (Plasmid #22418, deposited by Jayanta Debnath). Briefly, the retroviral vector was transfected into 293T cells (ATCC) with pCMV-VSV-G (Addgene, #8454) and pUMVC (Addgene, #8449) using FuGENE6® reagent (Roche Applied Science). Collected viruses were infected into Huh7 cells. JNK1- and 2-knockout MEF cells were kindly provided by Dr. Zigang Dong (University of Minnesota, Austin, MN, USA). The cells were maintained in Dulbecco's modified Eagle's medium (HyCloneTM, GE Healthcare) supplemented with 10% heat-inactivated fetal bovine serum (Atlas Biologicals) and antibiotics (Invitrogen) in an atmosphere of 5% CO2 at 37°C. The siRNA targeting human p62/SQSTM1, IRE1α, PERK, ATF6, ATF4, NRF2, and XBP1 and siRNA negative control were purchased from Santa Cruz Biotechnology. Huh7 cells were transfected for 24h with 10 nM of each siRNA by Lipofectamine® RNAiMAX reagent (Invitrogen) according to the manufacturer's instructions, and then further incubated with DC for 24h.
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6

Immunoblotting Analysis of Cellular Signaling Pathways

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Briefly, lysis was performed with NP40 lysis buffer. The lysates were electrophoresed on 4–12% NuPAGE Bis-Tris gels in MOPS SDS running buffer and transferred onto nitrocellulose membranes (Invitrogen) overnight. The membranes were blocked in 3% BSA and incubated with indicated primary antibodies where specified for: mouse CLEC16A, PINK1 (Abgent), GFP, Nrdp1 (Novus Biologicals), TOM20 (ProteinTech), Parkin, p62/SQSTM1, LC3 I/II, ATG16L1, cytochrome c, caspase-9, p-ERK1/2 and EK1/2 (Santa Cruz), cleaved Caspase-3, p-Akt (ser473), p-Akt (Ser308) and total Akt (Cell signaling). The membranes were washed and incubated with a respective mouse/rabbit secondary antibody and bound antibody was detected with WesternBright ECL kit (Advansta). Membranes were stripped and re-probed for β-actin as loading control.
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7

Antibody Detection in Protein Analysis

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Anti-β-actin was from Santa Cruz Biotechnology (sc-47778); anti-Hsp70 from Enzo Life Sciences (catalog no. ADI-SPA-810); anti-Hsc70 from StressMarq Biosciences Inc (catalog no. SMC-151) or anti-Hsp70 (BB70, Dr. David Toft, Mayo Clinic, Rochester, MN); anti-Hsp90β (H90.10, Dr. David Toft); anti-LC3B (Cell Signaling Technology, 3868S);, anti-cleaved LC3A (LC3AII) (Abgent Antibody, Abcepta, San Diego, CA, AP1805a); anti-GAPDH (Santa Cruz Biotechnology, sc-166545); and p62/SQSTM1 from Santa Cruz Biotechnology, Inc (catalog no. sc-28359).
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8

Western Blotting Analysis of Autophagy Markers

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The western blotting was performed as described previously.20 (link) Briefly, protein of the samples were separated in 12% SDS-gels, and then transferred to PVDF membranes at an hour for all gels. Subsequently, the blocking of membranes were done in 5% skim milk buffer containing 0.1% Tween-20 for 1.5 h and then probed with primary antibodies against microtubule-associated proteins 1A/1B light chain 3B (LC3B) (1:1000, Cell Signaling), P62/SQSTM1 (1:500, Santa Cruz) and β-actin (1:500, Cell Signaling) overnight at 4°C on a shaker incubator. After 4×5 min washing with Tris buffer saline containing 0.1% Tween-20, HRP-conjugated secondary antibody (1:7000, Cell Signaling) was added on the membranes. After for an hour incubation on shaker, the membranes were bathed in wash buffer and washed at least 3×5 min. Then, the membranes were incubated with the enhanced chemiluminescence (ECL, Amersham) reagents in dark room. This step was followed by the exposing of the membrane to an X-ray film and visualization of the chemiluminescence of the binding by means of a visualizing machine. The intensity of the bands was calculated using Image J software (IJ 1.46r version, NIH, USA) and normalized to each sample based on the intensity of β-actin as internal control.
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9

Molecular Mechanisms of Autophagy Regulation

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Anti-Vps34 (1:1,000, no. 4263), Beclin 1 (1:1,000, no. 3738), acetylated lysine (1:500, no. 9441), haemagglutinin (HA)-Tag (1:1,000, no. 3724, Rabbit) and HA-Tag (1:1,000, no. 2367, Mouse) antibodies were purchased from Cell Signaling Technology. Anti-UVRAG (1:1,000, NBP1–18885), Beclin 1 (1:1,000, NBP1–00088) and LC3 (1:5,000, NB100–2220) antibodies were obtained from NOVUS. Anti-Rubicon (1:1,000, ab92388) and p150 (1:1,000, ab128903) antibodies were obtained from Abcam. Anti-SIRT1 (1:1,000, AJ1717a), SIRT2 (1:1,000, AJ1718a) and HDAC1 (1:1,000, AP1101a) antibodies were purchased from Abgent. Anti-p300 (1:500, sc-585), p62/SQSTM1 (1:2,000, sc-28359) and HDAC2 (1:1,000, sc-55542) antibodies were purchased from Santa Cruz Biotechnology. Anti-a-tubulin (1:2,000, T6199), Flag (1:5,000, F3165) and Atg14L (1:1,000, A6358) antibodies were obtained from Sigma. Anti-phospho S409 Beclin 1 antibodies were generated by immunizing rabbits with the corresponding phosphopeptides. Bafilomycin A1, rapamycin, deacetylase inhibitors TSA and NAM, and CK1 inhibitor D4476 were purchased from Sigma.
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10

Cellular Localization of S. nigra Proteins

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HeLa cells were seeded on coverslips in a 12 well plate (3.8 × 104 cells/well) for at least 24 h, and cells were incubated with culture medium containing 50 nM FITC-labeled or non-labeled S. nigra proteins for fixed time periods. After washing with PBS, cells were fixed with 2% formaldehyde for 20 min, followed by three more PBS washes. Subsequently, cells were permeabilized in 0.5% Triton X-100 solution for 5 min, blocked with 50% fetal calf serum for 40 min at room temperature and incubated for 1 h at room temperature with one of the following primary antibodies: mouse anti-PDI (1:1000, Endoplasmic reticulum marker), anti-Golgin97 (1:2000, Golgi marker), rabbit anti-Rab5 (1:1000, Early endosome marker) or p62/SQSTM1 (1:100, autophagic flux marker, Santa Cruz Biotechnology Inc. Texas, USA). After three washes with PBS, cells were incubated for 1 h with goat anti-mouse IgG or goat anti-rabbit IgG Alexa Fluor-555 and after a final wash counterstained with DAPI (0.1 μg/ ml) and mounted with Vectashield (Vector Laboratories Inc., Burlingame, CA, USA).
Next to the immunostaining, lysosomes were visualized with LysoTracker (Life technologies, 50 nM) and lipid droplets were stained with BODIPY 493/503 (Life Technologies, 2 μg/ml).
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