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91 protocols using beclin 1

1

Western Blot Analysis of Hippocampal Proteins

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Hippocampal tissue was lysed and the supernatant was centrifuged to obtain hippocampal protein. Proteins were separated by electrophoresis on SDS-PAGE gels (10%). Proteins were then transferred to 0.45 μm polyvinylidene fluoride (PVDF) membranes by electrophoresis. The membranes were then blocked and incubated with primary antibodies overnight. The next day, imaging was performed after incubation with secondary antibodies. Antibodies against the following proteins were used for Western blot experiments: TLR4 (Abcam, Cat No: ab13556), LC3A/B (Cell Signaling Technology, 4108), P62 (Proteintech, Cat No.: 18,420-1-AP), and beclin1 (Proteintech, Cat No.: 11,306-1-AP).
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2

Investigating SSD-Induced Cellular Stress Responses

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SSD (purity ≥98%, high-performance liquid chromatography) was purchased from Shanghai Yuanye Bio-Technology (Shanghai, China). SSD was dissolved in dimethyl sulfoxide (Solarbio, Beijing, China) to prepare a stock solution at a concentration of 1 mM, wrapped in aluminum foil to protect against light, and stored at −20°C. The Cell Counting Kit-8 (CCK-8), Hoechst 33258 staining kit, Annexin V-FITC Apoptosis Kit, and Immunocytochemical staining (ICC) kit were purchased from BOSTER Biotechnology (Wuhan, China) and stored at 4°C. GRP78, CHOP, PERK, ATF6, Caspase-12, Caspase-9, Caspase-3, Beclin 1, β-actin, and peroxidase-conjugated anti-rabbit antibodies were purchased from Proteintech Group, Inc. (Wuhan, China). LC3 and poly (ADP-ribose) polymerase (PARP) antibodies were obtained from Abrasives Mart (Shanghai, China).
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3

Protein Fractionation and Immunoblotting

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The total protein extract was prepared by homogenizing the cells in a 1× SDS sample buffer. The NP-40-soluble and -insoluble protein fractions from the cells were prepared as previously described [34 (link)]. Immunoprecipitation and western blot were carried out as previously described [34 (link)]. Primary antibodies against the following proteins were used for western blot analysis: K48-linked Ub chain-specific antibody (Millipore, 05-1307); K63-linked Ub chain-specific antibody (Abcam, ab179434); ubiquitin (Abcam, ab134953); Phospho-SQSTM1 (Thr269/Ser272)-specific antibody (Phosphosolutions, P196-269); SQSTM1 (Santa Cruz Biotechnology (sc-28359); ATG5 (Cell Signaling Technology, 12994); LC3B (Cell Signaling Technology, 3868); ATG16L1 (Abcam, ab187671); WIPI2 (Abcam, ab105459); Beclin1 (Proteintech, 11306-1-AP); GFP (Rockland, 600-101-215); FLAG tag (Prospec, ANT-146-b); Myc Tag (Biolegend, MMS-150R); GAPDH (Zen Bioscience, 200306); β-actin (Zen Bioscience, 200068-6D7). See Supplementary Table S2 for further details and dilutions of all antibodies.
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4

PLGA-based Neuroprotective Formulation

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mPEG-poly lactic-co-glycolic acid (PLGA) (75:25, 45,000) was purchased from Daigang Biomaterial Co., Ltd (Jinan, Shandong, China). EGCG (purity > 98%; Yuanye Biotechnology Co., Ltd, Shanghai, China) was dissolved in water (pH 3.0) and stored at −20°C. Nimodipine was obtained from Ruiyang Pharmaceutical Co., Ltd (Yi Yuan, Shandong, China). Lactate dehydrogenase (LDH), glutathione (GSH), superoxide dismutase (SOD), total antioxidant capacity (T-AOC), and malondialdehyde (MDA) kits were obtained from the Nanjing Jiancheng Bioengineering Institute (Nanjing, Jiangsu, China). JC-1, Fluo-3 AM, DCFH-DA, Nissl staining kits, and enhanced chemiluminescence kits were purchased from Beyotime (Shanghai, China). CaMKII, Atg5, Beclin-1, and Mn-SOD antibodies were obtained from Proteintech Group, Inc (Rosemont, IL, USA). SP-9002 SPlink detection and DAB kits were purchased from Zhongshan Golden Bridge Biotechnology (Beijing, China).
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5

Baicalein Inhibits Mitochondrial Dynamics

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Baicalein (≥ 99%, Yousi Scientific Co., Ltd, Shanghai, China) was dissolved in DMSO at concentration of 200 mM and stored at -20 ℃. Mdivi-1, an inhibitor of Drp1, was purchased from Selleck (Huston, TX, USA). 3-Methyladenine (3-MA), an inhibitor of autophagosomes, and Bafilomycin A1 (Baf-A1), an inhibitor of H+-ATPase, were purchased from Selleck. Antibodies against PARP (#9542), Drp1 (#5391), AMPKα (#5831), p-AMPKα (Thr172) (#2535), LC3 (#12741), Bak (#6947) and β-actin (#3700) were obtained from Cell Signaling Technology (Boston, MA, USA). Antibodies against Caspase 3 (#19677-1-AP), Caspase 9 (#10380-1-AP), Bcl2 (#12789-1-AP), Bcl-xl (#10783-1-AP), Bax (#50599-1-AP), Cytochrome c (#10993-1-AP), Aif (#17984-1-AP), Cox IV (#11242-1-AP), Fis1 (#10956-1-AP), Opa1 (#27733-1-AP), Mfn1 (#13798-1-AP), Ndufs1 (#12444-1-AP), Sdha (#14865-1-AP), Uqcrc1 (#21705-1-AP), Atp5a1 (#14676-1-AP), p62 (#18420-1-AP), and Beclin1 (#11306-1-AP) were obtained from Proteintech (Wuhan, China). Antibody against p-Drp1 (Ser616) (#12749) was obtained from Signalway Antibody (College Park, MD, USA). Secondary goat anti-rabbit or rabbit anti-mouse antibodies were purchased from Proteintech. Fluorescent-labeled antibody Annexin V-FITC, Annexin V-APC, PI, 7-AAD and 10 × binding buffer were obtained from BD (Franklin Lakes, New Jersey, USA).
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6

Protein Expression Analysis in OC Cells

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Total protein in OC cells was extracted by a potent RIPA lysis reagent (Millipore, USA) containing 1% PMSF (Millipore, USA). The protein concentration of each sample was determined using the BCA method, and then samples (30 μg) were subjected to electrophoresis on an SDS-PAGE gel (Mellon, Dalian, China) and transferred onto PVDF membranes (Merck, USA). To prevent non-specific signals, the membranes were incubated with 5% BSA (Merck, USA) for 2 h. The primary antibodies, including LC3 (1:500; Cat No. 14600-1-AP, Proteintech, Wuhan, China), P62 (1:1000; Cat No. 18420-1-AP, Proteintech, Wuhan, China), FBXL11 (1:500; Cat No. 24311-1-AP, Proteintech, Wuhan, China), Beclin-1 (1:500; Cat No. 11306-1-AP, Proteintech, Wuhan, China), HA (1:5000; Cat No. 51064-2-AP, Proteintech, Wuhan, China), Flag (1:1000; Cat No. 80010-1-RR, Proteintech, Wuhan, China), and GAPDH (1:2000; Cat No. 60004-1-Ig, Proteintech, Wuhan, China) were added to incubate PVDF membranes at 4 °C overnight. After washing TBST for thrice, secondary antibodies were incubated for 2 h, and the protein signals in membranes were detected using the ECL reagent (Yeasen, Shanghai, China). GAPDH was set as a loading control to calculate the expression level of the target proteins.
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7

Triple Immunofluorescence Staining of LC3 and Beclin-1

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For triple immunofluorescence staining (IF), the coverslips with cells were rinsed by using phosphate-buffered saline (PBS, pH 7.4), fixed in 4% paraformaldehyde for 20 min, incubated in 0.1% Triton-X100 for 5 min, and closed with 3% BSA for 2 h. Primary antibodies LC3 ӀӀ/Ӏ (ABclonal, China, 1: 200) and Beclin-1 (Proteintech, Chicago, IL, USA, 1: 500) were mixed, and the coverslips were hatched overnight at 4°C overnight, coverslips were incubated with mouse anti-CoraLite488-conjugated goat anti-mouse IgG (H+L) and rabbit anti-Cy3-conjugated Affinipure goat anti-rabbit IgG (H+L) for 2 h. DAPI (Boster, California, USA) was incubated for 10 min to localize cell nuclei, mounted with an anti-fluorescence quenching sealing liquid (Solarbio, Beijing, China), observed and imaged in Laser Confocal Microscope (LSM800, ZEISS, Oberkochen, Germany).
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8

Protein Expression Analysis of Apoptosis and Autophagy

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Treated cells were lysed with RIPA lysis buffer (Bioswamp), and the protein concentrations in the lysates were measured with a BCA protein assay kit (Bioswamp). Equal amounts of proteins in each sample were loaded onto gels and subjected to SDS-PAGE. The separated proteins on the gels were then transferred to nitrocellulose membranes. Each immunoblot was blocked with 5% nonfat milk in TBST for 2 h prior to an overnight incubation at 4 °C with specific antibodies. The following primary antibodies were used for Western blotting: Bcl-2 (Proteintech, 60178-1-Ig), Bax (Proteintech, 50599-2-Ig), cleaved caspase-3 (Cell Signaling Technology, 9664), LC3B (Bioswamp, MAB43969), Beclin 1 (Proteintech, 66665-1-Ig), Parkin (Proteintech, 14060-1-AP), P62 (Proteintech, 18420-1-AP), Tim23 (Proteintech, 11123-1-AP), CoxIV (Cell Signaling Technology, 4844) and NDP52 (Cell Signaling Technology, 60732). The blots were washed with TBST three times for 15 min each and then incubated with secondary antibodies for 2 h at RT. Finally, enhanced chemiluminescence reagent was used to visualize the bands, and the intensities were determined to further evaluate the levels of each protein.
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9

Western Blot Analysis of Autophagy Proteins

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Western blot was performed as previously described [15 (link)]. The antibodies for the western blot were ATG3 (1:1000, Cell Signaling Technology, USA), ATG5 (1:1000, Cell Signaling Technology, USA), ATG7 (1:1000, Cell Signaling Technology, USA), ATG12 (1:1000, Cell Signaling Technology, USA), Beclin1 (1:1000, Proteintech, China), LC3 (1:1000, Novus, USA), p62 (1:1000, Proteintech, China), PGK1 (1:1000, Proteintech, China), Ubiquitin (1:1000, Proteintech, China) and β-actin (1:5000, Proteintech, China).
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10

Histological and Immunohistochemical Analysis of Osteoarthritic Rat Knees

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The whole knee joints of rats were collected and fixed in 4% paraformaldehyde for 24 h. After decalcification in 10% EDTA solution for 30 days, the samples were embedded in paraffin, cut into 5 μm–thick sections, and stained with H&E, Toluidine blue and Safranin O/Fast Green. The sections were next subjected to immunohistological staining using antibodies recognizing MMP13 (Abcam, 1;200), Cleaved-caspase3 (Cell Signaling Technology, 1:200) and Beclin1(Proteintech Group, 1:200). The Osteoarthritis Research Society International (OARSI) grade system were used to evaluate histopathologic changes in osteoarthritic cartilage [44 (link)]. All scorings were performed by three independent observers in a blinded manner. The rate of positive cells each section was quantitated from 6 rats of each group.
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