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5 protocols using protease inhibitors

1

Cardiac Autophagy Protein Analysis

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Cardiac slices were flash-frozen in liquid nitrogen, sonicated, and homogenized on ice in radio-immunoprecipitation assay buffer supplemented with protease inhibitors (Boston BioProducts) per manufacturer’s instructions. Proteins were extracted by constant agitation for 30 minutes before centrifugation. Protein concentration was measured by Bradford assay (BioRad), and 20–40 μg of total protein was loaded for electrophoresis and transferred to the polyvinylidene difluoride membrane. The membrane was processed for immunoblotting against LC3 (CST 3868, rabbit monoclonal, clone: D11; 1:1000, antibody ID: AB_2797680), p62 (CST 5114, rabbit polyclonal, 1:1000, antibody ID: AB_10624872), and actin (Sigma A5316, mouse monoclonal, clone: AC-74; 1:5000, antibody ID: AB_476743) and imaged with a ChemiDoc XRS molecular imager (BioRad). Immunoblot images are analyzed using ImageJ by measuring the LC3-I, LC3-II, p62, and actin signal intensity and calculating the LC3-II to LC3-I, LC3-II to actin, and p62 to actin ratios.
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2

Quantifying Intestinal Inflammatory Markers

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Immune indicators expression in colonic tissue homogenates was evaluated using an enzyme‐linked immunosorbent assay (ELISA) kit (R&D Systems). Briefly, dissected tissues were homogenized in RIPA buffer containing protease inhibitors (Boston Bioproducts). The protein concentrations in the homogenates were determined using the bicinchoninic acid assay. The concentrations of interleukin (IL)‐1β, IL‐6, IL‐17A, and tumor necrosis factor (TNF)‐α were analyzed using according to the manufacturer's instructions.
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3

Western Blot Analysis of Metabolic Regulators

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Cell culture reagents (DMEM, FBS, PenStrep, and trypsin-EDTA), as well as western blot reagents include NuPAGE 4–12% Bis-Tris Gel and MOPS SDS Running Buffer (20X) were from Life-Technologies (Grand Island, NY). NAO and DAPI were from Molecular Probes (Eugene, Oregon). DCFH, cytochrome c, n-Dodecyl-beta-maltoside, and DTT were from Sigma (St. Louis, MO). 5-Aminoimidazole-4-carboxamide riboside (AICAR) was from Cayman chemical company (Ann Arbor, MI). The antibodies for AMPK (AMP-activated protein kinase) and pAMPK (rabbit monocloncal anti-Phospho-Thr172-AMPKα), PGC1α, SIRT1, phospho-Ser47-SIRT1 (p-SIRT1) were from Cell Signaling Technology (Beverly, MA). Antibodies for SURF1 and Actin were from Santa Cruz Biotechnology (Dallas, TX). Protease inhibitors, phosphatase inhibitors, and RIPA buffer with EDTA were from Boston BioProducts (Ashland, MA). Pierce ECL Western blotting Substrate and Restore Western blot Stripping Buffer were from Thermo Scientific (Rockford, IL). Quick Start Bradford Dye Reagent for protein quantification was from Bio-Rad (Hercules, CA).
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4

Quantification of GLUT4 and IRS1 Proteins

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Total proteins were extracted using radio immunoprecipitation assay (RIPA) buffer with protease inhibitors (Boston Bio Products, Boston, MA, USA). Plasma membrane (PM) proteins were extracted using the Membrane Protein Extraction Kit (BestBio, Shanghai, China). Protein levels were quantified by the BCA protein assay. Total protein (25 μg) was loaded onto a 10% SDS-PAGE gel, separated by electrophoresis and transferred onto a polyvinylidene difluoride (PVDF) membrane. Blots were blocked with 6% skim milk and incubated overnight at 4 °C with primary antibody against GLUT4 (Abcam, Cambridge, UK)and IRS1 (Proteintech Group, Chicago, IL, USA), followed by incubation with secondary antibody for 1 h at room temperature and measured with a Fluor Chem M (ProteinSimple, Santa Clara, CA, USA). Protein expression was normalized by detection of β-actin (Abcam, Cambridge, UK). Duplicate experiments were conducted for all primary adipocyte proteins. The data were analyzed by Image J software (National Institutes of Health, Bethesda, MD, USA) and expressed as fold-change relative to the control group after normalizing against β-actin. Statistical differences between treatment and control groups were determined using Student’s t-test at p < 0.05.
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5

Western Blot Analysis of Hepatic Proteins

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Hepatic homogenates were prepared by homogenizing frozen livers in cold RIPA buffer containing protease inhibitors (Boston Bio Products, MA). Hepatic protein (20 μg) was subjected to NuPAGE 5–10% Bis-Tris gel electrophoresis and transferred to polyvinylidene fluoride membranes (0.45 μm), which were subsequently blocked with 5% milk, incubated overnight at 4 °C with primary antibodies against CPS1 (Santa Cruz Biotechnology, Santa Cruz, CA) and SIRT5 (Cell Signaling Technology, Inc., Danvers, USA) followed by secondary antibodies for 1 h at room temperature. β-actin (Abcam, Cambridge, UK) was used as the control. Duplicate experiments were carried out for all hepatic proteins. The blot was scanned in a FluorChem M (ProteinSimple, Santa Clara, California, USA). The data were analysed by Image J software and expressed as fold-change relative to the control group after normalizing against β-actin.
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