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4 protocols using clarity western substrate kit

1

Immunoblotting Protocol for Protein Analysis

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Immunoblotting was conducted as previously described [25 (link), 75 (link)]. Specifically, samples with equal amounts of protein (~10 μg) were dissolved in Laemmli buffer containing 5% β-mercaptoethanol (Bio Rad, #1610737) and subjected to sodium dodecyl sulfate-polyacrilamide gel electrophoresis (8–16% gradient), using pre-cast gels (BioRad, #1610710; Hercules, CA), followed by protein transfer onto polyvinylidene difluoride membranes (BioRad, #1704159). The membranes were incubated in 5% blocking buffer (BioRad, #1706404) dissolved in TBST (100 mM Tris-HCl, pH 7.4, 150 mM NaCl, and 0.05% Tween 20) for 1 h at room temperature, followed by an overnight incubation at 4°C with primary antibodies dissolved in blocking buffer. Membranes were then washed with TBST and incubated with appropriate HRP-conjugated secondary antibodies for 1 h at room temperature. Chemiluminescent technique using the Clarity Western Substrate kit (BioRad, #1705061) was employed to visualize protein bands in a ChemiDoc XRS + imaging system (BioRad). Membranes were subsequently stripped with Restore Stripping Buffer (ThermoFisher Scientific, #46430; Rockford, IL) and re-probed with anti-α-tubulin or anti-actin antibodies to serve as the loading control. Densitometric analysis of protein bands was performed with the ImageJ software (National Institutes of Health).
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2

Extracellular Vesicle Protein and LPS Analysis

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Following the purification of EVs, the proteins and associated lipopolysaccharides (LPS) were analyzed by dot blot on a nitrocellulose membrane (Bio-Rad, Hercules, CA, USA). Eight µg (lipid amount) of each type of EVs were spotted. The membrane was blocked for 30 min in 5% non-fat dry milk in [50 mM Tris, 200 mM NaCl, pH 7.5, 0.1% Tween-20] (TBS-T), then incubated overnight in 2.5% non-fat dry milk in TBS-T containing either mouse monoclonal anti-E. coli LPS IgGs (clone 2D7/1, ab35654, Abcam, Cambridge, UK) diluted 1/2000 or rabbit anti-OmpA polyclonal antibodies (Epigentek, East Farmingdale, NY, USA) diluted 1/2000. After two washes of 10 min each in TBS-T, the membranes were incubated for 3 h, respectively in 2.5% non-fat dry milk in TBS-T containing anti-mouse polyclonal antibodies coupled to horse radish peroxidase [HRP] and diluted 1/10,000 or containing HRP-conjugated anti-rabbit IgG F(ab′)2 fragment (Sigma) diluted 1/10,000. After washes in TBS-T, the membranes were revealed by chemiluminescence using a Clarity Western substrate kit (Bio-Rad) and photographed using a ChemiDoc apparatus (Bio-Rad).
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3

Western Blot Analysis of Tagged Proteins

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Cell pellets from nitrogen-depleted cultures (1 mL) were resuspended in loading buffer based on OD600. Equal volumes were separated on a 4–20% acrylamide gradient gel (Bio-Rad). Proteins were transferred to PVDF membrane and probed with M2 mouse anti-FLAG antibody (Sigma; 1 in 2,000 dilution) or mouse anti-β’ antibody (Neoclone; 1 in 7,000 dilution), and HRP-conjugated goat anti-mouse antibody (1 in 10,000 dilution). Tagged proteins were visualized using the Clarity Western Substrate kit (Bio-Rad).
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4

Outer Membrane Vesicle Characterization

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OMV solutions corresponding to 7.5 µg of each type of OMV lipids were mixed with 4 µL of 4X Laemmli sample buffer (Bio-Rad). Whole cell extracts of each bacterial clone (corresponding to 3 µg of proteins) were mixed with 4 µL of 4X Laemmli sample buffer (Bio-Rad). Following SDS-PAGE, the proteins and associated LPS were transferred from the polyacrylamide gel to a nitrocellulose membrane (Bio-Rad) using a Trans-Blot turbo apparatus (Bio-Rad) according to the manufacturer’s recommendations. The membrane was blocked for 30 min in 5% non-fat dry milk in TBS-T [50 mM Tris, 200 mM NaCl, pH 7.5, 0.1% Tween-20], then incubated overnight in 2.5% non-fat dry milk in TBS-T containing either mouse monoclonal anti E. coli LPS IgGs (clone 2D7/1 (ab35654), Abcam, Cambridge, United Kingdom) diluted 1/2000 or rabbit anti-OmpA polyclonal antibodies (Epigentek, Farmingdale, United States) diluted 1/2000. After two washes of 10 min each in TBS-T, the membranes were incubated for 3 h, respectively, in 2.5% non-fat dry milk in TBS-T containing anti-mouse polyclonal antibodies coupled to horse radish peroxidase [HRP] and diluted 1/10,000 or containing HRP-conjugated anti-rabbit IgG F(ab’)2 fragment (Sigma) diluted 1/10,000. After washes in TBS-T, the membranes were revealed by ECL using a Clarity Western substrate kit (Bio-Rad) and photographed using a ChemiDoc apparatus (Bio-Rad).
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