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6 protocols using image lab software ver 5

1

Evaluating TIG-R EV Transfer Activity

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To evaluate the transfer activity of TIG-R EVs to AB, bacterial growth (optical density, at 600 nm, OD600) of TIG-S AB treated with or without TIG-R EVs (5 μg; BCA quantified) under different concentrations of TIG (0–4 µg·mL−1) was monitored every 30 min for 24 h at 37 °C with 500 rpm using a SPECTROStar® Nano (BMG LABTECH GmbH, Ortenberg, Germany). Aliquots (5 μL) from cells grown for 24 h were spotted onto LB-agar plates to determine MIC values for bactericidal activity. The transfer activity of TIG-R EVs from AB to other bacteria was evaluated using a 96-well MIC assay [18 (link)]. LB-agar plates or 96-well plates were imaged by ChemiDocTM MP Imaging System (Bio-Rad, Hercules, CA, USA) and Image Lab Software (ver.5.2.1, Bio-Rad, Hercules, CA, USA). One of representative of the three is shown.
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2

Southern Blot Analysis of Genomic DNA

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Total genomic DNA for southern blot analysis was isolated from BY2 cells based on Shure et al. (1983) (link) with additional steps (Supplementary Method). Digested DNA was then separated on 0.8% agarose gel electrophoresis system at 100 V for 5 h in 1 × TAE. Separated DNA was then capillary transferred to a nylon membrane and immobilized by UV-crosslinking using Stratalinker (Stratagene, La Jolla, CA, United States). Hybridization was done using DIG probes. Signal intensity was scanned with high resolution chemiluminescence settings using a ChemiDoc Touch Imaging System (Bio Rad, Herculaes, CA, United States) with Image Lab Software ver 5.2.1 (Bio Rad, Herculaes, CA, United States).
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3

Comprehensive Characterization of Extracellular Vesicles

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Both a nanoparticle analyzer (NTA) and transmission electron microscopy (TEM), NanoSight NS300 (Malvern Panalytical, Malvern, UK) and Talos L120C TEM (Thermo Fisher Scientific, Waltham, MA, USA), respectively, were used to characterize the total particle concentration, size distribution, and morphology of EVs without disrupting their structure [20 (link),21 (link)]. The protein-based quantification of EVs was performed using Pierce BCA protein assay kit (Thermo Fisher Scientific, Waltham, MA, USA) [22 (link)] with a SPECTROStar® Nano (BMG LABTECH GmbH, Ortenberg, Germany). The protein components of EVs were characterized by 12% Mini-PROTEAN® TGXTM Stain-Free gel (Bio-Rad, Hercules, CA, USA) electrophoresis and imaged through the ChemiDocTM MP Imaging System (Bio-Rad, Hercules, CA, USA) and Image Lab Software (ver.5.2.1, Bio-Rad, Hercules, CA, USA) as described [23 (link)]. One representative of the three is shown.
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4

Evaluating TIG-R EVs Against Resistant Cells

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To determine the efficacy of TIG or TIG-R EVs on recurrent TIG-R, TIG-S cells (ATCC 17978) were initially cultured under different concentrations of TIG. To determine MIC, aliquots from individual samples were spotted on an LB-agar plate, followed by incubation at 37 °C (day 1; passage 0). The next day, the colonies grown at a sub-lethal concentration (0.125 µg·mL−1) were further cultured with or without TIG-R EVs (5 µg) under different concentrations of TIG for 16 h in LB broth. This step was performed for 10 days (passage 9) and the recurrence efficacy of TIG or TIG/TIG-R EVs was evaluated. All LB-agar plates were imaged and processed by ChemiDocTM MP Imaging System (Bio-Rad, Hercules, CA, USA) and Image Lab Software (ver.5.2.1, Bio-Rad, Hercules, CA, USA).
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5

Western Blot Analysis of CVZ Skin Samples

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On POD 1, skin samples (n = 6) from CVZ were collected and stored at −80 °C before Western blot analysis. Total protein was extracted using RIPA lysis buffer, supplemented with protease inhibitor (Beyotime Biotechnology, China). After homogenization and centrifugation of the samples, BCA Protein Assay Kit (Beyotime Biotechnology, China) was used to determine the protein concentrations of the supernatant. Proteins were fractionated by sodium dodecyl sulfate-polyacrylamide gels and transferred onto the PVDF membranes. After blocking with 5% non-fat milk or bovine serum albumin for 2 hours at room temperature, the membranes were incubated overnight with primary antibodies HIF-1α (1:200, Abcam), VEGF (1:1000, Abcam), Beclin 1 (1:1000, Cell Signaling Technology), p62(1:1000, Abcam), LC3 (1:1000, Sigma), Bcl-2 (1:1000, Cell Signaling Technology), Bax (1:1000, Cell Signaling Technology), cleaved Caspase-3 (1:1000, Cell Signaling Technology) and GAPDH (1:2000, Bioworld Technology) at 4 °C. Then the membranes were incubated with goat-anti-rabbit or goat-anti-mouse secondary antibodies for 2 hours, followed by detection with ECL plus reagent kit (Thermo Fisher Scientific, Rockford, IL). Finally, the band intensity was quantified using the Image Lab software (ver.5.2, Bio-Rad).
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6

Western Blot Analysis of Nrf-2 in Caco2 Cells

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Equal amounts of protein (30 µg) from treated and untreated Caco2 cells were electrophoresed through an SDS-polyacrylamide gel (10% resolving gel) in Tris-glycine buffer at 90 V for 2 h. The proteins were transferred from the SDS-polyacrylamide gel to Immun-Blot PVDF membrane (Bio-Rad, Hercules, CA, USA) using a wet transfer system. Membranes were developed using WesternBreeze Chromogenic Anti-Rabbit Kit (WB7105, Invitrogen, Carlsbad, CA, USA) and rabbit polyclonal primary anti-Nrf-2 antibody (sc-722, Santa Cruz Biotechnology, Heidelberg, Germany) according to the manufacturer’s instructions. The protein bands were detected by staining with the BCIP/NBT substrate and visualized with the ChemiDoc Imaging System (Bio-Rad, Hercules, CA, USA). Quantification of bands on Western images was done using the Image Lab software (ver. 5.2, Bio-Rad, Hercules, CA, USA). To normalize Nrf-2 levels, Nrf-2 band intensity was divided by β-actin (A1978, Sigma-Aldrich, St. Louis, MO, USA) band intensity (which serves as reference protein), and represented as percentages of control.
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