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25 protocols using gentamicin

1

Bacterial Infection of Mammalian Cells

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Bacterial suspension was added to mammalian cells at a multiplicity of infection (MOI) as described in the figure legends. BMDMs were washed 3 times with sterile PBS (Sangon Biotech) at 30 min after infection and other cells were washed at 1 h post-infection to remove extracellular bacteria. Infected cells were subsequently cultured in RPMI medium or DMEM medium containing 10% (vol/vol) heat-inactivated FBS (Biological Industries) and 50 μg/ml gentamicin (Sangon Biotech) for 2 h. Afterward, cell culture medium was replaced with those containing 10% (vol/vol) FBS (Biological Industries) and 10 μg/ml gentamicin (Sangon Biotech). Samples were collected for further experiments at the indicated time points as described in the figure legends. When appropriate, cells were pretreated or treated with GW806742X (HY-112292, MCE, New Jersey, USA), NSA (HY-100573, MCE), GSK’872 (HY-101872, MCE), zVAD (C1202, Beyotime), Nec-1 (HY-15760, MCE), (5Z)-7-Oxozeaenol (b7443, Ape×Bio, Houston, TX USA), SB239063 (HY-11068, MCE) and MK2-IN-1 (HY-12834, MCE) as described in the figure legends. To assess cell membrane permeability, Ethidium Homodimer-I (EthD-I; US Everbright, Suzhou, China) was used as previously described.24 (link)
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2

Isolation and Culture of T. musculis

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The cecal contents of HVEM−/− mice were harvested into sterile PBS and filtered three times through a 100-μm cell strainer. The filtrate was centrifuged at 200 × g for 5 min at 4°C. The pellet was washed twice with PBS. T. musculis enriched in the pellet was further purified using a 40%/80% Percoll gradient. For T. musculis culture, the isolated T. musculis was suspended with BHI broth (Oxoid, catalog no. CM1135) supplemented with a cocktail of broad-spectrum antibiotics, including 100 mg/mL streptomycin (Sangon Biotech, catalog no. A100382), 100 U/mL penicillin (Sangon Biotech, catalog no. A613460), 50 mg/mL vancomycin (Sangon Biotech, catalog no. A600983), 10 mg/mL ciprofloxacin (Sangon Biotech, catalog no. A600310), 20 mg/mL gentamicin (Sangon Biotech, catalog no. A506614), and 0.5 mg/mL amphotericin B (Sangon Biotech, catalog no. 171375). After suspension, T. musculis was then incubated in an anaerobic workstation (Don Whitley Scientific) at 37°C for 2 days.
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3

Allogeneic Bone Marrow Transplant in Mice

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For performing bone marrow transplant, the recipient mice (6 weeks old) were given antibiotic (Gentamicin,1 mg/mL, Sangon, China) in drinking water for 2 days before given 900 cGy irradiation. Donor bone marrow cells (5 × 106) were obtained from the donor mice (6 weeks old) were intravenous injected into the recipient mice (after irradiation) and followed with antibiotic drinking water for 1 week. The recipient mice and donor mice were maintained and housed separately in the same specific-pathogen-free environment at Sun Yat-sen University.
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4

Efficient Production of Antimicrobial Peptides

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Pseudomonas aeruginosa JCM5962 was preserved in our laboratory; E. coli DH5α and BL21(DE3) competent cells were purchased from Tiangen Biotech (China). Dulbecco’s-modified eagle medium (DMEM) and Fetal bovine serum (FBS) were purchased from Gibco (United States). The crystal violet, kanamycin, and gentamicin were obtained from Sangon Biotech Co. (China). Fluorescein isothiocyanate-labeled concanavalin A (FITC-ConA), 4′,6-diamidino-2-phenylindole (DAPI), Nile red, and SYPRO red were purchased from Sigma-Aldrich Co. (USA). The N-Phenyl-1-naphthylamine (NPN) and 3,3′- Dipropylthiadicarbocyanine iodide (DiSC3-5) were purchased from Aladdin (China). All other chemicals and reagents used in this study were of reagent grade.
PEW300 peptide was produced by our previous established protein expression and purification system (Wang et al., 2018 (link)). In this system, a high yield of AMPs can be acquired by simple centrifugation, with no expensive steps like NTA affinity chromatography and high-performance liquid phase separation. Purified PEW300 was dialyzed to PBS buffer and stored at-80°C for further experiment.
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5

ANKRD22 Overexpression in 293T Cells

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Recombinant ANKRD22-expressing lentivirus particles (100 µl/ml; multiplicity of infection=100; Cyagen Inc.) were used to infect 293T cells (Cell Bank of Shanghai Branch of the Chinese Academy of Sciences) which were maintained in high-glucose DMEM (Corning, Inc.) supplemented with 10% fetal bovine serum (Corning, Inc.) and 100 µg/ml gentamicin (Sangon Biotech Co., Ltd.) at 37°C in a humidified environment with 5% CO2. Following incubation for 48 h, cells were passaged and transferred to a new six-well plate and screened with 5 µg/ml puromycin for 7–10 days. After propagation, 293T cells with high expression levels of ANKRD22 were digested with 0.25% trypsin solution (Genom Biotechnology Co. Ltd.) at room temperature for 5 min and collected by centrifugation at 1,000 × g at room temperature for 5 min and washed twice with PBS. Following aspiration of the PBS, 500 µl ice-cold radioimmunoprecipitation assay lysis buffer (pH 7.5; 50 mM Tris-HCl buffer containing 150 mM NaCl, 1 mM EDTA, 0.25% deoxycholate acid and 1% NP-40 and 0.25% deoxycholate sodium) was added, and the solution was mixed by pipetting and gentle agitation. The solution was lysed on ice for 15 min, centrifuged at 13,000 × g at 4°C for 10 min, and the supernatant was aspirated for western blot analysis.
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6

Xanthine-based Compound Screening

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Xanthine (X8030) was purchased from Solarbio Life Science, Beijing, China. Middlebrook 7H9 Broth (271310) was purchased from BD/Difco, Franklin Lakes, NJ, United States. Amikacin (A602232), kanamycin (A100408), gentamicin (A100304), streptomycin (A100382), chloramphenicol (A100230), ciprofloxacin (A600310), rifampicin (A600812), and isoniazid (A600544) were purchased from Sangon Biotech, Shanghai, China. The Anti-His antibody (#9991) was purchased from Cell Signaling Technology, Danvers, MA, United States.
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7

Quantifying Intracellular UPEC Invasion

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MB49 or 5637 cells were seeded in 6-well plates and infected for 1 h with UPEC at a multiplicity of infection (MOI) of 10 when the cell confluence reached ~90%. The cells were then washed five times with phosphate-buffered saline (PBS) and digested using trypsin. Next, the cells were resuspended in 100 μL PBS, serially diluted, and plated on LB agar plates. In the invasion assays, the infected cells were treated with 100 μg/mL gentamicin (Sangon Biotech, Shanghai, China) for 1 h to kill any extracellular bacteria. After three washes with PBS, the cell suspension was lysed with 0.1% Triton X-100 for 10 min. Finally, the cell lysate was plated onto LB agar plates and the number of intracellular bacteria was quantified.
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8

Bacterial Strains and Antimicrobial Cultivation

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Bacterial strains used in this study were from the collection of our laboratory and listed in Table S1 in the supplemental material. The antimicrobial agents amikacin, gentamicin, and kanamycin were purchased from a commercial source (Shanghai Sangon Biological Engineering Technology & Services Co. Ltd., China). A single colony was propagated in 3% NaCl Luria-Bertani (LB) (tryptone [10 g/liter], yeast extract [5 g/liter], NaCl [30 g/liter]) broth for 8 h at 30°C. The cultures were diluted to 1:100 using fresh 3% NaCl LB medium and grown at 30°C.
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9

Cell Culture Conditions for Gastric Cancer and Macrophages

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The gastric cancer cells SGC7901 and BGC823 and human THP-1 macrophages were purchased from the Cell Bank of the Shanghai Branch of the Chinese Academy of Sciences. Mouse RAW264.7 macrophages were kindly provided by Professor Hongxiang Sun (College of Animal Sciences, Zhejiang University). Cells were cultured in the following media (Corning, Corning, NY) supplemented with 10% fetal bovine serum (FBS) (Corning) and 100 μg/mL gentamicin (Sangon Biotech, Shanghai, China) at 37°C in a humidified 5% CO2 atmosphere. Then, SGC7901 and BGC823 cells and human THP-1 macrophages were cultured in RPMI 1640 medium. Meanwhile, the mouse RAW264.7 macrophages were cultured in Dulbecco’s modified Eagle medium (DMEM).
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10

Lysogeny Broth Medium Preparation

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Lysogeny broth (LB) medium (g L−1) was composed as follows: peptone 10.0 g L−1, yeast extract 5.0 g L−1, NaCl 10.0 g L−1, pH 7.2, (solid, addition of 1.5% agar), and deionized water 1000 mL, which was sterilized at 121 °C for 20 min.
Proteinase K, lysozyme, ampicillin (Amp), kanamycin (Km), gentamicin (Gm), isopropyl-β-D-thiogalactopyranoside (IPTG), o-nitrophenyl β-D-galactopyranoside (ONPG), and o-nitrophenol (ONP) were purchased from Shanghai Sangon Biotech (Sangon Biotech, Shanghai, China). GA C15:1 standard was purchased from Shanghai Tauto Biotechnology (Shanghai, China). Other chemical reagents were analytical grade.
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