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22 protocols using neomycin trisulfate salt hydrate

1

Adoptive T cell transfer in mice

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Starting 3 days before adoptive T cell transfer, mice were placed on a high dose gavage treatment of 200 μL antibiotic, consisting of 1 mg/mL ampicillin (anhydrous, 96.0%–102.0%, Sigma-Aldrich), gentamicin sulphate (Sigma-Aldrich), metronidazole (Metronidazole BioXtra, Sigma-Aldrich), neomycin (trisulfate salt hydrate, Sigma-Aldrich), and 0.5 mg/mL vancomycin (vancomycin hydrochloride, Streptomycesorientalis, potency ≥900 μg/mg, Sigma-Aldrich) diluted in PBS. On day 0, mice received 2 × 106 WT CD4+CD3+CD25 T cells i.v. and were monitored for change in weight over 15 days.
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2

Cell Culture and Treatment Protocols

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All cells were cultured at 37°C and 5% CO2. HT1080 (human male), HEK293T/17 (human fetus), RKO (human, gender N/A), Lcells (mouse male), and WNT3A expressing Lcells (mouse male) were obtained from American Type Culture Collection (ATCC, Manassas, VA) and grown in DMEM with 10% FBS. Each cell line was tested for mycoplasma contamination and passaged no more than 20 passages from the original ATCC stock. Cells were treated at the indicated concentrations with the following compounds: CHIR99021 (Cayman Chemicals, Ann Arbor, MI), chlorpromazine HCL (Sigma-Aldrich, St. Louis, MO), bafilomycin A1 (Cayman Chemicals), rhWNT3A (PeproTech, Rocky Hill, NJ), rhWNT5A (R&D, Minneapolis, MN), neomycin trisulfate salt hydrate (Sigma-Aldrich) and carbachol (EMD Chemicals, Gibbstown, NJ).
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3

Gut microbiota depletion protocol

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An antibiotic mix consisting of ampicillin (ampicillin sodium salt, catalogue number A9518, Sigma-Aldrich, Vienna, Austria), bacitracin (bacitracin from Bacillus licheniformis, catalogue number 11702, Sigma-Aldrich), meropenem (OptinemR, AstraZeneca Österreich GmbH, Vienna, Austria), neomycin (neomycin trisulfate salt hydrate, catalogue number N5285, Sigma-Aldrich) and vancomycin (vancomycin hydrochloride from Streptomyces orientalis, catalogue number 4747, Sigma-Aldrich) was used to deplete the gut microbiota.
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4

Fluorescent Dextran Uptake Assay

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Lysine fixable 3 kDa and 10kDa-FITC or Texas Red-labeled dextrans were purchased form ThermoFisher scientific Inc (Waltham, MA.). Dextrans were diluted in Hanks' balanced salt solution without Ca2+ and Mg2+ (HBSS-CFM) at a final concentration of 10 mg/mL, aliquoted in black opaque tubes and stored at −30°C until use. As indicated by the manufacturer, the actual molecular weights of dextran molecules in each preparation has a distribution, and contains polymers with molecular weights ranging from 1.5 to 3.0 kDa (including the dye) in the case of 3 kDa dextran-TR, and 50% of the dextran molecules contains a dye, on average.
Hank’s balanced salt solution (HBSS), HBSS-CFM, phosphate buffered saline (PBS), Dulbecco’s Modified Eagle Medium (DMEM), DMEM media without calcium, and Leibovitz’s L-15 medium with GlutaMAX were also purchased from ThermoFisher scientific Inc. Cell impermeant BAPTA tetrapotassium salt (Molecular Probes, ThermoFisher scientific, Inc.) was dissolved at 50 mM in water. A stock solution of 30 mM benzamil hydrochloride hydrate (Sigma-Aldrich, St. Louis, MO) was prepared in DMSO. Amiloride hydrochloride (EMD MILLIPORE, Burlington, MA) was dissolved at 150 mM in DMSO. Aminoglycosides, dihydrostreptomycin sesquisulfate, and neomycin trisulfate salt hydrate (Sigma-Aldrich) were dissolved at 50 mM in water.
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5

NMR Analysis of RNA Complexes

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L-argininamide dihydrochloride (Sigma) and Neomycin trisulfate salt hydrate (Sigma) were purchased in powder form and dissolved in NMR buffer before being added to the RNA sample. DMA derivative 24 was obtained as described previously2 and was stored at 50 mM in 100% dimethyl sulfoxide (DMSO).
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6

Antibiotic Effects on Insect Rearing

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The rearing diet contained a mixture of powdered oat flakes, wheat germ and Pangamin, a dried yeast biomass (Rapeto, Bezdružice, CZ) (10/10/1 w/w/w). The rearing diet (control) was powdered by blender, sieved at 0.5 mm sieves and sterilized by heating to 70°C for 0.5 h. The diet of 50±5 mg was placed to every IWAKI chamber. The antibiotics, ampicillin sodium salt (cat No. A0166, Sigma-Aldrich, Saint Louis, USA), neomycin trisulfate salt hydrate (cat No. N6386, Sigma-Aldrich) and streptomycin sulfate salt (cat No. S9137, Sigma-Aldrich) were added to the rearing diets, separately. The treatments included antibiotic concentrations of 0.1, 1, 10, and 30 mg of antibiotics per g of diet (mgg−1). The control was the rearing diet without supplementation.
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7

Choline-deficient Diet Induced NASH in Rats

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Male six-week-old Fischer 344 rats (CLEA Japan, Inc., Osaka, Japan) were housed in a room under controlled temperature and a 12/12 h light-dark cycle. The animals were divided into the following three experimental groups and fed for 8 weeks: i) Choline-deficient amino acid diet (CDAA; n=10); ii) choline-deficient amino acid diet plus antibiotics (CDAA+AB; n=10) and iii) choline-supplemented amino acid diet (CSAA; n=5). All rats were sacrificed at the end of week 8. For selective intestinal decontamination, poorly absorbable antibiotics (1 g/l polymyxin B sulfate salt (Fluka, Buchs, Switzerland) and 3 g/l neomycin trisulfate salt hydrate (Sigma-Aldrich, St. Louis, MO, USA) were administered to the rats in the CDAA+AB group by adding them to drinking water during the experimental period, excluding the first and fifth week. All animal procedures were performed according to standard protocols and in accordance with the standard recommendations for the proper care and use of laboratory animals. This study was approved by the ethics committee of Nara Medical University, Kashihara, Japan.
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8

Gut Microbiome Depletion and TNBS Model

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Depletion of gut bacteria was achieved using the protocol described by Kelly et al. [23 (link)]. Mice were administrated with Abx cocktail containing 1 mg/mL ampicillin (Sigma-aldrich), 1 mg/mL neomycin trisulfate salt hydrate (Sigma-aldrich), 1 mg/mL metronidazole, 0.5 mg/mL vancomycin hydrochloride (Sigma-aldrich), 1 mg/mL gentamicin (Sigma-aldrich) via oral gavage at the volume of 10 μl/g body weight (BW) for consecutive 3 days. TNBS intrarectal administration was performed after three days of treatment.
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9

Commensal Bacteria Ablation Protocol

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For ablation of commensal bacteria, an antibiotic cocktail of 1 g/L each of Ampicillin sodium salt (Sigma Aldrich), Neomycin trisulfate salt hydrate (Sigma Aldrich), Metronidazole (Sigma Aldrich), and 0.5 g/L Vancomycin hydrochloride (Alvogen) was used during 14 days, as previously described26 . Antibiotics were replaced into the drinking water every other day. Antibiotic activity was confirmed at the day of the experiment by changes in cecum size due to bacterial death.
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10

Chemoenzymatic synthesis of acetylated aminoglycosides

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Neomycin trisulfate salt hydrate (Sigma-Aldrich), paromomycin sulfate salt (Sigma-Aldrich), ribostamycin sulfate salt (Sigma-Aldrich), neamine hydrochloride (Toronto Research Chemicals), puromycin dihydrochloride (Sigma-Aldrich) were used at the purity stated by the commercial suppliers (≥ 97%). Chemoenzymatic preparation of acetylated forms of neomycin is described below. 6′-deoxy-paromomycin pentaacetate salt was synthesized by the Vasella group (ETH Zurich) as described48 and was a kind gift from David Crich (Wayne State University). All smFRET experiments were performed in Tris-polymix buffer (pH 7.5) containing 50 mM Tris acetate, pH 7.5, 5 mM Mg(OAc)2, 100 mM KCl, 5 mM NH4OAc, 0.5 mM CaCl2, 0.1 mM EDTA, 5 mM putrescine and 1 mM spermidine.
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