Amoxicillin-clavulanic acid (150 mg/kg; Sandoz), ampicillin (200 mg/kg; Euromedex), colistin (600 μg/gavage; Sigma‒Aldrich), metronidazole (200 mg/kg; Toku-e), neomycin (200 mg/kg; Euromedex), vancomycin (100 mg/kg; Mylan) or a broad-spectrum antibiotic cocktail containing a mix of ampicillin (200 mg/kg; Euromedex), metronidazole (200 mg/kg; Toku-e), neomycin (200 mg/kg; Euromedex), and vancomycin (100 mg/kg; Mylan) were resuspended in NaCl as it is used in human intravenous treatments and administered to mice daily by intragastric gavage for 10 days.
Ampicillin
Manufactured by Euromedex
Sourced in France
Ampicillin is a lab equipment product used as an antibiotic in microbiological applications. It is a broad-spectrum penicillin-type antibiotic that inhibits the growth of various bacteria.
Automatically generated - may contain errors
Lab products found in correlation
Neomycin, by Euromedex (2 mentions)
Erythromycin, by Euromedex (2 mentions)
Rifampicin, by Euromedex (2 mentions)
Metronidazole, by Merck Group (2 mentions)
Glycerol, by Thermo Fisher Scientific (2 mentions)
Lysogeny broth medium, by Merck Group (2 mentions)
Phosphate buffered saline (pbs), by Thermo Fisher Scientific (2 mentions)
Isopropyl β d 1 thiogalactopyranoside (iptg), by Thermo Fisher Scientific (2 mentions)
Neb 5 alpha competent e coli high efficiency, by New England Biolabs (1 mentions)
Kanamycin, by Euromedex (1 mentions)
Terrific broth, by Thermo Fisher Scientific (1 mentions)
Hygromycin b, by Euromedex (1 mentions)
Glycerol, by Merck Group (1 mentions)
Glucose, by Thermo Fisher Scientific (1 mentions)
Propofol, by Thermo Fisher Scientific (1 mentions)
Quinidine, by Thermo Fisher Scientific (1 mentions)
Metformin, by Thermo Fisher Scientific (1 mentions)
Imidazole, by Merck Group (1 mentions)
Lb broth, by Thermo Fisher Scientific (1 mentions)
Nah2po4, by Thermo Fisher Scientific (1 mentions)
11 protocols using ampicillin
1
Broad-spectrum Antibiotics Administered to Mice
2
Antibiotic Modulation of Gut Microbiome
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WT and eif2ak4−/− littermates were treated with an antibiotic cocktail containing 500 mg/l metronidazole (Sigma-Aldrich, M3761), 500 mg/l vancomycin (Sigma-Aldrich, 861987), 1 g/l neomycin (Sigma-Aldrich, N6386) and 1 g/l ampicillin (Euromedex, EU0400-D) for 7 d as described,32 (link) and 24 h later were orally challenged with 109 CFU of LF82 or K12 MG1655 bacteria for 3 d. Fresh fecal samples (100-200 mg) were collected from individual mice every day post-infection and resuspended in PBS to determine bacterial persistence in the gut. At d 3 post-infection, mice were sacrificed, and 2-cm segments of ileal tissues were removed, opened longitudinally and homogenized in PBS to determine the number of bacteria associated with the intestinal mucosa. After serial dilution, fecal or ileal samples were plated on LB agar plates containing 50 µg/ml ampicillin and 20 µg/ml erythromycin (Euromedex, E002) to isolate LF82 bacteria, or containing 300 µg/ml rifampicin (Euromedex, 1059-B) to isolate K12 MG1655 bacteria, and incubated at 37°C overnight.
3
Competent E. coli Strain Cultivation
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NEB 5-alpha competent E. coli (high efficiency) (New England Biolabs) was grown at 37 °C in LB medium containing 100 μg/ml ampicillin (Euromedex). Yeast strains were grown in YPD or YNB medium at 30 °C. CEN-PK (MATa ura3-52) was used to construct the genomic library (see below). Isolation of the commercial wine strain EC1118 haploid derivative 59A was described previously (Ambroset et al. 2011 (link)). 59A MATα Δamn1-loxP (provided by V. Galeote, INRA SPO) and the S288c auxotrophic derivative BY4720 (MATα lys2Δ0 trp1Δ63 ura3Δ0) were used for mean expression and noise measurements at the genomic level. Both strains have been transformed by pJRL2 plasmids to integrate promoter variants fused to yEGFP in their LEU2 locus (see below and supplementary table S6 , Supplementary Material online, for the list of strains). Cells transformed with pJRL2 plasmids were grown on plates containing 200 µg/ml G418 (Euromedex). Induction by CuSO4 was performed either in YPD or in YNB medium.
4
Cultivation of Escherichia coli and Mycobacterium smegmatis
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Escherichia coli DH10β and E. coli C41 (DE3)/pLyS strain were cultured in LB broth or Terrific Broth (Invitrogen, France). M. smegmatis mc2 155 and M. smegmatis mc2 155 groEL1ΔC [31 (link)] strains were cultured in Middlebrook 7H9 broth (BD Difco, Le Pont-de-Claix, France) supplemented with 0.05% (v/v) Tween-80 and 0.2% (v/v) glycerol (Sigma–Aldrich, Saint-Quentin Fallavier, France) (7H9-S). When needed, ampicillin and kanamycin (Euromedex, Souffelweyersheim, France) were added to the medium at final concentrations of 100 and 50 µg/ml for both E. coli and mycobacterial species, respectively. Hygromycin B (Euromedex) was used at a final concentration of 200 and 50 µg/ml for recombinant E. coli and recombinant mycobacteria, respectively.
5
Investigating E. coli BL21 protein expression
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E. coli BL21 were purchased from Invitrogen. Plasmid pET-21A was purchased from Novagen. pDNR-LIR-hVDAC was purchased from Dharmacon. Ampicillin, IPTG, Triton 100X, Guanidine hydrochloride, Acrylamide: Bisacrylamide 37.5:1, SDS 10%, Temed, APS, TGS 10X, NH4Cl and CaCl2 were purchased from Euromedex. NaCl, NaH2PO4, K2HPO4, KH2PO4, glucose, LB-broth, Tris-HCl, NADH, propofol, quinidine, ubiquinone 0, Laemli 6X, β-mercaptoethanol, PBS, Na2HPO4, K2SO4 and metformin were purchased from ThermoFisher. Aspirin, catechin, curcumin, DCCD, DPC, emodin, fluoxetine, and MnCl2 were purchased from Fluorochem. Imidazole, DIDS, DMSO, ReadyBlue Protein Gel stain, EDTA, MgCl2, CoCl2, H2BO3, acetone and ethanol were purchased from Sigma-Aldrich. FeSO4 and ZnSo4 were purchased from Biobasic. CuCl2 and Mo7O24 were purchased from Roth. 15NH4Cl, D2O and deuterated glucose were purchased from Innova-Chem. LDAO was purchased from CliniSciences. Itraconazole was purchased from Cayman Chemical company. VBIT4 was purchased from Aobious. Cannabidiol was purchased from Carbosynth. Olesoxime was obtained from in-house chemical library.
6
One Shot TOP10 E. coli Cells Protocol
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One Shot TOP10 chemically competent E. coli cells from Invitrogen (K-12 strain, similar to the DH10B strain) were used in this study. Colonies were grown in LB medium (Sigma–Aldrich) with ampicillin (100 µg ml−1, Euromedex) at 37°C to an OD600 of ∼1 (∼8 × 108 cells ml−1). The cells were centrifuged (1000g, 4°C), washed and gently resuspended in nutrient-free and sterile-filtered phosphate-buffered saline (PBS) pH ∼7.4 to an OD600 of ∼10 for SAS experiments. PBS and deuterated PBS (D-PBS) were adjusted to pH ∼7.4 and pD ∼7.4, respectively. Contrast-matching measurements were carried out on bacteria resuspended in D-PBS or in various ratios of PBS and D-PBS (further details are provided in the Supporting Information).
7
Microdilution Assay for Ampicillin MIC
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The microdilution assay was performed in BHI broth containing 32 µg/ml of ampicillin (Euromedex) in 96-well plates. Each well (200 µl) was inoculated with overnight cultures to obtain 5 × 105 cfu/ml. Plates were incubated for 24 h at 37 °C and the minimal inhibitory concentration was defined as the minimal concentration that prevented visible growth.
8
Bacterial Growth and Oxidative Stress
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Lysogeny Broth (LB) medium and hydrogen peroxide (H2O2) solution 30% w/w in water were purchased from Sigma-Aldrich (Saint Quentin Fallavier, France). The phosphorylated oligonucleotide pCGTAGG was obtained from Eurogentec (Seraing, Belgium). Yeast extract was purchased from Biokar Diagnostics (FR). Ampicillin was obtained from Euromedex (Souffelweyersheim, France). Phosphate Buffer Saline (PBS) 10× purchased also from Euromedex was diluted to 1× for ELP solutions. Glycerol and isopropyl β-D-1-thiogalactopyranoside (IPTG) were obtained from Fisher Scientific (Illkirch Graffenstaden, France). Tris(2-carboxyethyl)phosphine hydrochloride (TCEP∙HCl) and N-ethylmaleimide (NEM) were obtained from TCI Chemicals (Belgium). N-ethyldiisopropylamine (DIPEA) and dimethylformamide (DMF) were purchased from Alfa Aesar (Schiltigheim, France). Ultrapure (UP) water (18 MΩ-cm) was obtained by using a Millipore Milli-Q Biocel A10 purification unit.
9
Intranasal CXCL5 and Anti-CXCL5 Antibody Treatment
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Mice were anesthetized by an intra-muscular injection of ketamine (10 mg/mL, Merial) and xylazine (0.2%, Bayer). Recombinant murine CXCL5/LIX (9-78 amino acid, 1 µg per mouse) was administered intranasally at days 2 and 4 between the second and the third daily CS exposure. Anti-CXCL5/LIX antibody was obtained from Jacques Van Snick. 150 µg per mouse was injected intraperitoneally at days 2 and 4 between the second and the third daily CS exposure. An antibiotic cocktail containing Vancomycin 0.5 g/L (Sandoz), Ampicillin 1 g/L (Euromedex), Neomycin 1 g/L (Euromedex), Metronidazole 1 g/L, and sucrose 1% (Sigma-Aldrich) diluted in sterile water was given in drinking water and replaced every 3 days.
10
Gut Colonization Dynamics in eif2ak4 Mice
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At age of 12 weeks, eif2ak4+/+ and eif2ak4−/− mice, or Tg/eif2ak4+/+ and Tg/eif2ak4−/− mice were administered orally by gavage during three days (once per day) with either 109 of ampicillin-erythromycin-resistant AIEC LF82 strain isolated from a CD patient14 (link) or the rifampicin-resistant non-pathogenic E. coli K12 MG1655 strain. Bacterial persistence in the gut was evaluated every day post-infection. For this, fresh fecal samples (100–200 mg) were homogenized in PBS. After serial dilutions, fecal samples were plated on LB agar plates containing 50 μg/ml ampicillin and 20 μg/ml erythromycin (Euromedex, E002) to isolate LF82 bacteria, or containing 300 μg/ml rifampicin (Euromedex, 1059-B) to isolate E. coli K12 bacteria, and were incubated overnight at 37 °C. The number of bacteria was determined by counting the colony-forming units (CFU).
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