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34 protocols using chloramphenicol

1

APEC17 Strain Genetic Manipulation Protocol

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The APEC17 strain is a serotype O2 strain isolated from a case of avian colibacillosis in Anhui Province, China (Tu et al., 2016 (link)). All strains and plasmids are listed in Table 1. Bacterial strains were grown in Luria-Bertani (LB) medium (Sangon, Shanghai, China) at 28°C or 37°C. If required, antibiotics were added at the following concentrations: ampicillin (100 µg/mL) and chloramphenicol (30 µg/mL) (Sangon).

Strains and plasmids used in this study.

Table 1
StrainsRelevant genotypeSource
AE17APEC wild-type strainLaboratory stock
AE17ΔenvZAE17 envZ-deletion mutant strainThis study
AE17C-envZCmr, AE17ΔenvZ with the complement plasmid pSTV28-envZThis study
Plasmids
pKD46Ampr, expresses λ red recombinase, temperature-sensitiveTakara
pKD3Ampr Cmr, cat gene, confers resistance to chloramphenicol template plasmidTakara
pCP20Ampr Cmr, temperature-sensitive plasmidTakara
pSTV28Cmr, cloning vector with pACYC184 replication starting pointTakara
pSTV28-envZCmr, pSTV28 with envZ geneThis study

Abbreviations: Cmr, chloramphenicol-resistant; Ampr, ampicillin-resistant; APEC, Avian pathogenic E. coli.

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2

Antibiotic Resistance Profiling of Lactobacillus

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Following the results of the resistance gene analysis, the minimum inhibitory concentrations (MICs) of GE2270A (Adipogen, San Diego, CA, USA) were determined against L. rhamnosus X253 and L. rhamnosus GG. In addition, the MICs of other antibiotics (Sangon Biotech, Shanghai, China)—including ampicillin, chloramphenicol, erythromycin, gentamicin, streptomycin, tetracycline, and vancomycin—were determined for these two strains in accordance with the ISO 10932:2010 standard (https://www.iso.org/standard/46434.html, accessed on 30 May 2022). In 96-well plates, suspensions of the two strains were combined with antibiotics at varying doses and incubated anaerobically at 37 °C for 48 h. The optical density at 625 nm was measured using a microplate reader (Thermo Labsystems, Franklin, MA, USA). The threshold values for resistance to each antibiotic were derived from the European Food Safety Authority (EFSA) [32 ].
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3

Bacterial Cultivation and Antibiotic Use

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This study complies with all relevant ethical regulations and the bacterial strains and plasmids used in this study are listed in Table S2. Unless otherwise noted, S. aureus strains were grown in tryptic soy broth (TSB, Difco) at 37 °C with shaking (250 rpm), or on tryptic soy agar (TSA, Difco) at 37 °C. Escherichia coli strains were grown in Luria-Bertani (LB) broth at 37 °C with shaking (250 rpm) or on LB agar plates at 37 °C. For plasmid maintenance, antibiotics were used at the following concentrations where appropriate: for S. aureus, erythromycin (Sangon Biotech) at 10 μg/ml for RN4220 and 80 μg/ml for USA300 LAC and its derivatives, chloramphenicol (Sangon Biotech) at 15 μg/ml; for E. coli, carbenicillin (Sangon Biotech) at 150 μg/ml. For other reagents, tunicamycin and vancomycin (Dalian Meilun Biotech Co., Ltd.), targocil (Shanghai TopScience Co, Ltd.), oxacillin (Shanghai Aladdin Biochemical Technology Co.,Ltd.), imipenem, cefuroxime, ceftizoxime, cefaclor, cefoxitin, and epicatechin gallate from MedChemExpress, cefotaxime, isopropyl β-D-1-thiogalactopyranoside (IPTG), and AIP from Sangon Biotech, anhydrotetracycline (aTc) from APExBIO, Tarocin A1 from Merck, moenomycin complex from GlpBio, and nile red from Yeasen Biotechnology Co., Ltd. were used in this study.
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4

Antibiotic Resistance Profiling of L. sakei

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The predicted antibiotic resistance gene information in the genome was obtained by comparing the amino acid sequences of the strains with the comprehensive antibiotic research database (CARD, http://arpcard.mcmaster.ca, accessed on 24 May 2021) [51 (link)]. The strains were clustered using HemI software [50 (link)].
The microbroth dilution method was used to determine antibiotic resistance of L. sakei according to ISO 10932:2010 [52 ]. The following 11 antibiotics were detected: chloramphenicol, rifampicin, streptomycin, kanamycin, gentamycin, tetracycline, clindamycin, neomycin, erythromycin, ciprofloxacin, and vancomycin (all purchased from Sangon Biotech Co., Ltd., Shanghai, China). OD625 was determined using an enzyme-labeled instrument (Varioskan Lux, Thermo, Waltham, MA, USA) to determine the MIC of strain to antibiotics.
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5

Bacterial Culture Media and Reagents

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Tryptic Soy Broth medium (TSB) and Lysogeny Broth medium (LB) were purchased from Huankai Biotech Limited (Guangzhou, China). All antibiotics including tetracycline, kanamycin, and chloramphenicol were purchased from Sangon Biotech Limited (Shanghai, China). DNA polymerase, T4 ligase, and restrictive endonucleases were obtained from Takara (Japan).
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6

Spinal Cord Injury Rat Model with ATL-III Treatment

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Seventy‐two rats were randomly divided into 3 groups: a sham group (Sham), a control group (Ctrl), and an ATL‐III treatment group (ATL‐III). Contusion SCI was established with an Infinite Horizon impactor (Precision Systems).12 In brief, the anaesthetization of rat was executed with pentobarbital (50 mg/kg, i.p.), and a T9 vertebral laminectomy was performed. Moderate SCI was established with a 2.5‐mm‐diameter rod (force 120 kdynes). The sham rats underwent the same surgical procedure without contusion injury. Postoperatively, the rats were placed in a room with controlled conditions (20 ± 2°C, 55 ± 10% humidity). To protect against infection, the rats were administered 50 mg/kg chloramphenicol (Sangon Biotech) by drinking water. ATL‐III (Phytomarker Ltd.) was mixed with 0.9% NaCl and dimethyl sulfoxide (DMSO, 1%). The rats were administered 5 mg/kg ATL‐III by gavage three hours after the operation and then once a day until sacrifice.6, 7, 8 The control rats were administered the same volume of saline.
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7

Synthesis and Characterization of Gold Nanoparticles

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Protamine sulfate salt, tetrachloroauric (III) acid tetrahydrate ( HAuCl 4 ⋅4H 2 O), andsodium citrate (C 6 H 5 Na 3 O 7 ⋅2H 2 O) were purchased from Sigma-Aldrich (USA). Kanamycin sulfate, tetracycline hydrochloride, p-hydroxy-ampicillin, chloramphenicol, ampicillin and gentamicin sulphate were obtained from Sangon Biotechnology Inc. (Shanghai, China). Kanamycin aptamer (5 ′ -TGG GGG TTG AGG CTA AGC CGA-3 ′ ) and cDNA (5 ′ -TCG GCT TAG CCT CAA-3 ′ ) were synthesized by Sangon Biotechnology Inc. (Shanghai, China). Sodium chloride (NaCl), sodium borohydride (NaBH 4 ), magnesium chloride (MgCl 2 ), glucose, and absolute ethyl alcohol were obtained from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China). Exonuclease I was purchased from New England Biolabs (Beijing, China). All other chemicals were of analytical reagent grade or higher and used without further purification. Double distilled water (18.2 MΩ, Pall Cascada) was used throughout the experiments.
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8

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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9

Cloning and Expression Optimization

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E. coli JM109 and E. coli BL21 (DE3) were used as the cloning host and the expression host, respectively. The plasmids pACYCDuet-1, pCOLADuet-1, pCDFDuet-1, pETDuet-1, and pRSFDuet-1 were from Novagen (Darmstadt, Germany). The DNA gel extraction kit, plasmid miniprep kit, and Taq DNA polymerases were from TaKaRa. The multiF seamless connection kits were from Abclonal (Wuhan, China). The isopropyl β-D-1-thiogalactopyranoside, ampicillin, kanamycin, chloramphenicol, and streptomycin were from Sangon Biotech (Shanghai, China). Standards: the L-arginine, agmatine sulfate, putrescine, and pyridoxal-5 -phosphate were from Aladdin (Shanghai, China). The methanol and tetrahydrofuran were chromatography grade, from Tedia (Fairfield, OH 45014, U.S.A.) and Rhawn (Shanghai, China), respectively. Primer synthesis and gene sequencing were performed by Talen-bio Scientific (Shanghai, China). The primers used are listed in Table 1.
Table 1. Primers used in the study.
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10

Profiling antibiotic resistance in Bifidobacterium bifidum

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B. bifidum genomes were aligned against sequences from the latest version of the Comprehensive Antibiotic Resistance Database [39 (link)], and a conservative threshold (amino acid identity ≥ 30%, comparison hit-bit score ≥ 37.0) was used to predict putative ARGs.
The antibiotic susceptibility of the B. bifidum strains was evaluated using the broth microdilution method, according to ISO 10932:2010 [40 ]. The following 10 antibiotics were tested: tetracycline, erythromycin, clindamycin, ampicillin, amoxicillin, trimethoprim, ciprofloxacin, chloramphenicol, rifampicin, and vancomycin (all purchased from Sangon Biotech Co., Ltd., Shanghai, China). The microbiological breakpoints of Bifidobacterium recommended by the European Food Safety Authority were used to distinguish susceptible strains from resistant strains.
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