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15 protocols using kanamycin

1

Nitrogen Sources' Impact on Ammonia Production

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Luria–Bertani (LB) medium was prepared with 10 g/L Bacto™ Tryptone (Becton, Dickinson and Company, Detroit, MI, USA), 5 g/L Bacto™ Yeast Extract (Becton) and 10 g/L NaCl (Wako chemicals, Osaka, Japan). M9-YE medium was prepared with 6 g/L K2HPO4, 3 g/L KH2PO4, 0.5 g/L NaCl, 7.25 g/L yeast extract, 0.1 mM CaCl2, and 1 mM MgSO4. In the experiment for the examination of effects of nitrogen sources on ammonia production, Bacto™ Tryptone (Becton), Bacto™ Peptone (Becton), or Bacto™ Casamino acids (Becton) were used instead of Bacto™ Yeast Extract in M9-YE medium. Ampicillin (Meiji Seika Pharma, Tokyo, Japan, 100 μg/mL) and kanamycin (Nacalai Tesque, Kyoto, Japan, 25 μg/mL) were added as appropriate.
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2

Pneumococcal Infection and Bacterial Load

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Streptococcus pneumoniae Xen10, which possesses a stable copy of the modified Photorhabdus luminescens lux operon at a single integration site on the bacterial chromosome (parental strain, A66.1 serotype 3; Caliper Life Sciences, Hopkinton, MA, USA), was cultured in brain-heart infusion broth (Becton, Dickinson and Company, Franklin Lakes, NJ, USA) at 37 °C under a 5% CO2 atmosphere with no aeration. After overnight culture, S. pneumoniae was collected by centrifugation at 4 °C, 9100× g, 3 min and washed twice with sterile PBS. One week after the final immunization, mice were nasally challenged with 5.0 × 106 CFU (40 µL per mouse) of S. pneumoniae under anesthesia. The survival and body weight of the infected mice were monitored for 14 days. After euthanizing infected mice, lungs and BALF were then collected from these mice and the collected lungs were homogenized for 1 min in 1 mL sterile PBS (Nacalai Tesque). The samples were plated on blood agar (BD Biosciences, San Jose, CA, USA) coating with kanamycin (100 µg/mL: 40 μL) (Nacalai Tesque). After sample culture overnight at 37 °C, the numbers of bacterial colonies on the blood agar plate were counted.
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3

Reticuline-Producing E. coli Culture Protocol

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Reticuline-producing E. coli harboring pCOLADuet-1 or pCOLADuet-1_AtDTX1 were cultured overnight in liquid LB containing 80 mg/L ampicillin (Sigma-Aldrich, St. Louis, MO, USA), 2 mg/L tetracycline (Nacalai Tesque), 100 mg/L spectinomycin (Nacalai Tesque), 30 mg/L chloramphenicol (Nacalai Tesque), and 50 mg/L kanamycin at 30 °C with shaking at 200 rpm. The overnight grown cultures were treated as described in section 2.5. Growth was measured by OD600.
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4

Heterologous Protein Expression in BL21(DE3) Cells

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BL21(DE3) cells harboring pCOLADuet-1, pCOLADuet-1_AtDTX1, or pCOLADuet-1_NtJAT1 were cultured overnight in liquid LB medium containing 50 mg/L kanamycin (Nacalai Tesque) at 30 °C with shaking at 200 rpm. Overnight cultures of OD600 = 0.1 were then inoculated in 90 mL LB medium containing 50 mg/L kanamycin and grown at 30 °C. Isopropyl β-D-thiogalactopyranoside (IPTG) (1 mM) was added when OD600 reached 0.6, then were incubated for another 3 h. Next, the cells were harvested via centrifugation at 9000×g for 2 min, re-suspended in 0.5 mL 1 × phosphate-buffered saline (PBS), and disrupted via sonication (nine cycles of 30 s on, 30 s off, performed on ice). The mixture was centrifuged at 3000×g for 15 min, and the supernatant was collected and centrifuged at 20,000×g for 20 min to pellet the membrane proteins. The membrane proteins were then denatured, subjected to electrophoresis on a 10% sodium dodecyl sulfate-polyacrylamide gel, and transferred to an Immobilon polyvinylidene difluoride membrane (Millipore, Tokyo, Japan). The membrane was treated with BlockingOne (Nacalai Tesque) and incubated with an anti-His monoclonal antibody (MBL Life Science, Nagoya, Japan) against His-AtDTX1 or an anti-NtJAT1 antibody (a generous gift from Dr. Y. Moriyama, Kurume University) against NtJAT1. The immunoreactive band was visualized using Chemi-Lumi One Super (Nacalai Tesque).
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5

Cytotoxicity Assay for Campylobacter Strains

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C. upsaliensis strains, ATCC 43954, 40-1, 48-1, 99-1 and 102-1, examined previously [16 (link)] were used in
this study. Recombinant Escherichia coli strain BL21 (DE3) with cdt-II(Chcdt-II) genes of C. hyointestinalis in TH-pET vector (rChCDT-II) [17 (link)] and C. jejuni strain K328 with 667 and 51 bp deleted regions in the cdt gene cluster [15 (link)], were used as positive and negative controls, respectively, for cytotoxicity assay. Campylobacter strains were grown on
blood agar [blood base agar no. 2 (Oxoid Ltd., Basingstoke, U. K.)] supplemented with 5% (v/v) defibrinated horse blood (Nippon Bio-Supp. Center, Tokyo, Japan)
under anaerobic condition (10% CO2, 10% H2 and 80% N2) at 37°C for 48 hr. E. coli strains, JM109 and BL21
(DE3), were used as cloning and expression vectors, respectively, and they were grown aerobically in Luria-Bertani (LB; Becton, Dickinson and Co., Frankline
Lakes, NJ, U.S.A.) agar at 37°C overnight. E. coli strains carrying a recombinant plasmid were grown in LB broth containing 30
µg/ml kanamycin (Nacalai Tesque Inc., Kyoto, Japan) at 37°C with vigorous shaking.
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6

Wash and Filter Mites and Eggs

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The study was conducted on 1000 whole adult mites and eggs, which were washed to reduce bacterial contamination, by modification of a previously reported method20 (link). Briefly, the raccoon dog’s skin and hair were washed at 37 °C for 1 h in washing solution [10% SDS, 0.1 μg/μL papain (Wako Pure Chemical Industries, Osaka, Japan), Pronase/ethylenediaminetetraacetic acid (EDTA) solution (Kyokuto Pharmaceutical Industrial, Tokyo, Japan)32 (link) containing 25 μg/mL kanamycin (Nacalai Tesque, Kyoto, Japan) and 35 μg/mL chloramphenicol (Wako Pure Chemical Industries)]. Undissolved mites and eggs were then collected using a filter (EASYstrainer, 50 μm mesh, Greiner Bio-One, Kremsmünster, Austria).
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7

Lung cancer and Leishmania assay protocol

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The lung adenocarcinoma cell line (A549) was obtained from the Japanese Collection of Research Bioresources (JCRB) Cell Bank, National Institute of Biomedical Innovation. Institute of Tropical Medicine, Nagasaki University supplied us with L. major, which was used as endorsed by the ethical board of the Institute of Tropical Medicine, Nagasaki University, Japan. M199 and Dulbecco’s Modified Eagle’s Media, kanamycin, dimethyl sulfoxide (DMSO), etoposide, miltefosine, fetal bovine serum, and MTT were obtained from Nacalai Tesque in Kyoto, Japan. The 96-well plates were purchased from Becton Dickinson (Franklin Lakes, NJ, USA). Solvents for the extraction, fractionation, and mass analysis were obtained from Sigma-Aldrich Inc., St. Louis, MO, USA.
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8

Antibacterial Evaluation via MTT Assay

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The antibacterial activities were evaluated using an MTT assay according to the previously published protocol, against Gram-positive bacteria (S. aureus NBRC 100910 and B. subtilis NBRC 13719), with slight modifications [25 (link)]. Bacterial strains were inoculated on YP agar plates [1% polypeptone (Nihon Pharmaceutical, Tokyo, Japan), 0.2% yeast extract (Difco Laboratories, Franklin Lakes, NJ, USA), 0.1% MgSO4⋅7H2O, and 1.5% agar (Fujifilm Wako Pure Chemical Corporation)] and incubated at 37 °C for 12 h. Solutions of compounds were prepared at 10 mM in DMSO and diluted to sixteen sample concentrations (0.078125, 0.15625, 0.3125, 0.625, 1.25, 1.5625 2.5, 3.125, 5, 6.25, 10, 12.5, 25, 50, 100, and 200 μM) in 96-well plates containing the microbial strains incubated in YP medium. A DMSO control was also included. The plates were incubated further at 37 °C for 12 h. Ampicillin (Nacalai Tesque, Kyoto, Japan) and kanamycin (Nacalai) were used as reference reagents. Finally, 10 µL of MTT solution (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (0.5 mg/mL in iPrOH- HCl) was added to each well and incubated further at 37 °C for 1 h. All MIC values were determined in triplicate. The MIC was defined as the lowest concentration at which no growth was observed.
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9

Antibiotic procurement and preparation

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Ampicillin, kanamycin, and chloramphenicol were purchased from Nacalai (Kyoto Japan). Neomycin, gentamicin, and apramycin were purchased from Sigma-Aldrich Co. (MO, USA). All other chemicals were of analytical grade. Fortimicin sulphate was kindly supplied from Kyowa Hakko Co. (Tokyo, Japan). Restriction enzymes were purchased from Takara Bio, Inc. (Shiga, Japan) and New England BioLabs (MA, USA).
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10

Expression, Purification, and Analysis of G. antarctica HSP70

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Expression was assessed in LB containing 50 μg/mL of kanamycin (Nacalai, Japan). Induction was performed using 0.5 mM isopropyl β-D-thiogalactopyrosidase (IPTG) (Nacalai, Japan) after reaching an OD600 of ~0.8 and inducing for 16 h at 20 °C. The overexpression of the G. antarctica HSP70 was analyzed using 15% SDS-PAGE (Figure S4). The protein bands were visualized by Coomassie brilliant blue R250 staining (Nacalai, Japan). Purification was performed using prepacked Ni-NTA columns and AKTA Avant based on the manufacturer’s instructions (GE Healthcare, Marlborough, MA, USA). The purified GaHSP70-1 and GaHSP70-2 were analyzed for purity using SDS-PAGE (Figure S5).
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