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Kanamycin

Manufactured by HiMedia
Sourced in India

Kanamycin is a broad-spectrum antibiotic commonly used in laboratory settings. It is an aminoglycoside antibiotic that inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome. Kanamycin is often used as a selective agent in bacterial cell cultures and genetic engineering applications to identify and maintain cells that have been successfully transformed or transfected.

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35 protocols using kanamycin

1

Purification of Recombinant Proteins

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Sodium chloride, imidazole, GdmCl, urea, glycine, ethanol, Tris buffer, etc. were brought from Merck (Darmstadt, Germany). Glycerol, N-lauroylsarcosine, and Triton X-100 were purchased from Sigma (St. Louis, MI, USA). Luria–Bertani broth, kanamycin, and imidazole were brought from Himedia, India. All the chemicals used for the experiments were of analytical grade.
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2

Mycobacterium tuberculosis Strain Maintenance

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M. tb strain H37Rv was obtained from ATCC (ATCC 27294 strain). Frozen stocks were revived and cultured in Middlebrooks 7H9 broth (Himedia) supplemented with 10% oleic acid-albumin-dextrose-catalase (OADC) (Himedia), 0.4% glycerol (Himedia) and 0.05% Tween-80 (Sigma) in a BSL3 facility. For estimation of colony forming units, Middlebrooks 7H11 agar (Himedia) supplemented with 10% oleic acid-albumin-dextrose-catalase (OADC) (Himedia) and 0.5% glycerol (Himedia) was used.
The knockdown strain of ribH gene of M.tb used in this study was derived from mc2 7902 (H37Rv ΔpanCD ΔleuCD ΔargB)41 (link) and was cultured in Middlebrook 7H9 broth or 7H11 agar supplemented with 10% oleic acid-albumin-dextrose-catalase (OADC) (Himedia) along with 0.5% glycerol, 0.05% tyloxapol and pantothenate, leucine and arginine (PLA) supplement containing l-pantothenate (24 mg/l); l-leucine (50 mg/l); and l-arginine (200 mg/l) to circumvent synthetic lethality41 (link). The knockdown strains were selected on Kanamycin (Kan) and hygromycin (Hyg) at concentrations of 25 μg/ml and 50 μg/ml, respectively as described42 (link).
DH5-α and BL21 (DE3) strains of E. coli (NEB) were used for cloning and protein expression studies. E. coli strains were cultured in Luria Bertani (LB) broth (Himedia) or LB agar containing Kanamycin (Himedia) (Supplementary Table 3).
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3

Bacterial Culture and Protein Purification

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Luria–Bertani (LB)
broth, Luria agar, and kanamycin were purchased from Himedia, India.
Sodium chloride, imidazole, boric acid, Tris–HCl buffer, EDTA,
ethanol, and the Amicon Ultra 10K device were purchased from Merck
(Darmstadt, Germany). Heparan sulfate, sodium dodecyl sulfate, Triton
X-100, and 3,30-diaminobenzidine (DAB) were bought from Sigma, Saint
Louis. All other chemicals used during the experiments were of molecular
biology grade.
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4

Antibiotic Susceptibility Profiling of Isolates

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The isolates were tested against 24 antibiotics using the Kirby-Bauer disc diffusion technique [45 (link)]. Antibiotic discs were placed on freshly prepared lawns of each isolate on Mueller-Hinton agar (MHA) plates and incubated at 37 °C for 24–48 hours. The diameter of the inhibition zones was measured, and the strains were classified following the standard antibiotic disc chart. Standard antibiotic discs were procured from ‘HiMedia’ which includes gentamicin (120 μg), vancomycin (30 μg), tetracycline (30 μg), polymixin-B (300 μg), kanamycin (30 μg), ofloxacin (5 μg), co-trimoxazole (25 μg), meropenem (10 μg), ceftriaxone (30 μg), clindamycin (2 μg), ampicillin (10 μg), norfloxacin (10 μg), rifampicin (5 μg), amikacin (30 μg), penicillin-G 10μg), cefdinir (5 μg), ciprofloxacin (5 μg), azithromycin (15 μg), methicilin (5 μg), and streptomycin (10 μg).
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5

Antibiotic Susceptibility Testing for Klebsiella

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Antibacterial susceptibility testing was performed using the disk diffusion method according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI) documents (13 ). The antibiotics used comprised of piperacillin (100 μg), ceftazidime (30 μg), cefotaxime (30 μg), cefazoline (30 μg), tetracycline (30 μg), kanamycin (30 μg), Imipenem (10 μg), and Meropenem (10 μg) (Himedia, Mombay, India). Minimum inhibitory concentration (MIC) for Imipenem was determined by E-test method (AB Biodisk, Solna, Sweden) for all K. pneumoniae isolates according to CLSI guideline (14 (link)).
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6

Antibiotic Susceptibility Profiling of Wild-Type Strains

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The susceptibility/resistance of wild-type strains to antibiotics was investigated using the disk diffusion assay. The antibiotics (HiMedia Laboratories, Mumbai, India) studied were gentamycin (10 μg/disk), kanamycin (30 μg), streptomycin (10 μg), tetracycline (30 μg), erythromycin (15 μg), clindamycin (2 μg), chloramphenicol (30 μg), ampicillin (10 μg), and vancomycin (30 μg). The method involved inoculating 4 mL of sterile agar at 45 °C with 200 μL of each culture separately, followed by coating the mixture on MRS agar Petri dishes. After 15 min, the antibiotic disks were placed on the surface, followed by incubation at 37 °C for 24 h and determination of inhibition bands around the disks [37 (link)]. The results were interpreted according to the cut-off levels proposed by Charteris et al. (1998), with strains considered resistant if inhibition zone diameters were equal to or smaller than 12 mm for gentamycin and ampicillin, 13 mm for kanamycin, erythromycin, and chloramphenicol, 11 mm for streptomycin, 14 mm for tetracycline and vancomycin, and 8 mm for clindamycin [37 (link)].
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7

Antibiotic Susceptibility Testing by Disk Diffusion

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Antibiotic susceptibility testing was done using disk diffusion method as described by Clinical and Laboratory Standards Institute [35 ]. 95 isolates were randomly selected for convenience from all bacteria isolated from the three counties. The isolates were tested for susceptibility to commonly used antibiotics including Ampicillin, Tetracycline, Streptomycin, Co-trimoxazole, Kanamycin, Gentamicin, Sulphamethoxazole, and Chloramphenicol (HiMedia).
Isolates were grown on blood agar for 24 hours; 5 colonies were picked from each plate and suspended in 5 ml of sterile normal saline which was then adjusted to a density approximately equal to McFarland Opacity Standard number 0.5. A dry sterile cotton swab was then placed inside the suspension; excess liquid from the swab was expressed against the wall of the tube and the swab used to spread the bacterial suspension evenly on the surface of Mueller-Hinton agar in order to get confluent growth. Antibiotic disks were then placed on the surface of the inoculum and incubated for 18–24 hours. Zones of inhibition were measured to the nearest millimeter and interpretation as to whether the bacterium was resistant or susceptible to the particular antibiotic was done according to specifications defined by Clinical and Laboratory Standards Institute (CLSI 2006).
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8

Bacterial Protein Expression and Purification

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The principal components of bacterial culture: LB broth, tryptone, and yeast extract; antibiotics: kanamycin; protein expression and extraction reagents: IPTG, Tris–HCL and base, glycine, lysozyme, PMSF, SDS, acrylamide/bis-acrylamide, ammonium persulfate, tetramethylethylenediamine (TEMED), DTT, and EDTA, and Coomassie G-250 were purchased from Himedia and VWR life science. Inclusion body solubilizing and protein refolding reagents: guanidine hydrochloride, urea, arginine hydrochloride, and isopropanol were from Sigma-Aldrich. PCR cloning kit: pJET1.2; Q5 high fidelity DNA polymerase and restriction enzymes, T4-DNA ligase, and rapid protein assay BCA kit were from New England Biolabs (NEB) and Thermo Scientific. Protein purification was performed by AKTA FPLC systems using superose 12 10/300 size-exclusion column which were purchased from GE Healthcare. Surface Plasmon Resonance instrument (Autolab ESPRIT) and BLI systems (Octet RED96) were used to measure the binding affinity.
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9

Antibacterial Activity of Ouabain against S. aureus

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Ouabain (OBN) and ATP (adenosine 5′-triphosphate), FITC (fluorescein isothiocyanate), Crystal violet, used in this study were purchased from the Sigma Aldrich (St. Louis, MO). Antibiotics such as ampicillin (AMP), tetracycline (TET), vancomycin (VAN), gentamycin (GEN), amikacin (AMK) and kanamycin (KAN) was procured from HiMedia (Mumbai, India).
The methicillin-sensitive S. aureus (MSSA); ATCC29213 was used in this study. Clinical S. aureus strains IGMS 002 and IGMS 007 received a kind gift from the Indira Gandhi Institute of Medical Science (IGIMS), Patna, were used for cell susceptibility analysis. Muller Hinton Agar/Broth (MHA/MHB) and Tryptic Soya Broth (TSB) were used to culture S. aureus and biofilm formation, respectively at 37 °C. Culture media was purchased from the Hi-media Laboratory.
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10

Gfp Tagging of Native B. thuringiensis Strain

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Native B. thuringiensis strain VKK-BB2 (GenBank accession number KT714045) was retrieved from the bacterial stock of Insect Physiology and Molecular Biology Laboratory, Division of Entomology, IARI, New Delhi which was originally isolated from the cabbage aphid, Brevicoryne brassicae (Mandla et al. 2017) . The BtVKK-BB2 strain was found to be the most potential out of 12 native strains screened against neonate of BSFB (data not shown here). Thus, BtVKK-BB2 strain was selected for gfp tagging through electroporation. This strain is resistant to ampicillin and penicillin therefore maintained on Luria Bertani agar (LA) supplemented with ampicillin and penicillin (HiMedia Laboratories Pvt Ltd, India) at 50 µg/ml at 30 °C. The Escherichia coli harboring pCAMBIA1302 plasmid (Fig. 1) was grown in Luria Bertani broth (LB) supplemented with 50 µg/ml kanamycin (HiMedia Laboratories Pvt Ltd, India) at 37 °C.
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