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11 protocols using ampicillin

1

Purification of truncated TtCBD and variants

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The genes for TtCBD (residues 78–285, gene id WP_011174503.1) and its H132A and H177A variant were synthesised (GeneArt) and cloned in pET21a (ampicillin resistant) with a C-terminal 6xHistag. A detailed protocol for expression and purification for full-length CarH9 (link), which has been published earlier, was adapted for the truncated TtCBD and its variants. Briefly, genes were transformed in E. coli BL21(DE3) (New England Biolabs) cells and fresh transformants were used to grow cultures in sterile auto-induction media (Formedium) supplied with 50 µg/ml of ampicillin (Formedium). In a typical purification experiment cells from 2 l culture were resuspended in buffer containing 50 mM Tris-HCl pH 7.5, 100 mM NaCl and 10 mM imidazole. A two-step purification protocol, consisting of an affinity chromatography step followed by size-exclusion chromatography, similar to that of full-length TtCarH was followed. TtCBD also eluted as a tetramer from the Superdex Hiload 26/60 gel-filtration column (Cytiva) with >95%purity in elution buffer containing 50 mM Tris-HCl pH 7.5, 100 mM NaCl. Protein concentration was determined using published molar extinction coefficient of 8.0 × 103 M−1 cm−1 for AdoCbl at 522 nm32 (link).
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2

Recombinant Protein Purification from E.coli

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Overexpression was carried out using E.coli BL21-DE3 cells grown in 2X YT Broth supplemented with 34μg/ml kanamycin, or 100mg/mL Ampicillin (Formedium, United Kingdom) at 37 °C. At an OD600 of 0.7 the culture was induced with 0.5 mM IPTG, after which cells were grown for a further 18 hours at 18 °C. Cells were harvested by centrifugation and the pellets were resuspended in His-tag extraction buffer (10 mM Tris-HCl, 300 mM NaCl, 20 mM imidazole and 10mM β-mercaptoethanol [pH 8.0]) (Sigma) along with 0.5 mM PMSF protease inhibitor (Fluka Analytical). Cells were lysed by sonication and the cell lysate was centrifuged at 16000 rpm for 25 minutes at 4 °C to remove any cellular debris. The supernatant was filtered and loaded onto a nickel agarose resin column (QIAGEN). The resin was washed repeatedly with extraction buffer prior to elution of the bound protein using extraction buffer supplemented with 200 mM imidazole. Soluble aggregates were removed by running the eluate through a superdex 200 16/60 column (GE Healthcare) equilibrated in column buffer (10 mM Tris-HCl, 100 mM NaCl, 1 mM DTT [pH 7.5]).
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3

Purification and Production of Enzymes

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All commercially available chemicals were
used without further purification. BaseMuncher endonuclease was purchased
from Abcam. Ampicillin, dithiothreitol (DTT), and isopropyl-β-D-1-thiogalactopyranoside
(IPTG) were purchased from Formedium. Escherichia coli (E. coli) DH5α (high efficiency)
and BL21(DE3) cells, Gibson Assembly Cloning Kit, and Dpn1 were purchased
from New England Biolabs. QIAprep Spin Miniprep, PCR clean-up, and
Plasmid Midi kits were purchased from Qiagen. Ethylenediaminetetraacetic
acid (EDTA)-free Complete protease inhibitor cocktail was purchased
from Roche. Ammonium bicarbonate, ammonium sulfate, ATP, deuterium
oxide (D2O), glycerol, histidine, imidazole, lysozyme,
PRPP, potassium chloride, d-ribose 5-phosphate, tricine,
phosphoenolpyruvate, Saccharomyces cerevisiae (S. cerevisiae) pyruvate kinase (ScPK), S. cerevisiae myokinase
(ScMK), NiCl2, and ZnCl2 were
purchased from Merck. Agarose, dNTPSs, kanamycin, 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic
acid (HEPES) EnzCheck Pyrophosphate Kit, MgCl2, NaCl, PageRuler
Plus Prestained protein ladder, and Phusion High-Fidelity polymerase
were purchased from ThermoFisher Scientific. Psychrobacter
arcticus
HisGS (PaHisGS), M. tuberculosis pyrophosphatase
(MtPPase), and tobacco etch virus protease (TEVP)
were produced as previously described,20 (link) as was E. coli PRPP synthetase (EcPRPPS).21 (link)
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4

Yeast Strain Maintenance and Selection

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The S. cerevisiae strains used in this study are described in Table S5 in the supplemental material. Stocks were stored at −80°C in 15% glycerol. Strains that contained the URA3_CEN plasmid were grown on agar with 1 mg/mL of 5-fluoroorotic acid (5-FOA) (Kaixuan Chemical Co.) to select for uracil auxotrophs before construction of the query strains. Gene deletion libraries were maintained in synthetic complete (SC), synthetic dropout (SD), enriched sporulation, or yeast-peptone-dextrose agar as previously described (89 ). The media and solutions used included agar, amino acids, peptone, yeast extract, yeast nitrogen base (Formedium), ampicillin, atorvastatin calcium, glucose, monosodium glutamate, potassium acetate (Sigma-Aldrich), Geneticin sulfate, l-canavanine sulfate, S-aminoethyl-l-cysteine hydrochloride (thyalisine) (Carbosynth), nourseothricin sulfate (Werner BioAgents), and hygromycin B (Life Technologies). All antibiotics and supplement stocks were filter sterilized with 22-μm-pore filters (Jet Biofil).
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5

Purification and Characterization of BaseMuncher Endonuclease

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All commercially available chemicals were
used without further purification. BaseMuncher endonuclease was purchased
from AbCam. Ampicillin, dithiothreitol (DTT), and isopropyl-β-D-1-thiogalactopyranoside (IPTG) were purchased from Formedium. Escherichia coli DH5α (high efficiency) and
BL21(DE3) cells and Gibson Assembly Cloning Kit were purchased from
New England Biolabs. Ethylenediaminetetraacetic acid (EDTA)-free Complete
protease inhibitor cocktail was purchased from Roche. Deuterium oxide
(D2O), sodium deuteroxide, 2-(N-morpholino)ethanesulfonic
acid (MES), N-[tris(hydroxymethyl)methyl]-3-aminopropanesulfonic
acid (TAPS), glycerol, imidazole, lysozyme, NiCl2, tris(hydroxymethyl)aminomethane
(Tris), polyethylene glycol 8000 (PEG-8000), and dUMP were purchased
from Merck. Agarose, dNTPs, 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic
acid (HEPES), NaCl, and Phusion high-fidelity polymerase were purchased
from ThermoFisher Scientific. Tobacco etch virus protease (TEVP) was
produced as previously described.11 (link)
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6

Recombinant Protein Purification Protocol

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All commercially available chemicals were used without further purification. BaseMuncher endonuclease was purchased from AbCam. Ampicillin, dithiothreitol (DTT), isopropyl β-D-1-thiogalactopyranoside (IPTG) and 2-(N-morpholino)ethanesulfonic acid-sodium dodecyl sulfate (MES-SDS) were purchased from Formedium. DH5α chemically competent Escherichia coli, DpnI were purchased from New England Biolabs (NEB). QIAprep Spin Miniprep, PCR clean-up and Plasmid Midi kits were from Qiagen. Ethylenediaminetetraacetic acid (EDTA)-free Complete protease inhibitor cocktail was from Roche. ATP, C43(DE3) and BL21(DE3) chemically competent E. coli, D2O, glycerol, histidine, imidazole, lysozyme, PRPP, potassium chloride, and tricine were purchased from Sigma-Aldrich. Agarose, dNTPSs, kanamycin, 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES), MgCl2, NaCl, PageRuler Plus Prestained protein ladder, PageRulerTM Plus Prestained protein ladder, and SYPRO orange protein gel stain were from ThermoFisher Scientific. DNA oligonucleotide primers were synthesised by Integrated DNA technologies (IDT).
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7

Antibiotic Resistance Screening Assay

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Spot titer tests were performed to determine the level of β-lactam antibiotic resistance of cells expressing the β-lactamase tripartite fusions. A single colony from fresh E. coli BL21 (DE3) cells (Stratagene) (transformed with the appropriate plasmid) was used to inoculate 100 mL sterile LB containing 10 μg/mL tetracycline (Formedium). Cultures were incubated overnight at 37 °C with shaking (200 rpm). 1 mL of overnight culture was used to inoculate 100 mL sterile LB containing 10 μg/mL tetracycline and grown at 37 °C (shaking at 200 rpm) until an OD600 of 0.6 was reached. Expression of the β-lactamase fusion construct was induced by the addition of filter-sterilized arabinose (Sigma) to a final concentration of 0.02 % (w/v). Cultures were incubated for a further 1 h, when the OD600 of the cells was adjusted to 1.0 using sterile LB, and the cultures were then serially diluted in 10-fold increments into sterile 170 mM NaCl solution. 3 μL of each dilution was then spotted onto LB agar plates, supplemented with 10 μg/mL tetracycline, 0.02 % (w/v) arabinose, and increasing concentrations of ampicillin (Formedium) (0–140 μg/mL). The plates were incubated at 37 °C for 18 h and the maximal cell dilution allowing cell growth (MCDGROWTH) was determined for each ampicillin concentration by visual inspection.
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8

Antibiotic Resistance Screening Assay

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Spot titer tests were performed to determine the level of β-lactam antibiotic resistance of cells expressing the β-lactamase tripartite fusions. A single colony from fresh E. coli BL21 (DE3) cells (Stratagene) (transformed with the appropriate plasmid) was used to inoculate 100 mL sterile LB containing 10 μg/mL tetracycline (Formedium). Cultures were incubated overnight at 37 °C with shaking (200 rpm). 1 mL of overnight culture was used to inoculate 100 mL sterile LB containing 10 μg/mL tetracycline and grown at 37 °C (shaking at 200 rpm) until an OD600 of 0.6 was reached. Expression of the β-lactamase fusion construct was induced by the addition of filter-sterilized arabinose (Sigma) to a final concentration of 0.02 % (w/v). Cultures were incubated for a further 1 h, when the OD600 of the cells was adjusted to 1.0 using sterile LB, and the cultures were then serially diluted in 10-fold increments into sterile 170 mM NaCl solution. 3 μL of each dilution was then spotted onto LB agar plates, supplemented with 10 μg/mL tetracycline, 0.02 % (w/v) arabinose, and increasing concentrations of ampicillin (Formedium) (0–140 μg/mL). The plates were incubated at 37 °C for 18 h and the maximal cell dilution allowing cell growth (MCDGROWTH) was determined for each ampicillin concentration by visual inspection.
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9

Bacterial Growth Media Preparation

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Growth media, ampicillin, 5-aminolevulenic acid and isopropyl-β-D-thiogalactopyranoside (IPTG) were purchased from Formedium, Ltd. (Hunstanton, UK). Chemicals used in the preparation of phosphate buffers were purchased from Fisher Scientific (Loughborough, UK). Voriconazole was purchased from Discovery Fine Chemicals (Dorset, UK). Palmitoleic acid (C16:1) was purchased from Tokyo Chemical Industry UK Ltd (Oxford, UK). All other fatty acids and chemicals were purchased from Sigma-Aldrich (Poole, UK), unless otherwise stated.
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10

Genome Editing of Kluyveromyces marxianus

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Kluyveromyces marxianus strain NBRC1777 from the Biological Resource Centre, NITE (NBRC; Tokyo Japan) was used as the base strain for all work in this study. For preliminary genome editing and knock-outs, strains were routinely grown in YPD broth (2% yeast extract, 1% peptone and 2% glucose; Formedium, Hunstanton, UK), or synthetic drop-out (SD) medium with the relevant supplements (0.5% ammonium sulphate, 0.19% yeast nitrogen base without amino acids or ammonia (Formedium), 2% glucose and the relevant drop-out supplement according to the manufacturer’s recommendations (Formedium)). When cells needed to be grown on solid media, the recipes above were supplemented with 2% agar (Formedium). For transformations involving CRISPR/Cas9, strains were grown on YPD agar with 200 mg L−1 hygromycin for selection. Bacterial transformations used E.coli DH5a grown in LB medium (1% NaCl, 1% peptone, 0.5% yeast extract; Formedium) or LB agar (+ 1.5% agar) with the appropriate antibiotic (100 mg L−1 ampicillin, 50 mg L−1 chloramphenicol or 50 mg L−1 kanamycin) as required. All antibiotics and reagents were purchased from Fisher Scientific (Dublin, Ireland) or Sigma-Alrdich/Merck (Haverhill, UK). All primers were obtained from Sigma-Aldrich.
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