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27 protocols using kh2po4

1

Purification and Characterization of Bacterial Enzymes

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Deuterium oxide (99.96%) was from Euriso-Top (Saint-Aubin Cedex, France). U, UMP, uracil, K2HPO4, KH2PO4, NaHCO3, MnCl2, HEPES, NaCl, IPTG, imidazole, tetra-n-butylammonium bromide, glycerol, and ATP were from Carl Roth (Karlsruhe, Germany). Glc1,6diP and SYPRO orange, was from Sigma Aldrich (St. Louis, USA). Rib5P was purchased from Biosynth (Staad, Switzerland). Expression vectors (pet15b or pet28a+) containing the genes for YeiN, DeoB, UP, and Yjjg were from Genescript (Leiden, The Netherlands).
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2

Analytical Quantification of Metabolites

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All reagents and chemicals were of analytical grade and applied without further purification. HPLC-grade deionized water was used during all experiments.
α-KG, 5-HMF, NASeLM, NALM, and glucose were supplied by CYL-Pharma (Lassnitzhöhe, Austria). NaCl, KCl, KH2PO4, MgSO4, CaCl2, NaHCO3, and dextrose were obtained from Roth (Karlsruhe, Germany). Acetonitrile, ammonium acetate, 1-butanol, ethanol, HPLC-grade water, hydrogen peroxide, and HCl were obtained from Merck (Darmstadt, Germany). Albumin from human serum, angiotensin 1-7 acetate salt hydrate, butylated hydroxytoluene (BHT), 2,4-dinitrophenylhydrazine (DNPH), ethyl acetate, guanidine-hydrochloride, malondialdehyde tetra-butyl-ammonium salt (MDA), 2-thiobarbituric acid (TBA), trichloroacetic acid (TCA), and tris(hydroxymethyl)aminomethane (Tris) were obtained from Sigma-Aldrich (Vienna, Austria).
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3

Nitrate Respiration Assay for Pseudomonas

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Dissimilatory nitrate reduction was checked by a physiological assay, monitoring growth of our Pseudomonas strains in presence or absence of NO32–. Therefore, a minimal medium was prepared containing 4.75 gl–1 K2HPO4 (Merck, Darmstadt, Germany), 4.55 gl–1 KH2PO4, 2 gl–1 yeast extract (Roth, Karlsruhe, Germany) and 20 mM glucose monohydrate. Medium was eighter supplemented with 20 mM NaNO3 or no NaNO3 and pH was adjusted to 6.69. After autoclaving, media was aliquoted into microplates and kept in an anaerobic chamber for 48 h to become anoxic prior to inoculation. Plates were inoculated with an OD600 = 0.1 of a freshly prepared preculture as described above. Growth was measured using a Fluostar Omega microplate reader (BMG LABTECH GmbH, Ortenberg, Germany) after 3 days of incubation within the anaerobic chamber at 25°C. P. aeruginosa DSM 1117 was used as a positive control for nitrate respiration. Significant growth differences were defined based on a two-side open t-test (p < 0.01) between samples containing NaNO3 and no NaNO3.
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4

Immuno-Affinity Assay Development for Antibiotic Detection

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Dimethyl sulfoxide (DMSO), 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride, EZ-Link™ NHS-PEG4 Biotinylation Kit, and NHS were acquired from Merck KGaA, Darmstadt, Germany. Albumin Fraction V (biotin-free), KCl, KH2PO4, NaCl, Na2(CO3), NaHCO3, Na2HPO4 × 12 H2O and Tween-20 were purchased from Carl Roth, Karlsruhe, Germany. Immuno-filtration columns (ABICAP HP columns) were purchased from Senova Gesellschaft für Biowissenschaft und Technik mbH, Weimar, Germany. Anti-Penicillin G monoclonal antibody was kindly provided by the Milchprüfring Bayern e.V. (MPR), Wolnzach, Germany. Anti-kanamycin monoclonal antibody (article number CSB-MA000511I0m) was purchased from Cusabio, Wuhan, China. Detection antibody goat anti-mouse IgG coupled to HRPO (article number 115-035-008) was purchased from Jackson ImmunoResearch Europe Ltd., Ely, UK. Penicillin G and kanamycin A were acquired from Duchefa Biochemie, Haarlem, Netherlands. Magnetic particles with streptavidin-functionalized shell and a hydrodynamic diameter of 70 nm [synomag®-D, article number 104-19-701] were purchased from micromod Partikeltechnologie GmbH, Rostock, Germany.
Coupling buffer, phosphate buffered saline (PBS), PBS-Tween (PBS-T) as well as blocking solutions for ELISA and magnetic immunodetection were prepared as described in [23 (link)].
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5

Analytical Reagent Quality Control

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Methanol (MeOH), acetonitrile (ACN), and toluene were obtained in gradient grade from Fisher Scientific (Schwerte, Germany). NaCl, formic acid, hexane, and Na2HCO3 were in pro analysi (p.a.) quality from Merck KGaA (Darmstadt, Germany). Potato dextrose agar (PDA), potato dextrose broth, and KH2PO4 were from Carl Roth (Karlsruhe, Germany), Xylene in p.a. quality was obtained from Honeywell (Seelze, Germany), NaHCO3 in p.a. quality was obtained from Grüssing (Filsum, Germany), and KCl in p.a. quality was obtained from VWR (Langenfeld, Germany). Purified water of ASTM type 1 quality was prepared with a Purelab Flex 2 system from Veolia Water Technologies (Celle, Germany).
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6

Reagents for Cellular Assays

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Diethylenetriaminepentaacetic acid (DTPA), dimethyl sulfoxide (DMSO), glucose, penicillin-streptomycin (PenStrep), phorbol-12-myristate-13-acetate (PMA) were obtained from Merck (Germany). Brain heart infusion (BHI, brain heart broth) medium, formaldehyde, hemin, superoxide dismutase (SOD) were purchased from Sigma (USA). Dihydroethidium (DHE) was from Fluka (Switzerland). Desferal (DFO) was from Novartis Pharma (Germany) and 1-hydroxy-3-methoxycarbonyl-2,2,5,5-tetramethylpyrrolidine-HCl (CMH) was from Noxygen (Germany). KCl, K2HPO4, KH2PO4 and NaCl were from Roth (Germany). Dulbecco’s Modified Eagle Medium (DMEM) was obtained from Gibco and fetal calf serum (FCS, low LPS) from Bio&Sell (Germany). Yeast extract powder was supplied by Amresco (USA). Nourseothricin (NTC) was bought from Jena Bioscience (Germany).
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7

Cultivation of Neisseria gonorrhoeae and E. coli

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Neisseria gonorrhoeae was grown overnight at 37°C and 5% CO2 on agar plates containing gonococcal base (GC) agar [10 g/l Bacto agar (BD Biosciences, Bedford, MA, United States), 5 g/l NaCl (Roth, Darmstadt, Germany), 4 g/l K2HPO4 (Roth), 1 g/l KH2PO4 (Roth), 15 g/l Proteose Peptone No. 3 (BD), 0.5 g/l soluble starch (Sigma-Aldrich, St. Louis, MO, United States)] supplemented with IsoVitaleX (IVX): 1 g/l D-Glucose (Roth), 0.1 g/l L-glutamine (Roth), 0.289 g/l L-cysteine-HCL × H20 (Roth), 1 mg/l thiamine pyrophosphate (Sigma-Aldrich), 0.2 mg/l Fe(NO3)3 (Sigma-Aldrich), 0.03 mg/l thiamine HCl (Roth), 0.13 mg/l 4-aminobenzoic acid (Sigma-Aldrich), 2.5 mg/l β-nicotinamide adenine dinucleotide (Roth) and 0.1 mg/l vitamin B12 (Sigma-Aldrich). GC medium is identical to the base agar composition but lacks agar and starch.
E. coli was grown in LB (Lysogeny Broth, Roth) medium or on LB agar plates (15 g/l Bacto agar (BD Biosciences, Bedford, MA, United States) at 37°C.
For N. gonorrhoeae antibiotics were used at the following concentrations: 2.5–5 μg/ml erythromycin (Thermo-Fisher), 100 μg/ml streptomycin (Sigma-Aldrich), 10 μg/ml chloramphenicol (Sigma-Aldrich). For E. coli antibiotics were used at the following concentrations: 50 μg/mL kanamycin (Roth).
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8

T Cell Activation Assay Protocol

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Culture medium (CM) was prepared using RPMI 1640 supplemented with 100 U/mL of penicillin, 100 μg/mg streptomycin (both from Sigma, Steinheim, Germany), and 2 mM L-glutamine (Biochrom, Berlin, Germany). Concanavalin A (ConA) (Sigma) was diluted in CM to a concentration of 600 μg/mL and stored at −70°C. Antibodies were purchased from Becton Dickinson (BD, Heidelberg, Germany). Phosphate buffered saline (PBS) was made by dissolving 7.013 g NaCl, 0.2 g KCl, 1.513 g Na2HPO4, and 0.2 g KH2PO4 (all purchased from Roth) in 1 liter distilled water and by adjusting the pH to 7.4. Red blood cell (RBC) lysing solution was purchased from Becton Dickinson and diluted 1 : 10 in distilled water before use. Washing buffer was obtained from BD Biosciences (San Diego, USA). Formaldehyde solution and absolute methanol was purchased from Merck (Darmstadt, Germany).
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9

Gonococcal Base Agar Composition

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Gonococcal base agar was made from 10 g/l dehydrated agar (BD Biosciences, Bedford, MA), 5 g/l NaCl (Roth, Darmstadt, Germany), 4 g/l K2HPO4 (Roth), 1 g/l KH2PO4 (Roth), 15 g/l Proteose Peptone No. 3 (BD Biosciences), 0.5 g/l soluble starch (Sigma-Aldrich, St. Louis, MO), and supplemented with 1% IsoVitaleX (IVX): 1 g/l D-glucose (Roth), 0.1 g/l L-glutamine (Roth), 0.289 g/l L-cysteine-HCL x H2O (Roth), 1 mg/l thiamine pyrophosphate (Sigma-Aldrich), 0.2 mg/l Fe(NO3)3 (Sigma-Aldrich), 0.03 mg/l thiamine HCl (Roth), 0.13 mg/l 4-aminobenzoic acid (Sigma-Aldrich), 2.5 mg/l β-nicotinamide adenine dinucleotide (Roth), and 0.1 mg/l vitamin B12 (Sigma-Aldrich). GC medium is identical to the base agar composition but lacks agar and starch.
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10

Evaluating Cellular Responses to ZnO Nanoparticles

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Alpha-amylase, CaCl2 ∙ 2H2O, 4′,6′-diamidino-2-phenylindole (DAPI), 2′,7′-dichlorofluorescin-diacetate (DCFH-DA), MgCl2 ∙ 6H2O, mucin, ox bile, pancreatin, paraformaldehyde, pepsin, trypsin and ZnO nanopowder (#677450 and #544906) were purchased from Sigma-Aldrich Chemie GmbH, Taufkirchen, Germany. Dulbecco’s Modified Eagle Medium (DMEM), foetal bovine serum (FBS), non-essential amino acids, penicillin/streptomycin, and trypsin/EDTA were obtained from PAN-Biotech GmbH, Aidenbach, Germany. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), dimethyl sulfoxide, fluorescein isothiocyanate (FITC)-dextran, hydrogen peroxide (30%), nitric acid (Suprapur), and triton X-100 were acquired from Merck KGaA, Darmstadt, Germany. 2-((3-Chlorophenyl) hydrazinylidene) propanedinitrile (CCCP) and ZnCl2 were procured from Thermo Fisher Scientific Inc., Waltham, MA, USA. Carbamide, ethylene glycol tetraacetic acid (EGTA), KCl, KH2PO4, NaCl, NaHCO3, and Na2HPO4 ∙ 2H2O were purchased from Carl Roth GmbH & Co. KG, Karlsruhe, Germany. Cacodylic acid and glutaraldehyde were bought from Serva Electrophoresis GmbH, Heidelberg, Germany. 5,5′,6,6′-Tetrachloro-1,1′,3,3′-tetraethylbenzimidazolylcarbocyanine iodide (JC-1) was obtained from Enzo Life Sciences GmbH, Lörrach, Germany. Phalloidin-iFlour 488 reagent was acquired from Abcam plc., Cambridge, UK.
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