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170 protocols using sodium chloride (nacl)

1

Comprehensive Media Preparation for Staphylococci and E. coli

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Basic medium (B medium) for Staphylococci consisted of Soy Peptone (10 g; Plato, Koblenz, Germany), Yeast Extract (5 g; Deutsche Hefewerke, Nuernberg, Germany), NaCl (5 g; Carl-Roth, Karlsruhe, Germany), Glucose (1 g; Carl Roth) and K2HPO4 (1 g; Applichem, Darmstadt, Germany). Deionized water was added to a final volume of 1 liter and pH was adjusted to 7.2.
LB medium for E. coli consisted of Peptone (10 g; Plato), Yeast Extract (5 g; Deutsche Hefewerke) and NaCl (5 g; Carl Roth). Deionized water was added to a final volume of 1 liter and pH was adjusted to 7.2. MacConkey agar was prepared according to the manufactures’ instructions (Carl Roth). Minimal media M9 for staphylococci consisted of Na2HPO4 (6 g; Carl Roth), KH2PO4 (3 g; Fisher Chemicals), NH4Cl (1 g; Merck Darmstadt, Germany) and NaCl (0.5 g; Carl Roth). Deionized water was added to a final volume of 1 L, the media was autoclaved and supplemented with thiamine (2 µg/mL; Sigma Aldrich, Munich, Germany), MgSO4 (1 mM; Carl Roth) and casamino acids (0.2%; BD Bioscience, Heidelberg, Germany). Cells were routinely grown at 37 °C either in liquid culture in baffled Erlenmeyer flasks (1:5 ratio) with shaking or on 1.5% agar plates.
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2

Sodium Iodide Sample Preparation

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Sodium iodide (>99.5%) was purchased
from Alfa Aesar. Sodium thiocyanate (99.99%), sodium tetraphenyl borate
(99.5%), and D2O (>99.9%) were obtained from Sigma-Aldrich
for the HD-SFG measurements. For the TR-SFG experiments, D2O (99.9%) was obtained by Eurisotop, and HCl (37%) was obtained from
VWR. Sodium perchlorate, anhydrous (>98%), was obtained from Thermo
Scientific. Sodium chloride (≥99.5%) and sodium sulfate (≥99%)
were purchased from Carl Roth GmbH. Sodium chloride was baked at 500
°C for 8 h before use. Other materials were used as received.
The DCl solution was prepared by mixing the HCl solution into D2O. To avoid the oxidation of iodide ions and BPh4 ions, we
dissolved the Sodium iodide salt into D2O under N2 atmosphere and in a dark room just before SFG experiments.
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3

Protein Purification and SDS-PAGE Analysis

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The purified protein sample was estimated to be 90% pure, based on SDS-PAGE gels. Tris buffer, sodium cacodylate buffer, LB broth, kanamycin, isopropyl-ß-D-thiogalacto-pyranoside (IPTG), imidazole, sodium dodecylsulphate (SDS), NaCl, acrylamide/bisacrylamide solution 29:1, (30% w/v), N,N,N′,N′-tetramethylethylenediamine (TEMED), ammonium peroxide, Rotigarose His/Ni beads, methanol, glycerol, glycine, sodium chloride, powdered milk, and acetic acid were acquired from Carl Roth (Karlsruhe, Germany). Amonium-acetate buffer, ammonium persulphate (APS), β-mercaptoethanol, Tween 20, bromphenol blue, MOPS buffer, and diphenylamine (DPA) were acquired from Sigma-Aldrich (St. Louis, MO, USA). The Arg2-2-naphthylamide (Arg-Arg–2NA) was produced by Bachem (Bubendorf, Switzerland); 2-naphthylamine (2-NA), 2-mercaptoethanol, and DNase I from bovine pancreas were produced by Merck (Darmstadt, Germany). For visualization of SDS-PAGE gels, we used PhastGel Blue R tablets (Pharmacia, Uppsala, Sweden). The EDTA was obtained from Kemika (Zagreb, Croatia), and metal (zinc, copper, cobalt, manganese) standard nitrate solutions were produced by Merck (Darmstadt, Germany).
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4

Microbial Growth Media Formulations

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The cells were grown in their respective medium to the needed OD. Basic medium (BM) for S. aureus consisted of Soy Peptone (10 g; Plato), Yeast Extract (5 g; Deutsche Hefewerke), NaCl (5 g; Carl-Roth), Glucose (1 g; Carl Roth) and K2HPO4 (1 g; Applichem). Deionized water was added to a final volume of 1 liter and pH was adjust to 7.2. LB medium for E. coli consisted of Peptone (10 g; Plato), Yeast Extract (5 g; Deutsche Hefewerke) and NaCl (5 g; Carl Roth). Deionized water was added to a final volume of 1 liter and pH was adjust to 7.2.
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5

Characterization of Sugar Beet Pectin

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Sugar beet pectin was provided by Herbstreith & Fox KG. (Neuenbürg, Germany). The main molecular characteristics are protein content: 4.1% ± 0.2%; molecular weight: 104 kDa ± 5 kDa; galacturonic acid: 66.1% ± 1.8%; degree of methylation: 52.1% ± 1.7%; degree of acetylation: 23.1% ± 0.5%; and trans-ferulic acid: 706 mg/100g ± 21 mg/100 g [18 (link)].
Medium chain triglyceride oil (MCT oil) was supplied by IOI Oleo GmbH (Hamburg, Germany). The MCT oil was composed of 60% C8 and 40% C10 chains and had a density of 0.95 kg/L at room temperature, according to supplier information. 1-Dodecanthiol (≥98%), hydrogen peroxide (30%), and sulfuric acid (98%) were purchased from Merck KGaA (Darmstadt, Germany). Sodium chloride, hydrochloric acid, sodium hydroxide, and Florisil were obtained from Carl Roth GmbH & Co. KG. (Karlsruhe, Germany). All chemicals were at least of analytical grade, and ultrapure water was used throughout the experiments.
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6

Oxidative Stress Biomarker Assay Protocol

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Uric acid, hexadecyltrimethylammonium bromide, epinephrine, O-dianisidin, and sodium azide were purchased from Sigma-Aldrich Chemical Co. (Taufkirchen, Germany). Sodium hydroxide, hydrochloric acid, bovine serum albumin, sodium chloride, and Dimethylsufoxide (DMSO) were purchased from Carl-Roth (Kalshur, Germany). Nitric acid was purchased from Qualikems. Allopurinol was obtained from Aspen-Pharma (Ireland). Ether was purchased from a local pharmacy (Dschang, Cameroon). Griess reagent, Biuret reagent, and carbonate buffer were prepared in the laboratory with ingredients from Sigma-Aldrich Chemical Co. (Taufkirchen, Germany). ThiobarbitUric acid was purchased from Shanghai Zhanyun Chemical Co. Ltd (China). Trichloroacetic acid was purchased from Guangdon Guanghua Sci-Tech Co. Ltd (China).
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7

Gardnerella Isolate Cultivation Protocol

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Gardnerella isolates of different species (52 (link)) were obtained from the Laboratory of Bacteriology, University of Ghent, Belgium. These isolates include strains purchased from culture collections and fresh isolates from BV patients obtained from the University Clinic Bruges. Gardnerella isolates were grown on chocolate (Choc) agar plates (Becton, Dickinson) under anaerobic conditions in an anaerobic chamber equipped with anaerobic atmosphere generation bags (Sigma-Aldrich) for 48 h. All isolates were cultured in New York City broth III (NYCB), consisting of 10 mM HEPES (Sigma-Aldrich), 15 g/L proteose peptone (Sigma-Aldrich), 3.8 g/L yeast extract (Thermo Fisher Scientific), 86 mM sodium chloride (Carl Roth), and 28 mM α-d-glucose (Sigma-Aldrich), supplemented with 10% horse serum (HS) (Thermo Fisher Scientific). Table S1 lists all Gardnerella and Lactobacillus isolates studied.
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8

SDS-PAGE Protein Analysis Protocol

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2-Amino-2-(hydroxymethyl)-1,3-propanediol (Tris), Tris hydrochloric acid (HCl), sodium chloride (NaCl), sodium hydroxide (NaOH), disodium ethylenediaminetetraacetate (Na2EDTA), acrylamide solution, urea, boric acid, N,N,N′,N′-tetramethylethylenediamine (TEMED), ammonium persulfate (APS), dimethyl sulfoxide (DMSO), methanol (MeOH), and normal melting point agarose were obtained from Roth (Karlsruhe, Germany). Acetylated bovine serum albumin (BSA), phenylmethanesulfonyl fluoride (PMSF), aprotinin, leupeptin, pepstatin, sodium fluoride (NaF), sodium orthovanadate (Na3VO4), dithiothreitol (DTT), APC, bicinchoninic acid (BCA) solution, formamide, blue dextran, Triton X-100, low melting point agarose, 1,4-Diazabicyclo[2.2.2]octane, potassium chloride (KCl), and potassium phosphate (KH2PO4) were obtained from Sigma/Merck (Darmstadt, Germany).
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9

Electrochemical Detection of SARS-CoV-2 Spike Protein

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All chemicals were used as received without further purification. The chemicals were purchased as follows: pyrrole 98% − from Alfa Aesar (Germany), sulfuric acid (H2SO4; 96%) from Lachner (Czech Republic), nitric acid (HNO3, 63%), sodium hydroxide (NaOH, 98%), and chloroplatinic acid (H2PtCl6, 40% Pt) from Merck (Germany), potassium phosphate (KH2PO4, 98%) from Honeywell Riedel-de Haen (Germany), sodium chloride (NaCl, 99,5%), potassium chloride (KCl, 99,5%), and disodium hydrogen phosphate (Na2HPO4, 99%) from Carl Roth (Germany). SARS-CoV-2 spike glycoproteins were purchased from UAB Baltymas (Lithuania).
The experiment was performed using potentiostat/galvanostat Metrohm-Autolab model μAutolabIII/FRA2 μ3AUT71079 controlled by NOVA 2.1.3 software (EcoChemie, The Netherlands). All measurements were done in a homemade cell. The total volume of the cell was 250 μL. Three-electrode system consisted of a working electrode (WE) – Pt disk with 1 mm diameter sealed in glass, reference electrode (RE) – Ag/AgCl, and counter electrode (CE) – Pt disk of 2 mm diameter.
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10

Heterologous Expression of Enzymes in P. pastoris

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All chemicals used were of analytical grade or highest purity available. All buffers and aqueous solutions were prepared with deionised water (>17 MΩ). 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) and yeast nitrogen base were from Amresco LLC (OH, USA). 2,6-dimethoxyphenol (DMP), acetic acid, boric acid, magnesium chloride, manganese sulphate, peptone from casein, potassium hydroxide, potassium sulphate, sodium hydrogen phosphate, sodium molybdate and sulfuric acid were from Fluka (St. Gallen, CH). Zeocin was from Invitrogen (Carlsbad, CA, USA). Sodium hydroxide was from Merck (Darmstadt, Germany). Agar, ammonium sulphate, glucose, glycerol, mEthanol, phosphoric acid (85%), potassium sulphate, potassium dihydrogen phosphate, potassium hydrogen phosphate and sodium chloride were from Roth (Karlsruhe, Germany). Agarose, biotin, calcium sulphate, citric acid, cobalt chloride, copper sulphate, EDTA, ferrous sulphate, magnesium sulphate, sodium iodide, Tris base, yeast extract and zinc chloride were from Sigma Aldrich (St. Louis, USA). Ethanol was from VWR (Radnor, USA). Escherichia coli NEB5α (New England Biolabs, Ipswich, MA, USA) was used for subcloning and Pichia pastoris × 33 (Invitrogen) for heterologous expression9 (link). A modified pGAPZ A vector (Invitrogen) under the control of the GAP promotor was used for expression in P. pastoris43 (link).
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