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52 protocols using naocl

1

Root Canal Instrumentation and Irrigation

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The root canal was prepared using MTWO files (VDW, Munich, Germany) adapted to an electric motor (VDW Silver motor; VDW) in rotary movement. The following files were used: size #10/0.04, #15/0.05, #20/0.06 and #25/0.06. The instrumentation was performed in a gentle in-and-out motion, taking the files to the working length.
During instrumentation, the canals were irrigated using 1 mL of distilled water following the use of each instrument. After the instrumentation was completed, the debris in the root canal was subjected to ultrasonic vibration. Then, the root canal opening was dried and sealed with flowing resin (Beautiful Flow Plus F00, Shofu, Japan).
The three groups were subdivided into four subgroups (n = 40) based on the irrigation solution used: subgroup A, distilled water; subgroup B, 1% NaOCl (Sigma-Aldrich Co., USA); subgroup C, 2% NaOCl (Sigma-Aldrich Co.); subgroup D, 5.25% NaOCl (Sigma-Aldrich Co.). Half of the samples in each subgroup were washed with CNI, and half were washed with PIPS (n = 20).
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2

Toxicant Effects on Stress Response Genes

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Exponential phase cells were used for toxicant treatments. Typical toxicants CuSO4 (Cat. number C1297, Sigma, MO), NaOCl (Cat. number 425044, Sigma, MO), and Aroclor 1016 (48701, Sigma, a type of PCBs) were employed in the present study. To test the doses effect of toxicants on CpHSP70 and CpHSP90 transcriptional expression, a series of concentrations of each toxicant were added in the C. polykrikoides cultures (with final concentration of CuSO4: 1, 5, and 8 mg L−1; NaClO3: 0.02, 0.1, 0.3, and 0.5 mg L−1; PCB: 0.05, 0.1, 0.2, and 0.5 mg L−1). The treated and untreated cultures were harvested for gene expression analysis at indicated time points. RNA extraction and cDNA were prepared with the same manner described previously. Gene expression and statistical analysis were followed by Guo et al. [27 (link)].
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3

Taurine Chloramine Synthesis Protocol

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Commercial chow diet (balanced diet), containing 67% carbohydrates, 10% fat, and 23% protein as the energy sources (overall calories: 3.6 kcal/g), was purchased from El Gomhorya company (Cairo, Egypt). Azathioprine (AZA): manufactured by EXCELLA Gmbh & Co. Feucht, Germany. Taurine (TAU): 2-amino ethane sulfonic acid was supplied by GALL Pharma, Austria Pharmaceutical. Taurine-chloramine (TAU-Cl), N-Monochlorotaurine, was synthesized freshly on the day of use by adding equimolar amounts of NaOCl (Sigma-Aldrich) to taurine. This was prepared by dropwise additions of 5 ml of 2 mM NaOC1 (Sigma) solution in 0.06 M phosphate buffer (pH 7.4-7.5) with vigorous stirring to 5 ml of 29 mM amine solution in the same buffer. The authenticity of TAU-Cl formation was monitored by UV absorption (200–400 nm). Its sodium salt form (molecular weight 181.57) was prepared, and its purity was checked according to a previously published method of Gottardi and Nagl (2002) [14 (link)]. Stock solution of taurine chloramine was kept at 4 ºC for a maximum period of 2 weeks before use.
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4

Oxidative Stress Resistance Assay

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Overnight cultures of different strains were sub-cultured in fresh LB broth (at the ratio of 1:100) and incubated in a shaking incubator at 37 °C. The mid log phase grown cultures were then exposed to different concentrations of paraquat, H2O2 and HOCl (sodium hypochlorite, NaOCl, Sigma) for 2 h. Aliquots were withdrawn, serially diluted and plated on HE agar plates. CFUs/ml were calculated following incubation of plates at 37 °C for overnight.
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5

Toxicant Impact on Photosynthetic Efficiency

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Exponential phase cells were used for toxicant treatments. Typical toxicants and biocides CuSO4 (cat. number C1297, Sigma, MO) and NaOCl (cat. number 425044, Sigma, MO) were employed in the present study.
The maximal photosynthesis efficiency (Fv/Fm) was assessed for different doses of toxicants. Before measuring the fluorescence for Fv/Fm, all the samples were allowed to adapt in the dark for 25 min. The fluorescence efficiency rates were measured using a Handy Plant Efficiency Analyser fluorometer (Handy PEA fluorimeter; Hansatech Instruments Ltd., King's Lynn, UK). The basic fluorescence parameters [36 (link)] are as follows:


Fo: minimal fluorescence in the dark-adapted state


Fm: maximal fluorescence in the dark-adapted state


Fv: variation in fluorescence


Fv/Fm = (FmFo/Fm): maximal quantum yield of PS II photochemistry

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6

Cultivation and Stress Exposures of Bacterial Strains

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Bacterial strains, plasmids and primers used in this study are listed in Supplementary Tables S1, S2, S3. For cloning and genetic manipulation, Escherichia coli was cultivated in LB medium. For stress experiments, S. aureus COL wild type and mutant strains were cultivated in LB, RPMI, or Belitsky minimal medium and exposed to the different compounds during the exponential growth as described previously (Loi et al., 2017 (link), 2018b (link)). NaOCl, methylglyoxal, diamide, methylhydroquinone, DTT, cumene hydroperoxide (80% w/v), H2O2 (35% w/v), and monobromobimane were purchased from Sigma Aldrich.
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7

Assay for Hemoglobin Oxidation by PIC1

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PIC1 (IALILEPICCQERAA-dPEG24) was manufactured by PolyPeptide Group (San Diego, CA) to ≥95% purity as verified by HPLC and mass spectrometry analysis. Lyophilized PIC1 was solubilized in normal saline with 0.01 M Na2HPO4 buffer to 15 mM. dPEG24 was purchased from PolyPeptide Group and dissolved in the same buffer. Pure human methemoglobin (metHb), myoglobin from equine skeletal muscle, and L-cysteine were purchased from Sigma (St. Louis, MO). 3,3′,5,5′-Tetramethylbenzidine (TMB) as a solution containing H2O2 was purchased from Thermo Fisher Scientific (Waltham, MA). 4-Aminobenzoic acid hydrazide (ABAH), O-dianisidine, and NaOCl were purchased from Sigma-Aldrich (St. Louis, MO). 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) solution was purchased from Thermo Fisher Scientific (Waltham, MA).
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8

Biofilm Susceptibility to Sodium Hypochlorite

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The biofilms were challenged with static application of 2% NaOCl (Sigma‐Aldrich, St Louis, MO, USA) in order to evaluate only the diffusion‐induced chemical effect. Volumes of 20‐ or 40 μL were gently pipetted over the biofilm samples and left undisturbed for 60‐, 120‐ or 300 s. To ensure the proper concentration of the NaOCl, a thiosulfate titration assay was performed before every experiment. After treatment application, NaOCl was neutralized by gently pipetting 4.23% sodium thiosulfate solution (Na2S2O3, Sigma‐Aldrich) over the biofilm samples.
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9

Preparation and Characterization of N-Chlorotaurine

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N-chlorotaurine (NCT) was obtained from two different sources. For dimerization assays, NCT was freshly prepared from the equimolar reaction between taurine (Sigma-Aldrich) and NaOCl (Sigma-Aldrich) in water (Klamt and Shacter, 2005 (link)). In the other assays, NCT was used as a crystalline sodium salt (MW 181.57 g/mol) (Gottardi and Nagl, 2002 (link)). Solutions of 250 mM NCT were freshly prepared in water and used for necessary dilutions in the experiments. H2O2 (30% v/v) was purchased from Sigma-Aldrich and fresh solutions of 500 mM were prepared in water before each experiment. All the other reagents were purchased from Sigma-Aldrich unless otherwise specified.
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10

Oxidative Treatment of MWCNTs Suspension

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Suspension of MWCNTs (500 µg/mL) in water was aliquoted (250 µL) into Eppendorf tubes immediately after rigorous stirring. MWCNTs were sonicated in an ultrasonic bath (Elma Ultrasonic, Singen, Germany) at 25 °C, power 90 W. Micro aliquots of freshly prepared NaOCl (Sigma-Aldrich, St. Louis, MO, USA) were added to the tubes once or twice daily over a period of 10 days. Concentrations of NaOCl were added in the samples as 1 mM (NaOCllow) and ~100 mM (NaOClhigh). During the incubation period, 1 mM NaOCl was added 11 times, and 70–100 mM NaOCl added 6 times. Control MWCNTs suspensions were supplemented with an equivalent volume of water. Treatment history is presented in Table S1 in the Supplementary Information. After the last addition, the incubation was continued for 5 days more. The samples were incubated at room temperature upon shaking during several hours a day. After the treatment with NaOCl the samples were centrifuged (10,000 g) several times and washed with an excess amount of distilled water in order to remove any possible residual NaOCl. The experiment was conducted twice for each type of MWCNTs.
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