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4 protocols using sodium acetate

1

Determination of Aromatic Amines

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Aromatic amines and reference substances with a purity of >97 % were purchased from Sigma-Aldrich, Steinheim, Germany and Alfa-Aesar, Karlsruhe, Germany. The reagents used for hydrolysis and derivatization, namely concentrated hydrochloric acid (37 %), hydriodic acid (55 %, unstabilized, A.C.S.), sodium nitrite (≥97 %), sodium sulphite (≥98 %), alizarinsulfonic acid (98 %), and amidosulfonic acid (99, 3 %) were all products of Sigma-Aldrich. Sodium hydroxide (99 %) was from VWR, Darmstadt, Germany, and sodium acetate (≥99 %) from Applichem, Darmstadt, Germany. Analytical grade methanol was purchased from KMF Laborchemie, Lohmar, Germany, and the ultra-filtered water used was a product of PureLab Ultra (ELGA LabWater, Celle, Germany).
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2

Doping Assay with BPA, Carbamazepine, and Ciprofloxacin

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BPA was obtained from Sigma-Aldrich Co. (St. Louis, MO, USA). A solution of BPA (97%; CAS No. 80-05-7; MW: 228.29 g/mol) was prepared by dissolving 2 mg of the compound [28 (link)] in 2 mL of HPLC-grade methanol (Merck, Darmstadt, Germany) [25 (link),37 (link)] and added to the respirometer during the homogenization phase of the doping assay. Moreover, 2 mL of methanol was added to the respirometer during the control homogenization assay to avoid side effects generated by methanol addition in the doping test.
A total of 1 mg of carbamazepine was added during the doping phase to reach a concentration of 1000 µg/L in the respirometer, and 0.1 mg of ciprofloxacin was added in the same way to maintain a concentration of 100 µg/L [38 (link)].
Sodium acetate was obtained from AppliChem GmbH (Darmstadt, Germany). A stock solution of Sodium acetate (99%; CAS No. 127-09-3; MW: 82.03 g/mol) of 500 mg/L was prepared; then, three different dilutions of 35, 70, and 100% [39 (link)] were used in the assays.
Mixture assays were carried out by adding the three above compounds at concentrations identical to those in the single-doping test.
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3

Fecal DNA Extraction and Purification

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Feces samples were collected and stored at −20 °C until processing for DNA-based 16S rRNA gene sequencing. DNA was extracted using an established phenol–chloroform-based method65 (link). In short, 500 µl of extraction buffer (200 mM Tris (Roth), 20 mM EDTA (Roth), 200 mM NaCl (Roth), pH 8.0), 200 µl of 20% SDS (AppliChem), 500 µl of phenol:chloroform:isoamyl alcohol (PCI) (24:24:1) (Roth) and 100 µl of zirconia/silica beads (0.1 mm diameter) (Roth) were added to each feces sample. Samples were lysed and homogenized twice using a Mini-BeadBeater-96 (BioSpec) for 2 min. After centrifugation and additional extraction with PCI (24:24:1), DNA was precipitated using 500 µl isopropanol (J.T.Baker) and 0.1 volume of 3 M sodium acetate (AppliChem). Samples were incubated at −20 °C overnight and centrifuged at 4 °C at maximum speed for 20 min. The resulting DNA pellet was dried, resuspended in TE buffer (AppliChem) with 100 µg/ml RNase I (Sigma-Aldrich) and column purified (BioBasic Inc.) to remove PCR inhibitors.
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4

Osteoclast Differentiation and TRAP Staining

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After verifying OC morphology, TRAP staining was performed on day 14 of OC differentiation to identify mature OCs and OC precursor cells. Therefore, the fixed cells were washed twice with PBS and incubated with TRAP buffer (pH 5; distilled water containing 6.56 g/L sodium acetate, AppliChem, Darmstadt, Germany; 23 g/L sodium tartrate dihydrate, Carl Roth, Karlsruhe, Germany) for 10 minutes. After another wash step, the cells were incubated with the TRAP staining solution (distilled water containing 0.1 g/L Naphtol aminoacid-MX phosphate, AppliChem, Darmstadt, Germany; 10 mL/L N,N-Dimethylformamide, AppliChem, Darmstadt, Germany; 0.6 g/L Fast Red Violet LB salt (Sigma-Aldrich, St. Louis, MO, USA) for 2 hours. After a final washing step with PBS, cover slides were applied.
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