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4 protocols using calcium oxalate

1

Autophagy Regulation via Calcium Oxalate

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Calcium oxalate (Sigma, 455997), 3-methyladenine (Sigma, M9281), rapamycin (Sigma, R0395), 4′,6-diamidino-2-phenylindole (Sigma, D8417), N-acetyl-L-cysteine (Sigma, A7250), catalase (Millipore, 219261-100KU), 2′,7′-dichlorofluorescin diacetate (Sigma, D6883), Lipofectamine 3000 (Invitrogen, L3000008), and rabbit anti-LC3B (Sigma, L7543) for western blot (WB) (1:2000), mouse anti-BECN1 (Cell Signaling Technology, 3495) for WB (1:1000). rabbit anti-LC3B (Abcam, ab51520) (1:1000) and mouse anti-BECN1 (Abcam, ab114071) were used for immunohistochemistry (IHC) (1:500). Mouse monoclonal anti-GAPDH (Proteintech, 60004-1-Ig) was used for WB (1:5000). Mouse and rabbit HRP-conjugated antibodies were obtained from Zhongshan Golden Bridge Biotechnology (ZB-2305, ZB- 2301).
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2

Surface Chemistry Analysis of Carbon Fibers

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The surface chemistry of the carbon fibers was analyzed by X-ray photoelectron spectroscopy (XPS) using a Thermo Scientific Kα spectrometer with an Al Kα monochromatic source (1486.6 eV) and a multidetection analyser under a residual pressure of 5 × 10–8 mbar. Temperature programmed desorption (TPD) experiments were carried out in a TGA-DSC instrument (TA Instruments, SDT Q600 Simultaneous) coupled to a mass spectrometer (Thermostar, Balzers, GSD 300 T3) by heating the samples (approx. 4 mg) up to 950 °C (heating rate: 20 °C min–1) in a helium atmosphere (flow rate: 100 ml min–1). The thermobalance was purged for 2 hours in a helium atmosphere prior to the heating of the sample. The calibration of the equipment for H2O, CO and CO2 evolved gases was carried out using the decomposition of a calcium oxalate (99.999%, Sigma Aldrich) standard.
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3

Characterizing Kidney Stone Composition

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The following reagents were purchased from Sigma-Aldrich (St. Louis, MO): Calcium oxalate (CaOx), calcium phosphate (CaP), cystine, sodium oxalate (NaOx), oligomycin, FCCP (carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone), antimycin A, Triton X-100, Trypan Blue solution, triethanolamine (TEA), 5-sulfosalicylic acid (5-SA), 2-metlyl-5-vinylpyridine (MVP), DTNB (Ellman's Reagent) and diethylenetriamine pentaacetate (DTPA). All other reagents or kits used are noted elsewhere.
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4

Inflammasome Activation Protocols

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Cells were stimulated with 100 ng ml−1 LPS for 3 hours (Ultra pure lipopolysaccharide from E. coli 0111:B4 strain, InvivoGen, San Diego, California, USA), followed by addition of a second stimulus for supplemental 6 hours. The second stimulus consisted either of calcium oxalate (100 μg ml−1 from a 1 mg ml−1 stock stored at 4 °C) (Sigma Aldrich, St. Louis, Montana, USA), ATP (5 mM from a prepared 100 mM stock solution stored at −20 °C) (InvivoGen, San Diego, California, USA) or monosodium urate crystals (300 μg ml−1 from 5 mg ml−1 stock solution stored at −20 °C) (InvivoGen, San Diego, California, USA). The selective P2X7 inhibitors A740003 or apyrase (both from Sigma Aldrich, St. Louis, Montana, USA) were applied 15 minutes prior to the addition of the second stimulus. A740003 was dissolved in pure DMSO and cells were treated with 100 μM A74000310 (link) or the equivalent amount of DMSO alone (0.5%). apyrase was dissolved in RPMI and cells were treated with 10U apyrase ml−1 or the corresponding amount of RPMI only. At the end of every series supernatants were collected and RIPA buffer (Sigma Aldrich, St. Louis, Montana, USA) containing complete EDTA-free protease inhibitor (Roche, Mannheim, Germany) was added to each well to gain whole cell lysates.
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