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8 protocols using ac yvad cmk

1

Neuroprotective Agents in Mouse Model

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Adenosine (Akorn, Lake Forest, IL) in PBS was administered IP at a dose of 2 mg/kg/mouse. Glyburide in 2%DMSO/PBS was administered IP at a dose of 6.6 mg/kg/mouse. Ac-YVAD-CMK (Bachem, Torrance, CA) was administered ICV, as we have described (Johnson et al., 2007 (link), Chiu et al., 2012 (link)), at a dose of 50 ng/uL/mouse, 30 min prior to IP Adenosine injection.
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2

Doxycycline Attenuates IL-1β Signaling

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Doxycycline (Dox) was purchased from AppliChem (Darmstadt, Germany), recombinant human IL-1Ra from Genzyme (Cambridge, MA, USA), recombinant human IL-1β from PeproTech (London, UK), Ac-YVAD-CMK from Bachem (Torrance, CA, USA), bafilomycin A1 from Fermenteck (Jerusalem, Israel), and CA-074Me from Merck (Darmstadt, Germany). Diphenyleneiodonium (DPI) was purchased from Enzo (Plymouth Meeting, PA, USA). LPS from Escherichia coli K235 was purchased from Sigma-Aldrich (St. Lois, MO, USA). ATP was purchased from YAMASA CORPORATION (Chiba, Japan). Cycloheximide (CHX) and MSU crystals were purchased from Wako Pure Chemical Industries (Osaka, Japan). Aluminum adjuvant (Imject Alum) was purchased from Pierce (Rockford, IL, USA). Ficoll-Paque PLUS was purchased from GE Healthcare Japan (Tokyo, Japan).
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3

Inflammasome Activation Assay Protocol

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LPS, ATP, nigericin, poly dA:dT, IAA94, and Duolink In Situ PLA kits were purchased from Sigma-Aldrich (St. Louis, MO, USA). Ac-YVAD-cmk was obtained from Bachem (Torrance, CA, USA). The dye, 2′,7′-bis(2-carboxyethyl)-5,6-carboxyfluorescein acetoxymethyl ester (BCECF-AM), MitoSOX, MQAE (N-(Ethoxycarbonylmethyl)-6-Methoxyquinolinium Bromide) and DAPI were obtained from Invitrogen (Waltham, MA, USA). Flagellin (FLA-ST Ultrapure) was obtained from InvivoGen (San Diego, CA, USA). Alexa fluor 488TM Phalloidin was purchased from ThermoFisher Scientific. Abs were purchased for the detection of NLRP3 (Adipogen, San Diego, CA, USA), ASC (Adipogen), IL-1β (R&D systems, Minneapolis, MN, USA), caspase-1 (Adipogen), β-actin (Santa-Cruz Biotechnology, Dallas, TX, USA), and CLIC1 (Proteintech, Rosemont, IL, USA) Na+-K+ ATPase (Cell Signaling Technology, Danvers, MA, USA), and α-tubulin (Santa-Cruz Biotechnology).
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4

Renal Cell Carcinoma Cell Lines Protocol

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Five renal cell carcinoma cell lines (786-O, ACHN, A498, CAKI-1, and OSRC-2) and a human renal tubule epithelial cell line (HK-2) were purchased from the American Type Culture Collection (Manassas, USA). 786-O and OSRC-2 cell lines were maintained in RPMI-1640 culture medium (GIBCO), ACHN and A498 cell lines were maintained in minimal essential medium with Earle’s balanced salts, and CAKI‑1 cells were cultured in McCoy’s 5A medium. All culture media were supplemented with 10% heat-inactivated FBS (FBS; GIBCO) and 1% streptomycin–penicillin. HK-2 cell line was cultured in complete medium containing K-SFM (keratinocyte serum-free medium). All cell lines were maintained in an incubator with 5% CO2 at 37 °C. JQ1 (Catalog NO. S7110), MCC950 (Catalog NO. S7809), and BAY 11-7082 (Catalog NO. S2913), Z-DEVD-FMK (Catalog NO. S7312) were all purchased from Selleckchem. Ac-YVAD-CMK (Catalog NO. N-1330) was purchased form BaChem, and TNF-α (Catalog NO. 300-01A) was obtained from PeproTech.
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5

Macrophage Activation and Apoptosis Assay

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RPMI 1640 and the Dulbecco’s modified Eagle’s medium (DMEM) were purchased from Gibco. DCFH-DA probe was from Beyotime (Shanghai, China). Anti-mouse/human PPARγ (sc-7273, sc-7196, the dilution ratio was 1:500), anti-mouse caspase-1 (G-19, sc-1597, the dilution ratio was 1:1,000), MCAD (sc-98926 Lot # G2809, the dilution ratio was 1:1,000), EF-Tu (sc-393924, Lot # B0514, the dilution ratio was 1:1,000), SFXN1 (sc-160797, Lot # F0311, the dilution ratio was 1:1,000) and HA (sc-7392, Lot # E0614, the dilution ratio was 1:1,000) antibodies were purchased from Santa Cruz Biotechnology, Dallas, TX, USA. Anti-mouse FITC-F4/80 was purchased from eBiosience (Ref: 11-4801, the dilution ratio was 1:1,000). Anti-human caspase-1 antibody (D7F10, the dilution ratio was 1:1,000) was from Cell Signaling (Boston, USA). HRP conjugated goat anti-mouse/rabbit antibodies were from Beyotime (Haimen, China, the dilution ratio was 1:10,000). All cytokines such as M-CSF were obtained from Peprotech Systems (Minneapolis, MN). The pan-caspase inhibitor z-VAD-FMK, caspase-1 inhibitor z-WEHD-FMK and the caspase-3 inhibitor z-DEVD-FMK were obtained from R&D systems. The caspase-1 inhibitor Ac-YVAD-CMK was obtained from Bachem. NCX-4016 (NO-aspirin) were purchased from Nicox (Sophia Antipolis, France). All of other chemicals were purchased from Sigma-Aldrich unless otherwise described.
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6

Investigating Inflammasome Activation and Apoptosis

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LPS, ATP, nigericin, poly dA:dT, staurosporine, cytochalasin D, valinomycin, and apyrase were purchased from Sigma-Aldrich (St. Louis, MO, USA). JC-1 and MitoSox were obtained from Invitrogen (San Diego, CA, USA). zVAD-FMK,and ac-YVAD-CMK were purchased from Bachem (Torrance, CA, USA). Mammalian expression constructs for mouse Sarm1 (pGW1-Myc-Sarm1) was purchased from Addgene (Watertown, MA, USA). The following antibodies were used for detecting mouse caspase-1 (Adipogen, San Diego, CA, USA), NLRP3 (Adipogen), IL-1β (R&D Systems, Minneapolis, MN, USA), ASC (Santa Cruz Biotechnology, Dallas, TX, USA), β-actin (Santa Cruz Biotechnology), caspase-3 (Cell Signaling, Beverly, MA, USA), gasdermin D (Abcam, Cambridge, MA, USA), and Sarm1 (Cell Signaling).
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7

Caspase-1 and Ion Efflux Regulation in Caco-2 Cells

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Caco-2 cells cultured on 12 or 6-well plates were pre-treated for 1h with 100μM of the irreversible caspase-1 inhibitor Ac-YVAD-cmk from Bachem. Potassium efflux was blocked with either 50μM of the ion-channel blocker glibenclamide or 130mM KCl both from Sigma Aldrich. For Rac 1 and FAK inhibition, 50 or 100μM of the Rac 1 inhibitor NSC23766 (EMD Millipore) and the indicated concentrations of the FAK inhibitor PF-431396 (Sigma Aldrich) were used. Solvents used were water for NSC23766 and DMSO for the remaining inhibitors; solvents also served as the negative (vehicle) controls. After pre-treatment with the inhibitors, cells were infected as indicated for 8hr with inhibitors maintained in culture throughout the infection.
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8

Signaling Inhibitors in CVA11 Infection

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Cells were exposed for 1 h before CVA11 infection to the PI3K inhibitor LY294002 (Santa Cruz Biotechnology), the MEK inhibitor PD0325901 (Wako), the pan‐caspase inhibitor Z‐VAD‐FMK (R&D Systems), the caspase‐3 inhibitor Z‐DEVD‐FMK (Selleck, Houston, TX), the caspase‐8 inhibitor Z‐IETD‐FMK (Selleck), the caspase‐1 inhibitor Ac‐YVAD‐CMK (Bachem), the caspase‐12 inhibitor Z‐ATAD‐FMK (R&D Systems), or the RIPK1 inhibitor necrostatin‐1 (Chemscene).
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