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7 protocols using ceramides

1

Diesel Particulate Extract Analyses

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Diesel particulate extract used in the present study is Standard Reference Material 1975 (SRM 1975), purchased from the National Institute of Standards and Technology (NIST) (Gaithersburg, MD, USA). Nicotinamide, NADPH, NADP, and 2, 7-dichlorofluorescin diacetate were obtained from Sigma-Aldrich (St. Louis, MO, USA). Apo, N-acetylcystine. C17-S1P, S1P (d18:1), sphingosine, ceramides (fatty acid lengths C8, C12, C16, C18, C22, C24, and C24:1), C17-ceramide (d17:1/C18:0), and C12-sphingomyeline sphingosine, ceramides (fatty acid lengths C12, C16, C18, C22, C24, and C24:1) were obtained from Avanti Polar Lipids (Alabaster, AL, USA). Organic solvents for sphingolipid extraction or LC-MS/MS analysis were purchased from Merck (Darmstadt, Germany).
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2

Quantification of Sphingolipids Using Mass Spectrometry

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Diesel particulate extract (DPE) used in the present study is Standard Reference Material 1975 (SRM 1975), purchased from the National Institute of Standards and Technology (NIST) (Gaithersburg, MD, USA). Nicotinamide, NADPH, NADP, 2,7-dichlorofluorescin diacetate, GW4869, NVP213 and acetylsalicylic acid were obtained from Sigma-Aldrich (St. Louis, MO, USA). C17-C1P, C17-S1P, S1P (d18:1), sphingosine, ceramides (fatty acid lengths C12, C16, C18, C22, C24, and C24:1), C17-ceramide (d17:1/C18:0), and C12-sphingomyeline sphingosine, ceramides (fatty acid lengths C12, C16, C18, C22, C24, and C24:1) were obtained from Avanti Polar Lipids (Alabaster, AL, USA). Organic solvents for sphingolipid extraction or LC-MS/MS analysis were purchased from Merck (Darmstadt, Germany).
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3

Lipid Extraction and Quantification

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Ceramides (acyl chain lengths of C14, C16, C18, C22, C24, and C24:1), C17‐ceramide (d17:1/C18:0), sphinganine, SP, S1P and C17‐SP, C17S1P as an internal standard were obtained from Avanti Polar Lipids (Alabaster, AL, USA). Organic solvents for SL extraction and HPLC analysis were purchased from Merck (Darmstadt, Germany). ACh, Bay11‐7082, IBTx, MG132, PGF, PKI, SN50, and tetrodotoxin were purchased from Sigma‐Aldrich (St Louis, MO, USA). The primary antibodies used in this study were anti‐Tyr‐458‐p‐p85 (Cell Signaling Technology, Boston, MA, USA), anti‐Thr‐560‐p‐PKCζ (Abcam, Cambridge, MA, USA), anti‐Thr‐183/Tyr‐185‐p‐JNK (Cell Signaling Technology), anti‐Ser‐19‐p‐MLC (Cell Signaling Technology), anti‐KCa1.1 (α‐subunit; Novus Biologicals, Littleton, CO, USA), anti‐KCa1.1 (β‐subunit; Abcam), anti‐CerS2 (Sigma‐Aldrich), anti‐CerS5 (Santa Cruz), and anti‐GAPDH (EMD Millipore, Darmstadt, Germany).
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4

Lipid Quantification Protocol

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Ceramides (C14:0, C16:0, C18:0, C18:1, C20:0, C24:0, C24:1 Ceramides), dihydroCeramides (C16:0, C18:0, C24:0, C24:1), sphinganine, sphingosine, sphingomyelins (SM; 16:0, C18:0, C18:1), and DAG (C16:0–C16:0, C18:1–C18:1, C16:0–C18:1, C18:0–C18:2, C18:0–C20:4) were obtained from Avanti Polar Lipids (Alabaster, AL, USA). Insulin was obtained from Eli Lilly and Company (Indianapolis, IN, USA).
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5

Lipid Modulation in Cell Signaling

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Tunicamycin, thapsigargin, and dimethyl sulfoxide (DMSO) were obtained from Sigma–Aldrich (St. Louis, MO, USA). Ceramides (C14:0, C16:0, C18:0, C18:1, C20:0, C24:0, and C24:1 Ceramides), dihydroCeramides (C16:0, C18:0, C24:0, and C24:1), sphinganine, sphingosine, sphingomyelins (SM 16:0, C18:0, and C18:1) and diacylglycerols (C16:0-C16:0, C18:1-C18:1, C16:0-C18:1, C18:0-C18:2, and C18:0-C20:4) were obtained from Avanti Polar Lipids (Alabaster, AL, USA). Insulin was obtained from Eli Lilly Corporate Center (Indianapolis, Indiana, USA). Activating transcription factor 4 (ATF4) and sXBP1 adenoviruses were obtained from Dr. Seung-Hoi Koo (Korea University, Seoul, Korea).
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6

Ceramide-Induced Autophagy Regulation

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Tissue culture medium was obtained from Lonza. Palmitate, fatty-acid-free BSA, bafilomycin A1 and C6-ceramide were obtained from Sigma–Aldrich. FB1, sphingosine kinase inhibitor (SKI), fumonisin B1 (FB1), D,L-threo-1-phenyl-2-palmitoylamino-3-morpholinopropan-1-ol (PPMP), and sphingosine-1-phosphate were from Biomol. Apo-ONE® Homogenous Caspase-3/7 Assay kits were from Promega. All solvents were from Merck Eurolab or Fisher Scientific. Ceramides and C17-sphingosine were from Avanti Polar Lipids. Anti-LC3 (Cell Signaling, clone 2775, dilution 1/1000 for Western-blot; clone D11, dilution 1/500 for immunofluorescence), and anti-β-actin (Sigma-Aldrich, St. Louis, MO, USA, clone 8H10D10, dilution 1/5000) antibodies were from Sigma-Aldrich. Secondary alexa fluor antibodies and ProLong™ Gold Antifade Mountant with DAPI were from Invitrogen™, Waltham, MA, USA.
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7

Comprehensive Lipid Extraction and Quantification

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Acetonitrile (ACN) was HPLC-grade and purchased from Acros Organics (Geel, Belgium). Methanol HPLC-grade (MeOH), Dichloromethane (CH2Cl2), Ammonium Formate (>99%) (AF), Boron trifluoride-methanol solution 14% (BF3-MeOH), Heptane, Ethyl acetate (EtOAc), potassium hydroxide (KOH), pentafluorobenzyl bromide (PFB-Br), and diisopropylethylamine (DIPEA), iodoacetamide, ammonium bicarbonate, trifluoroacetic acid, and trypsin was supplied by Sigma Aldrich Chemicals Co. (Saint Quentin Fallavier, France), acetic acid (AA) from Honeywell Fluka. Ultrapure water (18.2 MΩ) was obtained from a milliQ apparatus from Millipore (Guyancourt, France).
Internal synthetic standards of phospholipids (PL: PE 12:0/12:0, PC 13:0/13:0, PS 12:0/12:0), Ceramides (Cer: Cer d18:1/15:0), sphingomyelins (SM: SM d18:1/12:0), and sphingosine (So: So d17:1) and sphinganine (Sa: Sa d17:0) were purchased from Avanti Polar Lipids (Alabaster, AL, USA). Synthetic internal standard PI 16:0/17:0 was supplied by J. Clark (Cambridge). Synthetic internal standards for neutral lipid (LN: stigmasterol, cholesteryl heptadecanoate, glyceryl trinonadecanoate) and for free FAs (FFA: heptadecanoate) and total FAs (TFA: glyceryl triheptadecanoate, glyceryl trinonadecanoate) were purchased from Sigma Aldrich (St Quentin Fallavier, France).
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