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24 protocols using ar c155858

1

Lentiviral Knockdown of Thermogenic Genes

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Replication-incompetent lentiviral particles (Millipore Sigma, Inc.) encoding Ucp1 shRNA (1.8 × 107 TU/ml, clone # TRCN0000437754), Slc2a1 (GluT1) shRNA (2.1 × 107 TU/ml, clone # TRCN0000305719), and Slc16a1 (Mct1) shRNA (2 × 106 TU/ml, clone# TRCN0000079545) were bilaterally injected into the BAT pad of Th-Cre::ChR2 mice using a Hamilton syringe (1 μl per site and 5 sites per pad). For pharmacological experiments, drugs (AR-C155858, 1 μM, Tocris bioscience; SR59230A, 1 μM, Millipore Sigma Inc; Sodium Oxamate, 50 mM, Chem Cruz, sc-215880) were bilaterally injected to the BAT pad at five loci (1 μl per locus).
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2

Bumetanide Transport Assay Protocol

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Bumetanide and all of the other compounds (with the exception of AR-C155858) were purchased from Sigma-Aldrich (St. Louis, MO). AR-C155858 was purchased from Tocris Bioscience (Bristol, U.K.). [3H]Bumetanide (15–30 Ci/mmol) was purchased from American Radiolabeled Chemicals (St. Louis, MO). GIBCO Leibovitz’s L-15 medium with glutamine (Cat. No. 41300-039) and all Western blotting materials were supplied by Thermo Fisher Scientific (Rockford, IL). The pCR2.1-TOPO, TOPO TA cloning kit, TRIzol Reagent, and mMESSAGE mMACHINE T7 transcription kit were purchased from Thermo Fisher Scientific (Rockford, IL). pGH19 vector was kindly provided by Dr. Walter F. Boron (Case Western Reserve University, Department of Physiology and Biophysics, Cleveland, Ohio).24 (link) The FlashGel System was purchased from Lonza (Portsmouth, NH). All enzymes were purchased from New England Biotechnology (Ipswich, MA). The gel extraction and PCR purification kits were purchased from Qiagen (Valencia, CA). DNA purity and concentration were verified using a NanoDrop 1000 instrument (Thermo Fisher Scientific, Rockford, IL). A ZOE fluorescent cell imager made by Bio-Rad (Hercules, CA) was used for fluorescent microscopy. The mouse anti-Egfp antibody (JL-8, Cat. No. 632381) was purchased from Clontech (Mountain View, CA).
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3

Stable Isotope Tracing of Metabolic Pathways

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Antimycin A, Ascorbic acid, D-glucose, DL-malic acid, methylpyruvate, N, N, N′, N′-tetramethyl-p-phenylenediamine (TMPD), potassium dichloroacetate, pyruvic acid, rotenone, sodium L-lactate, succinic acid and UK-5099 were from Sigma-Aldrich. [U-13C]glucose tracer was from Cambridge Isotope Laboratories. 3H2O was from American Radiolabeled Chemicals and 14C tracers were from Perkin Elmer. AR-C155858 was purchased from Tocris Bioscience. 7ACC2 (7-aminocarboxycoumarin 2, see structure in Supplementary Note 1) and CPI-613 were synthesized and purified in our lab.
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4

Pharmacological Modulators of Acid-Sensing Receptors

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MCT-1/2 inhibitor AR-C155858, TDAG-8 agonist BTB09089 and OGR-1 agonist ISX-9 were purchased from Tocris Bioscience and OGR-1 allosteric agonist Ogerin was purchased from Sigma. Where drugs were not dissolvable in cell culture media, DMSO was used at final concentration <1% and appropriate vehicle controls included.
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5

Rat Cortical and Hippocampal Neuron Culture

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Cultures of cerebral cortical or hippocampal neurons were prepared from Sprague-Dawley rat embryos (male and female) at 18 days of gestation using methods similar to those described previously (Glazner et al., 2000 (link)). Dissociated cells were seeded into polyethyleneimine-coated plastic dishes or glass coverslips in MEM medium supplemented with 10% fetal bovine serum at a density of 80,000 cells/ cm2. After cells attached to the substrate, the medium was replaced with Neurobasal medium containing 5% B27 minus antioxidants, 1% GlutaMAX™ and 1% Anti-Anti (Gibco). Experiments were initiated on culture day 10. 3-D-hydroxybutyrate sodium salt and N-acetyl cysteine, cyclosporin A and sodium butyrate were obtained from Sigma. AR-C155858 was obtained from Tocris. SN-50 was purchased from Santa Cruz.
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6

Modulation of C. parvum Interaction with Bovine PMN

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Bovine PMN were pre-treated with the mentioned inhibitors for 30 min and then co-cultured with C. parvum sporozoites (1:3 PMN/sporozoite ratio, 3 h, 37 °C) with the purpose of blocking the ATP purinergic receptor P2X1, MCT1, MCT2, and glycolysis under hyperoxia 21% O2 = oxygen conditions widely used in most C. parvum-related studies) and physioxia (5% O2) conditions, simulating physiological oxygen pressure of small intestine in vivo as follows [4 (link),12 (link),54 (link),59 (link)]: AR-C 155858 (1 μM, MCT1- and MCT2-inhibitors, Tocris Bioscience, Wiesbaden, Germany), AR-C 141990 (1 μM, MCT1 inhibitor, Tocris Bioscience, Wiesbaden, Germany), NF449 (100 μM, purinergic receptor P2X1 antagonist, Tocris Bioscience, Wiesbaden, Germany), oligomycin A (5 μM, inhibitor of mitochondrial respiration, Sigma-Aldrich, Darmstadt, Germany) and 2-DG (2 mM; antagonist of glycolysis, Sigma-Aldrich, Darmstadt, Germany), were used in this study [37 (link),44 (link),60 (link),61 (link)].
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7

Bioenergetics Analysis of Liver Cell Lines

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Analysis of bioenergetics parameters was performed in HepG2 and Hep3B cells using the XF24 analyzer from Seahorse Bioscience (Billerica). OCR was measured using a Seahorse XF Cell Mito Stress Test kit (Seahorse Bioscience) in real time under culture conditions containing acetate (500 μM final concentration; Sigma-Aldrich) with or without AR-C155858 (100 μM final concentration; Tocris Bioscience) following the manufacturer’s protocol (1 μg/ml oligomycin, 0.5 μM final concentration of FCCP, 1 μM final concentration of antimycin A and rotenone).
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8

Preparation of DMEM with additives

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Penicillin G / streptomycin sulfate solution and powder to prepare Dulbecco’s modified Eagles medium (DMEM with 25 mM glucose; catalog number: 52100-021) were obtained from Thermo Fisher Scientific (Schwerte, Germany; RRID:SCR_008452). Glucose-free DMEM powder (catalog number: D5030), fetal calf serum (FCS), antimycin A, BAM15 and UK5099 were purchased from Sigma-Aldrich (Darmstadt, Germany; RRID:SCR_008988). AR-C155858 was purchased at Tocris Bioscience (Bristol, UK; RRID:SCR_003689). All enzymes used for the assays to determine pyruvate, lactate and glucose were purchased from Roche Diagnostics (Mannheim, Germany; RRID:SCR_001326). Other chemicals of the highest purity available were obtained from Merck (Darmstadt, Germany; RRID:SCR_001287), Sigma-Aldrich (Steinheim, Germany; RRID:SCR_008988), AppliChem (Darmstadt, Germany; RRID:SCR_005814) or Carl Roth (Karlsruhe, Germany; RRID:SCR_005711). Sterile cell culture materials and unsterile 96-well plates were from Sarstedt (Nümbrecht, Germany).
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9

Metabolic Regulation in Cancer Cells

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Unless specified, all reagents were obtained from Sigma and all the antibodies were from Santa Cruz Biotechnology, except for anti-HIF-1α (Becton Dickinson), anti-PKM2 and anti-Src-Tyr416 (Cell Signaling Technology) and anti phospho-Tyr (clone 4G10) (Millipore). HRP-conjugated streptavidin was from Pierce. HIF-1-siRNA and DEC1-siRNA were from Santa Cruz Biotechnology. N-(biotinoyl)-N-(iodoacetyl)ethylenediamine (BIAM) and 2′-7′-dichlorofluoresceindiacetate (H2-DCF-DA) were from Molecular Probe. [U-14C] lactate and [U-14C] glucose were from Perkin Elmer. All the kits used to perform miRNA extraction and quantitative reverse transcriptase PCR were from Qiagen. Lipofectamine 2000 was from Invitrogen. Metformin was obtained by Sigma. The chemical synthesis of the PKM2 activator DASA-58 was kindly performed by Dr. Richichi of the Department of Chemistry (University of Florence). The mitochondrial antioxidant MitoTEMPO was from Santa Cruz Biotechnology. The MCT1 inhibitor, AR-C155858, was from Tocris Bioscience.
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10

Fluorescent Dye Characterization Protocol

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The inhibitor AR-C155858, tetrodotoxin citrate (TTX) and sulforhodamine 101 (SR101) were acquired from Tocris, Wiesbaden-Germany, Abcam Biochemicals, Cambridge, UK, and Baseclick, Tutzing, Germany, respectively. Fluo-4-AM, SNARF-5-AM, and pluronic acid were obtained from Invitrogen. The fluorescent dyes, pluronic acid, AR-C155858 and SR101 were dissolved in DMSO.
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