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20 protocols using concanamycin a

1

Antibody Neutralization Assay with Bafilomycin

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Bafilomycin A1, bafilomycin B1 (Cayman Chemical Company), and concanamycin A (Santa Cruz Biotechnology) were resuspended in dimethyl sulfoxide (DMSO) and stored at −20°C until use. Cells were incubated with compounds for 1 h at 37°C prior to infection assay.
Antibody neutralization assays were conducted by preincubating cells with anti-CD164 clone N6B6 (BD Pharmingen) or mouse IgG isotype control (BD Pharmingen) for 1 h at 37°C prior to infection assay. Antibody details can be found in Table S3.
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2

Modulation of plant immunity by chemical treatments

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Seedlings were treated with 0.5 μM concanamycin A (Santa Cruz Biotechnology, 202111) or 15 μM AZD8055 (Santa Cruz Biotechnology, 364424) in liquid 1/2 MS (Duchefa biochemicals, M0221) for 10 h before analysis. Infected plants were treated at 21 DAI stage by vacuum-infiltration of 0.5 μM concanamycin A or DMSO (Sigma Aldrich, D8418) in liquid 1/2 MS and imaged after 10 h. For SA (Sigma Aldrich, 247588), 21 DAI plants were sprayed with 1 mM SA and 0.1 % EtOH and imaged 15 h later.
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3

Liposome-induced Macrophage Activation

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Lymphocytes fraction and type-1 macrophages were stimulated with different liposome formulations, used at the ratio of 1:1 (liposome:cell) for 18 h or, in the case of time course kinetics, as indicated in each figure legend. Where indicated, 10 nM RO 31-8220 (Sigma-Aldrich), a general inhibitor of protein kinase C (PKC), and 100 nM Gö 6976 (Sigma-Aldrich), an inhibitor of Ca2+-dependent PKC, were added, according to the instructions of the manufacturer, 30 min before liposome stimulation. Finally, in several experiments, 10 nM concanamycin A (Santa Cruz Biotechnology), was used to block the phagosome maturation, as described (24 (link), 25 (link)).
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4

Cellular Metabolism Inhibition Assay

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Oleyloxyethyl Phosphorylcholine and Concanamycin A were purchased from Santa Cruz Biotechnology. The Oleyloxyethyl Phosphorylcholine was initially dissolved in ethanol, and then diluted in cell culture medium before being added onto the cells. The Concanamycin A was initially dissolved in DMSO and then diluted in cell culture medium before being added onto the cells. Prior to the inhibitor treatment, HCT116 cells were cultured in medium containing 100 mM sucrose or medium alone (no treatment) for 24 h. Then, the medium was aspirated and replaced with fresh medium containing different concentrations of inhibitors, and the cells were further incubated for 6 h before being harvested for ET.
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5

Autophagy modulators in cell signaling

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BafA1 was obtained from Wako Chemicals or AdipoGen Life Sciences. Concanamycin A was obtained from Santa Cruz Biotechnology. Pepstatin A, E-64-d and leupeptin were obtained from Peptide Institute (Osaka, Japan). Wortmannin and MG-132 were obtained from Calbiochem. Ammonium chloride, novobiocin sodium salt, 3-MA, spautin-1 and 6-aminonicotinamide were obtained from Sigma. Recombinant mouse IL-1β was obtained from Cell Signaling Technology. The TLR2 ligand FSL-1 was obtained from InvivoGen. Other reagents were obtained from Wako Chemicals.
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6

Amino Acid Starvation and Stimulation

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HEK293T cells grown in RPMI were washed with PBS and starvation was performed by incubating the cells for 50 min in amino acid-free RPMI without serum. Cell were then stimulated for 10 or 20 min by the addition of RPMI containing a two time concentrated solution of amino acids. After stimulation, the final concentration of amino acids in the media was the same as in RPMI. In case of cycloheximide treatment, amino acid-starved cells were stimulated by addition of cycloheximide diluted in amino acid-free RPMI at a final concentration of 25 μg/ml. HeLa cells grown in RPMI were stimulated for 10 or 20 min by the addition of RPMI containing a two time concentrated solution of amino acids and insulin (1 uM final concentration, Sigma, I9278). Concanamycin A (sc202111 Santa Cruz) was used at 5μM and Torin 1 (4247, Tocris Bioscience,) at 250 nM. Amino acid-free RPMI medium powder (R8999-04A, US biological) was complemented with sodium bicarbonate and sodium phosphate, dissolved in water, adjusted to pH7.4 and filtered. RPMI containing a two time concentrated solution of amino acids was obtained by complementing amino acid-free RPMI medium with RPMI 1640 amino acids solution (R7131, Sigma), adjusted to pH7.4 and filtered. L-glutamine (59202C, Sigma) was added shortly before usage.
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7

Yeast Protein Expression and Purification

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Oligonucleotides were purchased from MWG Operon. Anti-FLAG-M2 resin, mouse anti-FLAG-M2 antibody, and FLAG peptide were purchased from Sigma. Amylose resin was purchased from New England Biolabs. Concanamycin A was purchased from Santa Cruz Biotechnology. Media for growth of yeast and Escherichia coli were purchased from Fisher Scientific. Yeast were maintained in yeast extract, peptone, 2% dextrose (YEPD) medium buffered to pH 5 with 50 mM potassium phosphate and 50 mM potassium succinate. Antibiotic selections in yeast were performed in YEPD containing 200 μg/ml G418 (Thermo Fisher Scientific), 100 μg/ml nourseothricin (Jena Bioscience), or 200 μg/ml hygromycin B (Invitrogen).
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8

Breast Cancer Cell Line Culture

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Three human breast cancer cell lines, MDA‐MB‐231, BT‐549, and MCF‐7 (kindly provided by Dr. K. Takenaga, Faculty of Medicine, Shimane University, Izumo, Japan), were maintained in DMEM (Sigma‐Aldrich) supplemented with 10% FCS (Invitrogen) and 20 μg/mL gentamicin (Sigma‐Aldrich) at 37°C in a humidified atmosphere of 5% CO2 in air. Doxorubicin (Sigma‐Aldrich) was diluted first in distilled water and subsequently in PBS. Anti‐tumor necrosis factor‐related apoptosis‐inducing ligand (TRAIL) Ab was purchased from BioLegend. Concanamycin A (CMA) was purchased from Santa Cruz Biotechnology. Recombinant TRAIL was purchased from PeproTech. Anti‐CD3 Ab (clone UCHT1) was purchased from Ancell.
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9

Lysosomal Function Imaging in MCF7 Cells

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A total of 45,000 MCF7 cells were seeded in an 8-well slide (Thermo Fisher Scientific #155361) and cultured for 8 hours. The cells were then treated for 16 hours with 1.25 mg/mL fluorescein (FITC)- and tetramethylrhodamine (TMR)-coupled dextran (Thermo Fisher Scientific) to allow them to enter lysosomes via endocytosis. The cells were then washed and fresh medium was added for a 1-hour chase period before being left untreated (DMSO) or treated with 10 nM concanamycin A (Santa Cruz, Dallas, TX, USA), 53 μM GalSph or 40 μM GlcSph for 1 or 5 hours. The medium was aspirated and cells washed once and fresh imaging solution was added (Thermo Fisher Scientific). The images were acquired immediately after on a LSM800 confocal microscope by acquiring FITC and TMR simultaneously using a plan-Apochromat 63×/1.40 Oil DIC M27 objective and Zen 2010 software (Carl Zeiss). Data was analyzed in ImageJ (Java 1.8.0_172 [64-bit]) and Excel (16.0.5332.1000), and illustrations made in Prism Software (8.0.2) and Adobe illustrator.
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10

Oxidative Stress Response in Cell Lines

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Negroid cervix epitheloid carcinoma (HeLa), Neuro2a (N2a) and mouse motor neuron-like cell line (NSC-34) were grown in DMEM supplemented with 10% FBS, 2 mml-glutamine, 1 mm non-essential amino acids and 1% ampicillin–streptomycin. For HeLa and N2a cells, cells were transiently transfected using FuGENE 6 (Roche Diagnostics). NSC-34 cells were transfected using Magnetofection (Oz Biosciences) as per manufacturer's instructions. One day after transfection, cells were treated with H2O2 (Sigma) or sodium arsenite (Sigma) for dose and duration indicated in text. For proteasome inhibition experiments, cells were treated with 10 µm MG-132 (Calbiochem) for 4 h before subsequent oxidative stress treatments. For inhibition of autophagy-lysosomal degradation or arginine methylation, cells were treated with 1 µm Concanamycin-A (Santa Cruz) or 100 µm AMI-1 (Sigma), respectively, for 12 h before subsequent oxidative stress treatments.
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