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30 protocols using bapta am

1

Prostate Cancer Signaling Pathway Analysis

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Antibodies recognizing YAP1, phospho-YAP1 (Ser-127 p-YAP1)(Cell Signaling Technology, Beverly, MA, USA), matrix metalloproteinase2 (MMP2), slug, twist, vimentin, AR, NK3 Homeobox 1 (NKX3.1), Myc, connective tissue growth factor (CTGF, Santa Cruz Biotechnology, Santa Cruz, CA, USA), E-cadherin, N-cadherin (BD Biosciences, San Jose, CA, USA), phospho-AR (ser-81 p-AR)(Milipore, Billerica, MA, USA), and ß-actin, GAPDH (Sigma-Aldrich, St. Louis, MO, USA) were used for immunoblottings. Horseradish peroxidase (HRP)-conjugated donkey anti-rabbit and anti-mouse IgGs were obtained from Cell Signaling Technology. GV1001 peptide was supplied by GemVax & KAEL (Seongnam, Kyeonggi-do, South Korea). Leuprolide acetate (LA) and cetrorelix acetate (CA) were synthesized by AnyGen (Gwangju, South Korea). KT5720 (Cat# K3761), forskolin (Cat# F6886), dihydrotestosterone (Cat# A8380), flutamide (Cat# F9397), pertussis toxin (Cat# P2980) and SQ22536 (Cat# S153) were purchased from Sigma-Aldrich (St. Louis, MO, USA). KH7 (Cat# 13243, Cayman Chemical, Ann Arbor, MI, USA) and 1,2-Bis(2-aminophenoxy) ethane-N,N,N’,N’-tetraacetic acid tetrakis(acetoxymethyl ester, BAPTA/AM)(Biovision, Mountain View, CA, USA) were used as signaling inhibitors for Gα-proteins.
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2

Optimization of A. alternata Extracts Dosage

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A. alternata extracts were purchased from Greer labs (catalog no. XPM1C3A25, Lenoir, NC) and dissolved in serum‐free (SF) DMEM. Treatment of the same fibroblasts with a different lot number of A. alternata extracts resulted in different cell viabilities. Therefore, the optimal doses of A. alternata extracts from each lot were determined based on cell viability (i.e., when control and IPF fibroblasts were treated with 100 μg/mL of lot no. 169626 and 400 μg/mL of lot no. 276920, a similar effect on their cell viability was observed). The soluble form of recombinant FasL (catalog No. ALX‐522‐020‐C005) was purchased from Enzo Life Sciences (Farmingdale, NY). N‐acetyl‐L‐cysteine (NAC), Thapsigargin, Resveratrol, tert‐Butyl hydroperoxide (tBHP), and sodium pyruvate were purchased from Sigma–Aldrich. BAPTA‐AM and Caspase 3/7 inhibitor I was obtained from Biovision Inc. (Milpitas, CA) and EMD Millipore (Billerica, MA), respectively. Hank's balanced salt solution (HBSS) and acetoxymethyl ester form of Fura‐2‐AM were purchased from ThermoFisher Scientific (Pittsburgh, PA) and Invitrogen/Life Technologies (Carlsbad, CA), respectively.
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3

Modulation of PIEZO1 in Red Blood Cells

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All treatments, except amitriptyline, were performed on diluted washed RBCs. To activate PIEZO1, RBCs were incubated with 0.5 µM Yoda1 (Biotechne, Minneapolis, MD, USA) for 20 s at 22 °C. To inhibit voltage-dependent Ca2+ channels, RBCs were incubated with 1 µM ω-agatoxin (Alomone Labs, Jerusalem, Israel) for 20 min at 22 °C. To modulate the intracellular Ca2+, RBCs were preincubated either in a Ca2+-free medium containing 1 mM EGTA (Sigma-Aldrich) for 10 min at 22 °C or with 20–40 µM BAPTA-AM (Abcam) for 60–90 min at 37 °C. For cholesterol depletion, RBCs were preincubated with 0.9 mM methyl-β-cyclodextrin (mβCD; Sigma-Aldrich) for 30 min at 37 °C. To decrease oxidative stress, RBCs were preincubated with 1 mM ascorbic acid for 1 h at 37 °C. Lysophosphatidylserine (lysoPS; Sigma) was inserted into membranes at 3 µM in 0.01% (w/v) defatted bovine serum albumin (BSA; Sigma)-containing medium for 5 or 40 min at 37 °C and was maintained during the whole experiment. For plasma acid sphingomyelinase (aSMase) inhibition, whole blood was incubated with 5 µM amitriptyline (Sigma-Aldrich, Saint-Louis, MO, USA) for 1 h at 37 °C, then diluted and washed as above.
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4

Measuring Calcium-Dependent Signaling

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Calcium concentrations were determined from the ratio of fura-2 fluorescence intensity at 340-nm excitation and 380-nm excitation. The 340-nm fluorescence of fura-2 increases and the 380-nm fluorescence decreases with increasing [Ca2+]i. For [Ca2+]i measurements HGECs and podocytes (20,000 cells/well) were plated on black 96-well plates with a clear bottom in complete medium. After 1 day the cells were serum-starved for 2-h. In the last 45 min of calcium-free serum-starvation, FURA-2AM (5 μM; Invitrogen) was added to the cells, then rinsed with Hanks Balanced Salt Solution (HBSS, Gibco BRL). FURA-2AM-loaded cells were sequentially excited at 340 and 380 nm by spectrophotometer microplate reader (Synergy MX; BioTek, Winooski, VT). Cinacalcet-induced [Ca2+]i were quantified by measurement of area under curve (AUC) and peak amplitude for the rise in relative [Ca2+]i. To evaluate cinacalcet-induced [Ca2+]i effects on CaMKKβ and LKB1, we used [Ca2+]i chelator BAPTA-AM (25 μM; Abcam).
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5

Modulating Red Blood Cell Properties

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All treatments were performed on washed isolated RBCs, except amitriptyline (AMI) which was applied on whole blood at 5 μM for 60 min at 37°C to inhibit the aSMase. To induce acute ATP depletion, RBCs were preincubated for 2 h in glucose-free DMEM (Life Technologies). ATP repletion was performed after RBC washing and resuspension in 4.5 g/l glucose-containing DMEM. To modulate the intracellular calcium content, RBCs were preincubated with 20 μM BAPTA-AM (Abcam): (i) for 15 min at 37°C, followed by a 60 min-reincubation at 37°C in the presence of Fluo-4 AM (see below), to measure its effect on the intracellular calcium content; or (ii) for 60 min at 37°C to determine EV abundance and PS exposure. To deplete membrane cholesterol, RBCs were preincubated with 0.9 mM methyl-β-cyclodextrin (mβCD; Sigma-Aldrich) for 30 min at 37°C. Cholesterol repletion was achieved with 7.5 and 15 μg/ml water-soluble cholesterol (Sigma-Aldrich) for 60 min at 37°C.
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6

Immunostaining of Drosophila Larval NMJs

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Third-instar larvae were dissected in modified HL3 saline and stained either with or without 0.03% Triton in PBS as described68 (link). The following primary antibodies were used: mouse anti-GluRIIΑ (8B4D2; 1:50; Developmental Studies Hybridoma Bank (DSHB)); rabbit anti-GluRIIIB70 (link) (1:1000); rabbit anti-GluRIIC71 (link) (1:2000); guinea pig anti-GluRIID70 (link) (1:1000); rabbit anti-parvalbumin (Pa1-933; 1:1000; Thermo Fisher); mouse anti-DLG (4F3; 1:100; DSHB). The following primary antibodies were generated in this study, where the following peptides were injected into animals by Cocalico Biologicals (Stevens, PA, U.S.A): affinity purified rabbit anti-pCaMKII using the peptide C-VHRQET(p)VDCLKK (1:2000); guinea pig anti-CaMKII using the peptide C-VHRQET(p)VDCLKK (1:1000); guinea pig anti-GluRIIΑtail using the peptide C-SGSRRSSKEKSRSKTVS (1:2000). Alexa Fluor-647 conjugated goat anti-HRP (1:200; Jackson ImmunoResearch) and Donkey anti-mouse, -guinea pig, and -rabbit conjugated Alexa Fluor 488, Cy3, and DyLight 405 secondary antibodies (Jackson ImmunoResearch) were used at 1:400. For the BAPTA-AM treatment, dissected larvae were incubated in HL-3 saline with 0.1 or 0.3 mM BAPTA-AM (#120503; Abcam) for 30 min before fixation and then stained as described above. For the control conditions, dissected larvae were incubated in HL-3 saline in 0 of 1.8 mM Ca2+.
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7

AMPK and Calcium Signaling Modulators

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cis-5,8,11,14,17-Eicosapentaenoic acid (EPA), metformin, compound C (AMPK inhibitor), insulin, STO-609 (CaMKK inhibitor), SB203580 (p38 MAPK inhibitor), fluo-3, AM and a monoclonal anti-β-actin antibody were purchased from Sigma Chemical Company (St. Louis, MO, USA). BAPTA-AM (intracellular calcium chelator), monoclonal antibody against ACC and polyclonal antibodies against GLUT4 were purchased from Abcam (Cambridge, MA, USA). Monoclonal antibodies against phosphorylated AMPKα, phosphorylated p38 MAPK, p38 MAPK, phosphorylated AS160, AS160, and the polyclonal antibody against AMPKα were obtained from Cell Signaling Technology (Danvers, MA, USA). The polyclonal antibody against phosphorylated ACC was provided by Merck (Rahway, NJ, USA). Fetal bovine serum (FBS) and penicillin-streptomycin were acquired from Thermo Fisher Scientific (Foster City, CA, USA). The monoclonal antibody against c-Myc was acquired from Santa Cruz Biotechnology (Dallas, TX, USA).
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8

Neutrophil Stimulation and Pathway Modulation

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Neutrophils were seeded on glass cover slips coated with 0.001% poly‐L‐lysine (Sigma‐Aldrich) with a concentration of 1 × 105 cells per well if not stated otherwise. PMNs were stimulated with 4 μM ionomycin (free acid, Sigma‐Aldrich), 100 nM phorbol 12‐myristate 13‐acetate (PMA, Sigma‐Aldrich), 15 μM Ece1 peptides including candidalysin (if not otherwise stated) or infected with C. albicans yeast (MOI 2) for a defined time period, following fixed using 2% paraformaldehyde (PFA) and stored at 4°C. In the infection experiments, the fungus was added to 1 × 104 PMNs 1 h after the cells were seeded.
For the pathway studies, neutrophils were incubated for 30 min before stimulation with 10 μM BB‐Cl‐amidine (PADi, Cayman Chemicals), 15 μM diphenyleneiodium (DPI, Sigma‐Aldrich), 15 μM 4‐hydroxy‐TEMPO (TEMPOL, Sigma‐Aldrich), 10/20 μM BAPTA‐AM (Abcam), 15 μM SYK inhibitors R406 (InvivoGen) and 12.5 μM piceatannol (InvivoGen), 15 μM PI3K blocker wortmannin (InvivoGen), 2.5 μM AKT inhibitor XI (InvivoGen) or NLRP3 blockage using compound 1 μM MCC950 (InvivoGen).
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9

Inhibitory Effect of Compounds on Infection

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We tested the inhibitory effect of the following compounds at the doses indicated except as otherwise stated, Tetrandrine (TETR 10 μM), Verapamil (VER 100 μM), Curcumin (CUR 75 μM), Bafilomycin (BAF 200 nM), Apilimod (APL 25 μM), Tamoxifen citrate (TMX 10 μM), Raloxifene hydrochloride (RLX 10 μM), Fulvestrant (ICI 182,780; FUL 100 μM) and β-Estradiol (EST 100 μM) were purchased from Sigma-Aldrich. Bapta-AM (BAP 10 μM) and YM201636 (YM 1 μM) and also controls Hydroxycloroquine (HCL 10 μM) endosomal acidification inhibitor and Teicoplanin (TEI 10 μM), an inhibitor of cathepsin L (Zhou et al., 2016 (link)) were purchased from Abcam. Stock solutions were dissolved in DMSO and working solutions were freshly prepared in DMEM 2% fetal bovine serum (FBS) at indicated concentrations. First, we pursued cell viability and cytotoxicity tests of all reagents using the CellTiter 96 Non-radioactive Cell Proliferation Assay (Promega) following the Manufacturer's instructions (Supplementary Fig. S2, Supplementary Fig. S3, Supplementary Fig. S4). We also studied the cytotoxic activity of the organic solvent DMSO. Based on these experiments we selected optimal non-toxic working concentrations for infection assays.
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10

Synthesis and Characterization of β-Lapachone

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β-Lap was synthesized and purified by Dr. William Bornmann (7 (link)). Dicoumarol (DIC), hydrogen peroxide (H2O2), Hoechst 33342, bovine serum albumin, cytochrome c, and Catalase, were purchased from Sigma-Aldrich (St. Louis, MO). 5-(and-6) chloromethyl-2,7-dichlorodihydrofluorescein diacetate (DCFDA) was purchased from Invitrogen Life Technologies (Eugene, OR). BAPTA-AM was purchased from Abcam (Cambridge, MA). HPβ-CD (>98% purity) was purchased from Cyclodextrin Technologies Development, Inc. (High Springs, FL). β-Lap-HPβ-CD was prepared as described (18 (link)).
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