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NBD-PE is a lipid fluorophore used for labeling and tracking lipid-containing structures in biological systems. It consists of a nitrobenzoxadiazole (NBD) fluorescent group covalently attached to a phosphatidylethanolamine (PE) headgroup. NBD-PE can be incorporated into lipid membranes and vesicles to visualize their dynamics and distribution.

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12 protocols using nbd pe

1

Quantifying Phospholipidosis in Cells

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To measure phospholipidosis (PLD), LipidTOX Red phospholipidosis detection reagent was used according to the instructions for HCS LipidTOX Phospholipidosis and Steatosis kit (ThermoFisher Scientific). Briefly, LipidTOX Red reagent was warmed up to 37 C, diluted in the culture medium and filtered through 0.8 mm pore filter and added to cells together with test compounds. After 72 h incubation, cells were stained with 20 mg/mL Hoechst 33342 in 4% paraformaldehyde solution in PBS for 30 min, washed in PBS 3 times, and imaged on ImageXpress Micro (Molecular Devices) high content analysis system. LipidTOX Red was imaged in the Texas Red channel (Ex 562/40, Em 624/40) and Hoechst in the DAPI channel (Ex 377/50, Em 447/60). Four images were taken per well using a 10Â objective.
Alternatively, in some experiments, PLD was measured by staining the cells with NBD-phosphatidylethanolamine (NBD-PE) (Molecular Probes, ThermoFisher Scientific) during 72-h incubation with test compounds (referred to as PLD NBD-PE) as described earlier. 19
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2

Fluorescent Lipid Vesicle Preparation

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Lipids 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPS), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), and 1-palmitoyl-2-oleoyl-sn-glycero-3- phosphocholine (POPC) were obtained from Avanti Polar Lipids (Alabaster, AL). Alexa Fluor® 488 (AF-488) C5-maleimide, BODIPY® FL DHPE (N-(4,4-Difluoro-5,7-Dimethyl-4-Bora-3a,4a-Diaza-s-Indacene-3-Propionyl)-1,2-Dihexadecanoyl-sn-Glycero-3-Phosphoethanolamine, Triethylammonium Salt), NBD-PE (N-(7-Nitrobenz-2-Oxa-1,3-Diazol-4-yl)-1,2-Dihexadecanoyl-sn-Glycero-3-Phosphoethanolamine, Triethylammonium Salt) and Texas Red-1,2-dihexadecanoyl-sn-glycero-3 phosphoethanolamine (Triethylammonium salt) were from Life Technologies (Grand Island, NY). Na2S2O4 (SDT), casein, Tris, HEPES, and EDTA were obtained from Fisher Scientific (Rochester, NY). All commercial reagents were used without further purification.
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3

Fluorescent Lipid Membrane Probes

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1,2-dioleoyl-sn-glycero-3-phophocholine (DOPC) was used in all membranes. Raft-forming mixtures included the sphingomyelin (SPM; brain, porcine) and the cholesterol (CHOL). For fluorescence microscopy, a variety of fluorescent lipid conjugates at trace concentrations (1–3 mol %) were mixed with the primary lipids. The probes used include: (i) Texas red 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (TR-DHPE, Life Technologies, Carlsbad, CA), (ii) two types of the NBD-labelled cholesterol, 5-cholesten-3ß-ol 6-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino] caproate (head-labelled NBD-CHOL) and 25-[N-[(7-nitro-2-1,3-benzoxadiazol-4-yl)methyl]amino]-27-norcholesterol (tail-labelled NBD-CHOL), (iii) N-[12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]dodecanoyl]-sphingosine-1-phosphocholine (NBD-SPM; tail-labelled NBD-SPM), and (iv) 1-palmitoyl-2-{12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]dodecanoyl}-sn-glycero-3phosphoethano lamine (tail-labeled NBD-PE). All lipids were purchased from Avanti Polar Lipids (Birmingham, Alabama). For protein binding assays, we used monosialoganglioside (GM1; brain, ovine-ammonium salt) and Alexa Fluor 488-labelled cholera toxin B subunit (CTxB-488, Life Technologies, Carlsbad, California).
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4

Lipid Fluorescence Labeling

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MF was purchased from Sigma-Aldrich (St. Louis, MO, USA); 2-(6-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)hexanoyl-1-hexadecanoyl-sn-glycero-3-phosphocholine and N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine, triethylammonium salt (NBD-PC and NBD-PE respectively) were obtained from Molecular Probes.
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5

FRET-based Evaluation of β2GPI Binding

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The ability of β2GPI to bind to and intercalate into phospholipid liposomes or into LPS R60 aggregates was investigated by FRET as described earlier [13] (link). Briefly, phospholipid liposomes from phosphatidylserine (PS), phosphatidylcholine (PC) or LPS R60 were doubly labeled with the fluorescent phospholipid dyes N-(7-nitrobenz-2-oxa-1,3-diazol-4yl)-phosphatidyl ethanolamine (NBD-PE) and N-(lissamine rhodamine B sulfonyl)-phosphatidylethanolamine (Rh-PE) (Molecular Probes). Intercalation of unlabeled molecules into the doubly labeled liposomes leads to probe dilution and thereby to a lower FRET efficiency. Thereby the emission intensity of the donor ID increases and that of the acceptor IA decreases (for clarity, only the quotient of the donor and acceptor emission intensity is shown here).
In all experiments 100 μl of 100 μM β2GPI were added to doubly labeled PC, PS or LPS R60 (900 μl of 10 μM) at 50 s after equilibration. NBD-PE was excited at 470 nm and the donor and acceptor fluorescence intensities were monitored at 531 and 593 nm respectively and the fluorescence signal ID/IA was recorded for further 250 s.
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6

COX-2 siRNA Mediated Inhibition

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All the reagents used in the study were of the highest purity available. The siRNAstargeting COX-2 gene was designed by and purchased from Santa Cruz Company (Finnell Street Dallas, TX, USA). The COX-2 siRNA target sequence was 5′-GCTGGGAAGCCTTCTCTAA-3′, the sense strand was 5′-GCUGGGAAGCCUUCUCUAAdTdT-3′, and the antisense strand was 5′-dTdTCGACCCUUCGGAAGAGAUU-3′. Anti-p53 wild type (wt), anti-Bax, anti-Cox-2, and anti-β-actin antibodies were purchased from BD Biosciences (San Diego, CA, USA). Liver enzymes were estimated using the kits from Span diagnostics (Bengaluru, India). L-Aminonapthaline-3,6,8-trisulfonic acid (ANTS) and N,N′-p-xylylene bis (pyridinium bromide) (DPX) were bought from Molecular Probes, Inc. The fluorescent probes, Rh-PE and NBD-PE (Avanti polar lipids), were kind gifts from Dr. Anu Puri (NIH, Frederick, MD, USA). All other reagents were of analytical grade and purchased from local suppliers.
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7

Nanoparticle Formulation and Characterization

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Sodium bicarbonate, cholesterol and Triton X-100 were purchased from Sigma-Aldrich, USA. DPPC was obtained from Lipoid, Germany, and PEG(2000)-DSPE-NH2 and PEG(2000)-DSPE from Avanti Polar Lipids, USA. NBD-PE, which fluoresces at 488 nm, was obtained from Molecular Probes, USA. The near-infrared fluorescent dye Alexa Fluor 750 NHS ester was purchased from Invitrogen, USA. N-Butylcyanoacrylate was purchased from Special Polymer Ltd., Bulgaria. MicroMarker MB were ordered from Fujifilm Sonosite, The Netherlands.
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8

Characterization of Coumarins' Physicochemical Properties

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The solvents acetonitrile and formic acid were obtained from Tedia (HPLC grade, Radnor, PA, USA), and ultrapure water was obtained from the Milli-Q® Plus apparatus by Millipore (Billerica, MA, USA). Methanol, ethanol, isopropanol, polysorbate 80 (Tween® 80), dimethyl sulfoxide (DMSO), and sodium hydroxide were obtained from Vetec (Duque de Caxias, Brazil), and medium chain triglycerides (MCT) and egg lecithin (Lipoid® E80) were purchased from Lipoid GmbH (Ludwigshafen am Rhein, Germany). Monobasic potassium phosphate was obtained from Dinâmica (São Paulo, Brazil), and NBD-PE [N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine, triethylammonium salt] fluorescent-labelled phospholipid was purchased from Thermo Fisher Scientific (Waltham, MA, USA). Roswell Park Memorial Institute 1640 broth medium (RPMI-1640), 3(N-morpholino) propane sulfonic acid (MOPS), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), and itraconazole were obtained from Sigma-Aldrich (St. Louis, MA, USA), and potato dextrose agar (PDA) was purchased from Acumedia (San Bernardino, CA, USA). Tissue-Tek® O.C.T.™ was purchased from Sakura Finetechnical Co. (Tokyo, Japan). Log P (calculated log P) values of the coumarins were assigned using SwissADME http://www.swissadme.ch/ (accessed on 10 March 2023).
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9

Phospholipidosis Quantification Assay

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Phospholipidosis was assessed as previously described.6 (link) Cells were treated with hydroxychloroquine in the presence of 7.5 μM nitrobenzoxadiazole-conjugated phosphoethanolamine (NBD-PE) (ThermoFisher). Images were taken and the fluorescence was quantified using a Spark Mulitmode microplate reader (TECAN).
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10

Reverse Phase Evaporation for GUV Formation

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GUVs were prepared by reverse phase evaporation based on a protocol previously described.60 (link) Lipid mixtures containing 79% 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC, Avanti Polar Lipids, Alabaster, AL), 20% cholesterol, and 1% N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (NBD-PE, ThermoFisher) were prepared in chloroform with 7% (vol %) methanol. In a round-bottom flask, 100 μL of the lipid mixture was injected below 3 mL of a 1× PBS, 10 mM EDTA solution and placed on a rotary evaporator immersed in a 40 °C water bath. Under vacuum, the evaporation of organic phase spontaneously forms GUVs in the aqueous phase.
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