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21 protocols using sphingomyelin

1

Liposomal Vaccine Formulation and Characterization

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Immunogens (selected peptide – Peptide 5 or LiAg) and PBS (as control) were encapsulated in liposomes, which were used as vaccine carrier. Sphingomyelin/Cholesterol multilamellar liposomes (ratio of 2:1) were prepared by dissolving 25 mg of Sphingomyelin (Sigma-Aldrich) and 6.5 mg Cholesterol (Sigma-Aldrich) in 20 ml chloroform together with traces of methanol. The solution was kept in a 1,000-ml round-bottom flask and the solvent was removed by flash evaporation on a rotary evaporator at 37°C. After drying under reduced pressure for 80 min, the aqueous phase containing 2.1 mg of immunogens in PBS, pH 7.4 was added to the flask. The lipid film was dislodged from the glass by the use of a vortex mixer. The liposomes were retrieved using a Pasteur pipette and then treated with ultrasonic vibration three times during 20s each. The liposome suspension was centrifuged at 8,000 g for 10 min at 4°C to remove non-encapsulated immunogens and the supernatant protein concentration was estimated by spectrophotometry. The encapsulation efficiency for the formulations was 85%. The pelleted liposomes were resuspended and washed three more times with PBS by centrifugation and 0.5 mg Aluminum Hydroxide was added (200 μg/animal). The compound was stored in PBS at 4°C.
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2

Regulation of ABCA5 in neural cells

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SK-N-SH neuronal cells were obtained from the ATCC (Manassas, VA). Primary human fetal brain cells were a kind gift from Prof Guillemin and were prepared as described previously33 (link)–35 (link), and the study was approved by the University of New South Wales Human Research Ethics Committee (approval number: HREC 03187). Cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum, 1% Glutamax, 0.5% glucose, 100 IU/ml penicillin and 100 μg/ml streptomycin at 37 °C in humidified air containing 5% CO2. SK-N-SH cells were transfected with ABCA5 cDNA or empty vector (control) using Lipofectamine 2000 (Thermo Fisher Scientific) following the manufacturer’s protocol. After 48 hours the cells were harvested and total RNA prepared for gene expression studies. In the sphingomyelin study, cells were cultured in 12-well plates and treated with 40 µM sphingomyelin (Sigma-Aldrich #85615), 50 µM D609 inhibitor or vehicle (control) for 24 hours. In the regulation study, cells were cultured in 12-well plates and treated with 10 µM T0901317, 10 µM 9-cis retinoic acid, 10 µM pioglitazone (Sigma-Aldrich) or vehicle (control) for 24 h. The cells were harvested and total RNA prepared for gene expression analysis.
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3

Quantification of Sphingomyelin Fatty Acids

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Tissue samples were pulverized in aluminum mortar precooled with liquid nitrogen and transferred to tubes containing a solution of methanol and antioxidant (0.01% butylated hydroxytoluene). Lipid fractions were then isolated by the method described by Bligh and Dyer (1959). sphingomyelin was extracted using thin‐lyer chromatography (TLC). The gel bands were scraped off from the plates after their reference to the distance traveled by standard (sphingomyelin, Sigma–Aldrich) and moved into tubes containing internal standard (pentadecanoic acid). After transmethylation the sphingomyelin fatty acids were analyzed using gas‐liquid chromatography (GLC). Hewlett–Packard 5890 Series II system equipped with a double flame‐ionization detector and Agilent CP‐Sil 88 capillary column was utilized. Total sphingomyelin concentration is shown as the sum of individual fatty acid species (expressed in nM/g of the tissue).
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4

Lipid-based Microscopy Sample Preparation

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Droplets of DMSO (30072418, Sinopharm Chemical Reagent Co., Ltd), MeOH (10014118, Sinopharm Chemical Reagent Co., Ltd), FA (dissolved in double steamed water, F7876, Sigma-Aldrich), TO (T7140, Sigma-Aldrich), powder of BSA (4240GR005, BioFroxx), and sphingomyelin (S0756, Sigma-Aldrich) were sealed between two cover glasses (48393-172, VWR) for different experiments.
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5

Antibodies and Lipids for Cell Biology

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Anti-His-tag (mouse), anti-Rac (mouse), anti-E-cadherin (rabbit), anti-GAPDH (rabbit), anti-histone H3 (rabbit), anti-α-tubulin (rabbit), anti-rabbit IgG (goat), anti-mouse IgG conjugated with Alexa Fluor® 488 (goat), anti-rabbit IgG conjugated with Alexa Fluor® 594 (goat) were purchased from Invitrogen (Oregon, USA); anti-mouse IgG was obtained from Dako (rabbit, California, USA). GDP and a non-hydrolyzable GTP analogue, guanosine 5′-[β,γ-imido]triphosphate (GppNHp), were obtained from Jena Bioscience GmbH (Jena, Germany). TC100 insect cell media, fetal bovine serum, antibiotics (penicillin and streptomycin) and 10% Pluronic F-68 were obtained from PAN-Biotech GmbH (Aidenbach, Germany). Phosphatidylserine (PS), Phosphatidylcholine (PC), phosphatidylethanolamine (PE) and sphingomyelin (SM), phosphatidylinositol 4,5-bisphosphate (PIP2), and Folch I and Folch III brain lipid extracts were purchased from Sigma-Aldrich (Munich, Germany). PIP3 is from Merck (Darmstadt, Germany). All other standard reagents, including detergents (Table S1 in File S1) were obtained from Carl Roth GmbH (Karlsruhe, Germany) or Merck-Millipore (Darmstadt, Germany).
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6

Lipid Extraction and Analysis

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Lyso-platelet activating factor (Lyso-PAF C18:0 and (9Z)-C18:1) were purchased from Avanti Polar Lipids (Alabaster, AL). Lysophosphatidylcholine (LPC, C18:0) and sphingomyelin were from Sigma (St Louis, MO).
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7

Synthetic Myelin Phantom for UTE Imaging

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A 520 mg synthetic myelin lipid phantom approximating the nonprotein portion of biological myelin was prepared using a previously described procedure [13 (link)]. It consisted of 3:2 solid to liquid mass ratio of13.5% cholesterol, 13% galactocerebroside, 19.3% phosphatidylcholine, and 4.2% sphingomyelin (Sigma-Aldrich, St. Louis, MO) and deionized D2O which was mixed into a paste and placed in a glass NMR tube. The phantom was then subject to UTE imaging for T2* measurement. A custom-made solenoid coil (5 mm in diameter) was used for signal excitation and reception. The following MR imaging parameters were used: field of view (FOV) = 4 cm, slice thickness = 3 mm, bandwidth (BW) = ±31.25 kHz, flip angle =60°, acquisition matrix = 128×128, number of projections = 403. For T2* measurements, a TR of 1000 ms and 14 TEs (8 μs, 0.1, 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.6, 2.0, 2.5, 3.2, 4.8, 6.4 ms) were used. A bi-component model (details below) was used to analyze the data.
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8

Megakaryocytic Differentiation Protocol

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Phospholipids and sphingolipids were dissolved in DMSO or alcohol-containing solution prior to application to cell culture media. For megakaryocytic differentiation, 3 × 104 cells were seeded in 6-well plate with 3 ml of culture media which contained indicated levels of phytosphingosine or (R)-TEMOSPho. On subsequent days, 1 ml of fresh media containing phytosphingosine or (R)-TEMOSPho was added to the culture media.
2-(Trimethylammonium) ethyl (R)-3-methoxy-3-oxo-2-stearamidopropyl phosphate ((R)-TEMOSPho) was synthesized following previously reported methods with modifications (10) (link). Sphingomyelin was purchased from Sigma Aldrich (St. Louis, MO), and Oleoyl phytosphingosine, Tetraacetyl phytosphingosine, Hexanoyl phytosphingosine, phytosphingosine, Acetyl phytosphingosine, Glucosyl cerarmide, Phosphatidyl choline were supplied by Doosan Biotech (Seoul, Korea). Phytosphingosine-1-phosphate, Lysophosphatidyl ethanolamine, Lysophosphatidyl choline, Lysophosphatidic acid, Lysophosphatidyl inositol were purchased from Avanti Polar Lipids, Inc. (Alabaster, AL).
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9

Lipid Extraction and Separation Protocol

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Lipids from samples of the DRM fractions were extracted according to the Bligh and Dyer method [49 (link)]. During the extraction, acetic acid (0.057 M) was added to the water phase, in order to increase the recovery of acidic phospholipids [50 (link)]. Briefly, 960 μL of chloroform/methanol (1:2), 400 μL of chloroform and 200 μL of 0.1 M acetic acid were added, in that order, to 200 μL of sample. After shaking the mixture, the tubes were centrifuged (1,000 rpm, 5 min), and the organic phase was extracted and evaporated using Speed-Vac. When necessary, evaporated samples were resuspended in 25 μL of chloroform/methanol (4:1) and resolved on silica high-performance TLC plates using chloroform/methanol/water (68:28:4) when sphingolipid detection was required, or using chloroform/methanol/NH4OH/water (40:48:5:10) in the case of phosphoinositides (PIs). Standards (sulfatide, sphingomyelin or monophosphorylated PIs, all from Sigma-Aldrich) were resolved in parallel and staining of lipids was performed using primuline.
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10

Lipid Biomarker Profiling Techniques

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1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 1,2-dioleoyl-3-trimethylammonium-propane (chloride salt) (DOTAP), TopFluor-cholesterol (Bodipy-Chol), TopFluor- phosphatidylethanolamine (Bodipy-PE), D-lactosyl-ß−1,1' N-palmitoyl-D-erythro-sphingosine [LacCer(d18:1/16:0)] and Lyso-Lactosylceramide (Lyso-LacCer) were purchased from Avanti Polar Lipids Inc (Alabaster, AL, US). Bodipy FL C5-ganglioside GM1 (Bodipy-GM1), Bodipy FL C5-ceramide (Bodipy-Cer), Bodipy FL C12-spinghomyelin (Bodipy-SM C12), Bodipy FL C5-spinghomyelin (Bodipy-SM C5) were obtained from Thermo Fisher Scientific (Waltham, MA, US). BODIPY Fl-C5 NHS ester (4,4-Difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-pentanoic acid, succinimidyl ester) was purchased from Setareh Biotech, LLC (Eugene, OR, US). Sphingomyelin (SM d18:1/16:0), cholesterol (Chol), d7-cholesterol, N,N-diisopropylethylamine, sphingomyelinase (SMase) from Bacillus cereus, myriocin from Mycelia sterilia, anhydrous dimethylforamide (DMF), chloroform (CHCl3), and methanol (MeOH) were purchased from Sigma-Aldrich (St. Louis, MO, US). LC-MS grade formic acid was purchased from VWR Chemicals (Radnor, PA, US). LC-MS grade 2-propanol and acetonitrile were from Merck Millipore (Billerica, MA, US). Milli-Q water (Merck Millipore) was used. All reagents and chemicals were used without further purification.
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