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33 protocols using phastsystem

1

SDS-PAGE and Western Blotting of OMVs

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SDS-PAGE was performed on OMV preparations (containing approximately 2.5–5 mg/ml protein) using 8–25% gradient gels in the PhastSystem (GE Healthcare, Piscataway, NJ). Molecular weights of the reduced and denatured OMV proteins from the three Cronobacter spp. were estimated by using the relative mobility method (Weber et al., 1972 (link)). Western blotting of OMV protein samples separated by SDS-PAGE was carried out by electro-blotting onto a Problott (Applied Biosystems, Foster City, CA) membrane in a transfer buffer (10 mM of 3-[cyclohexylamino]-1-propane sulfonic acid containing 10% methanol, pH 11).
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2

CIDE Domain Protein Interactions

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The protein interactions between the CIDE domains and various mutants were analyzed by native (non-denaturing) PAGE using a PhastSystem (GE Healthcare) with pre-made 8–25% acrylamide gradient gels (GE Healthcare). The separated and purified proteins were pre-incubated at room temperature for 1 h before loading onto the gel, and Coomassie Brilliant Blue was used to stain and detect the shifted bands.
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3

Protein Characterization by SDS-PAGE and IEF

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Protein concentration was determined with a Quick Start Bradford protein assay kit (Bio-Rad Laboratories, Hercules, CA, USA). The apparent molecular mass of the enzymes was determined by SDS-PAGE in a 10–15 % polyacrylamide gel gradient as described by Laemmli. 17) A BenchMark Ladder (Invitrogen, Carlsbad, CA, USA) provided the standard protein markers. The molecular mass of the native enzyme was determined by native-PAGE in an 8–25 % polyacrylamide gel gradient as described by Davis. 18) The HMW marker kit (GE Healthcare, Chicago, IL, USA) provided the standard protein markers. The p I for thyroglobulin (669 kDa), ferritin (440 kDa), catalase (232 kDa), lactate dehydrogenase (140 kDa), and albumin (66 kDa) in the protein marker mix were 4.5, 4.5, 5.4, 5.0, and 4.9, respectively. The apparent p I of the enzyme was determined by isoelectric focusing on a Phastgel IEF 3–9 using the Phastsystem (GE Healthcare, Chicago, IL, USA). The proteins were stained with Rapid CBB KANTO (Kanto Chemical Co. Inc., Chuo-ku, Japan).
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4

Pika Hemoglobin Isoform Analysis

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We used isoelectric focusing (PhastSystem, GE Healthcare Bio-Sciences, Piscataway, NJ) to characterize the Hb isoform composition of circulating red blood cells in both O. princeps and O. collaris. Native pika Hbs were purified by means of anion-exchange chromatography (HiTrap QHP, GE Healthcare, Piscataway, NJ), as described previously (Storz et al. 2012 (link); Revsbech et al. 2013 (link)). The column was pre-equilibrated with 20 mM Tris (pH 8.4) and the sample was eluted using a linear gradient of 0–0.2 M NaCl. Samples were desalted by dialysis against 10 mM HEPES buffer (pH 7.4) and were concentrated using Millipore centrifugal filter units (30-kDa cutoff). Hb concentrations were determined from absorbance spectra using standard extinction coefficients at 577 and 540 nm.
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5

Protein Characterization by SDS-PAGE and IEF

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Protein concentration was determined using Quick Start Bradford Protein Assay (Bio-Rad, USA). The apparent molecular mass of the enzymes was determined using SDS-PAGE in 10–15 % gradient polyacrylamide gels as described by Laemmli.11) (link) Benchmark Ladder (Invitrogen) was used as standard protein markers. The molecular mass of the native enzymes was determined using native-PAGE in 8–25 % gradient polyacrylamide gels as described by Davis.12) HMW Marker Kit (GE Healthcare) was used as standard protein markers. The pI values of thyroglobulin (669 kDa), ferritin (440 kDa), catalase (232 kDa), lactate dehydrogenase (140 kDa), and albumin (66 kDa) present in the protein marker are 4.5, 4.5, 5.4, 5.0, and 4.9, respectively. The apparent pI of the enzymes was determined using isoelectric focusing on a Phastgel IEF 3–9 and the Phastsystem (GE Healthcare). Proteins were stained using Rapid CBB KANTO (Kanto Chemical, Japan).
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6

CD1d Lipid Loading Analysis

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Recombinant mouse CD1d was expressed and purified as previously
reported53 . CD1d was
loaded with 3× molar excess of SLF (bovine brain, Avanti Polar Lipids;
dissolved at 5 mg ml−1 in DMSO) in 100 mM Tris (pH 7.0) 100 mM
NaCl at 37 °C for 2 h. After lipid loading, excess lipid was removed by
ultrafiltration using Amicon filter cartridges (30-kDa molecular weight
cut-off). CD1d-SLF complexes were then incubated overnight at room temperature
with increasing concentration of either sphingomyelin (C24:1) (synthetic, Avanti
Polar Lipids) or α-GalCer. Lipids were dissolved in DMSO (5 mg
ml−1) and incubated with CD1d in the presence of 0.01%
tyloxapol. As a control, CD1d-SLF complexes were incubated with only tyloxapol.
In a reversed experiment, CD1d was first loaded with 6× molar excess of
either sphingomyelin (10 mg ml−1 in DMSO) or α-GalCer
(0.2 mg ml−1 in vehicle) at room temperature overnight,
purified from excess lipid by ultrafiltration and incubated with 3× molar
excess of SLF for 1 h at 30 °C, which is the minimum dose and time
necessary for full loading of insect-cell-expressed mouse CD1d (data not shown).
Four microliters (2–4 μg) of the various CD1d-lipid-loading
products were analyzed using native IEF gel electrophoresis on pH 5–8
gels with a PhastSystem (GE Healthcare) and stained with Coomassie dye.
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7

Gel Electrophoresis of AuNP Conjugates

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Gel electrophoresis experiments were performed with a PhastSystem (GE Healthcare Bio-Sciences AB, Uppsala, Sweden) electrophoresis device, in a standard 0.3% agarose gel with a 125 × TAE buffer solution at an electrical differential of 180 V. The experiments were run for 15 min. In addition, 1 % Sodium dodecyl sulfate (SDS) was added to selected samples, which enabled the reliable separation of unconjugated and conjugated AuNPs within the method.
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8

Isoelectric Focusing Procedure with PhastSystem

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Isoelectric focusing was accomplished in PhastSystem (GE Healthcare) at 15°C. The pH gradient was formed on the PhastGel IEF media 3–10.5 (pH range 3–10.5) containing pharmalyte carrier ampholytes for 75 Vh at the voltage of 2000 V. Samples were applied to the gel for 15 Vh at 200 V, and they were then allowed to migrate to their isoelectric points for 410 Vh at 2000 V. After migration, the gel was fixed with fixing solution (20% TCA, Sigma Aldrich) followed by washing with 30% methanol and 10% acetic acid in distilled water. The staining was done in InstantBlue solution (Expedeon) for 1 hour followed by washing with distilled water until the desired background was achieved.
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9

Lipid Loading and Isoelectric Focusing of mCD1d

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Aliquots of 10 μl purified mCD1d at a concentration of 20 μM were loaded overnight at room temperature in the presence of 6-times molar excess of each lipid. Sulfatide was dissolved in DMSO (5 mg/ml), and PA was dissolved in CHCL3 (10 mg/ml). Loading was performed in the presence of 100 mM Tris-HCl (pH 7). After lipid loading, samples were centrifuged (14,000×g, 10 min), and 4 μl supernatant was used for isoelectric focusing (IEF) analysis. CD1d–lipid complexes were separated using precast gels (PhastGel 5–8 IEF) and the PhastSystem (GE Healthcare Biosciences, Piscataway, NJ). Staining of mCD1d was performed with Coomassie blue, and successful lipid loading was identified by a gel shift of the mCD1d band in relation to the control lanes.
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10

Isoelectric Point Determination

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Calculation of isoelectric point (pI) was carried out using the Protean module 8.1.4 of DNASTAR Lasergene (USA). Isoelectric focusing (IEF) was carried out using a pre-casted gel with PhastGel IEF 3–9 (17-0543-01; GE Healthcare) and PhastSystem (GE Healthcare, Uppsala, Sweden). The protein bands were visualized by PhastGel Blue R (17-0518-01, GE Healthcare) staining.
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