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22 protocols using minigel

1

Western Blot Analysis of Protein Expression

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Total cell lysates were prepared in a Tris pH 6.8–10% SDS solution (1:1) by heating at 95° for 20 mins. Protein concentration was measured using Pierce BCA protein assay kit as per the company instructions. For western blotting 10–40 ug of protein was resolved on 7.5% or 10% mini gels from Biorad, transferred to nitrocellulose membrane using semi-dry method and immunoblotted. 10% BSA was used for filter blocking in all conditions.
The following primary antibodies were used: against Notch1, Slug and Actin (Santa Cruz Biotechnology), against PlexinD1 (R&D Systems), against Vinculin (Sigma), against Notch3 (Cell Signaling technology), against E-cadherin (BD Transduction laboratories).
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2

SDS-PAGE Analysis of L. loa Worm Extract

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SDS-PAGE was performed on discontinuous gels according to Laemmli13 (link) under reducing conditions and using 12.5% acrylamide. A single adult worm was removed during ocular passage, that was then washed three times in water. Soluble extract was loaded into a single well after boiling for 5 min in an SDS-PAGE L. loa sample cocktail. Gels were run in BioRad mini gels, with the apparatus at 200 V for 1 h at room temperature.
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3

Glycerol-SDS-PAGE Analysis of Muscle MHC Isoforms

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Myosin heavy chain (MHC) isoforms expressed in the lateral gastrocnemius muscle was examined using glycerol-SDS-PAGE (16 (link), 17 (link)). Briefly, SDS-PAGE samples equivalent to 5 μg of muscle tissue (wet weight) were resolved on 8% polyacrylamide gel with acrylamide:bis-acrylamide ratio of 50:1, prepared in 200 mM Tris base, 100 mM glycine, pH 8.8, containing 0.4% SDS and 30% glycerol. The stacking gel contained 4% polyacrylamide with acrylamide:bis-acrylamide ratio of 50:1, 70 mM Tris-HCl (pH 6.7), 4 mM EDTA, 0.4% SDS, and 30% glycerol. The upper cathode running buffer consists of 100 mM Tris base, 150 mM glycine, 0.1% SDS, and 10 mM β-mercaptoethanol. The lower anode running buffer was 50% dilution of the upper running buffer without β-mercaptoethanol. The 0.75-mm-thick Bio-Rad minigels were run at 100 V in an icebox for 24 h. The resolved protein bands were visualized after staining with Coomassie blue R250.
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4

Protein Extraction and Western Blotting

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Tissues that were snap frozen in liquid N2 were homogenized in RIPA buffer containing protease and phosphatase inhibitors cocktail (Roche and Thermo Fisher Scientific), protein extracted, and then subjected to Western blotting. Equal amounts (30 µg) of protein were loaded onto minigels (Bio-Rad Laboratories) and transferred onto a polyvinylidene fluoride membrane using established protocols. Samples were probed for the indicated proteins as described previously (Jin et al., 2011 (link)) using the antibodies listed in the following section.
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5

Glycerol-SDS-PAGE Analysis of Myosin Heavy Chains

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Myosin heavy chain (MHC) isoforms expressed in muscle tissues were examined using glycerol-SDS-PAGE (Feng et al., 2011 (link)). Briefly, SDS-PAGE samples equivalent to 5 μg of muscle tissue (wet weight) were resolved on 8% polyacrylamide gel with acrylamide:bis-acrylamide ratio of 50:1, prepared in 200 mM Tris base, 100 mM glycine, pH 8.8, containing 0.4% SDS and 30% glycerol. The stacking gel contained 4% polyacrylamide with acrylamide:bis-acrylamide ratio of 50:1, 70 mM Tris-HCl (pH 6.7), 4 mM EDTA, 0.4% SDS, and 30% glycerol. The upper cathode running buffer consists of 100 mM Tris base, 150 mM glycine, 0.1% SDS, and 10 mM β-mercaptoethanol. The lower anode running buffer was 50% dilution of the upper running buffer without β-mercaptoethanol. The 0.75-mm-thick Bio-Rad minigels were run at 100 V in an icebox for 24 h. The resolved protein bands were visualized after staining with Coomassie blue R250.
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6

Immunoblotting Procedure for Protein Detection

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Samples were supplemented with an equal volume of 2× SDS-PAGE sample buffer and boiled for 5 min at 95 °C. A total of 20 µL of each sample was loaded on 15% SDS-PAGE gels (Mini-Gels, Bio-Rad). Gels were run at 100 mV for 20 min and then 150 mV for 40 min. Proteins were transferred to PVDF membranes using a semidry transfer system. Membranes were blocked overnight in PBS–0.1% TritonX–5% milk and then probed with the appropriate antibody (Table 2). Membranes were developed with ECL reagent (PerkinELmer Life Science), imaged on XAR-5 film (Kodak) and processed.
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7

Cytokine and Metabolite Assays

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Tumor necrosis factor (TNF)-α was purchased from Life Technologies. Interleukin (IL)-1β, IL6, transforming growth factor (TGF)-β, IGF1 and IGF2 were purchased from R&D Systems. Reagents for SDS-PAGE, mini-gels and blocking buffer were purchased from Bio-Rad Laboratories. Mannitol and d-glucose were purchased from Sigma-Aldrich. Advanced glycation end products (AGE), AGE
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8

Western Blot Analysis of CAV1 Protein

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Protein extracts were separated by SDS-PAGE on 12% minigels (BioRad), loading 50 μg total protein. Blots were blocked with 5% milk in 0.1% Tween-PBS and probed with antiactin (1 : 5000) or anti-CAV1 (1 : 3000) antibodies. Bound antibodies were detected with horseradish peroxidase-conjugated secondary antibodies. CAV1 protein levels were quantified by scanning densitometry, standardized to actin levels in the same samples and comparing in each set with normal human melanocytes assigned a reference value of 1 (mean±SD, from three different experiments).
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9

Immunoblot Analysis of Drosophila Larval Proteins

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Larval brain lysates were analyzed by SDS-PAGE according to Laemmli using 12% mini-gels (Bio-Rad). For immunoblotting, after SDS-PAGE, the gels were electrophoretically transferred to nitrocellulose with transfer buffer (25 mM Tris, 192 mM glycine, 20% methanol, and 0.1% SDS) at room temperature (RT) for 1.5 h and at 25 V. The membrane with transferred proteins was blocked for 60 min at RT in blocking solution (5% nonfat dry milk in PBS with 0.05% Tween-20) and then incubated at RT overnight with rabbit polyclonal antibody raised against the C-terminal peptide CHKEAGPAASASEPEAK of Drosophila melanogaster HSP67Bc (Carra et al. [8 (link)]) diluted 1:5000. The membrane was then incubated at RT for 2 h with goat anti-rabbit IgG conjugated with horseradish peroxidase (Jackson ImmunoResearch) diluted 1:10,000 in PBST. Membranes were then detected and documented with a chemiluminescent method using the Bio-Rad Imaging System.
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10

Protein Extraction and Analysis from SMCs

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SMCs were trypsinized and proteins were extracted as previously described.9 (link) Proteins were separated by SDS–PAGE on 12% mini gels (Bio-Rad) and stained with Coomassie brilliant blue (R250, Fluka). For Western blotting (see Supplementary material online, Table S1, for antibodies), 1 μg of proteins for α-SMA and 12 μg of proteins for total and phospho-NF-κB were electrophoresed and transferred to a nitrocellulose membrane (Protran® 0.2 μm; Schleicher and Schuell). About 12 μg of proteins for S100A4 were electrophoresed and transferred on PVDF membrane (0.45 μm, Immobilon™-P, Millipore Corporation). α-Tubulin was used as a housekeeping protein. Horseradish peroxidase-conjugated goat anti-mouse IgG or IgM and goat anti-rabbit IgG were used as secondary antibodies. Enhanced chemiluminescence was used for detection (Amersham). Signals were digitized with Epson perfection 4990 photo scanner and analysed by using ImageJ v1.49 software. Results were normalized to tubulin expression.
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