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123 protocols using hyperfilm

1

Arabidopsis AER Protein Extraction and Detection

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Seven-day-old WT and aer Arabidopsis seedlings were ground to a powder in liquid nitrogen using a mortar and pestle, and the resulting powder was suspended in the extraction buffer (100 mM Tris-HCl buffer, pH 7.5, containing 0.1mM EDTA, 7% (w/v) PVPP, 5% Suc, 0.0005% Triton X-100, 1 mM PMSF, 15 mM DTT, and a commercial cocktail of protease inhibitors (AEBSF, 1,10-phenantroline, pepstatin A, leupeptine, bestatine, and E-64 from Sigma-Aldrich; 1/2, FW/v). Then, the crude extracts were centrifuged twice at 3,000xg for 6 min. Total protein content was analyzed by Bradford assay and separated by 10% SDS-PAGE and transferred to PVDF membranes (Immobilon P, Millipore, Bedford, MA, USA). For AER immunodetection, an specific antibody against Arabidopsis AER (Mano et al., 2005 (link)) was used at a dilution of 1:1000 and the immunoreactive band was detected using a photographic film (Hyperfilm, Amersham Pharmacia Biotech) with an enhanced chemiluminescence kit (ECL-PLUS, Amersham Pharmacia Biotech).
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2

Activation of AKT and MAPK Pathways in Neuroblastoma

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The HTB11 neuroblastoma cell line were incubated overnight in EMEM medium containing low levels of BSA (0.5%) to render the cells quiescent. After the cells were stimulated with EPO (0.5 or 20 iU/ml), or the medium level with 10% FBS as a positive control at 37°C for 5 min, the cells were lysed for 10 min on ice in RIPA lysis buffer containing protease and phosphatase inhibitors (Santa Cruz Biotechnology). The extracted proteins were separated on a 4-12% SDS-PAGE gel and transferred to a PVDF membrane. Phosphorylation of the serine/threonine kinase AKT (yielding phospho-AKT473) and p44/42 mitogen-activated kinase (yielding phospho-44/42 MAPK) was detected by phosphospecific p44/42 MAPK mouse and AKT rabbit polyclonal antibodies (Cell Signaling Technology, Danvers, MA, USA) with HRP-conjugated goat anti-mouse and anti-rabbit secondary antibodies (Santa Cruz Biotechnology). Equal loading in the lanes was evaluated by stripping the blots and reprobing with anti-p42/44 MAPK monoclonal antibody (Cell Signaling Technology) and anti-AKT polyclonal antibody (Cell Signaling Technology). The membranes were developed with an enhanced chemiluminescence (ECL) reagent (Amersham Life Science, Arlington Heights, IL, USA), dried, and subsequently exposed to film (Hyperfilm; Amersham Life Science).
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3

Western Blot Analysis of Protein Expression

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VICs were washed two times in PBS, solubilised and homogenised in RIPA buffer solution (Sigma) supplemented with protease inhibitor cocktail 1X (Roche). Cells were scraped with a rubber policeman; the lysate was transferred into a 1.5ml microtube and vortexed. Proteins were quantified with a Pierce BCA protein assay (Thermo Scientific) after a 10,000g centrifugation for 10 minutes at 4°C. Total protein homogenates (7.5 μg) were denatured and separated on 10% Bis-Tris gels (Invitrogen). Electrophoretically resolved bands were then transferred on nitrocellulose membranes (Hybond C, Amersham). Membranes were blocked for 1 hour in Phosphate-Buffered Saline (PBS) containing 0.1% Tween-20 (PBS-T) and 5% (w/v) non-fat powdered milk. Then, they were incubated for 1 hour with primary antibodies (Table 1) in PBS-T containing 5% (w/v) non-fat powdered milk. Membranes were then washed three times in PBS-T and incubated with corresponding horseradish peroxidase conjugate secondary antibody (Table 1) for 1 h at room temperature in PBS-T. Membranes were washed five times in PBS-T. Visualization of the protein bands was accomplished using enhanced chemiluminescence (ECL) substrate (Amersham) and positivity was captured on Hyperfilm (Amersham). Films were scanned and bands were quantitated using the QuantityOne program (Biorad). Levels of expression were normalised to GAPDH.
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4

Aortic Protein Expression Analysis in Marfan Mice

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Ascending aortic medial tissue from 6-mo-old wild-type (male n = 6; female n = 6) and Marfan (male n = 6; female n = 6) mice was homogenized using a bullet blender, ø 0.9–2 and 3 mm stainless steel beads (Next Advance, NY, USA) in 300 μl radioimmunoprecipitation assay buffer (RIPA, 10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 7.5, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium desoxycholate, 0.1% SDS, 140 mM NaCl) and protease inhibitors. Protein concentrations were assessed using a colorimetric assay for protein concentration (Biorad, CA, USA). Twenty micrograms of protein per sample were analyzed by 10% (v/v) SDS-PAGE and transferred to nitrocellulose membranes. Primary antibodies to COX-1 (Santa Cruz, CA, USA), COX-2, eNOS, (p)eNOS (BD Transduction Laboratories, CA, USA), iNOS (Thermo Fisher, MA, USA) and actin (Sigma Aldrich, MO, USA) were incubated overnight in TBS 1% BSA. Protein bands were revealed using secondary IgG HRP conjugates (Promega, WI, USA) and Luminol Reagent together with Hyperfilm (Amersham Pharmacia Biotech, Uppsala, Sweden). Band intensities were measured by densitometry scanning using ImageJ software (National Institute of Health, Bethesda, MD, USA). Band intensities were relativized against actin as a loading control and the values of all groups were normalized for WT male average values.
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5

StAR and CRTC2 Protein Analysis

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Cells were harvested and lysed with ProteoJET™ membrane protein extraction buffer (Fermentas, USA) supplemented with 1 mM phenylmethanesulfonyl fluoride (PMSF), Phosphatase inhibitor (20×: 125 mM NaF, 250 mM B-glycerophosphate, 250 mM para-nitrophenyl phosphate, 25 mM NaVO3) and protease inhibitor (Sigma, P8340) were added. Extracts were quantified by BCA protein assay kit (Pierce Bio-technology, Inc., Rockford, IL, USA). Proteins were incubated with an antibody raised against recombinant mouse StAR protein (Dr. Dale Buck Hales, University of Illinois at Chicago, USA), CRTC2 (Dr. H. Takemori, National Institute of Biomedical Innovation, Osaka, Japan) for 1 h. Protein bands were visualized by ECL reagent (Amersham Biosciences) and exposing the membrane against Hyperfilm (Amersham Biosciences).
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6

Western Blot Analysis of Protein Targets

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Equal amounts of protein (10 μg) were resolved on 10% Criterion XT Bis-Tris Precast Gels (Bio-Rad, Hercules, CA) and transferred to PVDF membranes. Membranes were blocked with TBS-T (TBS and 0.5% Tween 20) containing 5% (w/v) non-fat dry milk or 5% BSA (depending on the primary antibody) for 30 minutes to 1 h and washed with TBS-T. Membranes were then incubated overnight at 4°C with different antibodies including FASN (clone 23, BD Biosciences, Pharmingen), p21 (F-5, Santa Cruz Biotechnologies, Santa Cruz, CA) and AMPK, p-AMPK, ACC and p-ACC (Cell Signaling Technology, Danvers, MA). After a further 3 washes with TBS-T, membranes were incubated with horseradish peroxidase-linked secondary antibodies. Blots were then stripped and re-probed with a monoclonal antibody to β-actin and horseradish peroxidase-linked goat anti-mouse IgG secondary antibody. Proteins were detected by an enhanced chemoluminescence reaction using Hyperfilm (Amersham-Pharmacia, Piscataway, NJ).
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7

Western Blot Analysis of TGF-β Signaling

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Neural progenitor cells or tissues from different brain regions were homogenized in 0.7% NP40, 50 mM Tris-HCl (pH 8.0), 0.1 mM EDTA (pH 8.0), 250 mM NaCl, 10% glycerol, 0.2 mM Na3VO4, 1 mM PMSF, 10 mM DTT, 2 μg/ml Aprotinin and 1 μg/ml Pepstatin and centrifuged at 17,900 × g for 15 min. at 4°C. The protein concentration in the supernatants was determined using the BCA kit (Sigma-Aldrich). Protein extracts were resolved on 12% SDS-PAGE and transferred onto nitrocellulose membranes (Schleicher and Schuell, Dassel, Germany) as described previously [10 (link)]. Antibodies for Wetern blots were as follows: rabbit anti-phospho smad 2, 1:500 (Cell Signaling); mouse anti-smad 2 (1:500; Cell Signaling); mouse anti-TGFbRII (1:500; Santa Cruz Biotechnology, USA); rabbit anti-TGFbR1 (1:1000; Santa Cruz Biotechnology, Dallas, TX, USA); rabbit anti-actin (1:5000; Sigma-Aldrich). Secondary goat antimouse or anti-rabbit IgG-HRP antibodies (1:10,000; Dianova) and detection was performed with the ECL plus chemiluminescence system (Amersham/Pharmacia, Freiburg, Germany) and exposed to Hyperfilm (Amersham Pharmacia). Blots were stripped and reprobed as described [23 (link)].
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8

Quantitative Southern Blot Analysis of HPV16

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Southern blots were prepared as previously described (Bodily et al., 2011 (link); Fehrmann et al., 2003 (link); Southern, 1975 (link)). Briefly, 5µg or 10µg of total cellular DNA was digested with either BamHI (cuts HPV16 once) or HindIII (does not cut HPV16) restriction enzymes (NEB) and resolved on a 0.8% agarose gel with 0.5 µg /ml of ethidium bromide. 7×106, 7×107, and 7×108 copies (equivalent to 10, 100, and 1,000 copies per cell) of an HPV16-positive pUC plasmid linearized with BamHI was included on the Southern blot analysis for estimation of viral copy number. DNA was transferred onto a nylon membrane (GE Water and Process Technologies or GeneScreen Plus) and hybridized with full length HPV16 genome labeled with α−32P dCTP using the Rediprime II Random Prime Labelling System (Amersham Biosciences) or the Invitrogen RadPrime DNA Labeling System according to the manufacturer’s instructions. Radioactive signals were visualized by autoradiography (Amersham Hyperfilm).
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9

Western Blot Analysis of Skin Scarring

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Mouse skin tissues (at the junction of normal and scar) of each group were isolated for western blot analysis. Samples were homogenized and proteins were extracted using RIPA buffer according to manufacturer’s protocol (Cell Signaling Technology, USA, for 30 minutes). Proteins were separated by SDS-PAGE (10% gel) and transferred onto polyvinylidene difluoride (PVDF) membrane (Sigma-Aldrich, USA). The membrane was blocked in 5% bovine serum albumin (BSA) for 2 hours at room temperature. Then, the blots were incubated with p-p38 (Cell Signaling Technology, USA, 1:1000, 4 °C overnight) or KGF-2 antibodies (R&D Systems, USA, 1 µg/mL, 4 °C overnight) in 5% BSA solution, followed by incubation with secondary antibodies conjugated with horseradish peroxidase for 1 hour. Signals were visualized with enhanced chemiluminescence (ECL) and exposure to Hyperfilm (Amersham Biosciences, UK). β-actin expression was served as a loading control.
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10

In Vitro Methylation Assay of SETDB1

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In vitro methylation assays were performed using normalized amount of flag immunoprecipitated (with the beads) SETDB1 (WT or CA or NLS) from total extract of stable ES cell lines, 1 μg recombinant H3.1 (NEB M2503S and 2 μl Adenosyl-L-methionine, S-[methyl-3H] (Perkin Elmer NET155V250C) in 50mM Tris pH8,20 mM KCl, 5 mM MgCl2, 1 mM DTT, 5% glycerol and incubated at 30°C for 2 hours. Samples were separated on 4-12% NUPAGE gels (Invitrogen NP0321BOX) in MOPS buffer (Invitrogen NP0001), Coomassie stained (Invitrogen LC6060). Then gel was dried and autoradiography performed on Amersham Hyperfilm (ref28906843) at -80°C.
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