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8 protocols using gs 700 densitometer

1

Quantifying COX-2 and Perilipin-2 in Macrophages

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COX-2 and perilipin-2 protein levels in cultured macrophages were detected by Western blotting. Aliquots of MT-III-stimulated and non-stimulated cells (1.5×106 cells) were lysed with 100 μL sample buffer (0.5 M Tris-HCl, pH 6.8, 20% SDS, 1% glycerol, 1 M β-mercapto ethanol, 0.1% bromophenol blue) and boiled for 10 min. Samples were resolved by SDS-PAGE on 10% bis-acrylamide gels overlaid with a 5% stacking gel. Proteins were then transferred to nitrocellulose membranes using a Mini Trans-Blot (Bio-Rad Laboratories, Richmond, CA, USA). The membranes were blocked for 1 h with 5% nonfat dry milk in Tris-buffered saline (TBS) (20 mM Tris, 100 mM NaCl, and 0.5% Tween 20, pH 7.2), and incubated with primary antibodies against COX-2 (1∶1000 dilution), perilipin-2 (1∶2000) and β-actin (1∶3000) for 1 h. They were then washed and incubated with the appropriate secondary antibody conjugated to horseradish peroxidase. The immunonereactive bands were detected by the entry-level peroxidase substrate for enhanced chemiluminescence (ECL), according to the instructions of the manufacturer (GE Healthcare). Band densities were quantified with a GS 700 densitometer (Bio- Rad Laboratories) using the image analysis software Molecular Analyst (Bio-Rad Laboratories).
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2

Immunoblot Analysis of Protein Dynamics

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Immunoblot (IB) experiments were performed as described previously (Jones et al., 2004 (link), 2007 (link); Balut et al., 2010a (link),b (link); Gao et al., 2010 (link); Bertuccio et al., 2014 (link); Farquhar et al., 2017 (link)). Briefly, cells were lysed and protein concentrations were determined by the BCA protein assay (Walker, 1994 (link)). Equal amounts of protein (30 μg) were loaded into wells of a gel (6 or 8%) and protein standard (8 μl) used (BenchMark™ pre-stained protein ladder; Invitrogen, Cat No. 10748-010) and resolved with SDS-PAGE for 150 mV for 90 min (Hoefer Mighty Small II system, Cat. No. 80-6149-35, Amersham Biosciences Corp. Piscataway, NJ, USA). Proteins were transferred (50 V, 2 h) with a semi-dry transfer unit (Hoefer, EPS 2A200) to polyvinylidene difluoride (PVDF) membranes for further IB analysis with α-streptavidin antibody. Proteins bands were visualized by enhanced chemiluminescence detection (Lumilight, Roche, Basel Switzerland). Blots were probed for β-actin as a protein loading control. The bands obtained from immunoblot analysis were quantified by densitometry, using the GS-700 densitometer (Bio-Rad) and the Quantity One programme (BioRad laboratories). The obtained band intensities for the various time points were normalized to β-actin and then compared relative to the intensity at time 0 (t = 0) and reported.
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3

Quantifying Apoptotic Protein Expression

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Bax, Bcl-2, Bad, and Bcl-xl protein expression was determined on nuclear proteins separated from neuronal nuclei by SDS–polyacrylamide gel electrophoresis and transferred to nitrocellulose membranes using a wet trans-blotting system (Ravishankar et al., 2001 (link)), as well as on cytosolic (Halat, 1992 (link)) and mitochondrial proteins (Lasso Pirot et al., 2007 (link)). The membranes were incubated with polyclonal anti-Bax, anti-Bcl2, anti-Bad, or anti–Bcl-xl antibodies (Santa Cruz Biotechnology). Immunoreactivity was then detected by incubation with horseradish peroxidase–conjugated secondary antibody (Rockland Immunochemicals). Specific complexes were detected by enhanced chemiluminescence method using the ECL detection system (Amersham Pharmacia Biotech) and analyzed by imaging densitometry (GS-700 densitometer, Bio-Rad). The densitometric scanning data were expressed as autoradiographic values per immunoblot protein. Concomitant actin protein gels were run to demonstrate the consistent amounts of protein in each sample. Samples were run in duplicates. Proteins were expressed as absorbance/OD (OD × mm2).
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4

Protein-Protein Interaction Assays

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The Y2H system (Lam et al., 2013 (link); Stanczyk et al., 2016 (link); Zissimopoulos et al., 2006 (link)), co-IP and WB (Stanczyk et al., 2016 (link); Zissimopoulos et al., 2012 (link), 2013 (link)), cardiac SR preparation (Zissimopoulos et al., 2012 (link)) and single-cell Ca2+ imaging (Handhle et al., 2016 (link); Seidel et al., 2015b (link)) were carried out as previously described. Densitometry analysis was carried out using GS700 densitometer (Bio-Rad) and Quantity-one (Bio-Rad) software. Microsoft Excel was used to store and plot numerical data (expressed as mean±s.e.m.), unless otherwise stated. Statistical analysis was performed using GraphPad prism (GraphPad Software Inc). Data were first subjected to the Brown–Forsythe test for the equality of group variances, and populations with equal variance (no significantly different standard deviations, P<0.05) were analysed using one-way ANOVA (with Bonferroni's post-test). Where data were non-normally distributed, the Kruskal–Wallis test (with Dunn's multiple comparisons test) was used.
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5

Quantitative Analysis of Bcl-2 and Bax Proteins

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Protein was extracted from frozen left ventricular tissue. Bovine serum albumin as a standard protein concentration was determined by the bicinchoninic acid protein assay (Pierce Rockford, IL). Equal proteins were loaded on 12% SDS-PAGE which were confirmed by Coomassie blue staining. The sample volume is 40 μg. Proteins were transferred to a polyvinylidene membrane [31 (link), 32 (link)]. Rat anti-Bcl-2 monoclonal antibody (Santa Cruz Biotechnology; Santa Cruz, CA) and mouse anti-Bax monoclonal antibody (Santa Cruz Biotechnology; Santa Cruz, CA) were used for Bcl-2 and Bax detection, respectively. The bands were visualized by Phototope-HRP Western blot detection kit (New England Biolabs, Beverly, MA) and were scanned by GS-700 densitometer (Bio-Rad Company, Hercules, CA) and then quantified by quantitative procedure. Optical density of the tissue samples was normalized to the control sample in arbitrary densitometry unit.
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6

Quantifying Neuronal pCREB Density

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Expression of phosphorylated cAMP response element binding protein (pCREB) density was determined through previously described Western blotting techniques (Mishra and Delivoria-Papadopoulos, 2002 (link); Fritz et al., 2005 (link)) on neuronal nuclear membranes. The membranes were incubated with anti-pCREB Ser133 antibodies. Specific Immunoreactivity was then detected by incubation with horseradish peroxidase–conjugated secondary antibody (Rockland Immunochemicals). Specific complexes were detected by enhanced chemiluminescence method using the ECL detection system (Amersham Pharmacia Biotech) and analyzed by imaging densitometry (GS-700 densitometer, Bio-Rad). The densitometric scanning data were expressed as autoradiographic values per immunoblot protein. Concomitant actin protein gels were run to demonstrate the consistent amounts of protein in each sample. Samples were run in duplicates. Proteins were expressed as absorbance/optical density (OD × mm2).
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7

Quantifying p53 Protein Expression

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The hippocampus was removed from the brains of the nine mice in each group. Proteins (40 μg per lane) were separated by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis and transferred to nitrocellulose membranes (Hybond-C, Amersham, Buckinghamshire, UK) by electroblotting. Membranes were incubated in 5% nonfat milk for 1 h and incubated with antibodies to anti-p53 (Santa Cruz), and developed using enhanced chemiluminescence (Amersham). The band density was measured by a GS-700 densitometer (Bio-Rad).
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8

Irr Binding Affinity to DNA Motifs

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Electrophoretic mobility shift assays (EMSA) were used to analyze the binding of purified Irr to various DNA probes in vitro as described previously (Friedman and O’Brian, 2004 (link)). The negative-control DNA corresponds to the sequence found in the multiple-cloning site of pBluescript SK+. The test DNA probes were 45 bp in length and contained 21-bp ICE (underlined in the sequences below) flanked either by the original genomic flanks or the genomic flanks of a different ICE motif. The sequences of the probes are shown in Fig. S1. EMSA reactions were analyzed as autoradiograms of 5% non-denaturing polyacrylamide gels. Autoradiograms were scanned using GS-700 densitometer (Bio-Rad), and signal intensities were determined and quantified by Quantity One software (Bio-Rad). To determine the dissociation binding constant (Kd), binding reactions containing 0.1 nM 32P-labelled DNA were titrated with various concentrations of Irr. Bound and unbound DNAs were quantified by comparing relative signal intensities and analyzed using GraphPad Prism software (GraphPad software Inc., San Diego, CA)
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