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To examine whether protein expression in the hypothalamus was altered in tumour-bearing anorexic mice compared with free-fed control mice and caloric-restricted pair-fed mice, extracts from the hypothalami were separated by high-resolution two-dimensional electrophoresis (2-DE) using three different narrow pH range IPG strips (IPG 3 6, IPG 5 8, and IPG 7 10; experiment 1).
Data for the six spots that were identified in the IPG 3 6 and IPG 5 8 strips but that could not be validated in the independent samples (IPG 3 10NL) are given in Supplementary Table 1.
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After centrifugation at 19,000 g for 40 min, at 4°C, the supernatant was added with 105 mg of urea, 1.25 mg of CHAPS, 2 µl of Pharmalyte, 2 µl of IPG, 2 mg of DTT in order to obtain a rehydration buffer (8 M urea, 0.5% CHAPS, 1.6% IPG buffer, 1.6% Pharmalyte, 1% DTT), and a trace of bromophenol blue.
Pre-cast immobilised pH gradient strips (IPG, 11 cm, pH 3 10, Proteome Systems, North Ryde, Australia) were passively rehydrated in 200 µg sample protein extract for 6 hr at room temperature.
The gel strip was then placed in the sample lane of a 10-20% Tris-HCl IPG +1 well, 1 mm Criterion gel (BioRad) and sealed with agarose sealing solution (25 mM tris, 192 mM glycine, 0.1% SDS (w/v), 0.5% agarose, and 0.002% (w/v) bromophenol blue.
Immobilised pH gradient (IPG) strips (17 cm) with pH range (IPG 3 6, IPG 5 8, IPG 7 10, and IPG 3 10NL; Bio-Rad Laboratories) were used for isoelectric focusing (IEF).
Three identical spots (spot 5, 10, and 12) were found independently in gels using IPG 3 6 and IPG 5 8.
For IPG 3 6, IPG 5 8, and IPG 3 10NL, the individual samples (200 μg of proteins) were loaded during rehydration of the IPG strips in 300 μl (total volume) of IEF buffer (7 M urea; 2 M thiourea; 4% CHAPS; 10 m M 1,4-dithioerythritol; IPG buffer, pH 3 10) for 18 h.
The sample mixture was loaded onto pH 4-7 IPG, 17 cm strips (GE Healthcare).
The preparation (60 μg protein) was added to DeStreak Rehydration Solution containing IPG (0.5% IPG buffer 3 10 nonlinear; Amersham Biosciences, Uppsala, Sweden).
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