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7 protocols using criterion stain free gel

1

Quantitative SDS-PAGE protein analysis

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Whole cell protein lysates were prepared as previously described or using denaturing lysis buffer followed by column homogenization per manufacturers’ instructions (101BIO, Mountainview, CA) (12 (link)). SDS-PAGE was performed using Bio-Rad Criterion Stain Free Gels (Hercules, CA) and after electrophoresis stain-free gels underwent activation using ultraviolet radiation on the ChemiDOC XRS+ platform to allow for visualization and quantification of protein loading. Total protein was quantified from the gel and/or the blot following transfer per manufacturer instructions. Chemiluminescence signals from bands of the expected sizes were detected and quantified on the ChemiDOC XRS+ platform and normalized to the corresponding total protein loaded from the corresponding sample.
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2

Quantifying GLUT4 Protein Distribution

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Immunoblotting of single fibers and wash solutions was performed by separating protein on 4–15% Criterion Stain‐Free gels (Bio‐Rad, Hercules, CA) as previously described (Murphy et al. 2012). Following transfer, nitrocellulose membranes were blocked and probed with GLUT4 antibody while being constantly rocked overnight at 4C and 2 h at room temperature. Following washes and exposure to the secondary antibody (goat anti‐rabbit IgG‐HRP, 1:20000, 31460, Pierce), chemiluminescent images were captured and quantified using densitometry (Chemidoc MP and ImageLab software, Bio‐Rad, Hercules, CA). The proportion of GLUT4 protein in a given pool was expressed as a percentage of the total GLUT4 in all four of the single fiber fractions, that is, %GLUT4 in Trit = GLUT4 density in Trit/sum densities GLUT4 (Diff + Amy + Trit + FSk).
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3

Quantification of Muscle Protein Levels

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The protein levels were quantified using cryosectioned slices of frozen soleus and EDL muscles using Western blotting procedures, as described in detail previously [39 (link),40 (link),41 (link)]. Proteins assessed included CSQ1, SERCA1, GLUT4, GS, glycogen branching enzyme (GBE), glycogen phosphorylase (GP), GDE, and COXIV as described by [40 (link)], with DHPR and RyR1 as described by [41 (link)]. In brief, proteins, including 4–5 amounts of a mixed muscle homogenate used as a calibration curve, were separated on 4–15% Criterion Stain Free gels (Bio-Rad, Hercules, CA). After transferring to nitrocellulose and a series of washes, including antibody probes, protein bands were visualized using West Femto chemiluminescent substrate (Thermo Scientific, Carlsbad, CA, USA), images collected, and densitometry performed using Chemidoc MP system and Image Lab version 5.2 (Bio-Rad, Hercules, CA, USA). Total protein on the gels was imaged prior to transfer (Stain Free imager, Bio-Rad) and Western blot signals of given proteins normalized to total protein with both total protein and protein of interest expressed relative to their respective calibration curves [39 (link)].
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4

Western Blot Analysis of Protein Fractions

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Nuclear and cytosplasmic fractions were separated with NE-PER extraction reagents, following the manufacturer’s instructions (Thermo Scientific). Protein yield was quantified via Coomassie Blue assay (Pierce), diluted in PBS, and combined with Laemmli sample buffer/2.5% β mercaptoethanol (1:1) (Bio Rad). Samples were heated to 95°C for 10 minutes and directly placed on ice. 10 ug protein were loaded to Criterion Stain-free gels and electrophoresed for 1 hour at 200v in 1X Tris/Glycine/SDS buffer (Bio Rad). Protein was transferred to PVDF membranes on a Trans-blot turbo transfer system following manufacturer’s instructions (Bio Rad) then blocked for 1 hour in 5% milk and TBST (0.1% tween). Membrane was incubated with primary antibody overnight at 4°C (1:200, Hmox 1: ab13243 (Abcam), actin: a2228 (Sigma) and Nrf2 sc-722 (Santa Cruz Biotechnology)) followed by secondary antibody at 1:10,000 concentration for one hour r.t. (HRP conjugated goat α rabbit, Invitrogen 31460). The membrane was developed with SuperSignal West Pico PLUS Chemiluminescent substrate (Thermo Scientific) and imaged for both total protein and HRP signal on a BioRad ChemiDoc MP imaging system.
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5

Quantifying Thermoascus Xylosidase Protein

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Example 15

The total protein content of the Thermoascus aurantiacus GH3 beta-xylosidase was determined by gel quantitation. Protein concentration was determined by SDS-PAGE using a 8-16% Tris HCl CRITERION STAIN FREE™ gel and a CRITERION STAIN FREE™ Imaging System SDS-PAGE (Bio-Rad Laboratories, Inc., Hercules, Calif., USA) in which the Talaromyces emersonii GH3 beta-xylosidase was used as a protein standard.

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6

Thermoascus aurantiacus GH3 Beta-Xylosidase Quantification

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Example 15

The total protein content of the Thermoascus aurantiacus GH3 beta-xylosidase was determined by gel quantitation. Protein concentration was determined by SDS-PAGE using a 8-16% Tris HCl CRITERION STAIN FREE™ gel and a CRITERION STAIN FREE™ Imaging System SDS-PAGE (Bio-Rad Laboratories, Inc., Hercules, Calif., USA) in which the Talaromyces emersonii GH3 beta-xylosidase was used as a protein standard.

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7

Quantifying Thermoascus Xylosidase Protein

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Example 15

The total protein content of the Thermoascus aurantiacus GH3 beta-xylosidase was determined by gel quantitation. Protein concentration was determined by SDS-PAGE using a 8-16% Tris HCl CRITERION STAIN FREE™ gel and a CRITERION STAIN FREE™ Imaging System SDS-PAGE (Bio-Rad Laboratories, Inc., Hercules, Calif., USA) in which the Talaromyces emersonii GH3 beta-xylosidase was used as a protein standard.

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