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31 protocols using ab110411

1

Western Blot Analysis of Endothelin-1, NOX2, and OXPHOS

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Protein concentrations of the LV tissues were determined by the BCA protein assay kit (Thermo Fisher, Erembodegem, Belgium). Western blot was performed as previously described40 (link). Briefly, equal amounts of proteins (15 µg) were separated on a 12% SDS-PAGE gel with a mini protean 3 electrophoresis system (Bio-rad Laboratories, Temse, Belgium), transferred to a polyvinylidene fluoride (PVDF) membrane and subsequently, blocked for 2 h with 5% milk in Tris-buffered solution containing 0.1% Tween-20 (TBS-T) followed by incubation overnight at 4 °C in the presence of a specific endothelin-1 antibody (1/2500, Abcam, ab117757, Cambridge, United Kingdom), NOX2 antibody (1/2500, Abcam, ab31092, Cambridge, United Kingdom) or an OXPHOS antibody (1/1000, Abcam, ab110411, Cambridge, United Kingdom). Horseradish peroxidase-conjugated secondary antibodies (DAKO, Belgium) at a dilution of 1/2000 were used. Both primary and secondary antibodies were diluted in 5% milk-TBS-T. Visualization was performed with the enhanced chemiluminescence (ECL) technique using the Pierce ECL Plus western Blotting Substrate (Thermo Fisher, Erembodegem, Belgium). Data were normalized to β-actin protein levels.
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2

Muscle Biopsy and Protein Analysis

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For both pre and post-intervention muscle biopsies, it was ensured that participants were fasted state (10–12 h) and refrained from physical activity for 72 h prior to collection. Final training sessions were staggered across all groups to ensure accurate timing of the 72 h post-training muscle samples. After administration of a local anaesthetic (2% plain Lignocaine) a muscle biopsy was obtained from the lateral portion of the m. vastus lateralis of each participant. Using a 5-mm Bergstrom needle an ~100 mg sample was obtained, blotted on filter paper, removed of fat and connective tissue, frozen in liquid nitrogen and stored at -80°C until further analysis. Samples were analyzed for total protein content of PGC-1α (Calbiochem ST1202), nuclear respiratory factor (NRF)1 (Abcam ab34682), NRF2 (Santa Cruz sc-22810), mitochondrial transcription factor (Tfam; Abcam ab47517), mitochondrial complex I-V (Mitoprofile Human Total OXPHOS antibody cocktail, Mitosciences ab110411), myocyte enhancer factor 2A (MEF2A; Abcam ab87975), SIRT 1 (Cell Signaling 8469), GLUT4 (Millipore CBL242), p53 (Cell Signaling 2527), AKT (Cell Signaling 9272) and α-tubulin (Cell Signaling 2125), which was used as a loading control.
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3

Mitochondrial Dynamics and Apoptosis Analysis

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Cell pellets were lysed in RIPA buffer containing 1× HaltTM protease inhibitor cocktail (78437, Thermo) and supernatants collected after 10 min centrifugation at 12000 × g for SDS-PAGE. Total proteins were transferred to PVDF membranes and blotted with the antibodies against FIS1 (ab71498, Abcam), MFN1 (ab104274, Abcam), β-Actin (ab8227, Abcam), Caspase-3 (9665, Cell Signaling), Caspase-8 (sc-5263, Santa Cruz), Caspase-9 (sc-8355, Santa Cruz), HSP70 (TA309356, Origene) and Total OXPHOS Human WB Antibody Cocktail (ab110411, Abcam).
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4

Profiling Mitochondrial Protein Levels

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The following primary antibodies were used in this study: MS601 (ab110411, Abcam, 1:1000 dilution), NDUFB8 (ab110242, Abcam, 1:1000 dilution), SDHA (ab14715, Abcam, 1:2000 dilution), UQCRC2 (ab14745, Abcam, 1:1000 dilution), COXI (ab14705, Abcam, 1:1000 dilution), ATP5A (ab14748, Abcam, 1:1000 dilution), and β-actin (Cloud Clone Corp. CAB340Hu22, 1:10 000 dilution). HRP-conjugated mouse secondary antibody was used (DAKO, P0260, 1:2000 dilution), followed by detection using the ECL (GE Healthcare) and BioRad imaging system (Image Lab).
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5

Analyzing Mitochondrial Protein Expression

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Protein expression was analyzed as previously described25 (link). Briefly, frozen human left ventricles (LV) in each group were homogenized in an ice-cold lysis buffer containing protease and phosphatase inhibitors (5872 S; Cell Signaling), centrifuged and the supernatant was transferred to a new tube. Total protein concentration was determined using a BCA protein assay kit according to the manufacturer’s instructions (23225; Thermo Scientific). Lysates were loaded and separated using SDS-PAGE and then transferred onto a PVDF membrane. The following antibodies were used in the present study: anti- phosphorylated (S616) (1:1000; 3455; Cell Signaling) and total Dynamin-like protein 1 (DRP1) (1:1000; ab56788; Abcam) anti- Mitofusin 1 (MFN1) (1:2000; ab57602; Abcam), anti-Mitofusin 2 (MFN2) (1:2000; ab56889; Abcam), anti- Optic Atrophy 1 (OPA1) (1:1000; 612606; DB Biosciences), total OXPHOS human WB antibody cocktail (1:2000; ab110411; Abcam), anti-ATP5A subunit (1:1000; sc-136178; Santa Cruz) and anti-GAPDH (1:1000; ab8245; Abcam).
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6

Protein Expression Analysis by Western Blot

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The tissues or cultured cell pellets were homogenized in RIPA lysis buffer (Tris-HCl pH7.4, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) by sonication on a Branson Digital Sonifier. Protein concentrations were determined with the BCA reagent (Pierce). Protein lysates (40 ug) were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and proteins were transferred onto nitrocellulose filters. The blots were saturated with 5% milk and probed with antibodies against SHMT2 (#HPA020543, Sigma, 1:1000), NDUFS1 (sc-271510, Santa Cruz, 1:1000), Total OXPHOS Antibody Cocktail (ab110411, Abcam, 1:1000), ACLY (#15421-1-AP, Proteintech, 1:1000), ACC1 (#21923-1AP, Proreintech, 1:1000), FASN (#10624, Proteintech, 1:1000) or β-actin (A2066, Sigma, 1:1000). Following a wash with PBST (PBS containing 0.1% Tween 20), the blots were incubated with peroxidase-coupled goat anti-rabbit immunoglobulin G (Sigma, 1:5000). The immunolabeled protein bands were detected by enhanced chemiluminescence (ECL) method (Perkin Elmer) on an Azure C600 imager.
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7

Protein Expression Analysis in Cells

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Cells were lysed using M-PER (Mammalian Protein Extraction Reagent) (Thermo Scientific) per manufacturer instructions. Amicon Centrifugal filters (Millipore) were used for protein concentration. Following protein estimation by DC™ Protein Assay Kit II, samples were loaded onto 4-12% SDS-PAGE gel (Novex) and transferred to a membrane utilizing a Trans-blot turbo system (Biorad). The membranes were blocked with 3% BSA for 1h and incubated overnight with a primary antibody against mGPDH (1:700; Abcam; ab188585), OCT1 (SLC22A1) (1:1000; Abcam; ab181022) and total OXPHOS (1:500; Abcam; ab110411). GAPDH (1:1000; Invitrogen; MA5-15738) and Porin (1:1000; Abcam; ab14734) were used as endogenous controls. After 3x washing with TBST, the membrane was incubated with the secondary antibody (1:10000) and washed 3x. The blot was visualized using ECL (Thermo Scientific) and imaging system (Bio-Rad). The relative protein expression was quantified by densitometry using Fiji - ImageJ software.
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8

Detecting POLRMT and OXPHOS Proteins

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2 × 106 OCI-AML2 cells were pelleted and frozen at −80 degrees. For the detection of POLRMT, cells were lysed in RIPA lysis buffer and proteins were separated on a 7.5% PAGE minigel (Bio-Rad Laboratories). For mitochondrial proteins, cells were lysed in 1.5% n-beta-maltoside (Sigma) dissolved in PBS. Lysates were supplemented with Halt protease inhibitors (Thermo Scientific) and 0.5 mM EDTA. For mitochondrial proteins, separation was performed on a 12% PAGE gel. Semi-dry transfer was performed (Trans-Blot SD, Bio-Rad) onto PVDF membranes. Primary antibodies and concentrations were: POLRMT, Abcam ab32988, 1:250; OXPHOS cocktail, Abcam ab110411, 1:1,000 (contains antibodies against complex I, NDUFB8, complex II, SDHB, complex III, UQCRC2, complex IV, COXII, complex V, ATP5A), and alpha-tubulin, 1:1000.
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9

Quantitative Protein Expression Analysis

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Twenty micrograms of patient skeletal muscle protein lysates were prepared using NuPAGE LDS sample buffer (Thermo) and NuPAGE reducing agent, denatured at room temperature for 10 minutes and loaded into 4–12% gradient SDS-PAGE gels (Thermo, NP0322). Proteins were separated and transferred to a PVDF membrane using an iBlot2 dry transfer system (Thermo). PVDF membranes were blocked using 5% milk in Tris buffer-saline with 1% tween-20 (TBS-T) at room temperature for 1 hour before probing using monoclonal antibodies targeting NDUFB8, SDHB, UQCRC2, COX2, and ATP5A (Abcam, ab110411) as well as antibodies targeting GAPDH (Abcam, ab8245) and VDAC1 (Abcam, ab14734). Membranes were washed in TBS-T and probed again for 1 h with HRP-conjugated anti-Mouse IgG (Abcam, ab97023) prior to chemiluminescent imaging. Quantification was performed using ImageJ.
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10

Mitochondrial Protein Expression Analysis

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Lipoic acid (437695, Calbiochem/Merck, Darmstadt, Germany); Hsp60 (AB1-SPA-807-E, Enzo Lifesciences Farmingdale, US); Human OXPHOS cocktail (ab110411, Abcam, Cambridge, UK; 1:1000); VDAC1 (ab14734, Abcam; 1:5000); SLC25A26 (ab175209, Abcam; 1:1000); GAPDH (600004, Proteintech; 1:5000) SDHA (ab14715, Abcam; 1:1000), COXI (ab14705, Abcam; 1:1000); NDUFB8 (ab110242, Abcam; 1:1000); UQCRC2 (ab14745, Abcam; 1:1000); ATP5A (ab14748, Abcam; 1:1000). Secondary antibodies used include Polyclonal Donkey Anti-Rabbit Ig/HRP (NA9340V, SigmaAldrich, St. Louis, US); Polyclonal Sheep Anti-Mouse Ig/HRP (NA9310V, SigmaAldrich); Polyclonal Rabbit Anti-Mouse Ig/HRP (P0161, Dako/Agilent; 1:2000) and Polyclonal Swine Anti-Rabbit Ig/HRP (P0399, Dako; 1:3000).
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