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97 protocols using ab110413

1

Western Blotting of Mitochondrial Complexes

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Cells were harvested in RIPA buffer followed by lysis by shaking the samples for 30 min at 950 rpm and 4 °C for 30 min. This was followed by centrifugation at 16,000g and 4 °C for 20 min to remove cell debris. Supernatants/lysates were kept at −80 °C until use. Then 10–20 μg of protein were separated on mini-PROTEAN TGX pre-stained gels (Bio-Rad) followed by activation of pre-stained Bio-Rad MP imager. The proteins were blotted onto Trans-Blot Turbo Transfer Packs (Bio-Rad), using Bio-Rad semidry blotter, and total protein for loading control was determined from the pre-stains. Membranes were blocked with 10% BSA or 5% skim milk (for mitochondrial complexes I–V experiments) in TRIS-buffered saline (TBS) unless otherwise stated and hybridized with antibodies for MICU2/EFHA1 (Abcam, ab101465), β-tubulin (Abcam, ab6046), α-tubulin (Abcam, ab7291), and mitochondrial complexes I–V (Abcam, ab110413).
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2

Mitochondrial Protein Quantification Protocol

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The primary antibodies used in this study were as follows: MitoProfile Total OXPHOS Rodent WB Antibody Cocktail [NADH dehydrogenase (ubiquinone) 1β subcomplex 8 (NDUFB8), succinate dehydrogenase complex subunit B (SDHB), ubiquinol-cytochrome c reductase core protein II (UQCRC2), ATP synthase, H+ transporting, mitochondrial F1 complex, α-subunit (ATP5A), ab110413, Abcam], NADH dehydrogenase (ubiquinone) iron-sulfur protein 4 (NDUFS4; ab139178, Abcam), cytochrome c oxidase subunit IV (COX IV; ab14744, Abcam), and CS (ab129095; Abcam). The following secondary antibodies were used in the present study: rabbit anti-goat IgG (H&L) (#A102PT; American Qualex, San Clemente, CA, United States ) and mouse anti-goat IgG (H&L) (#A106PU; American Qualex).
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3

Protein Extraction and Western Blot

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Tissue was homogenized in RIPA buffer containing protease (SIGMAFAST Protease Inhibitor Cocktail Tablet, Sigma) and phosphatase inhibitors (10 mM NaF, 1 mM Na3VO4) by steel bead disruption (3 x 90 sec at 30 Hz using the TissueLyser II, Qiagen). Protein amounts were normalized after determination of protein concentration using BCA protein assay kit (Pierce) in a standard laemmli buffer and subjected to SDS-PAGE, transferred to a PVDF membrane and blotted for DNMT3A (Abcam, #ab188470) or OXPHOS rodent cocktail (Abcam, #ab110413). Protein loading was determined using Bio-Rad stain-free technology.
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4

Western Blot Analysis of Brain Proteins

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Proteins from isolated brain microvessels and brain tissue were extracted using RIPA buffer with protease inhibitor and phosphatase inhibitor cocktail (Roche Applied Science, Vienna, Austria) described previously [12 (link)]. Protein samples were separated by SDS-PAGE and transferred to the PVDF membrane (Millipore, Burlington, MA, USA). Membranes were blocked with 5% skim milk for 1 h and then incubated at 4 ℃, overnight with specific primary antibodies against Crif1 (1:1000, sc-134882, Santa Cruz Biotechnology, CA, USA), Notch1 (1:1000, 3608, Cell Signaling, MA, USA), Hes1 (1:500, sc-166410. Santa Cruz Biotechnology, CA, USA), Total OXPHOS complex (1:1000, ab110413, Abcam), adropin (1:500, NBP1-26387, Novus biologicals, CO, USA), β-actin (1:1000, sc-47778, Santa Cruz Biotechnology, CA, USA). After washing three times for 10 min with TBS/T, membranes were incubated with secondary antibodies (1:1000, Sigma-Aldrich, St. Louis, MO, USA) for 2 h at room temperature. Membranes were washed, and signals were observed using an ECL solution (WEST-ZOL). Images were quantified with ImageJ software.
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5

Quantifying Mitochondrial Proteins in Quadriceps

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Quadriceps muscle was homogenised in radioimmunoprecipitation assay (RIPA) buffer, separated by SDS-PAGE and immunoblot analysis conducted as previously described [22 ,28 (link)]. Stain-free images were collected after transfer for loading control (ChemiDoc MP and ImageLab software version 4.1; Bio-Rad Laboratories, New South Wales, Australia). Membranes were probed with antibodies raised against PGC1α (cat: ab54481, Cell Signalling, USA) and total OXPHOS (cat: ab110413, Abcam, UK).
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6

Comprehensive Protein Analysis in Stem Cells

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The primary antibodies used were: OXPHOS (ab110413, Abcam), TOM20 (sc-11415, Santa Cruz), LC3 (B7931, Sigma for WB), LC3 (M152–3, MBL for immunostaining), pULK1 S757 (6888, Cell Signaling), p62 (610832, BD Bioscience), Ubiquitin (sc-8017, Santa Cruz), LAMP1 (sc-5570, Santa Cruz), TFEB (mbs120432, MyBiosource), Histone H3 (9715, Cell Signalling), GAPDH (ab8245, Abcam), Parkin (sc-32282, Santa Cruz), PINK1 (BC100–494, Novus), MTF2 (M6444, Sigma), OPA1 (612606, BD Bioscience), DLP1 (611113, BD Bioscience), Oct4 (09–0023, Stemgent), Nanog (4903, Cell Signaling Technologies), Sox2 (09–0024, Stemgent), SSEA4 (ab16287, Abcam), TRA 1–81 (09–0011, Stemgent), TRA 1–60 (09–0010, Stemgent) and Nestin (ab22035, Abcam). The secondary antibodies for immunoblot studies were horseradish peroxidase-conjugated anti-mouse (Jackson ImmunoResearch, West Grove, PA) or anti-rabbit (Thermo Fisher Scientific) and for immunofluorescence were anti-mouse or anti-rabbit Cyanine Cy2 or Cy3 labeled (Jackson ImmunoResearch) and anti-mouse or anti-rabbit Alexa Fluor 488 or 555 (Thermo Fisher Scientific).
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7

Mitochondrial Dynamics Regulation Assay

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Unless specified, all the chemicals were purchased from Sigma. Mdivi-1 was purchase from Enzo. Mouse anti-OXPHOS (Abcam, ab110413) and mouse anti-VDAC1 (Abcam, ab14734) were used in this study.
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8

Western Blotting for OXPHOS and GAPDH

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Western blotting was performed as previously described (17 (link),20 (link)). The cells were lysed in lysis buffer (20 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA and 1% Triton X-100) containing a protease inhibitor cocktail (Sigma-Aldrich; Merck KGaA). The total protein concentrations were measured by a BCA Protein Assay kit (Sigma-Aldrich; Merck KGaA). After heat-denaturing, equal quantities of proteins (20 µg) were separated by NuPAGE Novex 12% Bis-Tris Gel and electrophoresed in the XCell SureLock™ Mini-Cell (both from Invitrogen; Thermo Fisher Scientific, Inc.), and then transferred to polyvinylidene difluoride membranes and blocked with 5% non-fat milk in Tris-buffered saline (TBS) for 1.5 h at the room temperature. The membranes were incubated with primary antibodies against OXPHOS (ab110413; 1:1,000; Abcam, Cambridge, UK) or GAPDH (AB2302; 1:1,000; EMD Millipore, Billerica, MA, USA) overnight at 4°C. After washing three times with 1X TBS, the membranes were incubated with secondary antibodies [anti-mouse (AP181R) and anti-rabbit antibodies (AP187R); 1:10,333; EMD Millipore] for 1.5 h at room temperature. After washing steps, immunoreactive binding was detected with ECL detection reagent (Amersham Biosciences, Piscataway, NJ, USA) with MicroChemi 4.2. The band intensity was quantified using ImageJ 1.47 software.
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9

Immunoblotting of Signaling Pathways

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Primary antibodies used were anti-phospho-Akt (Ser473; #4060, Cell Signaling), anti-pan-Akt (#2920, Cell Signaling), anti-phospho-P44/42 MAP(ERK1/2) (#9101, Cell Signaling), anti- P44/42 MAPK (ERK1/2) (L34F12) (#4696, Cell Signaling), anti-phospho-mTOR (SER2448 (D9C2), #5536, Cell Signaling), anti-mTOR (# 2972, Cell Signaling), anti-oxidative phosphorylation (OXPHOS) complexes I to V (#ab110413, Abcam), anti-KLF10 (#ab73537, Abcam), and β-actin (#4970, Cell Signaling).
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10

Quantitative Western Blot Analysis of Mitochondrial Proteins

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Western blot analysis was performed for 4-HNE, LRP1, mitochondrial OXPHOS complex proteins, NDUFS1, PDGFR-β, and TFAM. Cell lysates were formed using RIPA buffer (150 mM NaCl, 1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 50 mM Tris, pH 8.0) and centrifuged at 16,100× g for 30 min, and the total protein levels were estimated from the supernatant using a BCA kit (23225, Thermofisher). Western blot samples were obtained using XT sample buffer (1610791, Biorad, Hercules, CA, USA) with DTT and boiled at 95 °C for 10 min. The samples (15–20 µg protein, Eastbourne, UK) were resolved in duplicate 4–12% BIS-TRIS gel (3450125, Biorad, Hercules, CA, USA) under reducing conditions and transferred to the PVDF membrane. Probing was performed against 4-HNE (1:2500; HNE11-S, alpha diagnostic international, San Antonio, TX, USA), LRP1 (1:1000; sc-57351, Santa Cruze biotechnology, Dallas, TX, USA), NDUFS1 (1:1000, ab169540, abcam, Cambridge, UK), total OXPHOS antibody cocktail (1:1000; ab110413, abcam), mtTFA (1:1000, ab131607, abcam), and beta-actin (1:5000; 8H10D10, Cell Signaling, Danvers, MA, USA). The signals were detected using IRDy 68RD goat anti-mouse (1: 10,000; 926-68070, Li-Cor, Lincoln, NE, USA) and IRDye 800 CW goat anti-rabbit (1:10,000; 926-32211, Li-Cor). The protein levels were quantified via densitometric analysis using ImageJ software.
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