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8 protocols using cox5a

1

Western Blot Analysis of Mitochondrial Proteins

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Whole heart or isolated mitochondrial samples were lysed with RIPA buffer and protein content was measured using a Bradford assay [6] (link). Protein samples and molecular weight standards were separated by 1D gel electrophoresis. After transfer to a PVDF membrane, the membrane was incubated with antibody that recognizes proteins such as mt-COX-1 (Cat#sc-58347) (Santa Cruz Biotechnologies Inc., Santa Cruz), mt-COX2 (Cat#A-6404) (Life Technologies, Carlsbad, CA), MCU (Cat#ab121499), TFAM (Cat#ab131607), COX 5A (Cat#ab180129), COX 5B (Cat#ab110263) and COX VIIa (Cat#ab110268) (Abcam, Cambridge, MA) and VDAC (Cat#4866) (Cell Signaling Technologies, Danvers, MA) in Tris-Buffered Saline (pH 7.4) with 1% TWEEN 20 (TBS-T) with 5% BSA or nonfat dry milk at 4°C overnight. Membranes were incubated with the secondary antibody, appropriate horseradish peroxidase–conjugated IgG in TBS-T with 5% nonfat dry milk for 1 hour at room temperature. Immunoreactive protein was visualized using an enhanced chemiluminescence analysis kit (GE HealthCare, Piscataway, NJ).
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2

Mitochondrial Protein Expression Analysis

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The Eu was purchased from National Institutes for Food and Drug Control (China). Dulbecco’s modified Eagle medium (DMEM), Nutrient Mixture F-12 (DMEM/F12) media, horse serum, trypsin and penicillin/streptomycin, were obtained from Life Technologies, GibcoBRL (Rockville,MD,USA). Antibodies against CPT-1C and Tomm20 were purchased from Santa Cruz Biotechnology (Santa Cruz, CA,USA). Antibodies against ERRα and c-Myc were obtained from Cell Signaling Technology (Beverly, MA,USA) and an antibody against the HRAS, PGC-1β, NDUFB8, SDH-B, UQCRC2, ATP5A, COX5A, MCAD and PPARα were obtained from Abcam (Cambridge, MA, USA). 10058F4 were purchased from Sigma-Aldrich (St.Lois, MO, USA). XF Palmitate-BSA FAO Substrate was obtained from seahorse Bioscience (North Billerica, MA, USA).
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3

Mitochondrial Protein Expression Analysis

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Stable H9c2 cells, mouse heart, and isolated mitochondrial fractions were lysed with RIPA buffer, and protein content was measured using the Bradford assay. Cell and tissue homogenate protein was separated by 1‐dimensional gel electrophoresis. After transfer to a polyvinylidene difluoride membrane, the membrane was incubated with antibodies that recognize proteins such as mt‐COX1 (Abcam, Cambridge, MA), mt‐COX2 (Life Technologies, Carlsbad, CA), mt‐COX3 (Life Technologies, Carlsbad, CA), COX 5A (Abcam, Cambridge, MA), COX 5B (Abcam, Cambridge, MA), COX VIIa (Abcam, Cambridge, MA), pAkt at Ser 473 (Cell Signaling, Danvers, MA), Akt (Cell Signaling, Danvers, MA), α‐tubulin (Abcam, Cambridge, MA), and VDAC (Abcam, Cambridge, MA) in Tris‐buffered saline (pH 7.4) with 1% TWEEN 20 (TBS‐T) and 5% BSA or nonfat dry milk at 4°C overnight. Membranes were incubated with the appropriate secondary antibody conjugated to horseradish peroxidase IgG in TBS‐T with 5% nonfat dry milk for 1 hour at room temperature. Immunoreactive protein was visualized using an enhanced chemiluminescence analysis kit (EMD Millipore, Temecula, CA).
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4

Synthesis and Analysis of Compound 29

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Compound 29 (4-{4-[(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]-2-methoxyphenoxy}-3-(trifluoromethyl)benzonitrile, 95%) (17 (link)) was synthesized by MolPort. Oligomycin, carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP), antimycin A and rotenone were all purchased from Sigma-Aldrich. The following antibodies were used: PGC1α (H300, Santa Cruz; ST1202, EMD Millipore), ERRα (N1, GeneTex), mtCOI (Abcam), actin (Cell Signaling), SOD2 (GeneTex), GPX1 (GeneTex), pFAK-Y397 (Cell Signaling), COX4 (Abcam), COX5A (Abcam), UQCRC2 (Abcam), tubulin (Abcam), histone H3 (Abcam), and Ki-67 (Thermo Fisher).
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5

Integrin and Transcription Factor Regulation

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PLX4032, PD98059, AZD6244 and PF-573228 were purchased from Selleck Chemicals. The siRNAs against TCF4 (sc-61657), c-Myc (sc-29226), TCF3 (sc-36618) or TCF12 (sc-35552) were purchased from Santa Cruz Biotechnology. Antibodies against ITGA4, ITGA5, ITGB1, ITGB3, ITGB4, ITGB5, FAK, c-Myc, TCF12, and Porin were purchased from Cell Signaling Technology; p-FAK (Y397) antibodies were from Cell Signaling and Thermo Fisher Scientific, ID2 antibodies were from Cell Signaling, Santa Cruz Biotechnology and Thermo Fisher; V5, HMB45, COX5A, NDUFS4 and NDUFA9 antibodies were from Abcam; TCF4 antibodies were from Abnova and Santa Cruz; and PGC1α antibodies were from Santa Cruz and Millipore.
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6

Immunoblotting of Mitochondrial Proteins

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Reagents were purchased from Merck-Life Sciences (Gillingham, UK) or Thermo Fisher Scientific (Loughborough, UK). Primary antibodies for: phosphor-AMPK (T172), AMPK, phospho-AKT (Ser473), AKT, phosphop44/42 (ERK1/2) (Thr202/Tyr204), ERK1/2,c-CBL, CAP, CBL-b, were from Cell Signaling (Leiden, NL); β-TUBULIN and ACTIN from Merck-Sigma-Aldrich; NDUFA from Thermo Fisher; CORE2, COX5A and SDHA from Abcam. HRP-conjugated secondary antibodies were from Thermo Fisher.
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7

Native PAGE Analysis of OXPHOS Subunits

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Native PAGE was carried out as previously reported [51 (link)]. Briefly, 3–13% acrylamide gradient gels were loaded with 60 μg of mitochondrial protein and processed as described. After electrophoresis, proteins were transferred to a PROTAN® nitrocellulose membrane (Schleicher and Schuell, Bioscience GmbH, Dassel, Germany) at 35 V, overnight, and probed with specific antibodies raised against the following human OXPHOS subunits: NDUFA9, CORE2, COX2, COX5A, and SDHA (from Mitosciences, Eugene, OR, USA). Peroxidase-conjugated anti-mouse IgG was used as a secondary antibody (Molecular Probes, Thermofisher Scientific, Gilligham, UK). The signal was detected with ECL® plus (Amersham Biosciences, Freiburg, Germany).
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8

Comprehensive Western Blot Analysis

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Western blot was performed using primary antibodies raised against COX7A2L (ProteinTech), Myc (Origene), turbo-GFP (Origene), HA (Roche), β-actin (Sigma), and against the following human OXPHOS subunits: NDUFS1 (GeneTex); NDUFA9, NDUFB8, CORE2, RISP, CYC1, UQCRB, UQCRQ, COX1, COX4, COX5A, COX6C, SDHA, SDHB (Mitosciences); and COX5B (Santa Cruz). Peroxidase-conjugated anti-mouse and anti-rabbit IgGs were used as secondary antibodies (Molecular Probes). Immunoreactive bands were detected with an ECL prime Western Blotting Detection Reagent (Amersham) in a ChemiDoc™ MP Imager (Biorad). Optical densities of the immunoreactive bands were measured using the ImageLab™ (Biorad) and ImageJ analysis softwares.
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