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PINK1 is a protein kinase that plays a crucial role in mitochondrial homeostasis. It is involved in the regulation of mitophagy, a process that selectively removes damaged or dysfunctional mitochondria from the cell. PINK1 acts as a sensor, detecting mitochondrial depolarization and initiating the recruitment of Parkin, an E3 ubiquitin ligase, to promote the degradation of these organelles.

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20 protocols using pink1

1

Western Blot Analysis of Mitochondrial Proteins

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Immunoblotting was performed as described in Supplemental Methods. The primary antibodies used were as follows: LC3A/B (Cell signaling), Porin/anti VDAC1 (Abcam), Drp1 (BD transduction laboratories), Pgc1a (H 300), PINK1, β-actin (Santa Cruz Biotechnology Inc.), Mfn1 (Abcam), Mfn2 (Abnova).
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2

Vasicinone's Neuroprotective Effects on Paraquat-Induced Oxidative Stress

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Vasicinone (purity > 98%) was purchased from Cayman Chemical (CAS-486-64-6, Ann Arbor, MI, USA). Paraquat, a Mitochondria Staining Kit (JC-1 stain) and 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyltetrazolium bromide (MTT) were purchased from Sigma-Aldrich (St. Louis, MO, USA). The MitoSOXTM Red kit (M36008) was purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dulbecco’s modified Eagle medium (DMEM:F12) and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Primary antibodies against SOD-1, SOD-2, GST, GPx, TOM-20, VDAC-1, Parkin, PINK-1 and GAPDH were purchased from Santa Cruz Technology (Dallas, TX, USA), antibodies against DJ-1, α-synuclein, p-ULK, ATG7, ATG12 and LC3B were purchased from Cell Signaling Technology (Danvers, MA, USA) and an antibody against Nrf-2 was purchased from Abcam (Cambridge, MA, USA). All fluorescent secondary antibodies were purchased from Thermo Fisher Scientific in the USA.
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3

Protein Expression Analysis in TH1 Cells and Renal Cortex

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The whole cell lysates, cytosol fraction lysates, or mitochondrial fraction lysates were prepared from TH1 cells and renal cortex tissue. Protein concentration was determined by employing the BCA method, and 30 μg of protein per sample was loaded for western blotting. Electrophoresis in 8–12% sodium dodecyl sulfate-polyacrylamide gel was followed by a transfer to polyvinylidene difluoride membranes. The blots were washed with TBST (10 mM Tris-HCl, 150 mM NaCl, 0.05% Tween-20) and blocked with 5% skim milk for 1 h at room temperature. Subsequently, we incubated the blot with the appropriate primary antibodies: against PINK1 (Santa Cruz Biotechnology, Dallas, TX, USA, sc-517353), SIAH3 (Novus, Littleton, CT, USA, NBP2-83524), LC3B (Novus, NB100-2220), P62/SQSTM1 (Novus, NBP1-48320), p-DRP1 (Ser637) (Cell Signaling Technology, #4867S), DRP1 (Santa Cruz Biotechnology, sc-271583), MFN1 (Santa Cruz Biotechnology, sc-166644), OPA1 (Novus, NBP1-71656), ubiquitin (Novus, NB300-130), VDAC1 (Novus, NB100-695), α-tubulin (Santa Cruz Biotechnology, sc-8035), and β-actin (Santa Cruz Biotechnology, sc-47778). Then, the membranes were washed again and incubated for detection with either goat anti-rabbit IgG or goat anti-mouse IgG secondary antibodies (Cell signaling, Danvers, MA, USA). The bands were detected by enhanced chemiluminescence (Amersham Pharmacia Biotech, Little Chalfont, UK).
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4

Western Blot Analysis of Mitochondrial and Apoptotic Proteins

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Total protein was extracted from intestinal tissue and Caco-2 cells using a commercial protein isolation kit (KeyGEN Biotech, Nanjing, China). Equal protein amounts from the samples were analyzed using 10%-15% SDS-PAGE (Bio-Rad, Hercules, CA, United States) and then transferred to PVDF membranes (Millipore, Bedford, MA, United States). The membranes were blocked with 5% nonfat milk or 5% BSA in TBS-Tween buffer (0.1% Tween-20; pH 7.5) for 1 h at 37 °C. After blocking, the membranes were incubated with primary antibodies against total DRP1, DRP1 Ser637 (Abcam, Cambridge, United Kingdom), PINK1 (Santa Cruz Biotechnology, Santa Cruz, CA, United States), caspase-3 (Proteintech, Wuhan, China), and β-actin (ZSGB-BIO, Beijing, China) overnight at 4 °C. After washing, the membranes were incubated with the corresponding homologous horseradish peroxide-conjugated secondary antibodies for two hours at 37 °C. The bands were visualized using enhanced Chemiluminescence Plus reagents (Beyotime Institute of Biotechnology, China). Spectrophotometric analysis was performed with a BioSpectrum-510 multispectral imaging system (UVP, Upland, CA, United States) and signals were analyzed using Gel-pro Analyzer Version 5.0 (Media Cybernetics, Rockville, MD, United States).
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5

siRNA Transfection for Gene Knockdown

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Cells were transfected with 10 nM of each siRNA using the Lipofectamine RNAiMAX transfection reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. Eif2ak1 (also called Hri), Atm, Pink1, Parkin, Il1b, Il18, Nlrp3, Slc25a11, and Control siRNA were purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Knockdown efficiency was analyzed by qPCR-based gene expression analysis (Supplementary Figure S2).
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6

Multiplex Immunoblotting for Mitochondrial Proteins

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The following primary antibodies were used: FLAG (Sigma and Proteintech, 1:1000), HA (Cell Signaling and Proteintech, 1:1000), Myc (Proteintech, 1:1000), CHCHD10 (Proteintech, 1:1000), CHCHD2 (Proteintech, 1:1000), TOM20 (Cell Signaling and Santa Cruz Biotechnology, 1:1000), TDP-43 (Proteintech and Santa Cruz Biotechnology, 1:1000), HSP60 (Cell Signaling Technology, 1:1000), COX2 (Abcam, 1:2000), LC3B (Cell Signaling Technology, 1:1000), phospho-ubiquitin (EMD Millipore, 1:1000), Actin (Santa Cruz Biotechnology and Proteintech, 1:3000), PINK1 (Santa Cruz Biotechnology and Novus, 1:1000), DRP1 (Cell Signaling Technology, 1:1000), MFN1 (Cell Signaling Technology, 1:1000), MFN2 (Cell Signaling Technology, 1:1000), NDP52 (Proteintech, 1:1000), and OPTN (Proteintech, 1:1000). Samples were collected and lysed in RIPA buffer (Cell Signaling Technology) containing a protease inhibitor cocktail (Sigma) and subsequently separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) after measuring protein concentration by bicinchoninic acid (BCA) (Pierce). Immunoblots were visualized and analyzed with the Odyssey FC System (LI-COR).
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Protein Extraction and Western Blot Analysis

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Frozen placental tissues and cultured cells were suspended with RIPA lysis buffer for protein extraction. A BCA Protein Assay Kit (Beyotime Biotechnology, China) was used to quantify protein concentrations. Protein samples were separated by SDS polyacrylamide gels and transferred to polyvinylidene difluoride membranes (Millipore, USA). 5% nonfat dry milk (Bio-Rad, California, USA) was used for nonspecific protein band blocking, and the results were quantified using a ChemiDoc™ XRS + (Bio-Rad, USA). The antibodies used in WB were anti-BNIP3 (1:1000, Abcam, Catalog#: ab109362), ATG3 (1:500, Santa Cruz, Catalog#: sc-393660), Beclin-1 (1:500, Santa Cruz, Catalog#: sc-48341), P62 (1:500, Santa Cruz, Catalog#: sc-25329), β-actin (1:2000, ZSGB-BIO, Catalog#: TA-09), LC3 (1:500; NOVUS, Catalog#: NB100-2220), PINK 1 (1:500, Santa Cruz, Catalog#: sc-517353) and Cathepsin D (1:500, Wanleibio, Catalog#: WL01234).
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8

Immunoblotting for Mitochondrial Dynamics

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Immunoblotting was performed as we have previously described (Brown et al. 2018 (link), 2015 (link); Lee et al. 2016a (link); Perry et al. 2016 (link); Rosa-Caldwell et al. 2017 (link)). The following antibodies were used to probe Western blot membranes: cytochrome c oxidase subunit IV (COXIV) (Cell Signaling Technology, Danvers, Mass., USA; 4844), voltage-dependent anion channel (VDAC) (Cell Signaling; 4661), PGC-1α (Santa Cruz Biotechnologies, Santa Cruz, Calif., USA; sc-13067), Parkin (Cell Signaling; 4211), phosphorylated (p)-Parkinser65 (Abcam, Cambridge, Mass., USA; ab154995), Pink1 (Santa Cruz; sc-517353), MFN1 (Santa Cruz; sc-50330), MFN2 (Santa Cruz; sc-50331), Fis1 (Santa Cruz; sc-48865), Opa1 (Santa Cruz; sc-367890), microtubule-associated proteins 1A/1B light chain 3A and 3B (LC3A/B) (also referred to as LC3II/I; Cell Signaling, 4108), BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (BNIP3) (Cell Signaling; 3769), p62/sequestosome-1 (SQSTM1) (MilliporeSigma, St. Louis, Mo., USA; p0067).
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9

Western Blot Analysis of Protein Biomarkers

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At the end of the experiments, cells were washed with PBS and proteins were extracted using RIPA buffer containing protease inhibitor mixture (Chemcruz, Santacruz, USA) and stored at −20 °C until analyzed. Protein concentrations were measured with the BCA assay (Interchim, Montlucon, France) and samples were subjected to Western blot analysis. Whole cell-lysates were separated by SDS-PAGE, transferred to PVDF membranes (Bio-Rad) and incubated with primary antibodies against PINK1 (1:200, Santa Cruz), Parkin (1:100, Santa Cruz), iNOS (1:1000, Novus Biologicals), COX-2 (1:1000, Abcam) and β-actin (1:5000, Sigma- Aldrich). Secondary antibodies, polyclonal goat anti-rabbit IgG/HRP and rabbit anti-mouse IgG/HRP (Dako, Jena, Germany) were used at a dilution of 1:800. Chemiluminescent bands on autoradiograms were visualized with a ChemiDocTM Touch Imaging System (Bio-Rad, Basel, Switzerland) and quantified using the Image Lab software (Biorad, Germany).
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10

Antibody Reagents for Autophagy Analysis

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The antibodies used in this study were purchased from the following vendors: CST (USA)-LC3B, cleaved caspase-3, AMPK, P-AMPK, mTOR, P-mTOR; Abcam (UK)-P62, BNIP3; Sigma (USA)-LC3B-II; Novus (USA)-PINK1, HIF-1α; Santa Cruz(USA)-BNIP3; Proteintech (China)-TOMM20, COX IV, β-actin, anti-mouse IgG, anti-rabbit IgG, HRP-linked antibody; Invitrogen (USA):-Alexa Fluor 488 donkey anti-Rabbit IgG(H + L), Alexa Fluor 594 donkey anti-mouse IgG(H + L). Bafilomycin A1 (Sigma, USA) was dissolved in dimethyl sulfoxide (DMSO; Sigma, USA) and added to media to the final concentrations described.
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