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28 protocols using pi 1000

1

Quantification of FoxO1 Protein Levels

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After homogenization and sonication, samples were centrifuged at 10,000 g for 10 minutes. Supernatants were collected and protein concentrations were determined using a standard bicinchoninic acid assay. Prior to electrophoresis, samples were heated for 5 min at 95°C and 50 μg protein was applied per lane. Samples subjected to SDS polyacrylamide gel electrophoresis under standard conditions were transferred onto polyvinylidene difluride (PVDF) membrane in a buffer containing 0.2 mol/L glycine, 25 mM Tris and 20% methanol, overnight at 4°C. After blocking with 5% non-fat dry milk, membranes were incubated with the following primary antibodies FoxO1 (1:300 dilution; Cell Signaling; Cat no:880S) and GAPDH (1:1000 dilution; Cell Signaling; Cat no:2118S) overnight at 4°C. After washing, membranes were incubated for 1 h at room temperature with horseradish peroxidase conjugated secondary anti-rabbit IgG diluted by 1:5000 (Vector; PI-1000). The reaction was visualized using chemiluminescence based Super Signal CL HRP Substrate System (Thermo Scientific; Cat no:34080) and the membranes were exposed to Hyperfilm. As an internal standard to confirm the equal loading of the proteins, GAPDH was loaded to the gels. ImageJ (NIH, Bethesda, MD, USA) was used to quantify the density of the western blot bands.
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2

TRPV1 Expression in Subcellular Fractions

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vHip samples underwent subcellular fractionation protocols as in [33 (link)]. Cellular and membrane samples (50 µg/subject) were then subjected to SDS-PAGE and Western Blot protocols using TRPV1 primary antibody (Thermo Fisher PA1-29421; 1:1000). Primary antibodies for Beta-actin (Thermo Fisher PA1-183; 1:1000) and Na+/K+ ATPase (MilliporeSigma 05-382; 1:1000) and associated secondaries (Vector PI-1000 and PI-2000; 1:1000) were used as respective loading controls for cellular and membrane samples. Optical density of all bands was imaged and quantified using ChemiDoc XRS (Bio-Rad) and Image Lab software. Bands were normalized by calculating the ratio of TRPV1 to loading control optical density for each animal. All data reflect the average of samples run in duplicate.
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3

Quantitative Western Blot Analysis of Cholesterol Regulators

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Protein lysates were collected at 4 °C in RIPA buffer (Sigma) supplemented with protease inhibitors (10uM leupeptin, 5ug/ml pepstatin A, 3ug/ml aprotinin, 25ug/ml ALLN, and 0.5mM PMSF). Conditioned growth medium was collected at 4 °C with protease/phosphatase inhibitors (Cell Signaling) and concentrated with Amicon Ultra-15 filters (30-kDa cut-off, EMD Millipore). Total protein concentration was determined by BCA method (ThermoFisher) and equal amounts of total protein were loaded onto 8% or 4–12% Bis-Tris Plus Gels (ThermoFisher). Following electrophoresis (100 V, 1h), proteins were transferred to iBlot® 2 Transfer Stacks, nitrocellulose membranes (ThermoFisher Scientific). Blots were probed overnight at 4 °C with 1:500 anti-HMG-CoA reductase (EMD Milipore, ABS229), 1:1,000 anti-APOE (Calbiochem, 178479), 1:200 anti-SREBP2 (Abcam, 30682), 1:1,000 anti-LAMP1 (Abcam, ab24170), or 1:700 anti-ABCA1 (Abcam, ab18180) followed by 1:2,000 HRP-conjugated secondary (Goat, life technologies, 611620; Rabbit, Vector Laboratories, PI-1000; Mouse, Vector Laboratories, PI-2000, 1 h at room temperature) and visualized with WesternBright™ ECL HRP Substrate reagents (Advansta) on the UVP System.
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4

Validating μ-Opioid Receptor Specificity

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Immunoblotting was used to validate the specificity of the anti-μ-OR antibody (1:5000; Abcam, ab10275, polyclonal; made in rabbit, which detects a band of 49–65 kDa) and peroxidase-labeled secondary antibody (anti-rabbit; 1:6000, Vector Laboratories, PI-1000) used to detect μ-ORs in zebra finches (Figure 1C; cf. Sen et al., 2019 (link)). The anti-μ-OR antibody (ab10275) was raised against a sequence of 15 amino acids on the C-terminal (384 to 398) of OPRM-1; NX_P35372, which is a synthetic rat μ-OR peptide. This 15 amino acid sequence has 80% (12/15) homology to a similar sequence found in μ-ORs present in songbirds [zebra finch, (XP_012428092.1) and in starlings, (XP_014741492.1; (Kelm et al., 2011 (link))]. Whereas the μ-OR sequence for zebra finch has 99.67% (299/300) homology to that of starlings, the target peptide sequence against which the Abcam antibody was raised is identical in both species of songbirds (Supplementary Information 1). The abcam 10275 anti-μ-OR antibody has also been used in many other species including the rodent striatum (rats: Chuhma et al., 2011 (link); Jedynak et al., 2012 (link); mouse: Lee et al., 2008 (link)).
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5

Antibody Validation for Cellular Protein Detection

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Antibodies against PEX5 were from Proteintech (12545–1-AP; 1:100). Antibodies against HRP-beta actin were from Sigma-Aldrich (#A3854, 1:50,000). Antibodies against ACAA1 were from Abcam (#ab110289, anti-mouse, 1:1000). Antibodies against NeuN were from Abcam (#702022, anti-mouse, 1:1000) and MilliporeSigma (#ABN78, anti-chicken, 1:500). Secondary antibodies against rabbit (#PI-1000, 1:3000) and mouse (#PI-2000, 1:3000) were from Vector Laboratories.
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6

Immunohistochemical analysis of Parkinson's disease

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Procedures for the preparation of brain tissues and immunohistochemistry are described in the Supplementary Methods (Additional file 1).
Primary antibodies (immunofluorescence): anti-TH (Millipore #AB152) 1:1000; anti-α-syn (Millipore #AB5334P) 1:1000; anti-α-syn clone 5G4 (AJ Roboscreen) 1:1000; anti-phospho S129 α-syn (Abcam ab59264) 1:1000. Secondary antibodies: Cy2-conjugated donkey anti-rabbit IgG (H + L) (Jackson ImmunoResearch Inc. #711–225-152) 1:1000; Cy3-conjugated F(ab’)2 fragment donkey anti-sheep IgG (H + L) (Jackson ImmunoResearch Inc. #713–166-147) 1:1000.
Primary antibodies (DAB): anti-TH (Millipore #AB152 1:1000); anti-DAT (Millipore #MAB369) 1:4000; anti-HA-tag (Covance clone 16B12 #MMS-101P) 1:1000. Secondary antibodies: peroxidase Goat anti-rabbit IgG (Vector Laboratories #PI-1000) 1:200; peroxidase goat anti-mouse IgG (Vector Laboratories #BA-9200) 1:200; biotinylated rabbit anti-rat IgG (Vector Laboratories #BA-4001).
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7

Hippocampal Microglial Activity and Neurogenesis

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To assess microglial activity within the hippocampus, immunohistochemical staining was performed using rabbit anti-Iba-1 polyclonal antibodies (1:500, ab108539) and anti-CD86 rabbit monoclonal antibodies (1:1000, ab53004) (Abcam, Cambridge, MA, USA). To assess neurogenesis intensity, the number of newly formed neurons in the dentate gyrus (DG) subgranular zone (SGZ) was determined using anti-doublecortin antibodies (anti-DCX) (1:500, ab18723; Abcam, Cambridge, MA, USA). Proliferative activity in the DG SGZ was determined by immunohistochemical staining of the nuclear antigen of proliferating cells (PCNA) using mouse monoclonal anti-PCNA antibodies (1:500, ab29) (Abcam, Cambridge, MA, USA). Secondary antibodies conjugated to horseradish peroxidase (PI-1000, anti-rabbit; PI-2000, anti-mouse) were used according to the manufacturer’s recommendations (1:100; Vector Laboratories, Burlingame, CA, USA).
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8

Signaling Pathway Analysis via Western Blotting

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Cells were treated with TDPN or DMSO in time-dependent and dose-dependent manners. The cells were harvested by scraping and underwent lysis in RIPA buffer. The BCA method (Thermo Scientific) was used for protein concentration determination. The extracts were analyzed by SDS-PAGE followed by Western blotting with appropriate antibodies.
The following antibodies were used for Western blotting: p21 (catalogue no. 2947), AKT (9272), phosphorylated AKT (9271S), ERK (4695), Slug (9585S), and GAPDH (2118) were from Cell Signaling Technology; E-cadherin (610181) and Zo-1 (610966) were from BD Science Transduction; cyclin E (sc-247), cyclin D1 (sc-246), p53 (sc-126), phosphorylated ERK (sc-7383), collagen I (sc-25974), collagen III (sc-28888), and fibronectin (sc-9068) were from Santa Cruz Biotechnology; and MMP-1 (444209) was from Calbiochem. The secondary antibodies used in the Western blotting were anti-mouse (PI-2000; Vector Laboratories) anti-rabbit (PI-1000; Vector Laboratories), and anti-goat (AP-107P; Millipore). The blots were analyzed using the ImageJ software. The relative change in the ratio of the target protein to the DMSO control was determined.
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9

Immunohistochemical Analysis of Hippocampal Microglia, Neurogenesis, and Proliferation

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In order to evaluate the activity of microglia/macrophages in the mouse hippocampi, immunostaining was performed using anti-Iba-1 rabbit polyclonal antibodies (1:500, ab108539) and anti-CD86 rabbit monoclonal antibodies (1:1,000, ab53004; both from Abcam, Cambridge, MA, USA). For the analysis of neurogenesis, the determination of the number of newly-formed neurons in the dentate gyrus (DG) subgranular zone (SGZ) was performed using anti-doublecortin (anti-DCX) antibody (1:500, ab18723; Abcam). Appropriate secondary antibodies conjugated to horseradish peroxidase (PI-1000, anti-rabbit; PI-2000, anti-mouse) were used according to the manufacturer's instructions (1:100; Vector Laboratories, Burlingame, CA, USA). Proliferating cell nuclear antigen (PCNA)-immunoreactivity was determined using anti-PCNA mouse monoclonal antibodies (1:500, ab29) and NeuN rabbit monoclonal antibodies (1:1,000, ab177487; both from Abcam) in the DG SGZ. Appropriate fluorescent secondary antibodies (anti-mouse, ab150108; anti-rabbit, ab150080) were used according to the manufacturer's instructions (1:500; Abcam). Following incubation with the antibodies (4°C, 24 h for primary antibodies and room temperature, 45 min for secondary antibodies), the sections were embedded in Fluoroshield mounting medium with DAPI (ab104139; Abcam).
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10

Western Blot Analysis of Cell Signaling Proteins

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Western blots were performed as described [52 (link)] using the following antibodies and dilutions: 1:1000 Uhrf1 (sc-373750, Santa Cruz Biotechnology), 1:1000 Rb (9313T, Cell Signaling), actin (A1978, Sigma), E2F1 (3742S, Cell Signaling), E2F2 (sc-9967, Santa Cruz Biotechnology), E2F3 (MA5-11319, Nalgene Nunc); 1:1000 SEMA3E (PA547469, Thermo Scientific); 1:1000 AMPK (5831S, Cell Signaling); 1:1000 pAMPK (ab133448, Abcam). Secondary antibodies were diluted 1:1000 (PI-1000, PI-2000 or PI-9500, Vector Laboratories). Bands were visualized using chemiluminescence (SuperSignal West Pico Chemiluminescent Substrate, Thermo Scientific). Band intensities were analyzed using ImageJ software.
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