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6 protocols using goat anti rabbit

1

Amplification and Characterization of PADI3 Domains

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Full-length of PADI3 was amplified using PCR with the primers PADI3-EcoRI-Fex and PADI3-AscI-Rex, the N-domain was amplified with the primers PADI3-N-OE-EcoRI-Fex and PADI3-N-OE-AscI-Rex, the M-domain was amplified with the primers PADI3-M-OE-EcoRI-Fex and PADI3-M-OE-AscI-Rex, the C-domain was amplified with the primers PADI3-C-OE-EcoRI-Fex and PADI3-C-OE-AscI-Rex, the NM-domain was amplified with the primers PADI3-N-OE-EcoRI-Fex and PADI3-M-OE-AscI-Rex, and the MC-domain was amplified with the primers PADI3-M-OE-EcoRI-Fex and PADI3-C-OE-AscI-Rex. The primer sequences were designed as shown in Supplementary Table S1.
The following primary antibodies used in this study were commercially obtained: anti-PADI3 (Abcam, ab172959), anti-GAPDH (Abcam, ab181603), anti-AKT (Santa Cruz Biotechnology, sc5298), anti-Sirt2 (Santa Cruz Biotechnology, sc28298), anti-p21 (Santa Cruz Biotechnology, sc6246), anti-phosphorylated AKT (p-AKT) (CST, #4060), anti-Snail (CST, #3879), anti-His-tag (CST, 12698S), anti-histone 3 (Affinity, AF0863) and anti-red fluorescent protein (RFP) (Abcam, ab28664). The following secondary antibodies were used in this study: goat anti-rabbit (Affinity, #s0001), goat anti-mouse (Affinity, #s0002) and donkey anti-goat (Abcam, ab6881).
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2

Western Blot Analysis of Corneal Proteins

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Corneas were crushed in liquid nitrogen. RIPA Lysis Buffer (Beyotime, China) was used to extract the protein. The proteins were separated by 10% sodium dodecyl sulfate polyacrylamide Tris-glycine gels. The proteins in the gels were transferred to polyvinylidene difluoride membrane. The membrane was cropped according to the position of proteins’ color marker. Then the membranes were blocked with 5% milk in TBS for 2 h and then incubated overnight at 4 °C with the following primary antibodies: VEGF (1:1000, Abcam), ERK1/2 (1:1000, Invitrogen), Akt (1:3000: Abnova) and GAPDH (1:1000, Abcam). After 3 washes with TBST (TBS + 20% Tween-20), the membranes were incubated for 1 h at room temperature with goat anti-mouse (1:3000, Affinity Biosciences) and goat anti-rabbit (1:3000, Affinity Biosciences) secondary antibodies. ECL reagent was used to detect the immunological complexes membranes. And the proteins’ bands from the membranes were imprinted on the film in the dark room. The band intensities were measured by ImageJ software. The results were normalized to the expression of GAPDH.
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3

Protein Expression Analysis in Tissue Samples

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Proteins were extracted from cells, liver tissues, and mitochondria using RIPA buffer (Beyotime) with protease and phosphatase inhibitors (Beyotime). Separated by 8−12% SDS‐PAGE, an equal amount of protein was transferred to PVDF membranes (Millipore, Inc.). After blocking with 5% nonfat dry milk in TBST, primary antibodies were added and left to incubate overnight. These antibodies include anti‐PISD (sc‐390070, 1:500; Santa Cruz, CA), anti‐p‐STAT3 (9145, 1:2000; Cell Signaling), anti‐STAT3 (9139, 1:1000; Cell Signaling), anti‐COX IV (4850, 1:1000; Cell Signaling), anti‐Bcl‐2 (AF6139, 1:1000; Affinity), anti‐Bax (AF0120, 1:1000; Affinity), anti‐cleaved caspase‐3 (AF7022, 1:1000; Affinity), anti‐actin (AF7018, 1:6000; Affinity), and OXPHOS rodent WB antibody cocktail (45‐8099, 1:1000; Thermo Fisher Scientific). The blot was then further incubated with HRP‐conjugated secondary antibodies, either goat anti‐rabbit (S0001; Affinity) or goat anti‐mouse (S0002; Affinity). Finally, proteins were visualized with an enhanced chemiluminescence kit (Bio‐Rad).
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4

Liver Protein Extraction and Analysis

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The homogenate of liver tissue or cells was prepared in lysis buffer (20 mM Tris–Cl pH7.5, 140 mM NaCl, 1 mM CaCl2 and MgCl2, 10 mM NaF, 1% NP-40, 10% glycerol, 2 mM Na-Vanadate, and 1 mM PMSF) supplemented with complete Protease Inhibitor Cocktail (cOmplete™, Sigma-Aldrich, Dallas, TX) for 30 min, centrifuged at 12,000 rpm at 4°C for 15 min. The protein samples were resolved by SDS-polyacrylamide gel electrophoresis and electrophoretically transferred to PVDF membranes. The membranes were blocked at room temperature for 2 h in 5% defatted milk dissolved in TBST (10 mM Tris–HCl, pH 7.4, and 150 mM NaCl), incubated at 4°C for overnight with the following antibodies: PPARγ (#AF6284, Affinity, 1:1000), FGF9 (#A6374, ABclonal, 1:500 and #ab206408, Abcam, 1:500), ChREBP (#A7630, ABclonal, 1:1000), Fasn (#DF6106, Affinity, 1:1000), or β-Actin (#AF7018, 1:10000), washed in TBST (0.1%Tween 20) for 15 min (repeated three times) and incubated with a goat anti-mouse (# S0002, Affinity) or goat anti-rabbit (# S0001, Affinity) IgG (H + L) HRP secondary antibody (1:5000 dilution in TBS) for 1 h at RT. Immunoreactivity was visualized and quantified by infrared scanning using the Odyssey system (LI-COR Biosciences).
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5

Mori Fructus Antioxidant Mechanism

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The Mori Fructus fruits (Morus nigra Linn.) samples were sourced from Guangxi Province (China), 30% hydrogen peroxide was bought from Chengdu Keen (Chengdu, China), ROS, SOD, Gpx, BCA protein quantification and plasmatic nucleus isolation protein extraction kits are all from Beyotime Institute of Biotechnology (Shanghai, China). Cell Counting Kit-8(CCK-8) bought from Everbright, MEM medium, phosphate buffer and NQO1 antibodies were obtained from Boster (California, America). Lamin B and Nrf2 antibodies were from Proteintech (Wuhan, China), HO-1, Gapdh, AKT, p-AKT p-PI3K and PI3K antibodies were all obtained from Affinity(America), goat anti-mouse from Beyotime and goat anti-rabbit from Affinity.
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6

Immunofluorescence Analysis of USP13 and NLRP3 in Brain and Cell Samples

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The levels of USP13 and NLRP3 in brain tissues and SV‐HUC‐1 cells were assessed by immunofluorescence. Brain tissues were removed, fixed in 4% paraformaldehyde solution for 24 hours at 4°C. After embedding in paraffin, the tissues were cut into 4‐µm‐thick continuous coronal brain slices. Brain tissues and cells were blocked with 5% BSA blocking solution for 60 minutes at room temperature, followed by washing with PBS. Samples were then incubated with USP13 antibody or NLRP3 antibody at 4°C overnight. Sections were washed 3 times (5 minutes each time) with ice‐cold PBS and further incubated with goat anti‐rabbit IgG‐AF488 (Affinity, USA) secondary antibody.
Cells were fixed with 4% paraformaldehyde for 20 minutes and permeabilized with 0.5% Triton X‐100 for 20 minutes. Cells were blocked for 60 minutes at room temperature using 5% BSA blocking solution and then washed with PBS. Thereafter, cells were incubated with 1:200 dilution of primary antibodies (rabbit anti‐NLRP3 antibody, Affinity, USA) for overnight at 4°C. Following overnight incubation, cells were washed three times with PBS and incubated for 2 hours in dark with second antibody (goat anti‐rabbit, Affinity).
Later, the nuclei of cells were stained with 4′,6‐diamidino‐2‐phenylindole (DAPI, C0060, Solarbio); representative fluorescence images were obtained using fluorescence microscope (BX63, Olympus).
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