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32 protocols using horseradish peroxidase

1

Polyclonal Antibody Generation and Validation for Lactobacillus Proteins

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The anti-LPH polyclonal antibody was generated using female New Zealand white rabbits, as female is sensitive with lower doses of antigen and have higher response to immunization than male56 . Female New Zealand white rabbits (6-8 weeks, 2 kg body weight) were immunized through repeated intradermal injections of LPH (1:1 emulsified in Freund’s adjuvant). After the final boost, blood was collected and serum was prepared. The polyclonal antibody was purified using Pierce™ Protein A IgG Purification Kit (Thermo Fisher Scientific). Immunoblot was performed to detect the presence of LPH in the culture supernatant of L. casei, L. rhamnosus, and L. paracasei. Probiotics were grown in Man, Rogosa, and Sharpe medium at 37 °C, 24 h without agitation. The cell lysates and culture supernatants were harvested, separated on SDS-polyacrylamide gel, and transferred onto polyvinylidene difluoride membranes. Membranes were blocked with 5 % skim milk and incubated with rabbit polyclonal LPH antibody (1:5000) overnight. Expression of LPH was detected using goat anti-rabbit IgG antibody conjugated with horseradish peroxidase (1:5000, Proteintech, catalog number SA00001-2) and enhanced chemiluminescence reagent kit. The uncropped scans of immunoblots were provided in the Source Data file.
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2

Quantitative Protein Analysis by Western Blot

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Cells were collected, and the protein was extracted with RIPA lysate. Then the protein was denatured by boiling at 99°C for 5 min, and quantified with BCA Protein Assay Kit (Beyotime Biotechnology Co, Jiangsu, China). After SDS-PAGE electrophoresis and transmembrane, the protein was binded to PVDF membrane, then blocked the nonspecific sites with 5% skimmed milk powder. Meanwhile, a primary antibody, including CREB1 (dilution of 1:1000, Cell signaling Technology, USA), p-CREB1 (dilution of 1:1000, Cell signaling Technology, USA), VASP (dilution of 1:1000, Cell signaling Technology, USA), HA (dilution of 1:1000, Cell signaling Technology, USA), GAPDH (dilution of 1:5000, Proteintech, USA), should be prepared, and then incubating the PVDF membrane overnight at 4°C. The membrane was incubated with the corresponding secondary antibody horseradish peroxidase (dilution of 1:1000, Proteintech, USA) for 1 h at room temperature, and finally detected by ECL reagents (Tanon, Shanghai, China). The optical density of bands was measured by a computer-assisted imaging analysis system (Tanon, Shanghai, China) and the relative protein expression levels were normalized to GAPDH.
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3

Western Blot Analysis of Epigenetic Regulators

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The cells were washed in PBS and lysed with RIPA buffer (Vazyme, China) supplemented with protease inhibitor cocktail (Roche, Germany). After quantification using One DropTM 1000+ (ANTPEDIA, China), proteins were separated by SDS-PAGE under denaturing conditions and transferred to PVDF membranes (Millipore, USA). Membranes were blocked with 5% fat-free milk for 2 h at room temperature and incubated with primary antibodies for Gapdh (Proteintech, 60004-1-Ig, 1:5,000), Mll1 (CST, D668N, 1:1,000), Mll2 (CST, E6A8V, 1:1,000), Pax6 (Abcam, ab5790, 1:500), and H2b (Abcam, ab52599, 1:10,000). The membranes were then incubated with secondary antibodies conjugated with horseradish peroxidase (Proteintech, USA). Protein signals were visualized using the ECL detection reagent (Thermo Scientific) on UVP (Analytik Jena AG, Germany).
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4

Profiling mTOR and AKT Signaling Cascades

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Total protein was extracted using ice cold radioimmunoprecipitation assay (RIPA) lysis buffer (Cwbio), containing a phosphatase inhibitor (Roche) and a protease inhibitor cocktail (Roche). Then, 25 µg of protein from each sample was electrophoresed in SDS polyacrylamide gels and then transferred to PVDF membranes. The membranes were blocked with 5% non-fat milk for 1 h at room temperature and then incubated with antibodies against SGK3 (serum/ glucocorticoid-regulated kinase family member 3; 1:500 dilution; Proteintech), mTOR (mammalian target of rapamycin kinase; 1:1000 dilution; Cell Signaling), Phospho-mTOR (1:1000 dilution; Ser2448, Cell Signaling), AKT (protein kinase B; 1:1000 dilution; Cell Signaling), Phospho-AKT (1:1000 dilution; Ser473, Cell Signaling) overnight at 4°C. After washing four times with Tris-buffered saline containing 0.1% Tween-20, the membranes were incubated with the appropriated secondary antibody, conjugated with horseradish peroxidase (Proteintech) for 1 h at room temperature. Bands with peroxidase activity were detected by an enhanced chemiluminescent detection system (Merck Millipore) and visualized using a G-Box chemiluminescence image capture system (Syngene). GAPDH (glyceraldehyde-3-phosphate dehydrogenase; 1:5000 dilution; Proteintech) as a protein loading control.
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5

Comprehensive Western Blotting Protocol

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Western blotting was conducted in accordance with previously described standard protocols [16 (link)]. Primary antibodies, including anti-Beta Actin (20536-1-AP, Proteintech, China), anti-α-SMA (14395-1-AP, Proteintech, China), anti-CD31 (11265-1-AP, Proteintech, China), anti-E-cadherin (20874-1-AP, Proteintech, China), anti-Vimentin (10366-1-AP, Proteintech, China), anti-ZEB1 (21544-1-AP, Proteintech, China), anti-HIF1α (20960-1-AP, Proteintech, China), anti-HIF1α-OH402 (ab72775, Abcam, USA), anti-HIF1α-OH564 (#3434, CST, USA), anti-PHD1 (12984-1-AP, Proteintech, China), anti-PHD2 (19886-1AP, Proteintech, China), and anti-PHD3 (18325-1-AP, Proteintech, China) were used. Secondary antibodies, consisting of goat anti-mouse and anti-rabbit antibodies conjugated with horseradish peroxidase (Proteintech, China), were utilized, and the blots were detected utilizing enhanced chemiluminescence (ECL) (P10300, NCM, China). Quantitative analysis of western blotting was performed using ImageJ.
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6

Western Blot Analysis of Protein Samples

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Liver tissues (30-50 mg) and cultured cells were prepared in lysis buffer containing 1% of PMSF and 1% phosphatase inhibitor, followed by centrifugation (12,000 × g, 10 min, 4 °C), and the protein concentration was determined by the BCA Protein Assay Kit (P0012, Beyotime, Shanghai, China). Thirty micrograms of protein per lane were separated by 10% SDS-PAGE gels and electrophoretically transferred onto polyvinylidene fluoride (PVDF) membranes. Membranes are further blocked with 5% skimmed milk for 2 h at room temperature and incubated overnight with primary antibodies at 4 °C. Then, the membranes were incubated with appropriate horseradish peroxidase (1:5000, Proteintech, China) conjugated secondary antibodies for 50 min at room temperature. The protein blots were detected by enhanced chemiluminescence (ECL) reagent (7 Sea Biotech, China) with a chemiluminescence detection system (Bio-Rad, Chemi Doc, CA, USA). The antibodies used are listed in Supplementary Table 3.
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7

Immunohistochemical Analysis of HO-1 in Mouse Liver

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Mouse liver tissues were fixed in 4% formalin overnight and embedded in paraffin. Tissue slicing (3 μm) dewaxing and antigen (citrate) repair were performed. Tissue sections were treated with 3% hydrogen peroxide (PV-6001, ZSGB-BIO, Beijing, China) for 15 min, and blocked with goat serum for 30 min. Tissue sections were incubated with the primary antibody anti-HO-1 (1:200) overnight at 4 °C. After overnight incubation, the slides were washed and the sections were incubated with appropriate horseradish peroxidase (1:5000, Proteintech, China) conjugated secondary antibody for 30 min at room temperature. Then the slices were incubated with diaminobenzidine (DAB) (ZLI-9018, ZSGB-BIO, Beijing, China) for 3 min, stained with hematoxylin for 3 min, rinsed for 10 min, and then dehydrated and sealed with neutral gum. Finally, the sections were visualized by a microscope at a magnification of ×40.
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8

Melatonin Modulates ER Stress-Induced Apoptosis

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Fetal bovine serum, Dulbecco’s modified Eagle medium (DMEM)/F12 medium, and phosphate-buffered saline (PBS) were purchased from HyClone (Logan, UT, United States). Melatonin (73314) was purchased from Med Chem Express (Princeton, NJ, United States). LPS (ST1470), tunicamycin (TM) (SC0393), 4′,6-diamidino-2-phenylindole (DAPI) (P0131), 0.25% trypsin (C0205), and EX527 were purchased from Beyotime (Shanghai, China). Primary antibodies against SIRT1 (13161-1-AP), Bax (50599–2–Ig), glucose-regulated protein 78 (GRP78) (11587-1-AP), CHOP (15204-1-AP), IRE1α (27528-1-AP), and β-actin (15204-1-p) were purchased from Proteintech (Wuhan, Hubei), as were horseradish peroxidase (HRP)-conjugated secondary antibodies. Phospho-IRE1α (P-IRE1α) (ab124945), Bcl-2 antibodies (ab32124), cleaved caspase-4 (ab22687), and cleaved caspase-10 (ab11475) were purchased from Abcam (Cambridge, United Kingdom), and XBP1S (#40435) and cleaved caspase-3 (Asp175) were purchased from Cell Signaling Technology (Danvers, MA, United States). Cell-counting kit 8 (CCK-8) was purchased from Beyotime.
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9

Quantitative Analysis of Tight Junction Proteins

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For western blot analysis, colon tissues were homogenized and lysed using RIPA buffer containing 1X protease inhibitors (Sigma Aldrich, MO, USA), and lysates were further processed for immunoblotting as previously described (63 (link)). The membranes were probed with ZO-1, Occludin, Cldn-4, and β-actin antibodies, followed by incubation with a secondary antibody conjugated with horseradish peroxidase (Proteintech, IL, USA). The protein bands were developed with Immobilon Forte Western HRP substrate (Millipore Sigma, MA, USA) and imaged using a Bio-Rad ChemiDoc Imaging System (Hercules, CA, USA). Densitometric analysis of the bands was performed using ImageJ software (64 (link)). A list of the antibodies, sources, and dilutions used is provided in Table S2.
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10

Western Blot Analysis of Srebp-1, Lamin B1, and β-Actin

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As previously described (Sun et al., 2020 (link)), sterol regulatory element-binding protein-1 (Srebp-1) and Lamin B1 or β-actin protein in both the nucleus and cytoplasm were extracted with kits, and the protein samples were separated by 10% SDS–polyacrylamide gel electrophoresis. Next, the protein samples were transferred to a PVDF membrane (0.22 µm), which was blocked with 5% skim milk for 4 h at room temperature. Subsequently, the membrane was incubated with primary antibodies, including Srebp-1 (1:1,000), β-actin (1:2,000), and Lamin B1 (1:2,000), which were diluted in Tris-buffered saline with Tween-20 containing 5% skim milk at 4°C overnight. The immune complexes were recognized by a secondary antibody (1:2,000) conjugated to horseradish peroxidase (ProteinTech, Chicago, United States). Peroxidase activity was visualized using an enhanced chemiluminescence kit (Solarbio, Beijing, China). Densitometric analysis of the immunoblots was performed using ImageJ software.
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