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9 protocols using anti nrf1

1

Mitochondrial Biogenesis Pathway Regulation

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The protein expression levels of peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1α), peroxisome proliferator-activated receptor alpha (PPARα), nuclear respiratory factor 1 (NRF1), and mitochondrial transcription factor A (mtTFA) were measured by Western blot (Chen et al., 2018 (link)). The specific methods and steps are shown in Part 2 of the Supplementary Materials. The following antibodies were used: anti-PGC-1α (batch number: ab54481), anti-PPARα (batch number: ab8934), anti-NRF1 (batch number: ab175932), and anti-mtTFA (mitochondrial marker, batch number: ab131607) were provided by Abcam (Cambridge, UK); anti-β-actin (batch number: TA-09) was supplied by Beijing Zhongshan Jinqiao Biotechnology Co., Ltd. (Beijing, China). The mRNA expression levels of PGC-1α, PPARα, NRF1, and mtTFA were measured by real-time PCR (RT-PCR) (Mocker et al., 2019 (link)). The specific methods and steps are shown in Part 3 of the Supplementary Materials. Mitochondrial DNA (mtDNA) was detected using the PCR-fluorescent probe method (Liu et al., 2016 (link)). The specific methods and steps are shown in Part 4 of the Supplementary Materials.
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2

Western Blot Analysis of Myocardium Proteins

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Myocardium tissue was harvested for Western blot as described previously [23 (link)]. Cells of each group were harvested at appropriate time. Cells were washed three times with PBS and collected after ice-cold lysis buffer digestion. Protein lysates were separated on 10% SDS-PAGE gels and transferred onto nitrocellulose (NC) membrane. Membranes were blocked with 5% milk in 1 × TBS-Tween-20 buffer and incubated overnight at 4°C with primary antibodies. Then, membranes were washed in Tris-buffered saline with Tween, followed by incubation with the corresponding secondary antibodies at room temperature for 1 h. The blots were developed using an enhanced chemiluminescence kit (Millipore, Billerica, MA, USA) and visualized with UVP Bio-Imaging Systems. Blot densities were analyzed using ImageJ Software (National Institutes of Health, Bethesda, MD).
Primary antibodies are the following: anti-SIRT1, anti-IRS2, anti-P-Akt S473, anti-P-Akt T308, anti-t-Akt, anti-acetylated protein, anti-PGC-1α, anti-NRF1, anti-NRF2, anti-ERR-α, anti-TFAM, anti-GAPDH, and anti-β-actin (all from Abcam, Cambridge, MA, USA). Secondary antibodies are the following: horseradish peroxidase-conjugated goat anti-rabbit and goat anti-rat (from Zhongshan Biotechnology Co. Ltd., Beijing, China).
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3

Protein Extraction and Western Blot Analysis

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Frozen hearts, livers and kidneys were homogenized in modified RIPA buffer containing 50 mM Tris/HCl, 150 mM NaCl, 1% Triton X-100, 0.5% sodium deoxychoilate, 0.1% SDS, 1 mM EDTA, 10 mM sodium fluoride, Protease inhibitor cocktail (Roche Life Sciences, Mannheim, Germany) and Phosphatase inhibitor cocktail 2 and 3 (Sigma-Aldrich, Taufkirchen, Germany), pH 7.5 using an Ultra-Turrax T10 basic homogenizer. Samples were separated by 10% SDS-PAGE and transferred to polyvinylidene fluoride (PVDF) membranes at 250 mA for 2 h and incubated with the following primary antibodies: anti-insulin receptor (1:1000, Cell Signaling Technologies, 3025), anti-NRF1 (1:2000, Abcam, ab175932). Anti-Rabbit IgG (H+L) Fab2 Alexa Fluor (1:5000; Cell Signaling, 4414) and anti-Mouse IgG (H+L) Fab2 Alexa Fluor (1:10000; Cell Signaling, 4408) served as secondary antibody. Detection and quantification of fluorescent bands was performed using the Bio-Rad Western Blot Imager. Loading control was performed using anti-alpha-tubulin (1:2000, Sigma-Aldrich, T9026). For blots investigating levels of MTHFD1L, ATP synthase β and alpha-tubulin performed using isolated mitochondria, the following primary antibodies were used: Anti-MTHFD1L (1:1000, Novus Biologicals NBP2-37864), anti-ATP synthase β (1:2000, BD Biosciences, 612519), anti-alpha-tubulin (1:2000, Sigma-Aldrich, T9026).
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4

Protein Expression Analysis in Cells

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Cells and tissues were lysed with RIPA buffer, and protein concentration was calculated by bicinchoninic acid assay. Proteins were isolated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis and transferred to polyvinylidene fluoride membranes. Membranes were blocked with 5% non-fat dry milk for 1 h at room temperature, and then incubated with primary antibodies including anti-AQP4 (Cell Signaling Technology, 59678S), anti-ASC (Cell Signaling Technology, 60824S), anti-AP2B1 (Santa Cruz, 74423), anti-CAV-1 (Santa Cruz, sc-53564), anti-NLRP3 (Life Science, mAG-20B-0014), anti-NRF1 (Abcam, ab175932), anti-Occludin (Proteintech, 66378), anti-p65 (Cell Signaling Technology, 8242), anti-p-p65 (Cell Signaling Technology, 3033S), anti-TFAM (Cell Signaling Technology, 8076S), and anti-β-actin (Sigma, A5316) overnight at 4°C. The binding of primary antibodies was visualized with goat anti-rabbit horseradish peroxidase (HRP)-conjugated secondary antibody (Jackson Laboratory, 115-035-033) or goat anti-mouse HRP-conjugated secondary antibody (Jackson Laboratory, 111-035-003).
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5

Kidney Protein Extraction and Western Blot Analysis

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Whole kidney protein was extracted with lysis buffer. After centrifugation (13,000 rpm, 4 °C, 15 min), the lysate was mixed with 5× sample buffer and heated at 95 °C for 6 min. Total protein concentrations were measured using Bradford methods (BioRad Laboratories, Hercules, CA, USA). The lysate was subjected to SDS-PAGE gel electrophoresis and transferred onto a polyvinylidene difluoride (PVDF) membrane. The PVDF membranes were incubated overnight at 4 °C with the primary antibodies: anti-p-Src (1:1000; Cell Signaling Technology), anti-p-Fyn (1:1000; Santa Cruz Biotechnology), anti-PGC-1α (1:1000; Abcam), anti-TFAM (1:1000; Abcam), anti-NRF1 (1:1000; Abcam), anti-Cox4i1 (1:1000; Cusabio Biotech Co., Baltimore, MD, USA), anti-β-actin (1:1000), and anti-heat shock 70 kDa protein 8 (HSC70, 1:1000; Santa Cruz Biotechnology). The blots were reacted with peroxidase-conjugated secondary antibodies (Vector Laboratories, Inc., Burlingame, CA, USA), followed by an enhanced chemiluminescent sensitive plus reaction (BioFX Laboratories, Inc., Owings Mills, MD, USA). The positive immunoreactive protein bands were detected by LAS-3000 film (FUJIFILM Corporation, Tokyo, Japan). Each blot density was normalized to β-actin or heat shock 70 kDa protein 8 and compared with that of each control.
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6

Protein Expression Analysis in Skeletal Muscle

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Skeletal muscle tissues and L6 cells were lysed in RIPA lysis buffer and centrifuged (12 000 × g, 10 min, 4 °C). The lysates were separated by 10% SDS-PAGE and transferred to polyvinylidene fluoride membrane, immunoblotted with following primary antibodies of rabbit monoclonal anti-Sirt1, anti-Sirt3, anti-PGC-1α (BBI, Shanghai, China), anti-TFAM, anti-NRF1 and anti-GAPDH (ABCAM, Cambridge, UK), and then incubated with secondary goat anti-rabbit antibody (Cell Signaling, USA). The bands were visualized with enhanced chemiluminescence solution (ECL, Biotanon) and detected by Image Lab camera (Bio-rad, Germany), and then quantified by densitometry scanning with ImageJ software.
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7

Mitochondrial Gene Expression in TIMP-3 KO Mice

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To determine the expression of mitochondria-related genes in TIMP-3 KO mice, soleus muscle was harvested and homogenized. Ten µg of protein from each sample was denatured with 4X Sample Buffer Solution with 3-mercapto-1,2-propanediol (Wako, Osaka, Japan) and subjected to SDS-PAGE. Separated proteins were transferred to a polyvinylidene difluoride (PVDF) membrane followed by blocking with PVDF Blocking Reagent for Can Get Signal (Toyobo, Osaka, Japan) for 1 h at room temperature. After blocking, membranes were probed with primary antibodies for 1 h at room temperature, secondary antibody for 1 h at room temperature, and visualized with the ECL detection system. The intensity of each band was quantified using NIH ImageJ analysis software v1.61 (National Institutes of Health, Bethesda, MD) and normalized to GAPDH signal. The antibodies used were anti-UCP-2 (1∶1000; Proteintech, Chicago, IL, USA), anti-NRF-1 (1∶1000; abcam, Cambridge, UK), anti-NRF-2 (1∶500; abcam, Cambridge, UK), anti-VDAC (1∶1000; Cell Signaling Technology, Danvers, MA, USA), anti-COX4 (1∶1000; GeneTex, Irvine, CA, USA) and anti-GAPDH (1∶30000; Cell Signaling Technology, Danvers, MA, USA).
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8

Mitochondrial Function and Oxidative Stress Assay

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Samples of rat liver were homogenized as previously described [38 (link)]. Liver lysates containing 30 µg protein were loaded in each lane and were electrophoresed on SDS-PAGE gels and transferred to nitrocellulose membrane. Membranes were blocked and after probed with the following antibodies: anti-PGC1α (Millipore, Burlington, MA, USA), anti-NRF1 (Abcam, Cambridge, UK), anti-TFAM (Abcam), anti-TOM20 (Cell signaling), anti-GPX4 (Abcam), anti-PRDX3 (Abcam), anti-SOD2/MnSOD (Abcam), anti-CAT (Abcam), anti-DRP1 (Abcam), anti-OPA1 (Abcam), anti-MNF2 (Abcam), anti-PAMPK Thr172 (Cell signaling, Danvers, MA, USA), anti-AMPK (Cell signaling), anti-PULK Ser555 (Cell signaling), anti-ULK1 (Cell signaling), anti-AMBRA1 (Cell signaling), anti-PINK1 (Cell signaling ) anti-PARKIN (Cell signaling), anti-LC3B (Novus biologicals), anti-POLγ (Novus biologicals, Bio-Techne SRL, Milano, Italy), anti-Total OXPHOS complexes cocktail (Abcam), and anti-βACTIN (Sigma Aldrich, St. Louis, MO, USA). As secondary antibodies, peroxidase anti-rabbit IgG (Vector Laboratories Burlingame, CA, USA) and peroxidase anti-mouse IgG (Vector Laboratories) were used. Horseradish peroxidase-conjugated secondary antibodies were detected with enhanced chemiluminescence.
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9

Western Blot Analysis of Protein Abundance

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Cells were collected and lysed with cell lysis buffer (Beyotime, Shanghai, China). Whole-cell extracts were resolved by 10% SDS-PAGE and electrophoretically transferred to polyvinylidene di uoride membranes (Roche Diagnostics, Mannheim, Germany). The membranes were blocked and then incubated with anti-NRF1, anti-β-actin or anti-E2F1 antibodies (Abcam, Cambridge, MA, USA) at 4 °C overnight, followed by incubation with the appropriate horseradish peroxidase-conjugated secondary antibodies (Jackson ImmunoResearch, PA, USA). The chemiluminescence reaction was performed using ECL reagent (Thermo Scienti c, IL, USA).
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