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Calcineurin

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Calcineurin is a protein phosphatase enzyme that plays a central role in the calcium-dependent signaling pathways within cells. It is involved in the regulation of various cellular processes, including gene expression, immune response, and neuronal function.

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13 protocols using calcineurin

1

Protein Lysate Preparation and Western Blot Analysis

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Whole protein lysates from all tissues were prepared as previously described.41 (link) Whole protein lysates from cell lines were prepared by using RIPA lysis buffer (Santa Cruz Biotechnology Inc., Dallas, Texas, USA) according to the manufacturer’s instructions. Nuclear proteins were purified using a nuclear extraction kit (EMD Millipore, Billerica, MA, USA). SDS-polyacrylamide gel electrophoresis and western blot analyses were performed as previously described.33 (link) Antibodies for nuclear factor of activated T cells c1 (1:1 000) and lamin B1 (1:1 000) were from Santa Cruz Biotechnology. Antibody to detect irisin (epitope 42–112, 1:500) and FNDC5 expression was purchased from Phoenix Pharmaceuticals Inc. (#067-17). Antibodies for β-catenin (1:10 000) were from Sigma and those from P-AKT-1 (1:1 000), calcineurin (1:1 000), P-JNK (1:1 000), and β-actin (1:1 000) were from Cell Signaling (Danvers, MA, USA). The secondary antibodies were horseradish peroxidase-linked goat-anti-rabbit IgG (Santa Cruz Biotechnology). Blots were visualized using Pierce ECL chemiluminescence kit (Thermo Fisher Scientific).
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2

Protein Expression Analysis from Aortic and Kidney Tissues

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For protein analyses from whole aortic and kidney tissue, tissue lysates were processed and total protein concentration was determined as described previously.9 (link) The blots were probed for Fibronectin (Abcam), E-selectin (Abcam), collagen (Millipore), calcineurin (Cell Signaling), and β-actin (Sigma) and were identified simultaneously (800 nm and 700 nm wavelengths, respectively) using near-infrared visualization (Odyssey System, LI-COR Biosciences). Densitometry was performed using the Odyssey software.
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3

Mitochondrial Dynamics and Apoptosis Assay

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Whole protein lysates were extracted from cells using PRO-PREP Protein Extraction Solution (Intron Biotechnology, Seongnam, Korea). Cytoplasmic and mitochondrial fractionation was performed using a mitochondrial isolation kit for cultured cell (Thermo Scientific, MA, USA) according to the manufacturer’s protocol. Proteins were separated by 8–12% SDS-PAGE and then transferred onto nitrocellulose membranes (Pall, FL, USA). Membranes were incubated with antibodies against dynamin-related protein 1 (Drp1) (Cat#sc-32898), Mfn1 (Cat#sc-50330), Mfn2 (Cat#sc-50331) (Santa Cruz, CA, USA), p-Drp1 (Ser637) (Cat#4897S), cleaved caspase-3 (Cat#9661s), calcineurin (Cat#2614S; Cell Signaling, Danvers, MA, USA), Prx5 (Cat#LF-PA0210), and β-actin (Cat#LF-PA0207) (Abfrontier, Korea). We used horseradish peroxidase-conjugated anti-mouse and anti-rabbit IgGs (Thermo Scientific) as secondary antibodies. Protein bands were visualized with Clarity Western ECL Substrate (Bio-Rad, CA, USA), and band intensities were analyzed with Multi Gauge version 3.0 software (Fujifilm, Japan).
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4

Immunophenotyping of B-cell Subsets

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Sorted BM B220+CD43+ pro-B and B220+CD43 pre-B cells from WT or Rag1−/− mice or B220+IL-7R+ pro-B and B220+IL-7Rpre-B cells from WT mice were immunostained with NFATc1, NFATc2 (both from ImmunoGlobe), or NFATc3 (Santa Cruz) Abs following a previously published protocol.39 (link) Counterstaining with 4,6-diamidino-2-phenylindole was performed to confirm nuclear staining. Image acquisition and data analysis were performed using a TCS SP2 Leica confocal microscope and software.
Whole-cell protein extracts from the WT pro- and pre-B cells were prepared as mentioned previously.40 (link) Fifty micrograms of total protein was analyzed in an 8% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and subjected to immunoblotting for detection of calcineurin (Cell Signaling Technology) and PLCγ2 (Santa Cruz) levels. Actin was used as a loading control.
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5

Western Blotting Protocol for Protein Analysis

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For Western blotting experiments, cells were lysed in RIPA buffer containing 50 mM of Tris/HCl, (pH of 7.4) with1% Nonidet P-40, 0.5% Nadeoxycholate, 150 mM of NaCl, 1 mM of EDTA, 1 mM of PMSF, 1 mM of Na3VO4, 1 mM of NaF, and protease inhibitor (Sigma). Then cells were separated via SDS/PAGE, followed by being transferred to a 0.45-mm-pore PVDF membrane (MilliporeSigma, Burlington, MA, USA). Later, the membrane was blocked with 5% milk for 1 h, incubated with the relevant primary antibodies at 4°C overnight, and was then incubated with horseradish-peroxidase-conjugated secondary antibodies (1:2000) at room temperature for 1 h. An ECL Kit (MilliporeSigma) was used to detect the immunoreactive bands. The primary antibodies: Carabin (1:500) (Cat#PA5-20394, Thermo Scientific), Calcineurin (1:1000) (Cat#2614S, Cell Signaling, Danvers, MA, USA), NFAT (1:1000) (Cat#5861S, Cell Signaling), Ras (1:1000) (Cat#3339S, Cell Signaling), ERK (1:1000) (Cat#4696S, Cell Signaling) and p-ERK (1:500) (Cat#8544S, Cell Signaling). Antibodies used in this study for WB were listed in Supplementary Materials.
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6

Quantitative Analysis of Bone and Muscle Proteins

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Total RNA of tissues and cells was isolated using TRIzol (Thermo Fisher Scientific) and the Quick‐RNATM MiniPrep Kit (Zymo, CA). RNA of each sample was reverse‐transcribed by M‐MLV Reverse Transcriptase (Promega, WI) and cDNAs were quantified by real‐time PCR with SYBR Green Supermix (Affymetrix) on Bio‐Rad iQ5 (Bio‐Rad Laboratories, CA). The primer sequences used are listed in Table S2.
The protein of the femurs, tibias, and skeletal muscles, and bone marrow–derived mesenchymal cells (BMSCs) and bone marrow–derived macrophage (BMM) cells, were extracted as previously described (J. Zhang, Valverde, et al., 2017 (link)). Whole protein samples were extracted using the RIPA lysis buffer (Santa Cruz Biotechnology Inc., TX). The nuclear and cytoplasm proteins were separated by a nuclear extraction kit (EMD Millipore, Germany) followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blot analyses. Antibodies for β‐catenin (1:2,000), β‐actin (1:1,000), P‐AKT1 (1:1,000), P‐p38 (1:1,000), AKT1 (1:1,000), p38 (1:1,000) and calcineurin (1:1,000) were purchased from Cell Signaling Technology and the antibodies for nuclear factor of activated T cells c1 (Nfatc1; 1:1,000) and lamin B1 (1:1,000) were from Santa Cruz Biotechnology. Irisin pAb (IN102; AG‐25B‐0027) antibody (1:1,000) to detect irisin and FNDC5 expression was purchased from AdipoGen Corporation.
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7

Protein Extraction and Western Blot Analysis

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Protein extraction was performed as previously described 52 (link). Cytosolic and nuclear proteins were extracted using NE-PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Fisher Scientific), following the manufacturer's protocol. Equivalent level of protein was resolved by 10% SDS-PAGE gel, transferred onto polyvinylidene fluoride (PVDF) membranes and then blocked with 5% bovine serum albumin (BSA). Membranes were incubated, overnight at 4 °C, with primary antibodies against MVP (1:1000, Santa Cruz), NFATc1 (1:500, Santa Cruz), PU.1 (1:1000, Cell Signaling Technology), c-Fos (1:1000, Abcam), MITF (1:1000, Abcam), CTSK (1:1000, Santa Cruz), p-NFATc1 (1:1000, Invitrogen), Calcineurin (1:1000, Cell Signaling Technology), H3 (1:1000, Cell Signaling Technology), Lamin B (1:1000, Cell Signaling Technology) and GAPDH (1:8000, Bioworld), and then washed with TBST, incubated with secondary antibodies, and visualized by enhanced chemiluminescence. Semi-quantitative measurements were performed using Image J software (National Institutes of Health, USA).
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8

Protein Expression Analysis in Tissue and Cells

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The procedure was adapted from our previous studies.13 Total proteins from the tissues and cells were extracted with lysis buffer including 1% protease inhibitor solution. Briefly, the protein concentrations were determined by BCA protein assay kit. Protein samples (100 mg) were separated by 10% SDS‐PAGE and transferred to nitrocellulose membranes and then blocked with 5% nonfat milk. The membranes were probed overnight at 4°C with the following antibodies: TRPV3 (1:200; Alomone labs, Jerusalem, Israel), p‐CAMKII and CAMKII (1:1000; Cell Signaling Technology, Boston, MA, USA), calcineurin (1:1000; Cell Signaling Technology), β‐MHC (1:3000; Sigma), NFATc3 (1:100; Santa Cruz Biotechnology, Santa Cruz, CA, USA), BNP (1:100; Santa Cruz Biotechnology), Hsp70 (1:300; Boster Inc., Wuhan, China), β‐actin (1:2000; Zhong Shan‐Golden Bridge Biological Technology, Beijing, China), GAPDH (1:2000; Zhong Shan‐Golden Bridge Biological Technology). β‐actin or GAPDH was as a loading control. After washing three times, members were incubated with a horseradish peroxidase‐conjugated secondary anti‐rabbit/mouse/goat IgG for 2 hours at room temperature. Proteins were visualized using ECL (Thermo Fisher Scientific, Inc., Waltham, MA, USA), and collected by using the Bio Imaging Systems (UVP Inc., Upland, CA, USA).
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9

Whole-Cell Lysate Preparation and Western Blot Analysis

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The whole-cell lysate was prepared using Radioimmunoprecipitation assay (RIPA) lysis buffer (25mM Tris–HCl pH 7.6, 150mM NaCl, 1% Triton, and 0.1% SDS) + protease inhibitor and phosphatase inhibitor cocktail. Protein concentrations were estimated using a Bradford Assay (Bio-Rad Catalog # 500–0006). Lysates (25 μg) were mixed with 6X loading dye containing b-ME followed by boiling at 95°C on a dry bath, then loaded. The gel was transferred to a nitrocellulose membrane. The membrane was blocked with 5% BSA for 1 hour at room temperature. Primary antibodies were prepared in a 5% BSA solution as well and the membranes were incubated overnight at 4°C with gentle shaking. Antibodies used to detect the target proteins: MCU (Santa Cruz), MCUR1 (Santa Cruz), Calcineurin (Cell Signaling), Drp1 (Novus), phosphor-Drp1S637 (Cell Signaling), Fis1 (Santa Cruz), and NMDAR (Cell Signaling). Species-specific secondary antibodies were used from Santa Cruz and the membranes were incubated for 1 hour at room temperature. Chemiluminescence was used to detect the signal. The densitometry ratio of the bands was determined using an ImageJ that was normalized to GAPDH.
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10

Imaging of gp120-transgenic Mice Brains

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Imaging for gp120-tg mice brains (HPX1481) and WT (HPX1477) was done in Dr. Kaul’s Lab (Sanford Burnham Presbys Medical Discovery Institute). WT and gp120 tg mice were provided by Dr. Lennart Mucke (Gladstone Institute of Neurological Disease, University of California) (Toggas et al., 1994 (link)). The mice were 9 months of age for both WT and gp120-tg where they were anesthetized with Isoflurane and transcardially perfused with 0.9% saline. The brains were quickly removed and fixed with 4% paraformaldehyde for 48 hours at 4°C. The brain sections (frontal cerebral cortex layer III) of 5 μm thickness were obtained for the histological studies. The slides were permeabilized with 1% Triton X-100 for 30 mins followed by blocking with 10% heat-inactivated goat serum in PBS containing 0.5% Tween-20 for 1.5 hours. The sections were then stained with Calcineurin (Cell Signaling) and MAP-2 (Sigma) overnight followed by Alexa Flour 488-labeled goat anti-rabbit (Molecular Probes). Nuclear DNA was labeled with H33342. Per animal, at least three sagittal sections were analyzed, and, in each section, five fields were recorded using Zeiss inverted Axiovert 100M fluorescence microscope. Fluorescence and volumetric quantitation were performed with the Slide book software package.
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