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125 protocols using dc protein assay kit 2

1

Muscle Protein Expression Analysis

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The peripheral parts of muscle specimens were immediately frozen in liquid nitrogen and stored at −80°C for biochemical studies. Western blotting was performed as previously described (Fujimura and Usuki, 2015 (link), 2017 (link)). Briefly, the samples were sonicated for 5 s in tissue lysis buffer (T-PER Mammalian Protein Extraction Reagent; Pierce Biotechnology, Rockford, USA) containing Protease Inhibitor Cocktail and Phosphatase Inhibitor Cocktail 2 and 3 (Sigma-Aldrich, St Louis, USA). The samples were centrifuged (14,000 g for 1 h), and the supernatants were collected. The protein content was determined using the DC Protein Assay Kit II (Bio-Rad Laboratories, Hercules, USA). The cell lysates (20 μg protein) were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) on a 10% gel (Tefco, Tokyo, Japan) and transferred to nitrocellulose membranes (GE Healthcare, Buckinghamshire, UK). The membranes were then subjected to the following antibody probes: anti-MGF (Millipore, Billerica, USA); anti-IGF-I (Santa Cruz Biotechnology, CA, USA); anti-YAP1 (Novus Biologicals, Centennial, CO, USA); anti-phospho-YAP1 (Abcam, Cambridge, UK); anti-PAX7 (Cytoskeleton Incorporated, Denver, USA); anti-phospho-ERK, anti-ERK, anti-AKT, anti-phospho-AKT, anti-phospho-4EBP1, and anti-phospho-p70 S6 kinase (Cell Signaling Technologies); and anti-β-actin (Sigma-Aldrich).
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2

Quantifying Cardiac Interleukin-6 Levels

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Hearts of mice were excised, lyophilized and the resulting dry heart powder was dissolved in glucopyranoside. After determination of protein levels with DC Protein Assay Kit II (Bio-Rad), tissue homogenates were diluted to 5 mg/ml protein and IL-6 levels per mg heart homogenate were determined with mouse IL-6 ELISA Ready-set-go (eBiosciences).
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3

Telomerase Activity Quantification in iPSCs

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DC patient iPS cells were cultured and maintained in the presence of
BCH001 versus DMSO for 10 days. Cells were harvested and lysed with CHAPS
lysis buffer and protein concentration measured using DC Protein assay kit
II (Bio-Rad, 5000112). 5-fold dilutions of equivalent total protein lysate
were subjected to TRAP (telomere repeat amplification protocol) assay per
the TRAPeze Telomerase Detection kit (EMD Millipore, S7700). Products were
resolved on 10% TBE polyacrylamide gels and visualized by staining with
GelRed Nucleic acid gel stain (Biotium, 41003). Relative telomerase activity
was quantified using ImageJ software, by pairwise comparison of the
intensity of the first six amplicons in corresponding lanes with and without
PAPD5 inhibitors, and averaging across the three dilutions for each
sample.
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4

Western Blot Analysis of Cellular Proteins

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Following chemical treatment or transfection, subconfluent cells were lysed in RIPA buffer supplemented with a cocktail of protease and phosphatase inhibitors (Thermo Fisher Scientific, 78444) and sonicated for five cycles of 30 seconds on and 15 s off, in a Bioruptor® (Diogenode). Following lysate clearance with centrifugation for 10 min at 13000 rpm and 4 °C, protein quantitation was performed with the DC™ Protein Assay Kit II (Bio-Rad, 5000112). 20 μg of cell lysate was boiled in Laemmli sample buffer for 5 min at 95 °C, loaded onto SDS-PAGE gels, and transferred onto nitrocellulose or PVDF membranes. Chemiluminescence signal was detected using SuperSignal™ West Dura (Thermo Fisher Scientific, 34076). Images were acquired with an Amersham Imager 600 scanner. Cell fractionation was performed as previously described [2 (link)]. TCA precipitation was used for protein extraction following polysome profiling.
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5

Characterization of PVP-Coated Silver Nanoparticles

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All solvents and chemicals were of analytical grade. Pure PVP-coated AgNP (5 nm) were obtained from nanoComposix (San Diego, CA). Ultrapure deionized water was obtained by an Arium® pro system (Sartorius, Goettingen, DE), TraceSELECT™ nitric acid (≥ 65% v/v) (Honeywell Fluka, Fisher Scientific, Waltham, MA, USA), TraceSELECT™ hydrochloric acid (30–32% v/v) (Honeywell Fluka) and Primar™ hydrogen peroxide (≥ 30–32% v/v) (Fisher Chemical, Loughborough, UK) were used throughout. Proteases inhibitor cocktail (Mini Complete™, Roche), phosphatases inhibitor cocktail (PhosSTOP, Roche), phosphate-buffered saline (PBS), hematoxylin (Mayer’s solution), and eosin were obtained from Merck (Darmstadt, DE). The commercial BD™ Cytometric Bead Array (CBA) Mouse Inflammatory Cytokines Kit was obtained from BD Biosciences (San Diego, CA, USA). Primary antibodies targeting IкBα and phospho-IкBα were obtained from Cell Signaling (Danvers, MA, USA) and anti-mouse IgG, HRP-conjugated, secondary antibodies were obtained from Santa Cruz Biotechnologies (Santa Cruz, CA, USA). DC™ Protein Assay kit II and Clarity ECL Western Blot Substrate kit were obtained from BioRad Laboratories (Hercules, CA, USA).
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6

Protein Extraction and DPP3 Activity Assay

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Total protein extracts were prepared from tail biopsies minced in 150 μL Tris–HCl, pH 7.8, and subjected to sonication and freeze-thawing cycles. For protein extracts from total bone, the tissue was frozen in liquid nitrogen and homogenized using aluminum beads and the TissueLyser II instrument (Qiagen, Hilden, Germany). Tissue debris were removed by centrifugation at 4°C. Protein concentration in the supernatants were estimated using the DC™ Protein Assay Kit II (Bio-Rad, Berkeley, CA, USA) following the manufacturer’s instructions, on a Synergy™ H4 Microplate Reader (BioTek Instruments, Inc., Winooski, VT, USA). DPP3 enzymatic activity was performed as reported,(31 (link)) with minor modifications. Briefly, 50 to 80 μg of protein extracts were assayed with 0.04 mM Arg-Arg-β-naphthylamide (Sigma-Aldrich, Saint Louis, MO, USA) in 250 μL Tris–HCl, pH 8.5, at room temperature (RT). The reaction was stopped by adding 50 μL of 2 M acetate buffer, pH 4.5, containing 10% Tween and 1.5 mg/mL Fast Blue B Salt (all chemicals from Sigma-Aldrich). The absorbance of the released product (β-naphthylamine) was measured at 530 nm, using SynergyTM H4 Microplate Reader. The enzymatic activity was expressed as percentage of the wild-type (WT) value.
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7

Phosphoprotein Regulation in Neutrophils

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For Bio-Plex Pro™ Cell Signaling Assay (Bio-Rad) human and murine neutrophils were pre-incubated with DMSO, NS8593 (30 µM, Alomone Labs), TG100-115 (20 µM, Selleckchem) or a combination of IPI-549 (160 nM, Selleckchem) and nemiralisib (100 nM, Selleckchem) for 30 min and then treated with LPS (10 ng/ml, Sigma-Aldrich) for 30 min at 37°C. Cells were then washed and lysed using Cell Signaling Reagent Kit (Bio-Rad, catalog #171-304006M). Protein amount was measured using DC™ protein assay kit II (Bio-Rad, catalog #500-0012). Afterward samples were stored at −80°C. Collected samples were processed for the assay according to manufacturer’s instructions with following phosphoprotein targets: Akt (Ser473, catalog #171-V50001M), Erk1/2 (Thr202/Tyr204, Thr185/Tyr187, catalog #171-V50006M), NF-κB p65 (Ser536, catalog #171-V50013M), mTOR (Ser2448, catalog #171-V50033M).
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8

Protein Expression Analysis by Western Blot

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Cells were lysed in RIPA buffer (50 mM Tris–HCl, pH 7.4, 150 mM NaCl, 1% NP-40, 0.25% sodium deoxycholate, 1 M EDTA, 1 mM Na3VO4, 1 mM NaF, and protease inhibitor cocktail). Protein samples were quantified using the Bio-Rad DC Protein Assay Kit II (Hercules, CA, USA), separated by electrophoresis on an 8%, 10%, or 15% SDS-PAGE gel, and transferred to a Hybond enhanced chemiluminescence (ECL) transfer membrane (Amersham Pharmacia, Piscataway, NJ, USA). The membranes were blocked with 3% nonfat skim milk and probed with primary antibodies for P21, CDK2, SKP2, cleaved caspase-3, cleaved caspase-9, E-cadherin (Cell Signaling Technology, Beverly, MA, USA), cyclin E, cyclin A, B-cell lymphoma 2 (Bcl-2), PARP, AKT, p-AKT, and MMP-9 (Santa Cruz Biotechnologies, Dallas, TX, USA), and β-actin (Sigma Aldrich). The membranes were exposed to horseradish peroxidase-conjugated anti-mouse or rabbit secondary antibodies. Protein expression was examined by using an enhanced chemiluminescence (ECL) system (Amersham Pharmacia).
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9

Quantitative Immunoblotting and Cell Lysis

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Subconfluent cells were directly lysed in RIPA buffer (Thermo, PI-89901) plus protease (cOmplete ULTRA, code 05892970001, Roche) and phosphatase inhibitors (PhosSTOP, code 04906837001 Roche) and sonicated during 3–5 cycles of 30 s on and 30 s off, in a Bioruptor® (Diogenode). Protein quantification was performed with the DC™ Protein Assay Kit II (Bio-Rad, 5000112). Five to 20 μg was boiled in Laemmli sample buffer during 5 min at 95 °C, loaded onto SDS-PAGE gels and transferred to nitrocellulose or PVDF membranes. Chemiluminiscence signal was detected using SuperSignal™ West Dura (Thermo, 34076). Images were acquired with an Amersham Imager 600 scanner. Antibodies and their applications are listed in Supplementary Table S2.
Quantitative immunoblot was performed with Wes™ following manufacturer instructions (Protein Simple). Briefly, cells were lysed with RIPA, sonicated and analyzed. RPA194 levels were quantitated and normalized using β-actin as internal control.
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10

Protein Quantification of A. penicilloides MMEs

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The protein concentration of the A. penicilloides MMEs was determined with the DC Protein Assay Kit II (Bio-Rad, Hercules, CA) according to manufacturer’s instructions. The protein concentrations of the MME used in the serological assays ranged from 1.5 to 5.0 mg/ml.
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