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28 protocols using protein ladder

1

Genipin-Induced UCP1 Proteoliposome Analysis

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15 μL UCP1 proteoliposomes (protein concentration was 63.1 μg/mL, internal charge was 84) were incubated with 10, 50, 100, 200, 500, and 1000 μM genipin and an appropriate amount of water as a vehicle for 30 min at 37°C. Proteins were degraded at 97°C for 10 min in sodium dodecyl sulfate (SDS) sample buffer (pH 6.0) containing 25 mM Tris, 2.5% glycerin, 1% SDS, 1% β-mercaptoethanol, and bromophenol blue. Samples and protein ladder (Bio-Rad Laboratories, Hercules, CA) were loaded on 15% SDS gels. Electrophoresis was performed at 120 mV for 3 h. Silver staining of the gel was performed following a standard protocol.
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2

Quantification of CD3ζ Protein Levels

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SKOV3-SpyCatcher-BBζ cells were incubated with either 2000 nM myc-RFP-SpyTag or myc-RFP-SpyTag-DA for 1 h at 37 °C. Cells were lysed using RIPA lysis buffer with protease-inhibitor cocktail (Roche, cat. no. 5892970001) and centrifuged for 5 min. Lysate was then collected, and protein concentrations were quantified using a BCA assay (Thermo Scientific). Protein samples (80 μg) were mixed with loading buffer (Lammeli buffer; BioRad) containing 5% β-mercaptoethanol (BioRad) and incubated at 95 °C for 5 min. Samples were loaded in 4–15% Minigels protean TGX (BioRad) and run at 150 V for 1 h. A protein ladder (BioRad) was run along with the samples. Protein samples were transferred to a PVDF membrane (Millipore) at 100 V for 1 h. The membranes were washed with TBST (1% Tween; BioRad) and incubated with primary and secondary antibodies, including purified mouse anti-human CD3ζ (BD Pharmigen; 1:1000), anti-human/mouse/rat GAPDH, (R&D; 1:20 000), and peroxidase AffiniPure goat anti-mouse IgG (Jackson Immunology; 1:10 000). Membranes were washed three times in between the primary and secondary antibody incubation steps. Membranes were developed using the ECL prime Western blotting detection reagent (GE Healthcare no. RPN2236) and imaged using a GE ImageQuant LAS 4000 series imaging system.
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3

Quantifying Cell Viability and Proliferation

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Growth factor-reduced Matrigel (Corning, 356231). Thirty kDa protein filters (VWR, 89131-984 or Millipore UFC803024), ten kDa protein filters (VWR, 89132-008), CIM-plate 16 (ACEA, 05665817001), E-plate 16 (ACEA, 5469813001), iscript cDNA synthesis kit (Bio-Rad, 1708890), SYBR green kit (Bio-Rad, 1725270), Drabkin’s reagent (Sigma Aldrich, D5941-6VL), lenti-X concentrator (TaKaRa bio USA Inc., #631232), polybrene (Santa Cruz Biotechnology, #134220). The protein ladder was obtained from Bio-Rad (#161-0374) and TMB substrate from Thermo Fisher scientific (#N301). Propidium iodide (PI) was from Calbiochem (#537060).
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4

Protein Profile Analysis of U. fasciata

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The protein profile of the total soluble protein of U. fasciata under the four different acidification levels was detected via Sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) (Laemmli, 1970 (link)). Ten μl of protein ladder (prestained dual-color standard, 14.4–116 kDa, Bio-Rad, USA) and 15 μg of protein from each treatment were loaded onto stacking gel of 5% and separating gel of 12% acrylamide in 25 mM Tris–HCl, pH 8.3, 0.18 M Glycine and 0.1% SDS. SDS PAGE was performed using a Protean II xi cell electrophoresis unit (Biorad, Hercules, CA, USA). The separation was carried out at 180 V for 2 h. Gels were stained for 30 min with 0.02% (w/v) Coomassie Brilliant Blue R-250 in 50% (v/v) methanol and 7.5% (v/v) acetic acid, followed by a distaining for 70 min with 50% (v/v) methanol and 7.5% (v/v) acetic acid. Pictures of the gels were taken with Gel documentation system (Geldoc-it, UVP, England), which was applied for data analysis using Totallab analysis software, ww.totallab.com, (Ver.1.0.1).
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5

Evaluating Antibody Conjugation and Hybridization

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To determine linker oligo conjugation efficiency of antibodies, the reaction mixture was analysed using 10% SDS PAGE gel (Thermo Fisher Scientific, NW04122BOX) following manufacturer’s instructions. Controls, including unmodified antibodies and a protein ladder (Bio-rad, #1610375) were also used. Subsequently, the gel was Coomassie stained (Thermo Fisher Scientific, #24617) to visualize the protein bands. To determine efficiency of hybridization reaction, the annealing reaction mixture was analysed using a 4% agarose gel containing a DNA stain (Thermo Fisher Scientific, #S33102). The bands were visualized using a UV transilluminator (Bio-Rad laboratories, Hercules, California).
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6

Evaluating Antibody Conjugation and Hybridization

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To determine linker oligo conjugation efficiency of antibodies, the reaction mixture was analysed using 10% SDS PAGE gel (Thermo Fisher Scientific, NW04122BOX) following manufacturer’s instructions. Controls, including unmodified antibodies and a protein ladder (Bio-rad, #1610375) were also used. Subsequently, the gel was Coomassie stained (Thermo Fisher Scientific, #24617) to visualize the protein bands. To determine efficiency of hybridization reaction, the annealing reaction mixture was analysed using a 4% agarose gel containing a DNA stain (Thermo Fisher Scientific, #S33102). The bands were visualized using a UV transilluminator (Bio-Rad laboratories, Hercules, California).
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7

Western Blot Analysis of TGF-β1 Signaling

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Cells were seeded at 10 x 104 cells/well into 6-well plates and incubated in presence or absence of 10 ng/ml TGF-ß1 with or without terfenadine, ebastine, and solifenacin at 10 μM for 72h. Protein was isolated using RIPA buffer (Sigma Aldrich, UK). 20 μg of protein mixed with Li-Cor 4x protein loading buffer (Li-Cor, UK) and heat denaturated at 95°C under reducing conditions. Samples were then loaded onto Any kD Mini-PROTEAN® TGX Precast Protein Gels (Bio-Rad) along with a protein ladder (Bio-Rad). After gel electrophoresis, the separated protein was transferred onto a methanol-activated PVDF membrane (Millipore) by wet blotting at 350 mA for 1h. The membrane was washed and left to dry for 1h before being blocked with Li-Cor Intercept Blocking Buffer (Li-Cor) for 1h. The membranes were incubated overnight with primary antibodies (anti–α-SMA antibody, 1:3000 (Sigma-Aldrich); anti-fibronectin antibody, 1:1000 (ThermoFisher); anti-GAPDH, 1:10,000 (Abcam)) at 4°C on a shaker. Membranes were washed 4x with Tris-buffered saline containing 0.1% Tween 20 before incubation with secondary antibodies (Li-Cor, 1:10,000) for 1h on a shaker in darkness. This was followed by 4 washes with Tris-buffered saline containing 0.1% Tween 20. Blots were visualised using an infrared imaging system (Odyssey CLx imager; LI-COR) at 700 and 800 nm wavelengths simultaneously.
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8

Protein Cleavage Assay Protocol

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Final concentration of 1 µM of each protein in 50 mM Tris pH 8.0 in the presence of 1 mol equiv of 1 with and without 0.2 mM DTT in a final volume of 500 µL was allowed to incubate at 30 °C for 30 min. Reactions were lyophilized and resuspended in 25 µL of 50 mM Tris, pH 8.0. Cleavage was analyzed by mixing with equal volume of 2× sample buffer. A volume of 30 µL was analyzed by NuPAGE 4–12% Bis-Tris Gels (Life technologies) using protein ladder (Bio-Rad) as size indicator.
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9

Molecular Cloning Reagents Protocol

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All chemicals were obtained from Sigma Aldrich (St. Louis, MO), unless otherwise stated. Restriction enzymes and DNA polymerases were purchased from New England Biolabs (Ipswich, MA) and were used according to manufacturers’ procedures. Protein ladder was purchased from Biorad (Hercules, CA).
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10

Antibody-Based Protein Detection Protocol

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Aspartame was obtained from Sigma Aldrich, St. Louis, MO, USA. All major chemicals were obtained from Himedia Laboratories Pvt. Ltd., Mumbai, India. All other chemicals were of analytical grade and obtained from Sisco Research Laboratory, Bombay, India. Anti-Goat IgG HRP conjugated (HAF017) and Goat Anti-Rabbit IgG (111-035-003) antibodies were purchased from Jackson ImmunoResearch Laboratories, PA, USA. Super Signal West Femto (34095) was purchased from Thermo Fisher Scientific, Waltham, MA, USA. Alexa Fluor 488 Goat Anti-Mouse IgG (A11001), Alexa Fluor 594 Goat Anti-Rabbit IgG (A11012), and Alexa Fluor 488 Goat Anti-Rabbit IgG (A11008) were purchased from Thermo Fisher Scientific, Waltham, MA, USA. 10X Tris/Glycine buffer (161–0771), 10X Tris/Glycine/SDS buffer (161–0772), 2X Laemmli sample buffer (161–0737), and Protein Ladder (26616) were purchased from BioRad, CA, USA. Anti- FOXO3a Polyclonal Antibody (PA5-27145), anti-SIRT1 Antibody (MA5-15677), and Anti-Actin Antibody (MA1-744) were purchased from Invitrogen and Thermo Fisher Scientific Waltham, MA, USA. Protease inhibitor (04,693,124 001), Fluorescence mounting media (S3023), 2-Mercaptoethanol (M6250), Phosphate buffered saline (P5368), and Paraformaldehyde (P6148) were purchased from Sigma Aldrich St. Louis, MO, USA.
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