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32 protocols using dc protein kit

1

Apolipoprotein Analysis of HDL

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Apo AI-null HDL, with and without SOF treatment, were analyzed for protein using the BioRad DC protein kit. HDL-triglyceride (TG), cholesteryl esters, free cholesterol, and phospholipids (PL) were determined using kits and standards from Wako. The apo compositions of HDL and the SOF reaction products were determined by SDS-PAGE and visualized on a BioRad Gel Doc EZ Imager after staining with Coomassie Blue and by immunoblotting for apos AI, AII, and E.
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2

Inflammatory Cytokine Effects on Thiamine Uptake

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Human neuroblastoma SH-SY5Y cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with FBS (10%), penicillin/streptomycin (100 U/mL) in a humidified environment at 37 °C with 5% CO2 incubator (Miao et al., 2020 (link); Zhang et al., 2020 (link)). After reaching 80% confluency, the cells were exposed to the pro-inflammatory cytokines IL-1β (50 ng/mL), IL-6 (50 ng/mL) and TNF-α (50 ng/mL) (Brosseron et al., 2014 (link); Veerhuis et al., 1999 (link)) for 48 h (unless otherwise stated), as described previously (Anandam et al., 2021 (link)). [3H] Thiamin uptake (15 nM; 10 min) was then examined at 37 °C in Krebs–Ringer (KR) buffer in the presence and absence of 1 mM unlabeled thiamin. Uptake was terminated by adding 1 mL of ice-cold KR buffer, followed by rinsing of the cells (with ice-cold KR buffer), digesting them (with 1 mL of 1 N NaOH and then neutralized with 10 N HCl), and counting for radioactive content using a liquid scintillation counter (Anandam et al., 2021 (link); Zhu et al., 2015 ). Protein contents of the digested cells were measured using the Dc protein kit (Bio-Rad).
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3

Quantitative Immunoblotting of THTR-1 in SH-SY5Y Cells

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Control and IL-1β (50 ng/mL)-treated SH-SY5Y cells were lysed in radioimmunoprecipitation assay buffer (Sigma) in the presence of a protease inhibitor cocktail (Roche, Branchburg, NJ). The soluble protein fraction was collected after centrifugation (14,000 rpm, 20 min) and quantified using the Dc protein kit (Bio-Rad). An equal amount of protein (40 μg) was loaded onto 4–12% bis-Tris gradient mini gels (Invitrogen) and transferred onto Immobilon polyvinylidene difluoride membrane (Fisher Scientific). The blots were then probed with anti-THTR-1 (1:1000), anti-Sp1 (1:500), and anti-β-actin (1:3000). The specificity of the THTR-1 polyclonal antibodies has been validated by us in previous studies (Ramamoorthy et al., 2020 (link)). The immune-reactive bands were detected with the corresponding secondary antibodies anti-rabbit IRDye-800 and anti-mouse IRDye-680 (both at 1: 30,000 dilution). The densities of the immune-reactive bands were quantified using LI-COR software (LI-COR Bioscience, Lincoln, NE).
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4

Molecular Signatures of Hepatic Stress

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Liver tissues were resuspended in RIPA lysis buffer. Lysates were centrifuged for 15 min at 12000 g and 4 °C, and protein contents of the supernatant were determined using DC protein kit (Bio-Rad Laboratories, CA, USA). Aliquots of the proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and transferred to PVDF membranes (Bio-Rad Laboratories, CA, USA). PVDF membranes were incubated with antibodies against phospho-Eif2α, GRP78, CHOP, ATF6 (90KD), ATF6 (50KD), shear-XBP1 (XBP1-s), unshear-XBP1 (XBP1-u), Cleaved-Capsase3 (Cleaved-Casp3), phospho-IRS1 (Ser307), phospho-Akt (Ser473), IRS1, Akt, phospho-NFκB-p65, phospho-IκBα, phospho- JNK, phospho-p38-MAPK, NFκB-p65, IκBα, JNK1, p38-MAPK and β-actin. All antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA).
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5

Quantitative Immunoblotting of THTR-1 in SH-SY5Y Cells

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Control and IL-1β (50 ng/mL)-treated SH-SY5Y cells were lysed in radioimmunoprecipitation assay buffer (Sigma) in the presence of a protease inhibitor cocktail (Roche, Branchburg, NJ). The soluble protein fraction was collected after centrifugation (14,000 rpm, 20 min) and quantified using the Dc protein kit (Bio-Rad). An equal amount of protein (40 μg) was loaded onto 4–12% bis-Tris gradient mini gels (Invitrogen) and transferred onto Immobilon polyvinylidene difluoride membrane (Fisher Scientific). The blots were then probed with anti-THTR-1 (1:1000), anti-Sp1 (1:500), and anti-β-actin (1:3000). The specificity of the THTR-1 polyclonal antibodies has been validated by us in previous studies (Ramamoorthy et al., 2020 (link)). The immune-reactive bands were detected with the corresponding secondary antibodies anti-rabbit IRDye-800 and anti-mouse IRDye-680 (both at 1: 30,000 dilution). The densities of the immune-reactive bands were quantified using LI-COR software (LI-COR Bioscience, Lincoln, NE).
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6

Western Blot Protein Quantification

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Proteins were extracted from cells with a lysis buffer (NP40 1%, SDS 0.1%) and quantified with the Dc protein kit (Biorad). Forty μg of total proteins were resolved by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred onto nitrocellulose membranes. We used the following primary antibodies: anti-SF3B1 (1:5000, #170854 Abcam), anti-FLAG (1:5000, #F3165, Sigma), anti-GAPDH (1:5000), and anti-b-actin (1:1000, #ab8226, Abcam). Donkey anti-mouse (1:5000, #926-32222, LI-COR) and goat anti-rabbit (1:5000, #926-32211, LI-COR) secondary antibodies were used. Immunofluorescence was detected using Odyssey Infrared Imaging system (LI-COR). Quantification was performed with Image Studio Lite software. β-actin or GAPDH were used as references to normalize quantification.
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7

Secretome Isolation and Characterization for Wound Healing

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The secretomes were obtained following a protocol adapted from Fong et al. [44 (link)] and previously described by our group [7 (link)]. In summary, DSCs or ASCs monolayers at 90% confluence were subjected to a triple wash with PBS and maintained in DMEM without FBS for 48 h. Cell supernatants were collected and processed by centrifugation (5 min, 300 g) to pellet and exclude eventual floating dead cells, and then filtered through a 0.22 µm filter to remove debris. The resulting secretome was concentrated tenfold using an Amicon Ultra-15-Centrifugal Filter 3 kDa MWCO (Millipore) by centrifugation (45 min, 5,000 g), following the manufacturer's instructions. The concentrated secretome was aliquoted and stored at − 80 °C for up to 4 months for downstream applications. The total protein content of the secretome was quantified using the DC Protein kit (Bio-Rad) according to the manufacturer’s protocol, and reading was carried out using the Tecan Infinite M200 microplate reader. Total protein secreted was similar in seDSC and seASC (average of 194.4 and 209.4 µg per 106 cells, respectively). Secretomes were diluted to a final concentration of 1 µg/µl and wound healing studies used a dosage of 200 µg of total protein per wound, in reference to cell group controls that received 106 DSC or ASC per wound.
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8

Quantitative Western Blot Analysis

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Cells were lysed in RIPA lysis buffer (50 mM Tris-HCl [pH 7.5], 150 mM NaCl, 1% NP-40, 0.1% SDS, and 1% sodium deoxycholate) supplemented with protease inhibitors (Roche), sonicated, and centrifuged at 13,200 rpm for 15 min. Protein concentrations were measured using the Dc-Protein Kit (Bio-Rad). Equal amounts of protein were separated on SDS-PAGE, blotted, probed for target proteins, and detected using ECL (Perkin Elmer). The primary antibodies used for detection were UBF (F-9; Santa Cruz Biotechnology), RRN3 (ab112052; Abcam), TAF1C (ab134394; Abcam), POLR1A/RPA194 (C-1; Santa Cruz Biotechnology), POLR1B/RPA135 (H-15; Santa Cruz Biotechnology), RPA43 (HPA022416; Sigma-Aldrich), α-tubulin (10D8; Santa Cruz Biotechnology), lamin A/C (H-110; Santa Cruz Biotechnology), and GAPDH (14C10; Cell Signaling Technology). Horseradish peroxidase (HRP)-conjugated secondary antibodies were from DAKO or Santa Cruz Biotechnology. Protein densitometry analysis was conducted using ImageJ software, and the mean value normalized with loading control was used as final protein band quantification.
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9

Hepatic Microsome Isolation Protocol

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Hepatic microsomes were prepared as described by Ivanova et al.35 All preparation steps were carried out on ice, unless otherwise stated. Frozen liver tissue was added to about 5 volumes (v/w) of ice-cold preparation buffer (0.1 M K PO4, adjusted to pH 7.5) and manually homogenized in a Potter-Elvehjem tissue grinder (Sigma-Aldrich). Homogenates were separated using a series of centrifugation steps carried out at 16 000g for 30 min to remove nuclear and cellular debris, and then at 100 000g for 1 h to isolate microsomal fractions. Ultracentrifugation steps were conducted using a swing-out rotor SW41Ti ultracentrifuge (Beckman Instruments, Palo Alto, CA, USA) maintained at 4 °C. The microsomal particulate fractions were resolubilized in preparation buffer, aliquoted into single-use volumes, and stored at −80 °C until use in metabolism assays. Triplicate measures of total microsomal protein concentrations were taken from one single-use aliquot for each batch of microsomes prepared according to the method by Lowry et al.36 (link) (Bio-Rad, DC Protein Kit, Hercules, CA, U.S.A.).
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10

Disaccharidase Activity in Nondiabetic Rats

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The assay was conducted following the procedure as described previously by Hannan et al. [27 (link)]. The ethanol extract of B. monosperma (250, 500, and 1000 mg/kg) was administered by gastric gavage to 20 hr fasted nondiabetic rats. After 60 min, the rats were sacrificed and the small intestine was isolated, cut longitudinally, rinsed with ice-cold saline, and homogenized in 10 mL saline (0.9% NaCl). Aliquots of homogenate were incubated with 40 mM sucrose at 37°C for 60 min. The amount of protein was determined by DC Protein Kit (Bio Rad, USA). Disaccharidase activity was determined from the glucose concentration converted from sucrose as μmol/mg protein/h.
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