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21 protocols using ultraviolet spectrophotometer

1

Quantifying Viral E Gene Expression

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Total RNA was extracted from the collected tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. The concentration of each sample was measured using an ultraviolet spectrophotometer (Shimadzu, Shimazu, Japan). First cDNA was synthesized from 1 μg total RNA using PrimeScript TM RT Regent Kit with gDNA Eraser Kit (TaKaRa, Dalian, China). The primers for viral E gene were designed as previously reported (Yu et al., 2012 ). For confirming the viral copy numbers in the infected ducks, the viral titers (log10) were normalized to 1 μg of total RNA (Sun et al., 2014 (link)). Quantitative RT-PCR (qRT-PCR) was performed with the Applied Biosystems 7500 Fast Real-Time PCR System (Applied Biosystems, CA, USA) using the SYBR Green PCR kit (Takara, Dalian, China). qRT-PCR was conducted in a total volume of 20 μl following the manufacturer’s instructions. PCR reaction conditions consisted of 95C for 30 s, 40 cycles of amplification at 95C for 5 s, and 60C for 34 s, followed by a dissociation curve analysis step. Each sample was analyzed in triplicate.
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2

DNA Quantification in Mesenchymal Stem Cells

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To quantify total DNA content, the composites were cut into 1 mm × 1 mm pieces, and these fragments were treated in an Ultrasonic Cell Crusher (Sonics VCX800, Newtown, CT, USA). Cell proliferation was quantified by measuring the DNA concentration with a DNA/RNA extraction kit (Wako, Osaka, Japan) according to the manufacturer's protocol. The lysis solution was centrifuged at 1,000 r/min for 5 minutes, and the supernatant was collected for DNA quantification by measuring the absorbance at 260 nm with an ultraviolet spectrophotometer (Shimadzu, Kyoto, Japan). The DNA concentration was normalized to the initial number of bone marrow mesenchymal stem cells (Lundborg; Gu et al., 2014).
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3

Extraction and Quantification of Total Saponins from Clinopodium chinense

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Dried C. chinense samples from leaves, stems, and roots were used for separation of total saponins using a similar method to that previously reported [37 ,38 ]. Dried powder (0.1 g) from each sample was mixed with 50% carbinol and then subjected to ultrasonic extraction for 40 min (300 W, 40 kHz). The supernatant was then collected, dried by distillation, and dissolved in carbinol. Absorbance was measured using an ultraviolet spectrophotometer (Shimadzu Corporation, Japan). Clinopodiside A was used as a standard and the standard curve of the relationship between concentration and absorbance was constructed (Supplementary Figure S14). The yield (%) of total saponins was calculated as Yield (%) = [saponin content of extraction (g)/C. chinense samples powder weight (g)] × 100%].
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4

Biochemical Profiling of Serum

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The action of biochemical parameters such as serum alanine transaminase (ALT), alkaline phosphate (ALP), bilirubin, total cholesterol (CHL), albumin (ALB), and serum lactate dehydrogenase (LDH) was determined using standard kit methods. All estimation was done using ultraviolet spectrophotometer (Shimadzu) as per standard kit methods.
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5

Determining DOXY Encapsulation Efficiency in PNPs

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The EE% for DOXY in the prepared PNPs was determined by an indirect method [65 ]. The entrapped drug was separated from the un-entrapped by centrifugation [66 (link)] for 30 min at 14,000 rpm (17,979× g) using a Hettich centrifuge (Hettich, Mikro 22 R, Germany). The amount of the un-entrapped DOXY in the supernatant was estimated spectrophotometrically at 269 nm utilizing an ultraviolet spectrophotometer (Shimadzu, Japan). The experiment was done in triplicate and the EE% was calculated using the next equation [67 (link)]: Encapsulation efficiency % =(Total DOXY)(Unentrapped DOXY)Total DOXY×100
Additionally, the loading capacity percentage which represents the percentage of the amount of drug (DOXY) in the prepared PNPs was determined. The loading capacity % was measured through the following equation [68 (link)]: Loading capacity %=Mass ofentrappe DOXYMass of prepared PNPs ×100
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6

Quantifying Total Phenolic Content

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Total phenolic content was measured using the Folin–Ciocalteu’s reagent as described [11 ]. Absorbance was measured at 760 nm using an ultraviolet spectrophotometer (Shimadzu, Japan). Gallic acid was used as a standard. A dose response linear regression was generated using the gallic acid standard absorbance, and the total phenolic content was expressed as mg gallic acid equivalents (GAE)/g dry weight of extract. Values were determined in triplicate.
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7

Hypocotyl Lignin Quantification Protocol

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The lignin content of hypocotyls was determined using a plant lignin ultraviolet spectrophotometer kit (Solarbio, Beijing, China). Briefly, the hypocotyl samples were dried at 80°C and then ground to powder. Moreover, 10 mg of the samples was placed into test tubes, and then 1 ml acetyl bromide solution (25% v/v acetyl bromide in glacial acetic acid) and 40 µl perchloric acid were added, fully mixed, and heated for 40 min at 80°C with vortexing every 10 min. After cooling (room temperature), 1 ml of a solution of glacial acetic acid and sodium hydroxide was added to end the reaction. Finally, after centrifugation at 8,000 g for 10 min, 20 µl of supernatant was mixed with 1.98 ml glacial acetic acid, and 1 ml liquid was added to a quartz cuvette to determine the absorbance using an ultraviolet spectrophotometer (Shimadzu Corp., Kyoto, Japan) at 280 nm. The results were expressed on dry weight basis as mg cm-1.
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8

Total RNA Extraction and cDNA Synthesis

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The collected tissues (0.1 g) were ground in liquid nitrogen and the total RNAs were extracted from the tissues with TRIzol Reagent (Takara, Dalian, China), according to the manufacturer’s instructions. The concentrations of the total RNAs were measured with an ultraviolet spectrophotometer (Shimadzu, Shimazu, Japan). A sample of each RNA (1 μg) was treated with DNase I (Thermo Scientific, Lithuania) and reverse transcribed with M-MLV reverse transcriptase (Promega, Madison, WI, USA). The synthesized cDNA was stored at –20°C until analysis.
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9

Quantifying Lipid Peroxidation via TBARS Assay

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It was used as a thiobarbituric acid reacting substances (TBARS) assay. It was performed as described by Jentzsch et al.18 (link) In the TBARS assay, one molecule of malondialdehyde (MDA) reacts with 2 molecules of thiobarbituric acid (TBA) to produce a pink pigment with absorption at 535 nm. Amplification of peroxidation during the assay is prevented by the addition of the chain-breaking antioxidant Butylated hydoxytoluene (BHT). Plasma (400 μL) or MDA standard (0.2-4 μmol/L) was prepared by hydrolysis of 1,1,3,3 tetramethoxypropane (Sigma Chemical Co, St Louis, Missouri) and was mixed with 400 μL orthophosphoric acid (0.2 mol/L) (Sigma Chemical Co) and 50 μL BHT (2 mmol/L) (Sigma Chemical Co) in 12 × 75 mm tubes. We added 50 μL TBA reagent (0.11 mol/L in 0.1 mol/L NaOH) (Fluka Chem., Buchs, Switzerland) and mixed the contents; the contents were then incubated in a water bath at 90°C for 45 min. The tubes were put on ice to stop the reaction. Thiobarbituric acid reacting substances were extracted once with 1000 mL n-butanol (Sigma Chemical Co, St. Louis, MO, USA). The upper butanol phase was read at 535 nm and 572 nm to correct for baseline absorption using an ultra violet spectrophotometer (Shimadzu Corporation, Japan). MDA equivalents (TBARS) were calculated using the difference in absorption at the 2 wavelengths, and quantification was done using the calibration curve.11
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10

Quantifying AFTSI in Phytovesicles

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Phytovesicles containing AFTSI were separated from untrapped drug by centrifugation at 9000 rpm for 45 min. The supernatant was recovered and assayed spectrophotometrically using Shimadzu ultraviolet spectrophotometer.
Where, Ct - concentration of total AFTSI; Cr - concentration of free AFTSI.
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