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251 protocols using smartspec plus spectrophotometer

1

Estimating Malondialdehyde and Proline in Plant Tissues

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The MDA concentration was estimated according to the method of Health and Packer [60 (link)]. Fresh tubers (0.2 g) were homogenized with 10% trichloroacetic acid (1 mL) and centrifuged at 10,000 rpm for 10 min. Thereafter, 1 mL of the supernatant was mixed with 20% trichloroacetic acid containing 0.25% thiobarbituric acid and was heated at 95 °C for 30 min., quickly cooled in an ice bath, and then centrifuged again at 10,000 rpm for 10 min. The absorbance of the supernatant was read at 532 and 600 nm (SmartSpecTM Plus spectrophotometer, Bio-Rad, Hercules, CA, USA). The MDA concentration was calculated using an extinction coefficient of 155 mM−1cm−1 and expressed as nmol g−1 FW.
Pro was determined according to Bates et al. [61 (link)]. Fresh tissue of stored tubers (0.5 g) was extracted with 2.5 mL of boiled water. Subsequently, 2.0 mL extract was mixed with an equal volume of ninhydrin solution (1.25 g ninhydrin dissolved in 30 mL glacial acetic acid, and 20 mL of 6 M phosphoric acid) and glacial acetic acid. The samples were then incubated at 100 °C for 1 h and the reaction was terminated by cooling the tubes in an ice bath. After cooling, Pro was determined at 522 nm (SmartSpecTM Plus spectrophotometer, Bio-Rad, Hercules, CA, USA).
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2

Quantifying Leaf Hydrogen Peroxide

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The methodology developed by Velikova et al. [40 (link)] was used to determine hydrogen peroxide (H2O2). Fresh leaf material (200 mg) was crushed under liquid nitrogen followed by homogenizing in 1.5 mL 0.1% (w/v) trichloroacetic acid (TCA). The homogenate was centrifuged at 12,000× g for 15 min at 4 °C. A 0.5 mL aliquot of supernatant was supplemented with 0.5 mL of 10 mM potassium phosphate (pH 7) and 1 mL of 1 M KI, followed by vortex mixing. The H2O2 concentration was determined by reading the absorbance at 390 nm (SmartSpecTM Plus spectrophotometer, BioRad) and using a standard curve.
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3

Screening Bacterial Herbicide Tolerance

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The herbicide tolerance of bacterial strains was assessed in triplicate by observing their growth on liquid LB medium supplemented with different Sekator® Turbo herbicide concentrations (0.25 mL L−1 (Hb50), 0.375 mL L−1 (Hb75), and 0.5 mL L−1 (Hb100)). The bacterial growth in liquid LB media was monitored by measuring the optical density at 600 nm using SmartSpecTM Plus spectrophotometer (Bio-Rad, Hercules, CA, USA). The significant growth of bacterial strains in the presence of herbicide during 24 h at 37 °C (180 rpm) was considered as herbicide tolerant.
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4

Quantitative Analysis of BM-MSC RNAs

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Total RNAs in passage 4 BM-MSCs were extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. RNA integrity was determined using formaldehyde denaturalization agarose gel electrophoresis. RNA concentrations were measured by the smartspecTM plus spectrophotometer (BIO-RAD, Hercules, CA, USA). cDNA was generated using SuperScript III First Strand Synthesis SuperMix (Takara, Dalian, China) or a TaqMan MicroRNA Reverse Transcript Kit (Applied Biosystems). TaqMan probes for individual miRNAs were purchased from Applied Biosystems. β-Actin and U6 was used as internal housekeeping controls, respectively. Quantification of mRNA and mature miRNA was performed on an ABI 7500 real-time PCR detection system (Applied Biosystems, USA) as previously described. The specific primers oligonucleotides (TaKaRa, Dalian, China) were used and relative expression of the target genes was calculated with the 2−ΔΔCt method.
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5

Proline Content Determination in Plants

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The level of proline was evaluated according to [39 (link)], with modifications [40 ]. Fresh plants (0.5 g) and boiling water (2.0 mL) were added to the test tubes. The test pieces were placed in a water bath and boiled over a period of 30 min. After, the tubes were removed and cooled. The extract (1 mL) was mixed with an equal volume of acid ninhydrin (C9H6O4) solution and glacial acetic acid (CH3COOH). The samples were then incubated at 100 °C for 1 h and cooled in an ice container. The optical densities of the solutions were measured at 520 nm (SmartSpecTM Plus spectrophotometer, Bio-Rad, Hercules, CA, USA). The proline contents (μmoL g−1 FW) were calculated using a calibration curve.
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6

Membrane Integrity and Oxidative Stress Assay

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Pro content was evaluated as described [30 (link)] with the modification [31 ]. Disturbance of the barrier properties of cell membranes was assayed by following electrolyte leakage (EL) from plant tissues using an OK 102/1 conductometer (Radelkis, Hungary), measuring the ohmic resistance of water extracts on constant current [32 (link)]. The lipid peroxidation was assessed by malondialdehyde (MDA) content [26 ]. The optical densities were measured using a SmartSpecTM Plus spectrophotometer (Bio–Rad, Hercules, CA, USA) at 522 nm (for Pro) and 532 nm and 600 nm (for MDA).
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7

Determination of SOD activity in RBC and PBMC

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The activity of SOD in RBC and PBMC was determined using modified pyrogallol auto-oxidation method40 (link). In brief, 62.5 mM tris-cacodylic acid buffer was mixed with cell fractions (RBC and PBMC in respective cases) followed by addition of 4 mM pyrogallol. The auto-oxidation of pyrogallol was monitored spectrophotometrically (Bio-RAD SmartSpecTM Plus Spectrophotometer) at 420 nm, followed by the estimation of the absorbance of the test samples at specific time intervals.
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8

Malondialdehyde Assay for Lipid Peroxidation

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The degree of lipid peroxidation of membranes was assessed by malondialdehyde (MDA) concentration [83 ]. Fresh leaf (0.5 g) was homogenate with dH2O (3 mL), with the subsequent addition of 20% trichloroacetic acid (3 mL), followed by centrifugation for 10 min at 10,000× g. Afterword, the supernatant (2 mL) was blended with 0.5% thiobarbituric acid (2 mL), heated (100 °C for 30 min), and then rapidly cooled. The optic density of the obtained solution was measured at 532 nm and 600 nm (SmartSpecTM Plus spectrophotometer, Bio-Rad, St. Louis, MO, USA). Using an extinction coefficient (155,000 L cm−1 moL−1), the concentration of MDA (nmoL g−1 FW) was calculated.
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9

Wheat Genome Analysis via SSR Markers

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Total genomic DNA was extracted from seven-day-old seedlings [49 (link)]. DNA concentration was determined using a SmartSpec TM Plus spectrophotometer (BioRad, Hercules, California, USA).
In the work 21 SSR markers were used selected so as to cover maximally the wheat genome, including Xgwm334, Xgwm437, Xgwm18, Xgwm357, Xgwm613, Xgwm3, Xtaglgap, Xgwm408, Xgwm577, Xgwm261, Xgwm95, Xgwm155, Xgwm186, Xgwm130, Xgwm389, Xgwm513, Xgwm160, Xgwm192, Xgwm148, Xgpw2255, Xgwm190, and Xgwm469. The PCR procedure was published in Roeder et al. [50 (link)]. PCR fragments were separated on ABI PRISM 3100 automatic sequencer (Applied Biosystems, Waltham, MA, USA). Fragment size was calculated using the ABI GeneScan software, version 2.1 (Applied Biosystems, Waltham, MA, USA).
SSR analysis data were used to study the genetic similarity of lines using PHYLIP software package (Version 3.69, Seattle, Washington, USA) [51 ]. To assess the reliability of constructed trees, bootstrap analysis was performed for 100 replicates.
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10

Isolation and Characterization of Bacillus subtilis

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The bacterium Bacillus subtilis (strain 10-4) was isolated from the arable soils at the Bashkir Research Institute of Agriculture of the Ufa Federal Research Center of the Russian Academy of Sciences (BRIA UFRC RAS) (Ufa, Russia), identified using 16S rRNA and characterized [11 (link)]. B. subtilis 10-4 cells were cultured in potato glucose agar (PGA) medium at 37 °C for 3–4 days [11 (link),25 ]. To obtain the initial inoculum of B. subtilis 10-4, a suspension culture was grown to a concentration of 108 CFU mL−1, according to the 0.5 McFarland Turbidity Standard, monitored at an optical density of 600 nm (OD600) (SmartSpecTM Plus spectrophotometer, Bio–Rad, Hercules, CA, USA), and then diluted down to 105 CFU mL−1 using distilled water [11 (link)].
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