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13 protocols using biomate 3s uv visible spectrophotometer

1

Comprehensive Characterization of Au/Ce Nanoclusters

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Transmission Electron Microscopy (TEM) images were recorded using a JEM-2100 microscope (JEOS, Japan) to characterize the size and size distribution, a certain concentration of sample solution was spotted on carbon coated copper grid (300 meshes) and was dried in desiccator at room temperature. Energy dispersive X-ray spectroscopy (EDS) analyses was done in a Zeiss Ultra Plus scanning electron microscopic (SEM). The valence state of gold and cerium atoms in the Au/Ce nanoclusters was investigated by a PHI 5000 VersaProbe X-ray photoelectron spectrometer (XPS), briefly, samples were droped on a silicon wafer and dried in laboratory ambience to form evenly spread film. Thermo BioMate 3S UV–visible spectrophotometer was used for the UV–Vis absorption measurements, spectra were typically measured in the range of 200–700 nm. Photoluminescence spectra were carried out using SHIMADZU RF-5301 PC instrument. Cells fluorescence imaging were collected by laser scanning confocal microscope Carl Zeiss LSM710 (Zeiss, Germany). Nude mice in vivo imaging were carried on vivo multispectral imaging system (Maestro EX).
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2

RT-qPCR Analysis of Whole Blood RNA

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Total RNA samples were extracted from whole blood for use in RT-qPCR using TRIzol (Invitrogen, Life Technologies, USA), according to the manufacturer’s instructions. Total RNA purity and concentration were evaluated using an ultraviolet spectrophotometer (BioMate 3S UV-visible spectrophotometer; ThermoFisher Scientific). Total RNA samples aliquots (1 µg) were used to synthesize cDNA, using a cDNA Synthesis Kit (Roche Applied Science, Indianapolis, USA), and qRT–PCR conducted with a reverse transcription system (LC-480, Roche, USA) using SYBR Master Mix (Roche Applied Science). The housekeeping genes, GAPDH and HPRT, served as internal controls for cDNA normalization. All primer sequences used in this study are listed in Table S3.
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3

Ethanol Production from Glucose Fermentation

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The fermentation medium consisted of YEP (1% Yeast extract, 2% Peptone) supplemented with 10% glucose and then inoculated with 1% and the fermentation lasted 24 h at 30 °C. The amount of ethanol produced was determined by the spectrophotometric method described by Rattanaporn et al. (2019) . Briefly, 1 ml of tri-n-butyl phosphate (TPB, Lobal Chemie, India) and 1 ml of sample were mixed, stirred vigorously for 1 min and then centrifuged (3420g, 5 min). Subsequently, 500 μl of the upper phase (clear and transparent) and potassium dichromate solution (10% w/v K2Cr2O7, 5M H2SO4) were mixed in a new microtube, shaken vigorously for 1 min, then allow to stand for 10 min at room temperature. Finally, 100 μl of the lower (green) phase was diluted in 900 μl of deionised water and the optical densities were read at 595 nm using a spectrophotometer (Thermo Scientific BioMate 3S UV-Visible spectrophotometer, Thermo Scientific, USA). The concentration of ethanol in the sample was estimated from the calibration curve showing the relationship between absorbance at 595 nm and ethanol concentrations.
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4

DPPH Radical Scavenging Assay for Antioxidant Evaluation

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The antioxidant activity of the different extracts was assessed in culture supernatants, ICCs and whole cells by the 2,2-diphenyl-1-picryl hydrazyl radical method as described by Chen et al. (2010) . The selected isolates were grown in YPD broth for 24 h at 30 °C. Then the culture supernatants were obtained by centrifugation (3500 g, 15min) and the ICCs by cell bursting in citrate buffer pH 5 at 50 °C. An aliquot (800 μl) of supernatant or ICC and 1000 μl of DPPH (0.2 mM) were mixed, left in the dark at 25 °C for 30 min. Optical densities were measured at 517 nm using a spectrophotometer (Thermo Scientific BioMate 3S UV-Visible spectrophotometer, Thermo Scientific, USA). The test was performed in triplicate and the blank was prepared in deionised water. Antiradical activity of the extracts (A) was calculated according to the formula (Eq. (4)): %A=(1Abssample)Absblank×100 where: A = Antiradical activity.
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5

Embryonic Development of Colored Eggs

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Eggs laid by Fuyin, Fuyin-lre, and re were separately treated and incubated [13 ]. Every 24 h after incubation, the eggs were treated with 20% NaOH at 100°C for 3-5s, and then, eggs were blew with a dropper to separate the embryo from eggshell in clean water. The embryonic morphology of these eggs was observed under a microscope to determine the developmental stages of the embryo.
Every 24 h after incubation, 0.5 g of normal eggs laid by Fuyin as well as red eggs laid by Fuyin-lre and re was collected for total RNA extraction using the RNAiso Plus (TaKaRa) kit. The extracted RNA was digested by DNase I (TaKaRa) to remove DNA residues. The concentration and purity of total RNA was determined using a BioMate 3S UV-visible spectrophotometer (Thermo Fisher Scientific), and the quality of total RNA was identified using an Agilent bioanalyzer (Agilent Technologies 2100).The qualified RNA was used in DGE and qRT-PCR.
Normal eggs laid by Fuyin and the red eggs laid by Fuyin-lre and re were selected to extract their genomic DNA according to the literature [14 ]. Each qualified DNA sample was confirmed by the BioMate 3S UV-visible spectrophotometer before dilution to 100 ng/μL and storage at—20°C.
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6

Spectrophotometric Quantification of Lactic Acid

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Lactic acid was quantified by the spectrophotometric method as described by Borshchevskaya et al. (2016) . One ml of the fermentation broth was centrifuged (4500 rpm for 30 min) and the supernatant was collected and diluted 10 times. Subsequently, 0.1ml of the previous dilution was added to 4 ml of a FeCl3 solution (0.2%); after homogenization, the optical density was measured with a spectrophotometer (Thermo Scientific BioMate 3S UV-Visible spectrophotometer, Thermo Scientific, USA) at a wavelength of 390 nm. The amount of lactic acid was calculated based on of a previously drawn calibration curve. The results obtained were the mean of three experiments.
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7

Quantifying Plasmid and Protein Encapsulation in PLGA Nanoparticles

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The amount of pcDNA3.1-SynORF5 plasmids loaded into PLGA NPs was determined as follows (Zhao et al., 2010 (link)). Lyophilized PLGA-SynORF5 NPs were immersed in 1 mL dichloromethane, to which 5 mL 0.1 M PBS (pH 7.4) were added. The mixture was stirred for 30 min followed by centrifugation at 4,000 rpm for 8 min. The supernatant was collected and the concentration of pcDNA3.1-SynORF5 was determined by measuring absorbance at 260 nm using Biomate 3S UV-Visible Spectrophotometer (Thermo Scientific, USA).
The amount of entrapped GP5 protein in NPs was determined as described previously (Corrigan and Li, 2009 (link)). Briefly, freeze-dried NPs were dispersed into 3 mL 0.1 M NaOH containing 5% (w/v) SDS. The suspension was incubated in a water bath at 60°C for 1 h. Following centrifugation at 10,000 rpm for 10 min, the concentration of the GP5 protein in the supernatant was measured by using RC DCTM Protein Assay (Bio-Rad, USA) for micro-BCA analysis.
The EE of the NPs were calculated using this formula (Park et al., 2003 (link); Manca et al., 2008 (link)):
Where m is the mass of the pcDNA3.1-SynORF5 or GP5 loaded in PLGA NPs and C and V are the concentration and volume of the supernatant, respectively. m0 is the initial amount of pcDNA3.1-SynORF5 or GP5.
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8

Synthesis and Characterization of Upconversion Nanoparticles

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NaYF4:Yb,Tm nanocrystals and monodisperse silica-coated NaYF4:Yb,Tm (NaYF4:Yb,Tm@silica, UCPs) were synthesized and characterized following the method described by Guo et al. (2010) [7] and Qian et al. (2009) [9] (link). The UCPs were modified using an amino group following the method described by Guo et al. (2011). DMNPE (Invitrogen) was used to cage siRNAs following the manufacturer's protocol, and UCPs/siRNA-DMNPE complexes were made as described previously by Guo et al. (2011) [14] (link). The ratio of UCPs to siRNA was determined by measuring the zeta potential using Nano-ZS ZEN 3600 (Malvern Instruments Ltd, UK) at 25°C. The UV absorption spectrum was gathered using BioMate 3S UV-visible spectrophotometer (Thermo Scientific) at 25°C.
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9

Pigment and Protoporphyrin IX Analysis

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For the pigment analysis, the leaves were collected from the sprl1 mutant and its wild type at the seedling stage and the heading stage, respectively. The pigments were extracted from 0.2 g of fresh leaves with 80% acetone in the dark at 4 °C for 48 h. The contents of chlorophyll (Chl) and carotenoids (Caro) were measured at wavelengths of 470 nm, 646 nm, and 663 nm using the BIOMATE 3S UV-Visible Spectrophotometer (Thermo scientific, Waltham, MA, USA) and were calculated according to the method of Lichtenthaler and Wellburn [52 (link)]:


For the Proto IX analysis, 0.1 g fresh leaves at the seedling stage were homogenized in 1 mL methanol/acetone/0.1 M NaOH (9:10:1, v/v/v), and the homogenates were centrifuged at 7197 g (Eppendorf 5430R; 7830 rpm) at 1 °C for 20 min. To oxidize the Protogen IX into Proto IX, 5 μL of 1 M acetic acid and 5μL of 2-butanone peroxide was added to 200 μL supernatant [28 (link)]. Then, the Proto IX was analyzed by HPLC on a C8 column (4.6 × 150 mm, 3.5μm; Waters) according to the method of Wang [53 (link)]. The elution profiles were detected by fluorescence, with excitation at 405 nm and emission at 625 nm [28 (link)]. The Proto IX was quantified by using the Proto IX standard (Frontier Scientific, Logan, UT, United States).
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10

Protein Purification and Analysis Methods

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Proteins isolated from immobilized metal ion chromatography were further purified by FPLC on an AKTAprime-Plus (GE Healthcare) with a HiLoad 16/600 Superdex 75pg column (GE Healthcare). Protein absorbance was monitored at 280 nm.
Protein concentrations were determined using a BioMate 3S UV–visible spectrophotometer (Thermo Scientific).
Luminescence images were captured on a Gel Doc XR+ system. Luminescence intensities were quantified using a SynergyH1 hybrid reader (BioTek). Plates were either Corning 96-well assay plates (3359) [white, half area, round-bottom, 120 μL reaction volume] or Corning 384-well assay plates (3824) [white, low volume, flat bottom, 40 μL reaction volume]. Luminescence readings in living bacteria were obtained 30 min after substrate addition; all other luminescence readings were acquired immediately after substrate addition, unless indicated otherwise. Relative luminescence data were obtained by dividing raw luminescence readings by the largest luminescence value obtained in each experiment.
Recipes for buffers and stock solutions can be found in the Supporting Information. TB medium is terrific broth.
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