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25 protocols using tskgel g2000swxl

1

Analyzing Protein Aggregate Molecular Weight

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The molecular weight distribution of the aggregates was measured by size-exclusion chromatography on a HPLC system (e2695, Waters Alliance, Milford, MA) equipped with a UV/visible detector (2489, Waters Alliance) and the analysis software Empower (Waters Alliance). Two columns in series, TSKgel G2000SW XL and TSKgel G3000SW XL (Tosoh Bioscience GmbH, Griesheim, Germany) with a guard column were used for the separation and analysis of the proteins. The dimension of the columns was 7.8 × 300 mm each, and the exclusion volume was equivalent to 5 × 10 5 Da. The absorbance was recorded at 280 nm. The buffer was 20 mM sodium phosphate (pH 7.0). The flow rate was 0.5 mL/min, and the total duration of each run was 60 min. The coefficient of partition was calculated for the standards (thyroglobulin, aldolase, BSA, β-LG, and α-LA) and the whey protein aggregates using the elution volume of blue dextran (2 × 10 6 Da) as exclusion volume.
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2

Size Exclusion Chromatography for Digestive Protein Analysis

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MW distribution of digestive production (supernatants) was analyzed by size exclusion chromatography (TSKgel G2000SWXL, Tosoh Corp., Tokyo, Japan) on a high performance liquid chromatography (HPLC) system (LC-AT20, Shimadzu Crop, Tokyo, Japan). Data were processed and acquired via Labsolutions software. Twenty microliters of each digestive production (2 mg/mL) were injected, eluted using 45% acetonitrile containing 0.1% trifluoroacetic acid at a flow rate of 1 mL/min, and monitored at 214 nm. The MW calibration curve was plotted using the following standards, GLY (75 Da), Glutathione (307 Da), Bacitracin (1422 Da), Insulin (5733 Da), and Cytochrome c (12,400 Da). The MW was calculated, as follows:
MW represents MW (Da) and t means elution (min).
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3

Gel-filtration HPLC analysis of F. oxysporum

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The extracts from F. oxysporum after ultrasonication were subjected to gel-filtration high performance liquid chromatography (HPLC) on a TSKgel G2000SWXL (7.8 mm × 300 mm, TOSOH, Tokyo, Japan). Elution was performed with a 50 mM ammonium acetate buffer solution (pH 5.7) at a flow rate of 0.6 mL/min and monitored by measuring fluorescence at excitation 310 nm/emission 410 nm.
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4

Protein Molecular Weight Distribution Analysis

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MW distribution of the hydrolyzed protein in hydrolysates was performed on an AKTA-purifier system using a TOSOH TSK gel G2000SWxl (30 cm × 7.8 mm) size exclusion analytical column with a TOSOH SWXL guard precolumn. All samples were filtered through a 0.2-µm filter before injection. Protein samples (100 µl) were run at a 0.7 ml/min flow rate using 0.1 M NaCl in RO water as the mobile phase. The protein in the effluent was detected using a UV detector at 280 nm. The retention volumes of a standard protein mixture (Bio-Rad) were used to assign MW to protein hydrolysate peaks.
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5

Size Exclusion Chromatography of Compounds

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A TSK® gel G2000 SWXL (7.8 mm × 300 mm) column (Tosoh, Tokyo, Japan) was used for separation. The mobile phase consisted of acetonitrile, water, and trifluoroacetic acid (40/60/0.05, v/v/v). The flow rate was 0.5 mL/min, and monitoring wavelength was 214 nm [29 (link)].
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6

Structural Characterization of YCH Biopolymer

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The YCH was structurally characterized using circular dichroism (CD) spectroscopy using a MOS-500 CD spectrometer (Bio-Logic Science Instruments). The YCH solution (0.1 mg/mL) was prepared in deionized water. Parameters were as follows: wavelength range, 190-250 nm; scan speed, 100 nm/min; path length, 1 mm. Ellipticity (θ) was measured in millidegrees (mdeg).
The conformational change of the YCH was assessed by ANS fluorescence spectroscopy. The YCH was dissolved in phosphate buffer (pH 7.0, 10 mM) at a concentration of 1 μg/mL. Then, 20 μL of 8 mM ANS was mixed with 1.5 mL of the YCH solution, and the fluorescence spectrum was recorded using an F-2500 fluorescence spectrometer (Hitachi Ltd.) in a wavelength range from 400 to 700 nm.
The molecular weight distribution of the YCH was further analyzed, as described previously (Sun et al., 2021) (link). In brief, the mobile phase was composed of acetonitrile, water, and trifluoroacetic acid (45/55/0.1, vol/vol/vol). The YCH was dissolved in the mobile phase and filtered through a 0.45-μm filter. Then, the YCH solution was loaded on a TSK gel G2000 SWXL (300 × 7.8 mm internal diameter) column (Tosoh) for separation at a flow rate of 0.5 mL/min under a detection wavelength of 220 nm. The standards of cytochrome C, aprotinin, bacitracin, Gly-Gly-Tyr-Arg, and Gly-Gly-Gly were used to prepare a calibration curve of molecular weight.
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7

Isolation and Characterization of Retinal Pericyte-Derived Peptides

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Semi-confluent retinal pericytes were washed twice with pre-warmed Dulbecco's Modified Eagle Medium (DMEM)/Ham's F-12 medium without phenol red. Subsequently, the cells were cultured in the same medium for 24 h. After incubation, the medium was collected and filtered through a 0.22 µm filter. The solution was then acidified to pH 3.0 with trifluoroacetic acid (TFA) and subjected to a C18 solid phase extraction cartridge (Empore 10 mm/6 mL; 3M Company, St. Paul, MN) equilibrated with 2% acetonitrile and 0.1% TFA (buffer A). The cartridge was washed with buffer A, and the fraction of crude peptides was eluted with 80% acetonitrile and 0.1% TFA (buffer B). The eluent was evaporated in a vacuum concentrator and dissolved in 100 µL of 30% acetonitrile and 0.1% TFA (buffer C). The sample was separated by gel filtration column chromatography (TSKgel G2000SWXL; Tosoh, Tokyo, Japan) in buffer C at a flow rate of 1 mL/min. Corresponding peptide fractions (from the 8th to 11th fractions) were collected, combined, and then loaded onto a strong cation exchange spin column (MonoSpin SCX; GL Science, Tokyo, Japan). The peptide sample was washed twice with buffer B, eluted with 4% NH 4 OH in MeOH, and evaporated to dryness. Samples were reconstituted in 50 mM ammonium bicarbonate and analyzed for total peptide concentration using BCA protein assay kit (ThermoFisher Pierce, Rockford, IL).
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8

Peptide Size Distribution Analysis

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The
peptide size distribution
profile was measured with high-performance size-exclusion chromatography
(HPSEC) using TSKgel G3000SWxl column (7.8 mm × 300 mm) and TSKgel
G2000SWxl (7.8 mm × 300 mm) (Tosoh Bioscience LLC, King of Prussia,
PA, U.S.A.) in an Ultimate 3000 UHPLC system (ThermoFisher Scientific
Inc., U.S.A.). Digested samples were first filtered using a 0.2 μm
Spartan 13/0.2 R 6 Whatman filter (VWR), and then 10 μL of sample
was injected for each measurement. The mobile phase was made with
30% acetonitrile, 0.1% trifluoroacetic acid, and 70% ultrapure water.
Signals were measured with a UV detector set at 214 nm, at 30 °C
and with a flow rate of 1.5 mL/min. The calibration was performed
with standard solutions of α-lactalbumin, aprotinin, insulin,
bacitracin, phenylalanine, g-globulin, and ovalbumin. Then the calibration
curve was made by plotting the retention time of each standard solution
as a function of the protein’s molecular weight. Data analysis
was performed in Dionex Chromeleon 7.2 Chromatography Data System
software (ThermoFisher Scientific Inc., U.S.A.). A chromatogram from
the system resulted in peaks showing the amount of molecules with
the sizes >50 kDa, 50–10 kDa, 10–4 kDa, 4–2
kDa,
and <2 kDa. The experiments were done in duplicate per digestion
sample, resulting in four experiments per sample.
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9

HPLC Analysis of PpSP15 Aggregation

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A Waters® HPLC system (Alliance® 2695 Separation Module) equipped with a TSKGel G2000SWxl (Tosoh bioscience, Cat # 0008540) connecting a guard column (Tosoh Bioscience, Cat # 0008543) was used to assess the aggregation of PpSP15. One hundred microliters of 0.68 mg/mL PpSP15 were injected onto the column and the protein was eluted in phosphate buffer (5.6 mM Na2HPO4, 1.1 mM KH2PO4 and 225 mM NaCl at pH 7.4) at 0.5 mL/min over 40 min. Gel filtration standard (Bio-Rad, Cat # 1511901) was used as a control. The eluted protein was monitored at 280 nm.
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10

Determining Polycyclic Aromatic Hydrocarbon Molecular Weights

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The MW distributions of PCHs were determined by high-performance gel-ltration chromatography (HPLC) using a TSK gel G2000 SWXL (300 mm × 7.8, TOSOH, Tokyo, Japan) (Eric et al. 2013) (link). HPLC analysis was performed on a Waters e2695 Alliance HPLC system (Water Co., Milford, MA, USA), which was equipped with a 2487 UV detector and Empower workstation. The ow rate was set at 0.5 mL/min with the mobile phase consisting of acetonitrile/water/tri uoroacetic acid (45/55/0.1, v/v/v). Sample (10.0 μL) was injected into the system, and the column was maintained at a temperature of 30 ℃. The following standards: cytochrome C (12,500 Da), aprotinin (6,500 Da), bacitracin (1,450 Da), Gly-Gly-Tyr-Arg (451 Da), and Gly-Gly-Gly (189 Da) were used to build the calibration curve used to evaluate the MW of the sample. UV absorbance was recorded at 200 nm, and data were processed with gel-permeation chromatography (GPC) software (Waters Co., Milford, US).
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