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28 protocols using hplc system

1

Quantification of Caffeic and Rosmarinic Acids

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The content of caffeic and rosmarinic acid in leaves was determined as previously described (Kiferle et al., 2011 (link)). Briefly, the analyses were performed by using a Waters Alliance HPLC system equipped with a LiChrospher RP-18 column 250 mm × 4.6 mm, 5 μm (Phenomenex, United States), and the elution was carried out at a flowrate of 1.0 mL min–1 at room temperature. Two mobile phases, A and B, were used: mobile phase A was acetonitrile, while mobile phase B was 0.1% phosphoric acid. The gradient used was 0–4 min, B 95%; 4–5 min, B 95–85%; 5–10 min, B 85–80%; 10–20 min, B 80–60%; 20–21 min, B 60–5%; 21–25 min, B 5%; 25–26 min, B 5–95%; and 26–30 min, B 95%. The volume injected was 20 μl, and the UV absorption was monitored at 325 nm.
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2

HPLC Analysis of Nucleotide Metabolites

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The reaction mixture was analyzed at different time points on a Shimadzu HPLC system using a reversed phase Phenomenex C 18 column (4.6 × 250 mm, 5 μm), with mobile phase A (5 mM potassium phosphate (pH 7.0), 5 mM tetrabutylammonium dihydrogen phosphate, and 5% acetonitrile) and mobile phase B (acetonitrile). The flow rate was 1 ml/min and the gradient was as follows: 100% A, 0-25 min; 100-10% A, 25-29 min; 10-100% A, 29-31 min; 100% A, 31-40 min. The injection volume for each sample was 50 μl and the autosampler was set at 4 °C. The standard solution of dUMP and dTMP were run to assign the retention times and the elution was monitored at 260nm. The experiment was performed in duplicate.
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3

HPLC Analysis of Protocatechuic Acid

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Protocatechuic acid was analyzed using a Dionex HPLC system equipped with a UV/VIS detector and a Phenomenex kinetex 2.6 μm Biphenyl 100 A (50 × 2.1 mm) column for separation using a mobile phase consisting of 93% Solution A containing methanol: acetic acid: water (10:2:88) and 7% Solution B made of methanol: acetic acid: water (90:2:8), at a flow rate of 0.3 mL/min. Glucose, organic acids, and alcohols were analyzed by separation in a Jasco HPLC system equipped with RI detector using a BioRad Aminex HPX87H (Fast Acid) (100 × 7.8 mm) column. The mobile phase was 0.5 mM sulfuric acid used at a flow rate of 0.6 mL/min. The sample injection volume was 10 μL and all samples were filtered through a 0.2 μm filter, diluted 10 times in MQ water to a final volume of 1 mL prior to injecting into the column. The concentration of PCA and other metabolites formed was calculated as gram per liter (g/L) of the medium. Yield of PCA with respect to glucose (YP/S) was calculated as mol/mol. Biomass concentration was calculated as dry weight in cmol/L. The yield of PCA with respect to biomass (YP/B) was calculated as cmol/cmol. The productivity (g/L/h) was calculated by dividing maximum PCA concentration (g/L) by the time in hours from induction.
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4

HPLC Analysis of Flavonoid and Phenolic Compounds

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The compounds were analyzed with a Shimadzu HPLC system on a Phenomenex C18 Gemini column (5 μm, 4.6 × 250 mm) equipped with a binary pump (SPD-20AD), a UV detector (SPD-20A), an autosampler (SIL-20A), a column oven (CTO-20AC), a degasser, (DGU-20A3) and an LC solution system (Shimadzu, Kyoto, Japan). The flavonoid and phenolic compound quantification was conducted using a calibration curve at ten concentrations over a linear range (0.0005–1.0 mg/mL), and the chromatographic analysis was performed using the method previously reported by Jin et al. [13 (link)].
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5

Analytical Characterization of Compounds

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UV spectra were recorded on a Perkin-Elmer Lambda 19 uv/vis spectrophotometer. Fluorescence spectra were recorded on a Cary Eclipse fluorimeter. 1H and 13C NMR were recorded using a Varian Mercury-VX spectrometer at 400 MHz (1H) and 100 MHz (13C) or a Bruker Avance III 500 at 500 MHz (1H) and 125 MHz (13C). Chemical shift values are given in ppm (δ). J values are given in Hz. Analytical RP-HPLC was performed on a Dionex Ultimate 3000 system (Dionex, UK), with a VWD-3400 variable wavelength detector, and a RF-2000 fluorescence detector. Analyses were performed at 35 ± 0.1 °C on a Gemini 5 μ C18 110 A column, (150 × 4.6 mm - Phenomenex, UK), equipped with a Security Guard C18 (ODS) 4 × 3.0 mm ID guard column (Phenomenex, UK), at a flow rate of 1 mL/min. Mobile phase A was 0.1% aq. TFA, mobile phase B was 0.1% TFA in MeCN. (Gradient: 0.0–10.0 min 0–95% B, 10.0–20.0 min 95% B, 20.0–20.1 min at 95–5% B, 20.1–23.0 min 5% B). Preparative RP-HPLC was performed on a Dionex HPLC system equipped with a Phenomenex Gemini 5 μ C18 (250 × 10w mm) column at a flow rate of 2.5 mL/min. High resolution mass spectrometry was performed using a Bruker MicroTOF autospec ESI mass spectrometer.
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6

Standardized Protein Characterization Methods

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General methods were as previously described.3 (link),29 Growth media and conditions used for E. coli strains and standard methods for strain manipulation were as described,29 unless otherwise noted. All DNA manipulations performed following standard procedures.29 DNA sequencing was carried out at the U. C. Davis Sequencing Facility, Davis, CA or by Genewiz. All proteins were handled at 4 °C unless otherwise stated. Protein concentrations were determined according to the method of Bradford,30 (link) using a Tecan Infinite M200 Microplate Reader with bovine serum albumin as the standard. Protein purity and size was estimated using SDS-PAGE and visualized using Coomassie Blue stain and analyzed with a Bio-Rad ChemiDoc MP System. Accurate protein molecular weight was determined by ESI-MS on an Agilent 6530 Accurate-Mass Q-TOF LC/MS. Reductase activity assays were carried out on the Tecan Microplate Reader and kinetic assays of KR-catalyzed reductions were also performed by GC/MS. 1H and 13C NMR spectra were obtained on a Bruker Avance III HD Ascend 600 MHz spectrometer. A Thermo LXQ equipped with Surveyor HPLC system and a Phenomenex Jupiter C4 column (150 mm×2 mm, 5.0 μm) was utilized for analysis of diketide-ACP compounds. LC-ESI-MS-MS analysis was carried out in positive ion mode for analysis of pantetheinate ejection fragments.
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7

HPLC Analysis with Phenomenex Luna

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HPLC experiments were performed on a YungLin HPLC system equipped with Phenomenex Luna C18, 5 mm (4.6 × 250 mm) column, LC10AT VP pumps, SCL-10AVP system controller, SIL-10 AD VP auto injector, SPD-M10 AVP photodiode array detector and class VP software was used [16 ].
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8

General Procedure for Organic Synthesis

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All chemicals for
synthesis were obtained
from commercial suppliers (Sigma-Aldrich, Combi-blocks, and Boom)
and used as received, unless stated otherwise. Solvents used were
reagent grade for synthesis and technical grade for isolation if not
otherwise stated. Thin-layer chromatography was carried out on aluminum
sheets coated with silica gel 60 F254 (Merck). The developed chromatogram
was analyzed by UV lamp (254 nm) for the detection of components.
Alternatively, oxidative staining using aqueous basic potassium permanganate
solution (KMnO4) or aqueous acidic cerium phosphomolybdic
acid solution (Seebach’s stain) was used. Flash chromatography
was performed on silica gel (Screening devices B.V.) with a particle
size of 40–64 μM and a pore size of 60 Å or on Buchi
FlashPure silica columns (4–25 g, 40–63 μM, 60
Å) using a Buchi Reveleris X2 system. Preparative HPLC purification
was performed on a Shimadzu HPLC system with a Phenomenex Kinetex
5 μm EVO C18 100 Å column. Schemes and detailed characterization
data are reported in the Supporting Information (SI).
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9

Analytical Characterization of Compounds

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Optical rotations were measured on a PerkinElmer 241 polarimeter, NMR spectra were obtained with a Bruker Avance III NMR spectrometer equipped with a 3 mm cryogenic probe and operating at 600 MHz for 1H and 150 MHz for 13C. Spectra were referenced to residual solvent signals at δH 2.50 and δC 39.5 (DMSO-d6). HRESIMS data were acquired on an Agilent Technology 6530 Accurate-mass Q-TOF LC/MS. HPLC separations were performed on a Gilson HPLC system using a Phenomenex Luna C18 (5 μm, 100 Å, 150 × 21.2 mm) column run with the indicated gradient. Samples were dried on a Thermo Savant Explorer-220 speed vacuum system.
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10

Biomass and Metabolite Quantification

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Biomass concentrations was determined by optical density measurements (OD620nm) using an Ultrospec 2100 pro UV/Visible spectrophotometer (Amersham Biosciences, Buckinghamshire, United Kingdom). Cell dry weight (CDW) measurements were performed by passing 5 mL of culture through a pre-weighed and dried 0.45 µm paper filter, the filter was then dried in a microwave for 10 min and placed in a desiccation chamber for 2 days prior to being weighed again.
Concentrations of extracellular metabolites such as glucose, xylose, xylitol, glycerol, acetate and ethanol were quantified using a Waters HPLC system (Milford, USA) equipped with a Phenomenex Rezex ROA-Organic Acid column operating at 60 °C. Isocratic 5 mM sulfuric acid was used as mobile phase was isocratic 5 mM sulfuric acid and the flow rate was maintained at 0.6 mL/min.
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