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50 protocols using gc 6890

1

Characterizing Soil Microbial Communities via PLFA Analysis

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Soil microbial community composition was characterized by analyzing PLFAs [36 (link)]. Briefly, lipids were extracted from soil with a chloroform: methanol: 0.05 M sodium phosphate buffer mixture (1:2:0.8 (v/v/v)); they were then separated into neutral lipids, glycolipids, and phospholipids using a pre-packed silica column. Phospholipids subjected to mild alkaline methanolysis and fatty acid methyl esters were identified using a gas chromatograph with a flame ionization detector (FID) (GC6890, Agilent Technologies, Bracknell, UK) with methyl nonadecanoate (19:0) as the internal standard. The abundance of individual fatty acid methylesters was expressed as nmol/g dry soil. The total microbial biomass was estimated as the sum of all the extracted PLFAs.
Lipid markers associated with microbial functional groups were analyzed by summing their concentrations. The groups detected included bacteria (15:0, i15:0, i16:0, a16:0, 16:1 w6c, a17:0, c17:0, i17:0, 17:1 w8c, i17:1 w9c, 18:1 w5c, 18:1 w7c, c19:0 w8c, 20:1 w9c) [37 (link),38 (link)], fungi (16:1 w5c, 18:1 w9c, 18:2 w6,9c) [37 (link),39 (link)], Gram-positive bacteria (GP) (a15:0, i15:0, i16:0, a16:0, a17:0, i17:0, i17:1 w9c), Gram-negative bacteria (GN) (16:1 w6c, c17:0, 17:1 w8c, 18:1 w5c, 18:1 w7c, c19:0 w8c, 20:1 w9c) [40 (link),41 (link)], and arbuscular mycorrhizal fungi (16:1 w5c) [37 (link)].
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2

Biogas Composition Analysis by GC

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The volume of biogas collected daily was measured by a medical syringe at room temperature, and the components quantitatively analyzed by gas chromatography (GC-6890, Agilent, United States). About 0.4 mL gas sample was injected into a GC equipped with a thermal conductivity detector and a packed TDX-01 stainless-steel column, with argon, the carrier gas, flowing at 50 mL/min. The inlet temperature, detector temperature, and constant oven temperature of the GC were 120, 150, and 100°C, respectively.
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3

GC-MS Analysis of Hexane Extracts

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The gas chromatography (GC) analyses were performed using Agilent GC 6890 coupled with a 5973 MS detector. Each hexane extract (1 µL) was injected into the GC–MS and the analytes were separated on an HP-5 capillary column (30 m × 0.25 mm, 0.25 mM, 5% polisilarilene, and 95% polydimethylsiloxane). Helium was used as the carrier gas at a rate of 1.0 mL min−1. The GC injector was maintained at 230 °C, while the oven temperature was held at 60 °C for 3 min, and then increased to 150 °C at 10 °C/min, increasing to 180 °C at 5 °C/min, and finally to 280 °C at 10 °C/min and held for 5 min, for a total separation time of 30 min. The analyzer temperature was kept at 250 °C. The collision energy was set to a value of 70 eV and the fragment ions generated were analyzed at a mass range of 20–500 m/z.
The identification of each compound was based on the comparison of retention time with the relative standard and fragmentation spectra matching those collected into the NIST 05 Mass Spectral Library.
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4

Deuterium Measurement in Aquatic Samples

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OBD concentrations in abalone and ulva were measured by the following method. Collected samples were lyophilized and powderized. 0.2 g of lyophilized samples were stirred for 24 h in 10 ml of deuterium depleted water at 4°C and lyophilized for three times to remove exchangeable OBD,9 (link) such as deuterium on hydroxyl group or amino group. Then, deuterium concentration was measured by elemental analyzer (vario PORO cube, Elmentar) and mass spectroscopy (IsoPrime 100, Isoprime).
Deuterium concentration in cultivating water was measured by gas chromatography system (GC-6890, Agilent Technologies). Porapak-Q (80/100 mesh, 1/8 in × 6 ft) was used as pre-column and Molecular Sieve 13X (45/60 mesh, 1/8 in × 10 ft) was used as analysis column. Hydrogen gas was used for carrier gas. Deuterium concentration in cultivating water was monitored one time per week. It was checked against and adjusted to designed concentration.
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5

AITC Analysis in Headspace Silos

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The AITC content in headspace was determined through a septum localized in the lip of a laboratory silo system (Figure 7). The air was recovered using a syringe of 1 mL, and aliquots of 200 µL were injected in a gas chromatograph (GC) with flame ionization detector (FID) (GC 6890, Agilent Technologies Inc., Santa Clara, CA, USA.). The chromatograph was equipped with a 30 × 0.25 mm CP-SIL 88 fused capillary column (Varian, Middelburg, Netherlands). The temperature of the detector arrived at 200 °C with a gradient of temperature that starts at 60 °C. This temperature was maintained for 1 min and increased 8 °C per min up to 100 °C, then maintained for 5 min and finally increased in 15 °C per min up to 200 °C. The gas utilized as the carrier was H2 at 5 mL/min. The ionization was realized with H2 at 40 mL/min and purified air at 450 mL/min.
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6

GC-MS Analysis of Purified Fractions

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The partially purified active fractions were analyzed by GC–MS. The analyses of the compounds in the active fractions were run on a GC–MS system (Agilent GC: 6890, with a 7683B Autosampler). The fused-silica Rxi-5Sil MS capillary column (30 m 0.25 mm ID, film thickness of 0.25 mm) was directly coupled to an Agilent variant. Oven temperature was programmed (35 °C for 5 min, then 35–300 °C at 10 °C/min) and subsequently, held isothermal for 20 min. The injector port; was 250 °C, the transfer line: 290 °C, splitless. Volume injected: 0.2 ml and the column flow rate was 1 ml/min of 1 mg/ml solution (diluted in chloroform). The peaks of components in gas chromatography were subjected to mass-spectral analysis.
The MS was a LECO Pegasus 4D recording with a EI-source at − 70 eV; the solvent delay was 9 min. Scan time 1.5 s; acquisition rate 10 spectra/second; mass range 50–1000 amu; detector voltage 1800 V, and Ion source temperature: 250 °C. Data were recorded in TIC mode. The software adopted to handle the mass spectra and chromatograms was an Agilent chemstation software. The constituents were identified after comparing with available data in the GC–MS library in the literatures.
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7

Cholesterol Oxidation Product Analysis

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COPs were prepared by heating CHO with H2O2 at 150°C for 72 h. As evaluated using gas chromatography (GC 6890, Agilent, Wilmington, DE, USA) mass spectrometry, the final extract contained 7α-hydroxycholesterol (8.5%), 7β-hydroxycholesterol (14.8%), 5α- and 6α-epoxycholesterol (18.8%), 5β- and 6β-epoxycholesterol (20.2%), a mixture of 6-ketocholesterol and 25-hydroxycholesterol (6.3%), and 7-ketocholesterol (24.8%).
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8

Fatty Acid Composition Analysis

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The extracted lipids were dissolved in hexane to obtain a final concentration of 0.1 g fat/mL hexane and were then used in the following step. We added 1 mL of hexane and 1 mL of a methylating reagent (3N-HCl in methanol) to 100 μL of lipid extracts (of liver) and incubated the samples at 90°C in a water bath for 1 h. After cooling to room temperature, 2 mL of hexane and 5 mL of water were added to the samples, which were mixed thoroughly and incubated at room temperature overnight to allow phase separation. The top hexane layer containing the methylated fatty acids was analyzed for fatty acid composition by using a gas chromatograph (GC 6890, Agilent). Gas chromatography conditions were the same as those used for COPs analysis.
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9

Analytical Workflow for Lipid Profiling

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Lipid extraction was conducted following previously described procedures (Fărcaş et al., 2015 (link)). The derivatization of lipids into fatty acid methyl esters (FAMEs) was assessed following the procedures described in previous work (Nowacki et al., 2017 (link)). The fatty acid profile was analyzed using a gas chromatograph (GC6890, Agilent Technologies Inc. CA, USA) coupled with a mass spectrometer 5983 MS equipped with a quadrupole mass detector (Agilent Technologies Inc. CA, USA). Separation was performed in a 0.25 mm × 100 m HP-88 capillary column filled with an 88:12 cyanopropyl-aryl poly-siloxane bed (grain size 0.2 μm). Helium at a flow rate of 1 mL/min was used as the mobile phase, and the sample was injected in split mode (split 4:1). The program was set as follows: initial temperature at 60 °C (2 min) and heating at 20 °C/min to reach 180 °C followed by 3 °C/min to 220 °C. The temperature was maintained for 15 min. Heating continued at a rate of 5 °C/min to reach 250 °C, and the temperature was maintained for 8 min. Spectra were identified using an algorithm for searching the National Institute of Standards and Technology's (NIST) library (version of 2008).
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10

AITC Extraction and Quantification in Pita Bread

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The AITC extraction and quantification from pita bread were carried out as described by Nazareth et al. [35 (link)] with some modifications.
Each pita bread (40 g) was added to hermetic tubes of 150 mL containing 80 mL of methanol. The mixture was extracted for 30 min in a water bath at 40 °C and 10 min in an ultrasonic bath. Then, the extract was centrifuged at 4000× g for 5 min at 20 °C. The supernatant was recovered and filtered through a nylon membrane filter (0.22 μm) and an aliquot of 10 μL was injected in a gas chromatograph.
The residual AITC absorbed by samples was quantified using a gas chromatograph (GC) coupled a flame ionization detector (FID) (GC 6890, Agilent Technologies Inc., Santa Clara, CA, USA), equipped with a fused capillary column (CP-SIL 0.25mm × 30m) (Varian, Middelburg, Netherlands). The inlet temperature was set at 200 °C with 250 °C of detector temperature. H2 at 5 ml/min was the carrier gas, and the FID gasses were H2 at 40 mL/min, and purified air at 450 mL/min. The temperature program was a gradient when the initial temperature was 60 °C for 1 min, increased at 8 °C/min up to 100 °C and held for 5 min, then the temperature was raised at 15 °C/min up to 200 °C, the time of analysis was 16.6 min per sample.
Identification and quantification of AITC were carried out comparing the samples areas with points standards curve (1–100 mg/L).
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