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37 protocols using methoxylamine hydrochloride

1

HPLC-based Metabolite Profiling

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High-performance liquid chromatography (HPLC)-grade methanol, chloroform, and water were purchased from Fisher Scientific (Pittsburg, PA). HPLC-grade hexane was purchased from Honeywell Burdick & Jackson (Muskegon, MI). Butylated hydroxytoluene (BHT), myristic-d27 acid, methoxylamine hydrochloride, pyridine, and ammonium acetate were purchased from Sigma-Aldrich (St. Louis, MO). BSTFA [N,O-bis(trimethylsilyl) trifluoroacetamide] containing 1% trimethylchlorosilane (TMCS) was purchased from Alfa Aesar (Ward Hill, MA).
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2

Metabolomic Profiling via HPLC-GC-MS

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High-performance liquid chromatography (HPLC)-grade methanol was obtained from Thermo Fisher Scientific (Hampton, NH, USA). HPLC-grade hexanes were obtained from Honeywell Burdick & Jackson (Muskegon, MI, USA). Myristic-d27 acid, methoxylamine hydrochloride, and pyridine were obtained from Sigma Aldrich (St. Louis, MO, USA). N,O-bis(trimethylsilyl) trifluoroacetamide containing 1% trimethylchlorosilane was obtained from Alfa Aesar (Ward Hill, MA, USA).
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3

Metabolomic Analysis of Dendrobium Species

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The experiment was conducted using one-, two- and three-year-old basin-cultured D. officinale and D. huoshanense seedlings (Fig 1) grown in a greenhouse (Hefei Anhui Mulong Mountain Dendrobium Biotechnology Development Co., Ltd) under the conditions of day 24°C and night 18°C, with natural light. Six replicates of each sample, including one- to three-year-old stems of the two species, were collected from the same pot. Surface soil was removed by washing with water, and the materials were dried with filter paper. Then, the samples were immediately frozen in liquid nitrogen and stored at -80°C until use for metabolomics analysis.
Methanol and chloroform (HPLC grade) were purchased from TEDIA (Fairfield, OH, USA). Pyridine was obtained from Dr. Ehrenstorfer (Augsburg, Germany). Adonitol and methoxylamine hydrochloride were purchased from Sigma-Aldrich. N,O-bis (trimethylsilyl)-trifluoroacetamide (BSTFA) containing 1% trimethylchlorosilane (TMCS) was purchased from SUPELO (Bellefonte, PA, USA). Ultra-pure water was obtained from Wahaha Group Co., Ltd. (Hangzhou, China).
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4

Metabolite Profiling Protocol

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First grade methanol, hexane, water, D2O [99.%, containing 0.05% 3-(trimethylsilyl)-propionic-2,2,3,3-d4 acid sodium salt (TSP) as internal standard for NMR], methoxylamine hydrochloride, pyridine, L-ascorbic acid, 1,1-diphenyl-2-picrylhydrzyl (DPPH), Folin-Ciocalteu's phenol reagent, gallic acid, and sodium carbonate were purchased from Sigma (St. Louis, MO, USA). NaOD were obtained from Cortec (Paris, France). BSTFA [N,O-bis (trimethylsilyl) trifluoroacetamide containing 1% TMCS (trimethyl chlorosilane)] were purchased from Alfa Aesar (Ward Hill, MA, USA) and 2-Chloronaphtahalene as internal standard for GC-MS were purchased from Tokyo Chemical Industry Co., Ltd (Tokyo, Japan).
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5

Metabolomic Profiling of Silkworm Heads

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Silkworms, strain Dazao (P50), were reared on fresh mulberry leaves at 26 ± 1 °C and 70% ± 10% relative humidity. Larval heads were dissected on the third day of the fifth instar and immediately stored at −80 °C. Each group (with 3 biological replicates) containing 30 heads was homogenized in a mortar with liquid nitrogen. Powdered samples (100 mg) from each group were suspended with a 500 μL methanol-water (v/v, 4:1) mixture and sonicated for 20 min, followed by incubation on ice for 40 min. Thereafter, the samples were centrifuged at 15,000× g for 30 min. The supernatant was transferred to a centrifuge tube and lyophilized for 5 h in a vacuum concentrator [10 (link)]. The lyophilized samples were then re-dissolved in 65 μL pyridine (containing 15 mg/mL methoxylamine hydrochloride; Sigma-Aldrich, St. Louis, MO, USA) for GC-MS analysis or in a 80 μL methanol-water (v/v, 4:1) mixture for LC-MS/MS analysis.
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6

Metabolite Profiling by GC-MS

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Methoxylamine hydrochloride, N-methyl-(trimethylsilyl)trifluoracetamide (MSTFA), chlorotrimethylsilane (TMCS), pyridine and ribitol (used as internal standard), and all the authentic standards were purchased from Sigma-Aldrich (St Louis, MO, US). Methanol and acetonitrile were purchased from TEDIA (Fairfield, OH, USA). Dextran sulfate sodium (DSS) was purchased from MP Biomedicals (Solon, OH, USA) (MW = 36000–50000).
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7

Fecal Microbiome Analysis Protocol

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BBR, γ-oryzanol, pyridoxine (vitamin B6), urease, pyridine, methoxylamine hydrochloride, L-phenylalanine-13C9-15N, dulcitol, L-leucine-13C6, L-isoleucine-13C6-15N, L-valine-13C5-15N, L-alanine-13C3-15N and N,O-bis(trimethylsilyl)-trifluoroacetamide (BSTFA) with 1 % trimethylchlorosflane (TMCS) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Pure water was obtained from Millipore Alpha-Q water system (Bedford, MA, USA). Methanol and ethanol for HPLC grade were purchased from Merck Chemicals (Darmstadt, Germany). Chloroform for analytical grade from Sinopharm Chemical Reagent Company (Shanghai, China). KAPA HiFi polymerase (KAPA Biosystems, USA), Agencourt AMPure XP beads (Beckman Coulter, USA), Qubit dsDNA HS assay kit (Invitrogen, CA), Agilent high sensitivity DNA Kit (Agilent, USA), Ion PGM template OT2 200 kit, Ion PGM sequencing 200 kit v2 and Ion 316 chip kit v2 (Life Technology, CA) and QIAamp® Fast DNA stool mini kit (Qiagen, Germany) were obtain for fecal microbiota analysis.
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8

Quantitative Analysis of Hormones and Metabolites

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N,O-Bis(trimethylsilyl) trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS) of analytical grade was from Regis (Morton Grove, IL, USA). Methanol and chloroform of analytical grade were purchased from CNW Technologies GmbH (Düsseldorf, Germany). Methoxylamine hydrochloride and anhydrous pyridine were purchased from Sigma-Aldrich (St. Louis, MO, USA). Commercial kit used for determining adrenocorticotropic hormone (ACTH) was obtained from Phoenix Pharmaceuticals (Burlingame, CA, USA). Commercial kit used for determining thyroid-stimulating hormone (TSH) was purchased from R&D Systems (Minneapolis, USA). Commercial kit used for determining corticosterone (CORT) was obtained from Cayman Chemical Co. Ltd (MI, USA). Commercial kits used for determining, catecholamine (CA), testosterone, and serotonin were purchased from Cusabio Biotech Co. Ltd, (Wuhan, China). Total ginsenosides (GS, purity ≥ 80%, UV method) extracted from the roots of P. ginseng were purchased from Nanjing Zelang Biomedical Technology Co. Ltd. (Nanjing, China).
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9

Metabolomic Analysis of LP Toxicity on C. acutatum

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All the chemicals and reagents used in the study of LP toxicity to C. acutatum were of the highest commercially available grade. The extraction of the fungal metabolome for GC/EI/MS analyses was performed using ethyl acetate (EtOAc) and methanol (MeOH) (GC/MS grade, 99.9% purity, Carlo Erba Reagents, val de Reuil, France). For 1H NMR metabolomics, metabolite extraction was performed using deuterium oxide (D2O, 99.9%) containing 0.05 wt.% 3-(trimethylsilyl)propionic acid-2,2,3,3-d4-sodium salt (TSP, Sigma-Aldrich Ltd., Steinheim, Germany). Pyridine (99.8%, v/v), methoxylamine hydrochloride (98% w/w), and ribitol were purchased from Sigma-Aldrich Ltd. (Steinheim, Germany), and N-methyl-N-(trimethyl-silyl) trifluoroacetamide (MSTFA), used in sample preparation for GC/EI/MS metabolomics, was purchased from Macherey-Nagel (Düren, Germany).
The LP extract used in the study was obtained from liquid cultures of the isolate Bacillus sp. PTA13, as previously described [6 (link)]. Stock solutions of the LP extract (10,000 ppm) were prepared in methanol (MeOH) (GC/MS grade, 99.9% purity, Carlo Erba Reagents, val de Reuil, France) into 2 mL Eppendorf tubes, which were kept at −30 °C until further utilization.
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10

Metabolic Profiling and Cytokine Analysis

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CPT-11 (≥ 98%), L-(+)-lactic acid, D-sorbitol and CIF hydrochloride monohydrate were purchased from Aladdin Bio-Chem Technology Co., Ltd (Shanghai, China). Methoxylamine hydrochloride, 1,2-13C myristic acid and N,O-bis(trimethylsilyl)trifluoroacetamide were bought from Sigma-Aldrich (St. Louis, MO, USA). Mouse TNF-α, IL-1β, and IL-6 kits were purchased from Cell Signaling Technology (Beverly, MA, USA). The primers used for amplification were ordered in Sangon Biotech Co., Ltd. (Shanghai, China). Bicinchoninic acid (BCA) protein assay kit was purchased from Jiangsu KeyGEN Bio-Tech Corp., Ltd (Nanjing, China). E.Z.N.A.® Stool DNA Kit was purchased from Omega Bio-Tek (Norcross, GA, USA). TransStart Fastpfu DNA Polymerase and AxyPrep DNA Gel Extraction Kits were purchased from Axygen Scientific Inc. (Silicon Valley, USA). QuantiFluor™-ST blue fluorescent quantitative system was purchased from Promega Biotech Co., Ltd. (Beijing, China). SDS-PAGE Gel Kit was purchased from Solarbio Life Sciences Co., Ltd. (Beijing, China).
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