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Bbiorefcode 2 0 0

Manufactured by Bruker
Sourced in Canada

The BBIOREFCODE-2–0–0 is a laboratory equipment product by Bruker. It serves as a core function within the laboratory setting, though a detailed description while maintaining an unbiased and factual approach is not available.

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5 protocols using bbiorefcode 2 0 0

1

NMR Spectroscopy Metabolite Identification Protocol

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NMR spectra were acquired on a Bruker Avance III HD 500 NMR spectrometer (University of Aveiro, Portuguese NMR Network, Aveiro, Portugal) operating at 500.13 MHz for 1H observation, at 298 K. One-dimensional (1D) 1H spectra were recorded with 32 k points, 7002.80 Hz spectral width, a 2 s relaxation delay, and 512 scans, using the pulse programs “noesypr1d” and “zg” for aqueous and lipidic samples, respectively. Spectral processing was carried out in TopSpin 4.0.3 (Bruker BioSpin, Rheinstetten, Germany), and consisted of cosine multiplication (ssb 2), zero-filling to 64 k data points, manual phasing, baseline correction, and calibration to TSP-d4/TMS signals (0 ppm). Two-dimensional (2D) NMR spectra, namely, 1H-1H TOCSY, J-resolved, and 1H-13C HSQC spectra, were also recorded for selected samples to aid metabolite identification. Signal assignment was based on matching 1D and 2D spectral information to reference spectra available in Chenomx 9.0 (Edmonton, AB, Canada), BBIOREFCODE-2–0–0 (Bruker Biospin, Rheinstetten, Germany), and HMDB.
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2

NMR Analysis of Aqueous and Lipid Extracts

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For NMR analysis, dried aqueous and lipid extracts were dissolved, respectively, in 600 μL of deuterated phosphate buffer (PBS 100 mM, pH 7.4) containing 0.1 mM 3-(trimethylsilyl) propionic acid (TSP-d4), and 600 μL of deuterated chloroform containing 0.03% tetramethylsilane (TMS). After transferring 550 μL of each sample to 5 mm NMR tubes, analysis was performed on a Bruker Avance III HD 500 NMR spectrometer (University of Aveiro, Portuguese NMR Network) operating at 500.13 MHz for 1H observation, at 298 K. Standard 1D 1H spectra (pulse programs ‘noesypr1d’ and ‘zg’ for aqueous and lipid samples, respectively) were recorded with 32 k points, 7002.80 Hz spectral width, a 2 s relaxation delay and 512 scans. Spectral processing in TopSpin 4.0.3 (Bruker BioSpin, Rheinstetten, Germany) comprised cosine multiplication (ssb 2), zero-filling to 64 k data points, manual phasing, baseline correction and calibration to TSP-d4/TMS signals (δ 0 ppm). Two-dimensional NMR spectra, namely, 1H-1H TOCSY, J-resolved and 1H-13C HSQC spectra, were also recorded for selected samples to aid metabolite identification. Signal assignment was based on matching 1D and 2D spectral information to reference spectra available in Chenomx 9.0 (Edmonton, AB, Canada), BBIOREFCODE-2–0–0 (Bruker Biospin, Rheinstetten, Germany) and HMDB.
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3

NMR Analysis of Aqueous Extracts

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At the time of NMR analysis, the dried aqueous extracts were suspended in 600 μL of deuterated phosphate buffer (PBS 100 mM, pH 7) containing 0.1 mM of 3-(trimethylsilyl)propionic acid (TSP-d4), and 550 μL of each sample were transferred to 5 mm NMR tubes. All samples were analyzed in a Bruker Avance III HD 500 NMR spectrometer (University of Aveiro, Portuguese NMR Network) operating at 500.13 MHz for 1H observation, at 298 K. Standard 1D 1H spectra with water presaturation (pulse program ‘noesypr1d’, Bruker library) were recorded with 32 k points, 7002.801 Hz spectral width, a 2 s relaxation delay and 2048 scans. Spectral processing in TopSpin 4.0.3 (Bruker BioSpin, Rheinstetten, Germany) comprised cosine multiplication (ssb 2), zero-filling to 64 k data points, manual phasing and baseline correction, and calibration to the TSP-d4 signal (δ 0 ppm). Two-dimensional NMR spectra, namely 1H-1H TOCSY, J-resolved and 1H-13C HSQC spectra, were also recorded for selected samples to aid metabolite identification. Metabolite assignment was based on matching 1D and 2D spectral information to reference spectra available in Chenomx (Edmonton, Canada), BBIOREFCODE-2–0–0 (Bruker Biospin, Rheinstetten, Germany) and HMDB28 (link).
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4

NMR Metabolite Profiling and Statistical Analysis

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Metabolite signals in the NMR spectra were assigned using the Bruker NMR Metabolic profiling database BBIOREFCODE 2.0.0 (Bruker BioSpin), in combination with other publicly available databases [55 (link),56 (link)]. Both singlets and multiplets of the same metabolite were used, when possible, for identification and integration. Spectra were baseline corrected, aligned, and metabolite signals were integrated and quantified using NMRProcFlow v.1.2.28 [57 (link)]. The statistical significance of the differences between the means of the groups of the study was assessed using the Mann–Whitney U test. A p-value < 0.05 was considered statistically significant.
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5

C. elegans Metabolomics via HR-MAS NMR

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C. elegans HR-MAS NMR spectroscopy
was performed as previously described by Blaise et al.9 (link),10 (link) Spectra were reduced over the chemical range of 0.55–8.75
ppm to 8200 bins (10–3 ppm wide) with integration
of signal intensity. The residual water signal (δ = 4.5–5
ppm), residual methanol signal resulting from the formaldehyde fixation
step (δ = 3.32–3.39 ppm), and a noise area (δ =
5.5–6.5 ppm) were discarded prior to analysis. Spectra were
normalized using the probabilistic quotient normalization approach14 (link) with a median of all spectra as a reference
spectrum. We applied Pareto scaling on the data set for multivariate
analysis only.
Metabolite assignment was completed exploiting
reference data from the literature,9 (link),25 (link) the HMDB,15 (link) MMCD,16 (link) bbiorefcode-2-0-0
(Bruker, GmbH, Rheinstetten, Germany), and Chenomx NMR Suite 7.0 (Chenomx
Inc., Edmonton, Canada) spectral databases.
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