Summary of Study ST001103
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000738. The data can be accessed directly via it's Project DOI: 10.21228/M88X0P This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001103 |
| Study Title | Continuous in vivo metabolism by NMR |
| Study Summary | Metabolomics relies on analytical methods to provide holistic information about metabolites, their distributions across samples, and their underlying dynamic properties. The latter is gaining increasing attention due to advances in modeling and new analytical methods that provide dense time-series data. We extended high-resolution-magic angle spinning (HR-MAS) NMR—an established technique to measure metabolites from tissues and live organisms—into a flexible, untargeted, and continuous recording of in vivo metabolism. We call this technique “continuous in vivo metabolism by NMR” (CIVM-NMR). We used isotope-edited CIVM-NMR to reproduce a recent amino acid flux result in chronic lymphoid leukemia cells. We then collected untargeted CIVM-NMR datasets for Neurospora crassa, a classic multicellular model of biochemistry, genetics, and metabolism. CIVM-NMR requires virtually no sample preparation and allows for continuous collection of data over hours to days at ~4-min temporal resolution with little noise. CIVM-NMR provided real-time measurements that unambiguously reproduced the direction of flux of branched-chain amino acid accumulation in leukemia cells. It also revealed the dynamics of central carbon metabolism, amino acid metabolism, energy storage molecules, and lipid and cell wall precursors in N. crassa. CIVM-NMR is simple and readily adapted to different types of cells and microorganisms, making it ideally suited to experimentally complement kinetic models of metabolism for diverse biological systems. |
| Institute | University of Georgia |
| Last Name | Judge |
| First Name | Michael |
| Address | 315 Riverbend Rd., Edison Lab, Athens, GA, 30605, USA |
| judgemt@uga.edu | |
| Phone | 7046771037 |
| Submit Date | 2018-11-27 |
| Num Groups | 2 |
| Total Subjects | 6 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2019-07-17 |
| Release Version | 1 |
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Project:
| Project ID: | PR000738 |
| Project DOI: | doi: 10.21228/M88X0P |
| Project Title: | Continuous in vivo metabolism by NMR |
| Project Summary: | Metabolomics relies on analytical methods to provide holistic information about metabolites, their distributions across samples, and their underlying dynamic properties. The latter is gaining increasing attention due to advances in modeling and new analytical methods that provide dense time-series data. We extended high-resolution-magic angle spinning (HR-MAS) NMR—an established technique to measure metabolites from tissues and live organisms—into a flexible, untargeted, and continuous recording of in vivo metabolism. We call this technique “continuous in vivo metabolism by NMR” (CIVM-NMR). We used isotope-edited CIVM-NMR to reproduce a recent amino acid flux result in chronic lymphoid leukemia cells. We then collected untargeted CIVM-NMR datasets for Neurospora crassa, a classic multicellular model of biochemistry, genetics, and metabolism. CIVM-NMR requires virtually no sample preparation and allows for continuous collection of data over hours to days at ~4-min temporal resolution with little noise. CIVM-NMR provided real-time measurements that unambiguously reproduced the direction of flux of branched-chain amino acid accumulation in leukemia cells. It also revealed the dynamics of central carbon metabolism, amino acid metabolism, energy storage molecules, and lipid and cell wall precursors in N. crassa. CIVM-NMR is simple and readily adapted to different types of cells and microorganisms, making it ideally suited to experimentally complement kinetic models of metabolism for diverse biological systems. |
| Institute: | University of Georgia |
| Department: | Genetics; Biochemistry and Molecular Biology |
| Laboratory: | Arthur S. Edison |
| Last Name: | Judge |
| First Name: | Michael |
| Address: | 315 Riverbend Rd., Edison Lab, Athens, GA, 30605, USA |
| Email: | judgemt@uga.edu |
| Phone: | 7046771037 |
| Funding Source: | NSF 1713746; NSF ERC 1648035 (CMaT); Georgia Research Alliance |
| Contributors: | Michael T. Judge, Yue Wu, Fariba Tayyari, John Glushka, Ayuna Hattori, Takahiro Ito, Jonathan Arnold, Arthur S. Edison |
Subject:
| Subject ID: | SU001147 |
| Subject Type: | Fungi |
| Subject Species: | Neurospora crassa |
| Taxonomy ID: | 5141 |
| Genotype Strain: | bd1859 |
Factors:
Subject type: Fungi; Subject species: Neurospora crassa (Factor headings shown in green)
| mb_sample_id | local_sample_id | Condition |
|---|---|---|
| SA075125 | aer_4 | aerobic |
| SA075126 | aer_6 | aerobic |
| SA075127 | aer_5 | aerobic |
| SA075128 | anaer_12 | anaerobic |
| SA075129 | anaer_10 | anaerobic |
| SA075130 | anaer_11 | anaerobic |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO001141 |
| Collection Summary: | Mycelia were added with fresh media to a 4mm zirconia HR-MAS rotor with a sealed cap (anaerobic) or a cap with a drilled hole (aerobic). Sample was spun at 6KHz, and spectra were collected continuously over the course of 12h (4.2 min resolution). |
| Sample Type: | mycelia in media |
Treatment:
| Treatment ID: | TR001161 |
| Treatment Summary: | Time series were taken on aerobic and anaerobic cultures |
Sample Preparation:
| Sampleprep ID: | SP001154 |
| Sampleprep Summary: | Mycelia were added to the HR-MAS rotor with fresh media containing 1mM DSS as a reference. |
Analysis:
| Analysis ID: | AN001793 |
| Analysis Type: | NMR |
| Num Factors: | 2 |
NMR:
| NMR ID: | NM000136 |
| Analysis ID: | AN001793 |
| Instrument Name: | Bruker NEO |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Spectrometer Frequency: | 600 MHz |
| NMR Probe: | 4mm CMP HR-MAS Probe |
| NMR Solvent: | Vogels Media containing 5% D2O and 1mM DSS |
| NMR Tube Size: | 5mm |
