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Joseph D, Sukumaran S, Chandra K, Pudakalakatti SM, Dubey A, Singh A, Atreya HS. Rapid nuclear magnetic resonance data acquisition with improved resolution and sensitivity for high-throughput metabolomic analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:300-314. [PMID: 33030750 DOI: 10.1002/mrc.5106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/18/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Nuclear magnetic resonance (NMR)-based metabolomics has witnessed rapid advancements in recent years with the continuous development of new methods to enhance the sensitivity, resolution, and speed of data acquisition. Some of the approaches were earlier used for peptide and protein resonance assignments and have now been adapted to metabolomics. At the same time, new NMR methods involving novel data acquisition techniques, suited particularly for high-throughput analysis in metabolomics, have been developed. In this review, we focus on the different sampling strategies or data acquisition methods that have been developed in our laboratory and other groups to acquire NMR spectra rapidly with high sensitivity and resolution for metabolomics. In particular, we focus on the use of multiple receivers, phase modulation NMR spectroscopy, and fast-pulsing methods for identification and assignments of metabolites.
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Affiliation(s)
- David Joseph
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Sujeesh Sukumaran
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Kousik Chandra
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | | | - Abhinav Dubey
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Amrinder Singh
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Hanudatta S Atreya
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
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2
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Bennett CD, Gill SK, Kohe SE, Wilson MP, Davies NP, Arvanitis TN, Tennant DA, Peet AC. Ex vivo metabolite profiling of paediatric central nervous system tumours reveals prognostic markers. Sci Rep 2019; 9:10473. [PMID: 31324817 PMCID: PMC6642141 DOI: 10.1038/s41598-019-45900-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/03/2019] [Indexed: 02/06/2023] Open
Abstract
Brain tumours are the most common cause of cancer death in children. Molecular studies have greatly improved our understanding of these tumours but tumour metabolism is underexplored. Metabolites measured in vivo have been reported as prognostic biomarkers of these tumours but analysis of surgically resected tumour tissue allows a more extensive set of metabolites to be measured aiding biomarker discovery and providing validation of in vivo findings. In this study, metabolites were quantified across a range of paediatric brain tumours using 1H-High-Resolution Magic Angle Spinning nuclear magnetic resonance spectroscopy (HR-MAS) and their prognostic potential investigated. HR-MAS was performed on pre-treatment frozen tumour tissue from a single centre. Univariate and multivariate Cox regression was used to examine the ability of metabolites to predict survival. The models were cross validated using C-indices and further validated by splitting the cohort into two. Higher concentrations of glutamine were predictive of a longer overall survival, whilst higher concentrations of lipids were predictive of a shorter overall survival. These metabolites were predictive independent of diagnosis, as demonstrated in multivariate Cox regression models. Whilst accurate quantification of metabolites such as glutamine in vivo is challenging, metabolites show promise as prognostic markers due to development of optimised detection methods and increasing use of 3 T clinical scanners.
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Affiliation(s)
- Christopher D Bennett
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom
| | - Simrandip K Gill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom
| | - Sarah E Kohe
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom
| | - Martin P Wilson
- Birmingham University Imaging Centre, School of Psychology, University of Birmingham, Birmingham, United Kingdom
| | - Nigel P Davies
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Theodoros N Arvanitis
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Digital Healthcare, WMG, University of Warwick, Coventry, United Kingdom
| | - Daniel A Tennant
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Andrew C Peet
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom.
- Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom.
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Melikian M, Gramüller J, Hioe J, Greindl J, Gschwind RM. Brønsted acid catalysis - the effect of 3,3'-substituents on the structural space and the stabilization of imine/phosphoric acid complexes. Chem Sci 2019; 10:5226-5234. [PMID: 31191877 PMCID: PMC6540909 DOI: 10.1039/c9sc01044k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 04/08/2019] [Indexed: 11/21/2022] Open
Abstract
BINOL derived chiral phosphoric acids (CPAs) are widely known for their high selectivity. Numerous 3,3'-substituents are used for a variety of stereoselective reactions and theoretical models of their effects are provided. However, experimental data about the structural space of CPA complexes in solution is extremely rare and so far restricted to NMR investigations of binary TRIP/imine complexes featuring two E- and two Z-imine conformations. Therefore, in this paper the structural space of 16 CPA/imine binary complexes is screened and 8 of them are investigated in detail by NMR. For the first time dimers of CPA/imine complexes in solution were experimentally identified, which show an imine position similar to the transition state in transfer hydrogenations. Furthermore, our experimental and computational data revealed an astonishing invariance of the four core structures regardless of the different steric and electronic properties of the 3,3'-substituent. However, a significant variation of E/Z-ratios is observed, demonstrating a strong influence of the 3,3'-substituents on the stabilization of the imine in the complexes. These experimental E/Z-ratios cannot be reproduced by calculations commonly applied for mechanistic studies, despite extensive conformational scans and treatment of the electronic structure at a high level of theory with various implicit solvent corrections. Thus, these first detailed experimental data about the structural space and influence of the 3,3'-substituent on the energetics of CPA/imine complexes can serve as basis to validate and improve theoretical predictive models.
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Affiliation(s)
- Maxime Melikian
- Institut für Organische Chemie , Universität Regensburg , D-93053 Regensburg , Germany .
| | - Johannes Gramüller
- Institut für Organische Chemie , Universität Regensburg , D-93053 Regensburg , Germany .
| | - Johnny Hioe
- Institut für Organische Chemie , Universität Regensburg , D-93053 Regensburg , Germany .
| | - Julian Greindl
- Institut für Organische Chemie , Universität Regensburg , D-93053 Regensburg , Germany .
| | - Ruth M Gschwind
- Institut für Organische Chemie , Universität Regensburg , D-93053 Regensburg , Germany .
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Koos MRM, Luy B. Polarization recovery during ASAP and SOFAST/ALSOFAST-type experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 300:61-75. [PMID: 30711784 DOI: 10.1016/j.jmr.2018.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/03/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
Experiments with fast repetition schemes significantly enhance the capabilities of modern NMR spectroscopy. Two schemes for heteronuclear correlation experiments that have been presented are the ASAP and the ALSOFAST method. The first method is Acceleration by Sharing Adjacent Polarization (ASAP) for samples at natural abundance isotope level. It was originally derived in the ASAP-HMQC and recently received renewed attention in the ASAP-HSQC. Sharing the polarization of active protons with the surrounding reservoir can result in seemingly instant polarization recovery and therefore enormous gains in sensitivity, but can also lead to a slight reduction of polarization and spectral intensity, depending on sample and setup. A second type of setup has been introduced with the so-called Alternate SOFAST (ALSOFAST-) HMQC and ALSOFAST-HSQC for natural abundance 1H,13C-correlation experiments and in the SOFAST-HMQC for 1H,15N-correlations. In these cases, the reservoir spins are only maintained through the pulse sequence without Hartmann-Hahn-type mixing. A model for the estimation of the available polarization in the fast repetition schemes could be a valuable tool for experimentalists and pulse sequence developers. Starting from the well-known Ernst angle model, we derive in this article several mathematical models that describe the polarization over the course of ALSOFAST and ASAP type experiments. The models can be used to visualize the initial scans of an experiment and even more importantly, show the polarization and achievable signal intensity in the steady state of an experiment. In this way the two extreme applications of ASAP- and ALSOFAST-type acquisition schemes are covered: (i) acquisition using progressive excitation for experiments with few increments and shortest possible overall acquisition times and (ii) steady-state-type experiments with ultrahigh resolution and correspondingly large number of increments. The two resulting excitation strategies are applied to maximize SNR in different situations. To test the models, experimental data was obtained by special pulse sequences and examples are shown for different spin environments. The results show good agreement between theory and experiment.
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Affiliation(s)
- Martin R M Koos
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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Dumez JN. Spatial encoding and spatial selection methods in high-resolution NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:101-134. [PMID: 30527133 DOI: 10.1016/j.pnmrs.2018.08.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/01/2018] [Accepted: 08/01/2018] [Indexed: 06/09/2023]
Abstract
A family of high-resolution NMR methods share the common concept of acquiring in parallel different sub-experiments in different spatial regions of the NMR tube. These spatial encoding and spatial selection methods were for the most part introduced independently from each other and serve different purposes, but they share common ingredients, often derived from magnetic resonance imaging, and they all benefit from a greatly improved time-efficiency. This review article provides a description of several spatial encoding and spatial selection methods, including single-scan multidimensional experiments (ultrafast 2D NMR, DOSY, Z spectroscopy, inversion recovery and Laplace NMR), pure shift and selective refocusing experiments (including Zangger-Sterk decoupling, G-SERF and PSYCHE), a Z filter, and fast-pulsing slice-selective experiments. Some key elements for spatial parallelisation are introduced and when possible a common framework is used for the analysis of each method. Sensitivity considerations are discussed, and a selection of applications is analysed to illustrate which questions can be answered thanks to spatial encoding and spatial selection methods, and discuss the perspectives for future developments and applications.
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Affiliation(s)
- Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France.
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6
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Zhang G, Ahola S, Lerche MH, Telkki VV, Hilty C. Identification of Intracellular and Extracellular Metabolites in Cancer Cells Using 13C Hyperpolarized Ultrafast Laplace NMR. Anal Chem 2018; 90:11131-11137. [PMID: 30125087 PMCID: PMC6168181 DOI: 10.1021/acs.analchem.8b03096] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Ultrafast
Laplace NMR (UF-LNMR), which is based on the spatial
encoding of multidimensional data, enables one to carry out 2D relaxation
and diffusion measurements in a single scan. Besides reducing the
experiment time to a fraction, it significantly facilitates the use
of nuclear spin hyperpolarization to boost experimental sensitivity,
because the time-consuming polarization step does not need to be repeated.
Here we demonstrate the usability of hyperpolarized UF-LNMR in the
context of cell metabolism, by investigating the conversion of pyruvate
to lactate in the cultures of mouse 4T1 cancer cells. We show that 13C ultrafast diffusion–T2 relaxation correlation measurements, with the sensitivity enhanced
by several orders of magnitude by dissolution dynamic nuclear polarization
(D-DNP), allows the determination of the extra- vs intracellular
location of metabolites because of their significantly different values
of diffusion coefficients and T2 relaxation
times. Under the current conditions, pyruvate was located predominantly
in the extracellular pool, while lactate remained primarily intracellular.
Contrary to the small flip angle diffusion methods reported in the
literature, the UF-LNMR method does not require several scans with
varying gradient strength, and it provides a combined diffusion and T2 contrast. Furthermore, the ultrafast concept
can be extended to various other multidimensional LNMR experiments,
which will provide detailed information about the dynamics and exchange
processes of cell metabolites.
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Affiliation(s)
- Guannan Zhang
- Department of Chemistry , Texas A&M University , 3255 TAMU, College Station , Texas 77843 , United States
| | - Susanna Ahola
- NMR Research Unit, Faculty of Science , University of Oulu , P.O. Box 3000, 90014 Oulu , Finland
| | - Mathilde H Lerche
- Department of Electrical Engineering, Center for Hyperpolarization in Magnetic Resonance , Technical University of Denmark , Building 349, DK-2800 Kgs Lyngby , Denmark
| | - Ville-Veikko Telkki
- NMR Research Unit, Faculty of Science , University of Oulu , P.O. Box 3000, 90014 Oulu , Finland
| | - Christian Hilty
- Department of Chemistry , Texas A&M University , 3255 TAMU, College Station , Texas 77843 , United States
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King JN, Fallorina A, Yu J, Zhang G, Telkki VV, Hilty C, Meldrum T. Probing molecular dynamics with hyperpolarized ultrafast Laplace NMR using a low-field, single-sided magnet. Chem Sci 2018; 9:6143-6149. [PMID: 30090302 PMCID: PMC6053973 DOI: 10.1039/c8sc01329b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/27/2018] [Indexed: 11/21/2022] Open
Abstract
Laplace NMR (LNMR) offers deep insights on diffusional and rotational motion of molecules. The so-called "ultrafast" approach, based on spatial data encoding, enables one to carry out a multidimensional LNMR experiment in a single scan, providing from 10 to 1000-fold acceleration of the experiment. Here, we demonstrate the feasibility of ultrafast diffusion-T2 relaxation correlation (D-T2) measurements with a mobile, low-field, relatively low-cost, single-sided NMR magnet. We show that the method can probe a broad range of diffusion coefficients (at least from 10-8 to 10-12 m2 s-1) and reveal multiple components of fluids in heterogeneous materials. The single-scan approach is demonstrably compatible with nuclear spin hyperpolarization techniques because the time-consuming hyperpolarization process does not need to be repeated. Using dynamic nuclear polarization (DNP), we improved the NMR sensitivity of water molecules by a factor of 105 relative to non-hyperpolarized NMR in the 0.3 T field of the single-sided magnet. This enabled us to acquire a D-T2 map in a single, 22 ms scan, despite the low field and relatively low mole fraction (0.003) of hyperpolarized water. Consequently, low-field, hyperpolarized ultrafast LNMR offers significant prospects for advanced, mobile, low-cost and high-sensitivity chemical and medical analysis.
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Affiliation(s)
- Jared N King
- Department of Chemistry , The College of William & Mary , Williamsburg , Virginia 23187-8795 , USA .
| | - Alfredo Fallorina
- Department of Chemistry , The College of William & Mary , Williamsburg , Virginia 23187-8795 , USA .
| | - Justin Yu
- Department of Chemistry , The College of William & Mary , Williamsburg , Virginia 23187-8795 , USA .
| | - Guannan Zhang
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , Texas 77843 , USA
| | - Ville-Veikko Telkki
- NMR Research Unit , Faculty of Science , University of Oulu , 90014 Oulu , Finland
| | - Christian Hilty
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , Texas 77843 , USA
| | - Tyler Meldrum
- Department of Chemistry , The College of William & Mary , Williamsburg , Virginia 23187-8795 , USA .
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Marchand J, Martineau E, Guitton Y, Le Bizec B, Dervilly-Pinel G, Giraudeau P. A multidimensional 1H NMR lipidomics workflow to address chemical food safety issues. Metabolomics 2018; 14:60. [PMID: 30830413 DOI: 10.1007/s11306-018-1360-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Although it is still at a very early stage compared to its mass spectrometry (MS) counterpart, proton nuclear magnetic resonance (NMR) lipidomics is worth being investigated as an original and complementary solution for lipidomics. Dedicated sample preparation protocols and adapted data acquisition methods have to be developed to set up an NMR lipidomics workflow; in particular, the considerable overlap observed for lipid signals on 1D spectra may hamper its applicability. OBJECTIVES The study describes the development of a complete proton NMR lipidomics workflow for application to serum fingerprinting. It includes the assessment of fast 2D NMR strategies, which, besides reducing signal overlap by spreading the signals along a second dimension, offer compatibility with the high-throughput requirements of food quality characterization. METHOD The robustness of the developed sample preparation protocol is assessed in terms of repeatability and ability to provide informative fingerprints; further, different NMR acquisition schemes-including classical 1D, fast 2D based on non-uniform sampling or ultrafast schemes-are evaluated and compared. Finally, as a proof of concept, the developed workflow is applied to characterize lipid profiles disruption in serum from β-agonists diet fed pigs. RESULTS Our results show the ability of the workflow to discriminate efficiently sample groups based on their lipidic profile, while using fast 2D NMR methods in an automated acquisition framework. CONCLUSION This work demonstrates the potential of fast multidimensional 1H NMR-suited with an appropriate sample preparation-for lipidomics fingerprinting as well as its applicability to address chemical food safety issues.
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Affiliation(s)
- Jérémy Marchand
- EBSI Team, Chimie et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, BP 92208, 2 rue de la Houssinière, 44322, Nantes, France
- Laberca, Oniris, INRA, Université Bretagne Loire, 44307, Nantes, France
| | - Estelle Martineau
- EBSI Team, Chimie et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, BP 92208, 2 rue de la Houssinière, 44322, Nantes, France
- SpectroMaitrise, CAPACITES SAS, 26 Bd Vincent Gâche, 44200, Nantes, France
| | - Yann Guitton
- Laberca, Oniris, INRA, Université Bretagne Loire, 44307, Nantes, France
| | - Bruno Le Bizec
- Laberca, Oniris, INRA, Université Bretagne Loire, 44307, Nantes, France
| | | | - Patrick Giraudeau
- EBSI Team, Chimie et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes, CNRS, UMR 6230, BP 92208, 2 rue de la Houssinière, 44322, Nantes, France.
- Institut Universitaire de France, 1 rue Descartes, 75005, Paris Cedex 05, France.
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Deborde C, Moing A, Roch L, Jacob D, Rolin D, Giraudeau P. Plant metabolism as studied by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:61-97. [PMID: 29157494 DOI: 10.1016/j.pnmrs.2017.05.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 05/07/2023]
Abstract
The study of plant metabolism impacts a broad range of domains such as plant cultural practices, plant breeding, human or animal nutrition, phytochemistry and green biotechnologies. Plant metabolites are extremely diverse in terms of structure or compound families as well as concentrations. This review attempts to illustrate how NMR spectroscopy, with its broad variety of experimental approaches, has contributed widely to the study of plant primary or specialized metabolism in very diverse ways. The review presents recent developments of one-dimensional and multi-dimensional NMR methods to study various aspects of plant metabolism. Through recent examples, it highlights how NMR has proved to be an invaluable tool for the global characterization of sample composition within metabolomic studies, and shows some examples of use for targeted phytochemistry, with a special focus on compound identification and quantitation. In such cases, NMR approaches are often used to provide snapshots of the plant sample composition. The review also covers dynamic aspects of metabolism, with a description of NMR techniques to measure metabolic fluxes - in most cases after stable isotope labelling. It is mainly intended for NMR specialists who would be interested to learn more about the potential of their favourite technique in plant sciences and about specific details of NMR approaches in this field. Therefore, as a practical guide, a paragraph on the specific precautions that should be taken for sample preparation is also included. In addition, since the quality of NMR metabolic studies is highly dependent on approaches to data processing and data sharing, a specific part is dedicated to these aspects. The review concludes with perspectives on the emerging methods that could change significantly the role of NMR in the field of plant metabolism by boosting its sensitivity. The review is illustrated throughout with examples of studies selected to represent diverse applications of liquid-state or HR-MAS NMR.
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Affiliation(s)
- Catherine Deborde
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Annick Moing
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Léa Roch
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Daniel Jacob
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Dominique Rolin
- Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Univ. Bordeaux, UMR1332, Biologie du Fruit et Pathologie, 71 av Edouard Bourlaux, 33140 Villenave d'Ornon, France
| | - Patrick Giraudeau
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR 6230, CNRS, Université de Nantes, Faculté des Sciences, BP 92208, 2 rue de la Houssinière, F-44322 Nantes Cedex 03, France; Institut Universitaire de France, 1 rue Descartes, 75005 Paris, France.
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10
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Chen H, Cai S, Chen Z. A method for longitudinal relaxation time measurement in inhomogeneous fields. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 281:118-124. [PMID: 28586739 DOI: 10.1016/j.jmr.2017.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/13/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
The spin-lattice relaxation time (T1) plays a crucial role in the study of spin dynamics, signal optimization and data quantification. However, the measurement of chemical shift-specific T1 constants is hampered by the magnetic field inhomogeneity due to poorly shimmed external magnetic fields or intrinsic magnetic susceptibility heterogeneity in samples. In this study, we present a new protocol to determine chemical shift-specific T1 constants in inhomogeneous fields. Based on intermolecular double-quantum coherences, the new method can resolve overlapped peaks in inhomogeneous fields. The measurement results are in consistent with the measurements in homogeneous fields using the conventional method. Since spatial encoding technique is involved, the experimental time for the new method is very close to that for the conventional method. With the aid of T1 knowledge, some concealed information can be exploited by T1 weighting experiments.
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Affiliation(s)
- Hao Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuhui Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005, China.
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005, China
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11
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Rouger L, Yon M, Sarou-Kanian V, Fayon F, Dumez JN, Giraudeau P. Ultrafast acquisition of 1H- 1H dipolar correlation experiments in spinning elastomers. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 277:30-35. [PMID: 28219822 DOI: 10.1016/j.jmr.2017.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/03/2017] [Accepted: 02/07/2017] [Indexed: 06/06/2023]
Abstract
We show that two widely used 2D solid-state NMR (ssNMR) pulse sequences can be implemented in an ultrafast (UF) manner, and yield 2D spectra of elastomers in a single scan, under magic-angle spinning. UF 2D ssNMR provides an acceleration of one to several orders of magnitude for classic experiments.
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Affiliation(s)
| | - Maxime Yon
- CNRS UPR 3079 CEMHTI, Université d'Orléans, Orléans, France
| | | | - Franck Fayon
- CNRS UPR 3079 CEMHTI, Université d'Orléans, Orléans, France
| | - Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
| | - Patrick Giraudeau
- CNRS UMR 6230 CEISAM, Université de Nantes, Nantes, France; Institut Universitaire de France, Paris, France.
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12
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Lane AN, Fan TWM. NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry. Arch Biochem Biophys 2017; 628:123-131. [PMID: 28263717 DOI: 10.1016/j.abb.2017.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/24/2017] [Accepted: 02/27/2017] [Indexed: 01/23/2023]
Abstract
Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA.
| | - Teresa W-M Fan
- Center for Environmental Systems Biochemistry, University of Kentucky, USA; Department of Toxicology and Cancer Biology, University of Kentucky, USA
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Gouilleux B, Charrier B, Akoka S, Felpin FX, Rodriguez-Zubiri M, Giraudeau P. Ultrafast 2D NMR on a benchtop spectrometer: Applications and perspectives. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Marchand J, Martineau E, Guitton Y, Dervilly-Pinel G, Giraudeau P. Multidimensional NMR approaches towards highly resolved, sensitive and high-throughput quantitative metabolomics. Curr Opin Biotechnol 2016; 43:49-55. [PMID: 27639136 DOI: 10.1016/j.copbio.2016.08.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 11/25/2022]
Abstract
Multi-dimensional NMR is an appealing approach for dealing with the challenging complexity of biological samples in metabolomics. This article describes how spectroscopists have recently challenged their imagination in order to make 2D NMR a powerful tool for quantitative metabolomics, based on innovative pulse sequences combined with meticulous analytical chemistry approaches. Clever time-saving strategies have also been explored to make 2D NMR a high-throughput tool for metabolomics, relying on alternative data acquisition schemes such as ultrafast NMR. Currently, much work is aimed at drastically boosting the NMR sensitivity thanks to hyperpolarisation techniques, which have been used in combination with fast acquisition methods and could greatly expand the application potential of NMR metabolomics.
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Affiliation(s)
- Jérémy Marchand
- CEISAM, UMR6230, Université de Nantes, BP 92208, 2 rue de la Houssinière, 44322 Nantes, France; LUNAM Université, Oniris, Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), 44307 Nantes, France
| | - Estelle Martineau
- CEISAM, UMR6230, Université de Nantes, BP 92208, 2 rue de la Houssinière, 44322 Nantes, France; Spectromaîtrise, CAPACITÉS SAS, 26 Bd Vincent Gâche, 44200 Nantes, France
| | - Yann Guitton
- LUNAM Université, Oniris, Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), 44307 Nantes, France
| | - Gaud Dervilly-Pinel
- LUNAM Université, Oniris, Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), 44307 Nantes, France
| | - Patrick Giraudeau
- CEISAM, UMR6230, Université de Nantes, BP 92208, 2 rue de la Houssinière, 44322 Nantes, France; Institut Universitaire de France, 1 rue Descartes, 75005 Paris Cedex 5, France.
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Fan TWM, Lane AN. Applications of NMR spectroscopy to systems biochemistry. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:18-53. [PMID: 26952191 PMCID: PMC4850081 DOI: 10.1016/j.pnmrs.2016.01.005] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 05/05/2023]
Abstract
The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective in vivo imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied in vitro, ex vivo, or in vivo in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other 'omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.
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Affiliation(s)
- Teresa W-M Fan
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
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Lesot P, Berdagué P, Giraudeau P. Detection of quadrupolar nuclei by ultrafast 2D NMR: exploring the case of deuterated analytes aligned in chiral oriented solvents. Chem Commun (Camb) 2016; 52:2122-2125. [DOI: 10.1039/c5cc09409g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Anisotropic 2H ultrafast (ADUF) 2D NMR spectroscopy for studying deuterated analytes dissolved in chiral liquid crystals is investigated and its analytical possibilities are evaluated.
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Affiliation(s)
- Philippe Lesot
- Equipe RMN en Milieu Orienté
- ICMMO
- UMR-CNRS 8182
- Université de Paris-Sud
- Université Paris-Saclay
| | - Philippe Berdagué
- Equipe RMN en Milieu Orienté
- ICMMO
- UMR-CNRS 8182
- Université de Paris-Sud
- Université Paris-Saclay
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Gouilleux B, Charrier B, Danieli E, Dumez JN, Akoka S, Felpin FX, Rodriguez-Zubiri M, Giraudeau P. Real-time reaction monitoring by ultrafast 2D NMR on a benchtop spectrometer. Analyst 2015; 140:7854-8. [DOI: 10.1039/c5an01998b] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast 2D NMR spectra are recorded on a compact spectrometer to follow in real time a reaction in the synthetic chemistry laboratory. Complex reactions can be monitored in non-deuterated solvents to confirm in real time the molecular structure of the compounds involved in the reaction while giving access to relevant kinetic parameters.
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Affiliation(s)
| | | | - Ernesto Danieli
- Institut für Technische und Makromolekulare Chemie (ITMC)
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - Jean-Nicolas Dumez
- CNRS UPR2301
- Institut de Chimie des Substances Naturelles
- 91198 Gif-sur-Yvette Cedex
- France
| | - Serge Akoka
- CEISAM CNRS
- UMR6230
- Université de Nantes
- 44322 Nantes
- France
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