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An L, Liu H, Li M, Ma J, Zheng L, Zhou J, Zhang J, Yuan Y, Wu X. Unveiling the impact of harvest time on Dioscorea opposita Thunb. cv. Tiegun maturity by NMR-based metabolomics and LC-MS/MS analysis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:6342-6349. [PMID: 38415792 DOI: 10.1002/jsfa.13418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/29/2024] [Accepted: 02/25/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Dioscorea opposita Thunb. cv. Tiegun maturity (DM) is an important factor influencing its quality. However, there are few studies on the impact of harvest time on its maturation. In the present study, a NMR-based metabolomics approach was applied to investigate the dynamic metabolic changes of D. opposita Thunb. cv. Tiegun at six different harvest stages: stage 1 (S1), stage 2 (S2), Stage 3 (S3), stage 4 (S4), stage 5 (S5) and stage 6 (S6). RESULTS Principal component analysis showed distinct segregation of samples obtained from S1, S2 and S3 compared to those derived from S4, S5 and S6. Interestingly, these samples from the two periods were obtained before and after frost, indicating that frost descent might be important for DM. Eight differential metabolites responsible for good separation of different groups were identified by the principal component analysis loading plot and partial least squares-discriminant analysis. In addition, quantitative analysis of these metabolites using liquid chromatography-tandem mass spectrometry determined the effects of harvest time on these metabolite contents, two of which, sucrose and allantoin, were considered as potential biomarkers to determine DM. CONCLUSION The present study demonstrated that NMR-based metabolomics approach could serve as a powerful tool to identify differential metabolites during harvesting processes, also offering a fresh insight into understanding the DM and the potential mechanism of quality formation. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Li An
- Institute of Quality and Safety for Agro-products, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Grain Quality and Safety and Testing Henan Province, Zhengzhou, China
| | - Hao Liu
- International Joint Research Laboratory for Global Change Ecology, School of Life Sciences, Henan University, Kaifeng, China
| | - Meng Li
- Institute of Quality and Safety for Agro-products, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Grain Quality and Safety and Testing Henan Province, Zhengzhou, China
| | - Jingwei Ma
- Institute of Quality and Safety for Agro-products, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Grain Quality and Safety and Testing Henan Province, Zhengzhou, China
| | - Lufei Zheng
- Institute of Quality Standards and Testing Technology for Agro-products of CAAS, Beijing, China
| | - Juan Zhou
- Institute of Quality and Safety for Agro-products, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Grain Quality and Safety and Testing Henan Province, Zhengzhou, China
| | - Junfeng Zhang
- Institute of Quality and Safety for Agro-products, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Grain Quality and Safety and Testing Henan Province, Zhengzhou, China
| | - Yongliang Yuan
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xujin Wu
- Institute of Quality and Safety for Agro-products, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Grain Quality and Safety and Testing Henan Province, Zhengzhou, China
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Yu B, Bolik-Coulon N, Rangadurai AK, Kay LE, Iwahara J. Gadolinium-Based NMR Spin Relaxation Measurements of Near-Surface Electrostatic Potentials of Biomolecules. J Am Chem Soc 2024. [PMID: 39028837 DOI: 10.1021/jacs.4c04433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
NMR spectroscopy is an important tool for the measurement of the electrostatic properties of biomolecules. To this point, paramagnetic relaxation enhancements (PREs) of 1H nuclei arising from nitroxide cosolutes in biomolecular solutions have been used to measure effective near-surface electrostatic potentials (ϕENS) of proteins and nucleic acids. Here, we present a gadolinium (Gd)-based NMR method, exploiting Gd chelates with different net charges, for measuring ϕENS values and demonstrate its utility through applications to a number of biomolecular systems. The use of Gd-based cosolutes offers several advantages over nitroxides for ϕENS measurements. First, unlike nitroxide compounds, Gd chelates enable electrostatic potential measurements on oxidation-sensitive proteins that require reducing agents. Second, the large electron spin quantum number of Gd (7/2) results in notably larger PREs for Gd chelates when used at the same concentrations as nitroxide radicals. Thus, it is possible to measure ϕENS values exclusively from + and - charged compounds even for highly charged biomolecules, avoiding the use of neutral cosolutes that, as we further establish here, limits the accuracy of the measured electrostatic potentials. In addition, the smaller concentrations of cosolutes required minimize potential binding to sites on macromolecules. Fourth, the closer proximity of the paramagnetic center and charged groups within Gd chelates, in comparison to the corresponding nitroxide compounds, enables more accurate predictions of ϕENS potentials for cross-validation of the experimental results. The Gd-based method described here, thus, broadens the applicability of studies of biomolecular electrostatics using solution NMR spectroscopy.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
| | - Nicolas Bolik-Coulon
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Atul K Rangadurai
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-1068, United States
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Sun X, Yu Y, Qian K, Wang J, Huang L. Recent Progress in Mass Spectrometry-Based Single-Cell Metabolic Analysis. SMALL METHODS 2024; 8:e2301317. [PMID: 38032130 DOI: 10.1002/smtd.202301317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/10/2023] [Indexed: 12/01/2023]
Abstract
Single-cell analysis enables the measurement of biomolecules at the level of individual cells, facilitating in-depth investigations into cellular heterogeneity and precise interpretation of the related biological mechanisms. Among these biomolecules, cellular metabolites exhibit remarkable sensitivity to environmental and biochemical changes, unveiling a hidden world underlying cellular heterogeneity and allowing for the determination of cell physiological states. However, the metabolic analysis of single cells is challenging due to the extremely low concentrations, substantial content variations, and rapid turnover rates of cellular metabolites. Mass spectrometry (MS), characterized by its high sensitivity, wide dynamic range, and excellent selectivity, is employed in single-cell metabolic analysis. This review focuses on recent advances and applications of MS-based single-cell metabolic analysis, encompassing three key steps of single-cell isolation, detection, and application. It is anticipated that MS will bring profound implications in biomedical practices, serving as advanced tools to depict the single-cell metabolic landscape.
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Affiliation(s)
- Xuming Sun
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Yi Yu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
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Ghini V, Meoni G, Vignoli A, Di Cesare F, Tenori L, Turano P, Luchinat C. Fingerprinting and profiling in metabolomics of biosamples. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 138-139:105-135. [PMID: 38065666 DOI: 10.1016/j.pnmrs.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 12/18/2023]
Abstract
This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all researchers who wish to approach metabolomics with a clear idea of what they wish to achieve but not necessarily with a deep knowledge of NMR. For this reason, some technical parts may seem a bit naïve to the experts. The review starts by describing standard metabolomics procedures, which imply the use of a dedicated 600 MHz instrument and of four properly standardized 1D experiments. Standardization is a must if one wants to directly compare NMR results obtained in different labs. A brief mention is also made of standardized pre-analytical procedures, which are even more essential. Attention is paid to the distinction between fingerprinting and profiling, and the advantages and disadvantages of fingerprinting are clarified. This aspect is often not fully appreciated. Then profiling, and the associated problems of signal assignment and quantitation, are discussed. We also describe less conventional approaches, such as the use of different magnetic fields, the use of signal enhancement techniques to increase sensitivity, and the potential of field-shuttling NMR. A few examples of biomedical applications are also given, again with the focus on NMR techniques that are most suitable to achieve each particular goal, including a description of the most common heteronuclear experiments. Finally, the growing applications of metabolomics to foodstuffs are described.
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Affiliation(s)
- Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Francesca Di Cesare
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy; Giotto Biotech S.r.l., Sesto Fiorentino, Italy.
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Saviano G, Paris D, Iorizzi M. Editorial: Exploring metabolomic diversity in plant species by NMR-based and mass-based spectrometry. FRONTIERS IN PLANT SCIENCE 2023; 14:1248781. [PMID: 37534294 PMCID: PMC10392922 DOI: 10.3389/fpls.2023.1248781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 08/04/2023]
Affiliation(s)
- Gabriella Saviano
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
- Institute of Biomolecular Chemistry, National Research Council (CNR), Pozzuoli, Italy
| | - Debora Paris
- Institute of Biomolecular Chemistry, National Research Council (CNR), Pozzuoli, Italy
| | - Maria Iorizzi
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
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