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Zhan H, Chen Y, Cui Y, Zeng Y, Feng X, Tan C, Huang C, Lin E, Huang Y, Chen Z. Pure-Shift-Based Proton Magnetic Resonance Spectroscopy for High-Resolution Studies of Biological Samples. Int J Mol Sci 2024; 25:4698. [PMID: 38731917 PMCID: PMC11083948 DOI: 10.3390/ijms25094698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Proton magnetic resonance spectroscopy (1H MRS) presents a powerful tool for revealing molecular-level metabolite information, complementary to the anatomical insight delivered by magnetic resonance imaging (MRI), thus playing a significant role in in vivo/in vitro biological studies. However, its further applications are generally confined by spectral congestion caused by numerous biological metabolites contained within the limited proton frequency range. Herein, we propose a pure-shift-based 1H localized MRS method as a proof of concept for high-resolution studies of biological samples. Benefitting from the spectral simplification from multiplets to singlet peaks, this method addresses the challenge of spectral congestion encountered in conventional MRS experiments and facilitates metabolite analysis from crowded NMR resonances. The performance of the proposed pure-shift 1H MRS method is demonstrated on different kinds of samples, including brain metabolite phantom and in vitro biological samples of intact pig brain tissue and grape tissue, using a 7.0 T animal MRI scanner. This proposed MRS method is readily implemented in common commercial NMR/MRI instruments because of its generally adopted pulse-sequence modules. Therefore, this study takes a meaningful step for MRS studies toward potential applications in metabolite analysis and disease diagnosis.
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Affiliation(s)
- Haolin Zhan
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
- Department of Biomedical Engineering, Anhui Provincial Engineering Research Center of Semiconductor Inspection Technology and Instrument, Anhui Province Key Laboratory of Measuring Theory and Precision Instrument, Hefei University of Technology, Hefei 230009, China
| | - Yulei Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yinping Cui
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yunsong Zeng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Xiaozhen Feng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Chunhua Tan
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Chengda Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Enping Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yuqing Huang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
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Botton A, Girardi F, Ruperti B, Brilli M, Tijero V, Eccher G, Populin F, Schievano E, Riello T, Munné-Bosch S, Canton M, Rasori A, Cardillo V, Meggio F. Grape Berry Responses to Sequential Flooding and Heatwave Events: A Physiological, Transcriptional, and Metabolic Overview. PLANTS (BASEL, SWITZERLAND) 2022; 11:3574. [PMID: 36559686 PMCID: PMC9788187 DOI: 10.3390/plants11243574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Grapevine cultivation, such as the whole horticulture, is currently challenged by several factors, among which the extreme weather events occurring under the climate change scenario are the most relevant. Within this context, the present study aims at characterizing at the berry level the physiological response of Vitis vinifera cv. Sauvignon Blanc to sequential stresses simulated under a semi-controlled environment: flooding at bud-break followed by multiple summer stress (drought plus heatwave) occurring at pre-vèraison. Transcriptomic and metabolomic assessments were performed through RNASeq and NMR, respectively. A comprehensive hormone profiling was also carried out. Results pointed out a different response to the heatwave in the two situations. Flooding caused a developmental advance, determining a different physiological background in the berry, thus affecting its response to the summer stress at both transcriptional levels, with the upregulation of genes involved in oxidative stress responses, and metabolic level, with the increase in osmoprotectants, such as proline and other amino acids. In conclusion, sequential stress, including a flooding event at bud-break followed by a summer heatwave, may impact phenological development and berry ripening, with possible consequences on berry and wine quality. A berry physiological model is presented that may support the development of sustainable vineyard management solutions to improve the water use efficiency and adaptation capacity of actual viticultural systems to future scenarios.
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Affiliation(s)
- Alessandro Botton
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
- Interdepartmental Research Centre for Viticulture and Enology—CIRVE, University of Padova, Via XXVIII Aprile 14, Conegliano, 31015 Treviso, Italy
| | - Francesco Girardi
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Benedetto Ruperti
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
- Interdepartmental Research Centre for Viticulture and Enology—CIRVE, University of Padova, Via XXVIII Aprile 14, Conegliano, 31015 Treviso, Italy
| | - Matteo Brilli
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Veronica Tijero
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Giulia Eccher
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Francesca Populin
- Unit of Fruit Crop Genetics and Breeding, Research and Innovation Centre—CRI, Edmund Mach Foundation—FEM, Via E. Mach 1, San Michele all’Adige, 38098 Trento, Italy
| | - Elisabetta Schievano
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Tobia Riello
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Diagonal 643, 08017 Barcelona, Spain
| | - Monica Canton
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Angela Rasori
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Valerio Cardillo
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
| | - Franco Meggio
- Department of Agronomy, Food, Natural Resources, Animals and Environment—DAFNAE, University of Padova, Agripolis, Viale dell’università 16, Legnaro, 35020 Padova, Italy
- Interdepartmental Research Centre for Viticulture and Enology—CIRVE, University of Padova, Via XXVIII Aprile 14, Conegliano, 31015 Treviso, Italy
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Dimitrakopoulou ME, Matzarapi K, Chasapi S, Vantarakis A, Spyroulias GA. Nontargeted 1 H NMR fingerprinting and multivariate statistical analysis for traceability of Greek PDO Vostizza currants. J Food Sci 2021; 86:4417-4429. [PMID: 34459510 DOI: 10.1111/1750-3841.15873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/28/2021] [Accepted: 07/02/2021] [Indexed: 11/28/2022]
Abstract
In this study, non-targeted 1 H NMR fingerprinting was used in combination with multivariate statistical analyses for the classification of Greek currants based on their geographical origins (Aeghion, Nemea, Kalamata, Zante, and Amaliada). As classification techniques, Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) were carried out. To elucidate different components according to PDO (Protected Designation of Origin), products from Aeghion (Vostizza) were statistically compared with each one of the four other regions. PLS-DA plots ensure that currants from Kalamata, Nemea, Zante, and Amaliada are well classified with respect to the PDO currants, according to differences observed in metabolites. Results suggest that composition differences in carbohydrates, amino, and organic acids of currants are sufficient to discriminate them in correlation to their geographical origin. In conclusion, currants metabolites which mostly contribute to classification performance of such discriminant analysis model present a suitable alternative technique for currants traceability. The study results contribute information to the currants' metabolite fingerprinting by NMR spectroscopy and their geographical origin. PRACTICAL APPLICATION: This study presents an analytical approach for a high nutritional value Greek PDO product, Vostizza currant. A further research and implementation of this method in food industry, can be the key to food fraud incidents. Thus, application of this work opens up posibilities to "farm to table" mission.
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Affiliation(s)
| | - Konstantina Matzarapi
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Styliani Chasapi
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Apostolos Vantarakis
- Department of Public Health, Medical School, University of Patras, Patras, Greece
| | - Georgios A Spyroulias
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
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Ciubotaru RM, Franceschi P, Zulini L, Stefanini M, Škrab D, Rossarolla MD, Robatscher P, Oberhuber M, Vrhovsek U, Chitarrini G. Mono-Locus and Pyramided Resistant Grapevine Cultivars Reveal Early Putative Biomarkers Upon Artificial Inoculation With Plasmopara viticola. FRONTIERS IN PLANT SCIENCE 2021; 12:693887. [PMID: 34276743 PMCID: PMC8281963 DOI: 10.3389/fpls.2021.693887] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/04/2021] [Indexed: 06/02/2023]
Abstract
One of the most economically important grapevine diseases is Downy mildew (DM) caused by the oomycete Plasmopara viticola. A strategy to reduce the use of fungicides to compensate for the high susceptibility of V. vinifera is the selection of grapevine varieties showing pathogen-specific resistance. We applied a metabolomics approach to evaluate the metabolic modulation in mono-locus resistant genotypes carrying one locus associated with P. viticola resistance (Rpv) (BC4- Rpv1, Bianca- Rpv3-1, F12P160- Rpv12, Solaris- Rpv10), as well as in pyramided resistant genotypes carrying more than one Rpv (F12P60- Rpv3-1; Rpv12 and F12P127- Rpv3-1, Rpv3-3; Rpv10) taking as a reference the susceptible genotype Pinot Noir. In order to understand if different sources of resistance are associated with different degrees of resistance and, implicitly, with different responses to the pathogen, we considered the most important classes of plant metabolite primary compounds, lipids, phenols and volatile organic compounds at 0, 12, 48, and 96 h post-artificial inoculation (hpi). We identified 264 modulated compounds; among these, 22 metabolites were found accumulated in significant quantities in the resistant cultivars compared to Pinot Noir. In mono-locus genotypes, the highest modulation of the metabolites was noticed at 48 and 96 hpi, except for Solaris, that showed a behavior similar to the pyramided genotypes in which the changes started to occur as early as 12 hpi. Bianca, Solaris and F12P60 showed the highest number of interesting compounds accumulated after the artificial infection and with a putative effect against the pathogen. In contrast, Pinot Noir showed a less effective defense response in containing DM growth.
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Affiliation(s)
- Ramona Mihaela Ciubotaru
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Pietro Franceschi
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Luca Zulini
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Marco Stefanini
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Domen Škrab
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | | | | | | | - Urska Vrhovsek
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giulia Chitarrini
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Laimburg Research Centre, Auer, Italy
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5
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Roch L, Prigent S, Klose H, Cakpo CB, Beauvoit B, Deborde C, Fouillen L, van Delft P, Jacob D, Usadel B, Dai Z, Génard M, Vercambre G, Colombié S, Moing A, Gibon Y. Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5823-5836. [PMID: 32592486 PMCID: PMC7540837 DOI: 10.1093/jxb/eraa302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/23/2020] [Indexed: 05/13/2023]
Abstract
Fleshy fruits are very varied, whether in terms of their composition, physiology, or rate and duration of growth. To understand the mechanisms that link metabolism to phenotypes, which would help the targeting of breeding strategies, we compared eight fleshy fruit species during development and ripening. Three herbaceous (eggplant, pepper, and cucumber), three tree (apple, peach, and clementine) and two vine (kiwifruit and grape) species were selected for their diversity. Fruit fresh weight and biomass composition, including the major soluble and insoluble components, were determined throughout fruit development and ripening. Best-fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84), stearate (R=0.72), palmitate (R=0.72), and lignocerate (R=0.68). The strong link between biomass composition and RGR was further evidenced by generalized linear models that predicted RGR with R-values exceeding 0.9. Comparison of the fruit also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall glucose and fucose, and more starch, than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.
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Affiliation(s)
- Léa Roch
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Sylvain Prigent
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Holger Klose
- Institute for Biology, BioSC, RWTH Aachen University, Worringer Weg, Aachen, Germany
- Institute of Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Bertrand Beauvoit
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Catherine Deborde
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Laetitia Fouillen
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- UMR 5200, CNRS, Univ. Bordeaux, Laboratoire de Biogenèse Membranaire, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Pierre van Delft
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- UMR 5200, CNRS, Univ. Bordeaux, Laboratoire de Biogenèse Membranaire, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Daniel Jacob
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Björn Usadel
- Institute for Biology, BioSC, RWTH Aachen University, Worringer Weg, Aachen, Germany
- Institute of Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Zhanwu Dai
- UMR 1287 EGFV, INRAE, Univ. Bordeaux, Bordeaux Sci Agro, Villenave d’Ornon, France
| | | | | | - Sophie Colombié
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Annick Moing
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
| | - Yves Gibon
- UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine – Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
- Bordeaux Metabolome, MetaboHUB, INRAE, Univ. Bordeaux, Avenue Edouard Bourlaux, Villenave d’Ornon, France
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Zhan H, Huang Y, Chen Z. High-Resolution Probing of Heterogeneous Samples by Spatially Selective Pure Shift NMR Spectroscopy. J Phys Chem Lett 2019; 10:7356-7361. [PMID: 31718190 DOI: 10.1021/acs.jpclett.9b03092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Liquid NMR spectroscopy generally encounters two major challenges for high-resolution measurements of heterogeneous samples, namely, magnetic field inhomogeneity caused by spatial variations in magnetic susceptibility and spectral congestion induced by crowded NMR resonances. In this study, we demonstrate a spatially selective pure shift NMR approach for high-resolution probing of heterogeneous samples by suppressing effects of field inhomogeneity and J coupling simultaneously. A Fourier phase encoding strategy is proposed and implemented for spatially selective pure shift experiments to enhance signal intensity and further boost the applicability. The spatially selective pure shift method can serve as an effective tool for high-resolution probing of heterogeneous samples, thus presenting interesting prospects for extensive applications in the fields of chemistry, physics, biology, and food science.
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Affiliation(s)
- Haolin Zhan
- Department of Electronic Science, State Key Laboratory of Physical Chemistry of Solid Surfaces , Xiamen University , Xiamen 361005 , China
| | - Yuqing Huang
- Department of Electronic Science, State Key Laboratory of Physical Chemistry of Solid Surfaces , Xiamen University , Xiamen 361005 , China
| | - Zhong Chen
- Department of Electronic Science, State Key Laboratory of Physical Chemistry of Solid Surfaces , Xiamen University , Xiamen 361005 , China
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7
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Mazzei P, Celano G, Palese AM, Lardo E, Drosos M, Piccolo A. HRMAS-NMR metabolomics of Aglianicone grapes pulp to evaluate terroir and vintage effects, and, as assessed by the electromagnetic induction (EMI) technique, spatial variability of vineyard soils. Food Chem 2019; 283:215-223. [DOI: 10.1016/j.foodchem.2019.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/04/2019] [Accepted: 01/06/2019] [Indexed: 12/21/2022]
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Grape and Wine Metabolomics to Develop New Insights Using Untargeted and Targeted Approaches. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4040092] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chemical analysis of grape juice and wine has been performed for over 50 years in a targeted manner to determine a limited number of compounds using Gas Chromatography, Mass-Spectrometry (GC-MS) and High Pressure Liquid Chromatography (HPLC). Therefore, it only allowed the determination of metabolites that are present in high concentration, including major sugars, amino acids and some important carboxylic acids. Thus, the roles of many significant but less concentrated metabolites during wine making process are still not known. This is where metabolomics shows its enormous potential, mainly because of its capability in analyzing over 1000 metabolites in a single run due to the recent advancements of high resolution and sensitive analytical instruments. Metabolomics has predominantly been adopted by many wine scientists as a hypothesis-generating tool in an unbiased and non-targeted way to address various issues, including characterization of geographical origin (terroir) and wine yeast metabolic traits, determination of biomarkers for aroma compounds, and the monitoring of growth developments of grape vines and grapes. The aim of this review is to explore the published literature that made use of both targeted and untargeted metabolomics to study grapes and wines and also the fermentation process. In addition, insights are also provided into many other possible avenues where metabolomics shows tremendous potential as a question-driven approach in grape and wine research.
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9
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Chitarrini G, Soini E, Riccadonna S, Franceschi P, Zulini L, Masuero D, Vecchione A, Stefanini M, Di Gaspero G, Mattivi F, Vrhovsek U. Identification of Biomarkers for Defense Response to Plasmopara viticola in a Resistant Grape Variety. FRONTIERS IN PLANT SCIENCE 2017; 8:1524. [PMID: 28928759 PMCID: PMC5591819 DOI: 10.3389/fpls.2017.01524] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/21/2017] [Indexed: 05/20/2023]
Abstract
Downy mildew (Plasmopara viticola) is one of the most destructive diseases of the cultivated species Vitis vinifera. The use of resistant varieties, originally derived from backcrosses of North American Vitis spp., is a promising solution to reduce disease damage in the vineyards. To shed light on the type and the timing of pathogen-triggered resistance, this work aimed at discovering biomarkers for the defense response in the resistant variety Bianca, using leaf discs after inoculation with a suspension of P. viticola. We investigated primary and secondary metabolism at 12, 24, 48, and 96 h post-inoculation (hpi). We used methods of identification and quantification for lipids (LC-MS/MS), phenols (LC-MS/MS), primary compounds (GC-MS), and semi-quantification for volatile compounds (GC-MS). We were able to identify and quantify or semi-quantify 176 metabolites, among which 53 were modulated in response to pathogen infection. The earliest changes occurred in primary metabolism at 24-48 hpi and involved lipid compounds, specifically unsaturated fatty acid and ceramide; amino acids, in particular proline; and some acids and sugars. At 48 hpi, we also found changes in volatile compounds and accumulation of benzaldehyde, a promoter of salicylic acid-mediated defense. Secondary metabolism was strongly induced only at later stages. The classes of compounds that increased at 96 hpi included phenylpropanoids, flavonols, stilbenes, and stilbenoids. Among stilbenoids we found an accumulation of ampelopsin H + vaticanol C, pallidol, ampelopsin D + quadrangularin A, Z-miyabenol C, and α-viniferin in inoculated samples. Some of these compounds are known as phytoalexins, while others are novel biomarkers for the defense response in Bianca. This work highlighted some important aspects of the host response to P. viticola in a commercial variety under controlled conditions, providing biomarkers for a better understanding of the mechanism of plant defense and a potential application in field studies of resistant varieties.
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Affiliation(s)
- Giulia Chitarrini
- Food Quality and Nutrition Department, Fondazione Edmund MachSan Michele all’Adige, Italy
- Department of Agricultural and Environmental Sciences, University of UdineUdine, Italy
| | - Evelyn Soini
- Food Quality and Nutrition Department, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Samantha Riccadonna
- Computational Biology Unit, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Pietro Franceschi
- Computational Biology Unit, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Luca Zulini
- Genomics and Biology of Fruit Crop Department, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Domenico Masuero
- Food Quality and Nutrition Department, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Antonella Vecchione
- Genomics and Biology of Fruit Crop Department, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Marco Stefanini
- Genomics and Biology of Fruit Crop Department, Fondazione Edmund MachSan Michele all’Adige, Italy
| | | | - Fulvio Mattivi
- Food Quality and Nutrition Department, Fondazione Edmund MachSan Michele all’Adige, Italy
- Center Agriculture Food Environment, University of TrentoTrento, Italy
| | - Urska Vrhovsek
- Food Quality and Nutrition Department, Fondazione Edmund MachSan Michele all’Adige, Italy
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Fabres PJ, Collins C, Cavagnaro TR, Rodríguez López CM. A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera. FRONTIERS IN PLANT SCIENCE 2017; 8:1065. [PMID: 28676813 PMCID: PMC5477006 DOI: 10.3389/fpls.2017.01065] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/02/2017] [Indexed: 05/19/2023]
Abstract
Vitis vinifera (grapevine) is one of the most important fruit crops, both for fresh consumption and wine and spirit production. The term terroir is frequently used in viticulture and the wine industry to relate wine sensory attributes to its geographic origin. Although, it can be cultivated in a wide range of environments, differences in growing conditions have a significant impact on fruit traits that ultimately affect wine quality. Understanding how fruit quality and yield are controlled at a molecular level in grapevine in response to environmental cues has been a major driver of research. Advances in the area of genomics, epigenomics, transcriptomics, proteomics and metabolomics, have significantly increased our knowledge on the abiotic regulation of yield and quality in many crop species, including V. vinifera. The integrated analysis of multiple 'omics' can give us the opportunity to better understand how plants modulate their response to different environments. However, 'omics' technologies provide a large amount of biological data and its interpretation is not always straightforward, especially when different 'omic' results are combined. Here we examine the current strategies used to integrate multi-omics, and how these have been used in V. vinifera. In addition, we also discuss the importance of including epigenomics data when integrating omics data as epigenetic mechanisms could play a major role as an intermediary between the environment and the genome.
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Affiliation(s)
- Pastor Jullian Fabres
- Environmental Epigenetics and Genetics Group, Plant Research Centre, School of Agriculture, Food and Wine, University of Adelaide, Glen OsmondSA, Australia
| | - Cassandra Collins
- The Waite Research Institute, The School of Agriculture, Food and Wine, The University of Adelaide, Glen OsmondSA, Australia
| | - Timothy R. Cavagnaro
- The Waite Research Institute, The School of Agriculture, Food and Wine, The University of Adelaide, Glen OsmondSA, Australia
| | - Carlos M. Rodríguez López
- Environmental Epigenetics and Genetics Group, Plant Research Centre, School of Agriculture, Food and Wine, University of Adelaide, Glen OsmondSA, Australia
- *Correspondence: Carlos M. Rodríguez López,
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11
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Picone G, Trimigno A, Tessarin P, Donnini S, Rombolà AD, Capozzi F. 1 H NMR foodomics reveals that the biodynamic and the organic cultivation managements produce different grape berries ( Vitis vinifera L. cv. Sangiovese). Food Chem 2016; 213:187-195. [DOI: 10.1016/j.foodchem.2016.06.077] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/05/2016] [Accepted: 06/22/2016] [Indexed: 10/21/2022]
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12
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Cozzolino D. Metabolomics in Grape and Wine: Definition, Current Status and Future Prospects. FOOD ANAL METHOD 2016. [DOI: 10.1007/s12161-016-0502-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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13
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Shiratake K, Suzuki M. Omics studies of citrus, grape and rosaceae fruit trees. BREEDING SCIENCE 2016; 66:122-38. [PMID: 27069397 PMCID: PMC4780796 DOI: 10.1270/jsbbs.66.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/01/2015] [Indexed: 05/06/2023]
Abstract
Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.
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Affiliation(s)
- Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
- Corresponding author (e-mail: )
| | - Mami Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
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14
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Tuberoso CIG, Congiu F, Serreli G, Mameli S. Determination of dansylated amino acids and biogenic amines in Cannonau and Vermentino wines by HPLC-FLD. Food Chem 2014; 175:29-35. [PMID: 25577047 DOI: 10.1016/j.foodchem.2014.11.120] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/21/2014] [Accepted: 11/20/2014] [Indexed: 01/02/2023]
Abstract
Free amino acids (AA) and biogenic amines (BA) were quantified for the first time in Cannonau and Vermentino wines, the two most popular "Controlled Designation of Origin" wines from Sardinia (Italy). An analytical method for the simultaneous determination of AA and BA was developed, using selective derivatization with dansyl chloride followed by HPLC with fluorescence detection. Thirty-two compounds were identified in the wines analysed. High levels of AA were found, with proline being the most abundant with average levels of 1244 ± 398 and 1008 ± 281 mg/L in Cannonau and Vermentino wines, respectively. BA were detected at average concentrations <10mg/L, except putrescine which reached 20.5 ± 10.2mg/L in Cannonau wines. Histamine was never detected in any Vermentino wines. γ-Aminobutyric acid, 4-hydroxyproline, glycine, leucine+isoleucine and putrescine proved to be useful for differentiating Cannonau wines from Vermentino wines.
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Affiliation(s)
| | - Francesca Congiu
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale 72, 09124 Cagliari, Italy
| | - Gabriele Serreli
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale 72, 09124 Cagliari, Italy
| | - Stefano Mameli
- Department of Life and Environmental Sciences, University of Cagliari, Via Ospedale 72, 09124 Cagliari, Italy
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15
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Gallo V, Mastrorilli P, Cafagna I, Nitti GI, Latronico M, Longobardi F, Minoja AP, Napoli C, Romito VA, Schäfer H, Schütz B, Spraul M. Effects of agronomical practices on chemical composition of table grapes evaluated by NMR spectroscopy. J Food Compost Anal 2014. [DOI: 10.1016/j.jfca.2014.04.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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16
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Fotakis C, Kokkotou K, Zoumpoulakis P, Zervou M. NMR metabolite fingerprinting in grape derived products: An overview. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.03.032] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Anedda R, Piga C, Santercole V, Spada S, Bonaglini E, Cappuccinelli R, Mulas G, Roggio T, Uzzau S. Multidisciplinary analytical investigation of phospholipids and triglycerides in offshore farmed gilthead sea bream (Sparus aurata) fed commercial diets. Food Chem 2013; 138:1135-44. [DOI: 10.1016/j.foodchem.2012.11.098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 11/21/2012] [Accepted: 11/22/2012] [Indexed: 10/27/2022]
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18
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Rizzuti A, Caliandro R, Gallo V, Mastrorilli P, Chita G, Latronico M. A combined approach for characterisation of fresh and brined vine leaves by X-ray powder diffraction, NMR spectroscopy and direct infusion high resolution mass spectrometry. Food Chem 2013; 141:1908-15. [PMID: 23870909 DOI: 10.1016/j.foodchem.2013.05.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/04/2013] [Accepted: 05/13/2013] [Indexed: 12/16/2022]
Abstract
X-ray powder diffraction was combined, for the first time, with Nuclear Magnetic Resonance spectroscopy and direct infusion mass spectrometry to characterise fresh and brined grape leaves. Covariance analysis of data generated by the three techniques was performed with the aim to correlate information deriving from the solid part with those obtained for soluble metabolites. The results obtained indicate that crystalline components can be correlated to the metabolites contained in the grape leaves, paving the way to the use of X-ray diffraction analysis for food fingerprinting purposes. Moreover it was ascertained that, differently from most of the metabolites present in the fresh vine leaves, linolenic acid (an omega-3-fatty acid) and quercetin-3-O-glucuronide (a polyphenol metabolite) do not undergo sensible degradation during the brining process, which is used as preservative method for the grape leaves.
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Affiliation(s)
- Antonino Rizzuti
- Dipartimento di Ingegneria Civile Ambientale del Territorio Edile e di Chimica, Politecnico di Bari, Via Orabona 4, I-70125 Bari, Italy
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19
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Gupta V, Thakur RS, Reddy CRK, Jha B. Central metabolic processes of marine macrophytic algae revealed from NMR based metabolome analysis. RSC Adv 2013. [DOI: 10.1039/c3ra23017a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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20
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Hong YS, Martinez A, Liger-Belair G, Jeandet P, Nuzillard JM, Cilindre C. Metabolomics reveals simultaneous influences of plant defence system and fungal growth in Botrytis cinerea-infected Vitis vinifera cv. Chardonnay berries. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5773-5785. [PMID: 22945941 DOI: 10.1093/jxb/ers228] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Botrytis cinerea is a fungal plant pathogen of grape berries, leading to economic and quality losses in wine production. The global metabolite changes induced by B. cinerea infection in grape have not been established to date, even though B. cinerea infection is known to cause significant changes in chemicals or metabolites. In order to better understand metabolic mechanisms linked to the infection process and to identify the metabolites associated with B. cinerea infection, (1)H NMR spectroscopy was used in global metabolite profiling and multivariate statistical analysis of berries from healthy and botrytized bunches. Pattern recognition methods, such as principal component analysis, revealed clear metabolic discriminations between healthy and botrytized berries of botrytized bunches and healthy berries of healthy bunches. Significantly high levels of proline, glutamate, arginine, and alanine, which are accumulated upon plant stress, were found in healthy and botrytized berries of botrytized bunches. Moreover, largely degraded phenylpropanoids, flavonoid compounds, and sucrose together with markedly produced glycerol, gluconic acid, and succinate, all being directly associated with B. cinerea growth, were only found in botrytized berries of botrytized bunches. This study reports that B. cinerea infection causes significant metabolic changes in grape berry and highlights that both the metabolic perturbations associated with the plant defence system and those directly derived from fungal pathogen growth should be considered to better understand the interaction between metabolic variation and biotic pathogen stress in plants.
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Affiliation(s)
- Young-Shick Hong
- Laboratoire d'Oenologie et Chimie Appliquée, URVVC UPRES EA 4707, Faculté des Sciences, Université de Reims Champagne-Ardenne: BP 1039, 51687 Reims Cedex 2, France.
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21
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Pauli GF, Gödecke T, Jaki BU, Lankin DC. Quantitative 1H NMR. Development and potential of an analytical method: an update. JOURNAL OF NATURAL PRODUCTS 2012; 75:834-51. [PMID: 22482996 PMCID: PMC3384681 DOI: 10.1021/np200993k] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Covering the literature from mid-2004 until the end of 2011, this review continues a previous literature overview on quantitative (1)H NMR (qHNMR) methodology and its applications in the analysis of natural products. Among the foremost advantages of qHNMR is its accurate function with external calibration, the lack of any requirement for identical reference materials, a high precision and accuracy when properly validated, and an ability to quantitate multiple analytes simultaneously. As a result of the inclusion of over 170 new references, this updated review summarizes a wealth of detailed experiential evidence and newly developed methodology that supports qHNMR as a valuable and unbiased analytical tool for natural product and other areas of research.
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Affiliation(s)
- Guido F Pauli
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, USA.
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22
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Hong YS. NMR-based metabolomics in wine science. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49 Suppl 1:S13-S21. [PMID: 22290704 DOI: 10.1002/mrc.2832] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
As metabolomics is becoming an emerging field of 'omics' research, NMR serves as one of the major analytical approaches of the decade in metabolomic study, producing information-rich, highly reliable and reproducible data set in non-targeted or global and multivariate statistical analysis. Recently, NMR is successfully being used to characterize wine and find an association of wine metabolite with environmental and fermentative factors in vineyard and making wine. This review describes important analytical features and recent applications in/of NMR-based metabolomics in wine science.
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Affiliation(s)
- Young-Shick Hong
- Laboratoire d'Oenology et Chimie Appliquée, URVVC, UFR Sciences Exactes et Naturelles, Reims, France.
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