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Pandian K, Matsui M, Hankemeier T, Ali A, Okubo-Kurihara E. Advances in single-cell metabolomics to unravel cellular heterogeneity in plant biology. PLANT PHYSIOLOGY 2023; 193:949-965. [PMID: 37338502 PMCID: PMC10517197 DOI: 10.1093/plphys/kiad357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/03/2023] [Accepted: 05/17/2023] [Indexed: 06/21/2023]
Abstract
Single-cell metabolomics is a powerful tool that can reveal cellular heterogeneity and can elucidate the mechanisms of biological phenomena in detail. It is a promising approach in studying plants, especially when cellular heterogeneity has an impact on different biological processes. In addition, metabolomics, which can be regarded as a detailed phenotypic analysis, is expected to answer previously unrequited questions which will lead to expansion of crop production, increased understanding of resistance to diseases, and in other applications as well. In this review, we will introduce the flow of sample acquisition and single-cell techniques to facilitate the adoption of single-cell metabolomics. Furthermore, the applications of single-cell metabolomics will be summarized and reviewed.
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Affiliation(s)
- Kanchana Pandian
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Minami Matsui
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Emiko Okubo-Kurihara
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
- College of Science, Rikkyo University, Tokyo 171-8501, Japan
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Long ZG, Le JV, Katz BB, Lopez BG, Tenenbaum ED, Semmling B, Schmidt RJ, Grün F, Butts CT, Martin RW. Spatially resolved detection of small molecules from press-dried plant tissue using MALDI imaging. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11539. [PMID: 37915436 PMCID: PMC10617318 DOI: 10.1002/aps3.11539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 11/03/2023]
Abstract
Premise Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a chemical imaging method that can visualize spatial distributions of particular molecules. Plant tissue imaging has so far mostly used cryosectioning, which can be impractical for the preparation of large-area imaging samples, such as full flower petals. Imaging unsectioned plant tissue presents its own difficulties in extracting metabolites to the surface due to the waxy cuticle. Methods We address this by using established delipidation techniques combined with a solvent vapor extraction prior to applying the matrix with many low-concentration sprays. Results Using this procedure, we imaged tissue from three different plant species (two flowers and one carnivorous plant leaf). Material factorization analysis of the resulting data reveals a wide range of plant-specific small molecules with varying degrees of localization to specific portions of the tissue samples, while facilitating detection and removal of signal from background sources. Conclusions This work demonstrates applicability of MALDI-MSI to press-dried plant samples without freezing or cryosectioning, setting the stage for spatially resolved molecule identification. Increased mass resolution and inclusion of tandem mass spectrometry are necessary next steps to allow more specific and reliable compound identification.
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Affiliation(s)
- Zane G. Long
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
| | - Jonathan V. Le
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCalifornia92697‐3900USA
| | - Benjamin B. Katz
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
| | - Belen G. Lopez
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
| | | | - Bonnie Semmling
- The Chrysler Herbarium and Mycological Collection, School of Environmental and Biological SciencesRutgers UniversityNew BrunswickNew Jersey08901USA
| | - Ryan J. Schmidt
- Department of Ecology, Evolution, and Natural ResourcesRutgers UniversityNew BrunswickNew Jersey08901USA
| | - Felix Grün
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
| | - Carter T. Butts
- Departments of Sociology, Statistics, Computer Science, and Electrical Engineering and Computer ScienceUniversity of CaliforniaIrvineCalifornia92697USA
| | - Rachel W. Martin
- Department of ChemistryUniversity of CaliforniaIrvineCalifornia92697‐2025USA
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCalifornia92697‐3900USA
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Chen J, Li P, Han Y, Li Y, Du Y. Highly photoluminescent nitrogen-doped carbon quantum dots as a green fluorescence probe for determination of myricetin. Food Chem 2023; 417:135920. [PMID: 36933427 DOI: 10.1016/j.foodchem.2023.135920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023]
Abstract
Highly photoluminescent N-doped carbon quantum dots (N-CDs) which the quantum yield reached 63% were prepared through hydrothermal treatment. The obtained N-CDs displayed a uniform distribution of particle size, superior stability in high-salt conditions, and excellent sensitivity. A green fluorescence probe based on N-CDs was constructed for ultrasensitive determination of myricetin in vine tea on account of the static quenching. The N-CDs presented excellent linear fluorescence response in the concentration range of 0.2-40 μM and 56-112 μM and with a low detection limit of 56 nM. Additionally, the practicability of the probe was verified in spiked vine tea sample, and the satisfactory recoveries of myricetin varied from 98.8% to 101.2%, with relative standard deviations in the range of 1.52%-3.48%. It is the first time to employ N-CDs without any material modification as a fluorescence sensor to detect myricetin, which is a promising approach to expand the path for myricetin screening.
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Affiliation(s)
- Jingjing Chen
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Peipei Li
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yixiu Han
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yuchen Li
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yingxiang Du
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing 210009, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, PR China.
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Araujo dos Santos N, Kerpel dos Santos M, Almirall J, Romão W. Cannabinomics studies – A review from colorimetric tests to modern analytical techniques: Part II. Forensic Chem 2023. [DOI: 10.1016/j.forc.2023.100477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Yamagaki T, Osawa T, Fujikawa K, Watanabe T, Sugahara K. Multimatrix Variation Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry as a Tool for Determining the Bonding of Nitrogen Atoms in Alkaloids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2243-2249. [PMID: 36379021 PMCID: PMC9732872 DOI: 10.1021/jasms.2c00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/18/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
The reactivity of alkaloids in dehydrogenation was investigated using multimatrix variation matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of over 20 different alkaloids with six matrices. The dehydrogenated molecular ions [M - H]+ generated by in-source decay were detected in the MALDI mass spectra of some types of alkaloids such as reserpine. The dehydrogenation proceeded at the cyclic tertiary amine rather than double-bonded nitrogen atoms and indole rings involved in the electron-delocalized systems. The stable protonated primary amines hindered dehydrogenation. The laser-induced dehydrogenation correlated with the chemical properties and structures of alkaloids. Alkaloids were classified into three types by the ratio of dehydrogenation by comparing the relative abundances of [M - H]+, [M]•+, and [M + H]+ ions in α-cyano-4-hydroxycinnamic acid and 5-formylsalicylic acid matrices. Structural isomers were also discriminated by this method of analyzing the three molecular ions' ratio using multimatrix variation MALDI-MS.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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Yamagaki T, Sugahara K, Fujikawa K, Washida K. Fragmentation and Ionization Efficiency of Positional and Functional Isomers of Paeoniflorin Derivatives in Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Mass Spectrom (Tokyo) 2022; 11:A0101. [PMID: 35291502 PMCID: PMC8900252 DOI: 10.5702/massspectrometry.a0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/17/2021] [Indexed: 11/28/2022] Open
Abstract
Paeoniflorin and albiflorin, which are functional isomers, are the major constituents of an herbal medicine derived from Paeonia lactiflora. Those functional isomers and their galloylated derivatives, which are positional isomers, were studied by matrix-assisted laser desorption/ionization–tandem mass spectrometry (MALDI-MS/MS). The resulting mass spectra are discussed based on the fragmentation patterns of the sodium adducts. The product ion spectra of 4-O-galloylalbiflorin and 4′-O-galloylpaeoniflorin differed, even though they were positional isomers. The fragmentations of the ester parts were influenced by the neighboring hydroxyl groups. The ionization efficiency of the sodium adduct of albiflorin was higher than that for paeoniflorin. These results indicate that the carboxylic ester group has a higher affinity for sodium ions than the acetal group, which can be attributed to the carbonyl oxygen being negatively polarized, allowing it to function as a Lewis base.
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Affiliation(s)
- Tohru Yamagaki
- Suntory Institute for Bioorganic Research, Suntory Foundation of Life Sciences
| | - Kohtaro Sugahara
- Suntory Institute for Bioorganic Research, Suntory Foundation of Life Sciences
| | - Kohki Fujikawa
- Suntory Institute for Bioorganic Research, Suntory Foundation of Life Sciences
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A comprehensive review on innovative and advanced stabilization approaches of anthocyanin by modifying structure and controlling environmental factors. Food Chem 2021; 366:130611. [PMID: 34388403 DOI: 10.1016/j.foodchem.2021.130611] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 12/27/2022]
Abstract
Anthocyanins are pigments abundant in fruits and vegetables, and commonly applied in foods due to attractive colour and health-promoting benefits. However, instability of anthocyanins leads to their easy degradation, reduced bioactivity, and colour fading in food processing, limiting their application and causing economic losses. Stability of anthocyanins depends on their own structures and environmental factors. For structural factors, modification including copigmentation, acylation and biosynthesis is a potential solution to increase anthocyanin stability due to forming stable structures. With regard to environmental factors, encapsulation such as microencapsulation, liposome and nanoparticles has been shown effectively to enhance the stability. We proposed the potential challenges and perspectives for the diversification of anthocyanin-rich products for food application, particularly, introduction of hazards, technical limitations, interaction with other ingredients in food system and exploration of pyranoanthocyanins. The integrated strategies are warranted for improving anthocyanin stabilization for promoting their further application in food industry.
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Mizuno T, Sugahara K, Tsutsumi C, Iino M, Koi S, Noda N, Iwashina T. Identification of anthocyanin and other flavonoids from the green-blue petals of Puya alpestris (Bromeliaceae) and a clarification of their coloration mechanism. PHYTOCHEMISTRY 2021; 181:112581. [PMID: 33246305 DOI: 10.1016/j.phytochem.2020.112581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/19/2020] [Accepted: 11/01/2020] [Indexed: 06/11/2023]
Abstract
To understand the unique green-blue color of Puya alpestris (Bromeliaceae) flowers, we investigated their constituent anthocyanin and related compounds. An anthocyanin, two undescribed flavonols, and two flavones were isolated and identified as delphinidin 3,3',5'-tri-O-β-glucopyranoside, myricetin 3-O-[α-rhamnopyranosyl-(1 → 6)-β-glucopyranoside]-3',5'-di-O-β-glucopyranoside, myricetin 3,3',5'-tri-O-β-glucopyranoside, luteolin 4'-O-glucoside, and apigenin 4'-O-glucoside. Furthermore, the presence of chlorophyll has also been revealed. P. alpestris petals show a gradient color appearance: Green-blue at the tip and blue at the base. This color difference between the tip and base was used to analyze the pigment components underlying the green-blue color expression. It was found that the petal tip contains the anthocyanin, flavonols, flavones, and chlorophyll in high quantities. Furthermore, the pH of petal juice was 6.2 and 5.6 at the tip and base, respectively. In vitro reconstruction revealed the blue color expression occurred via an intermolecular copigmentation between the anthocyanin and flavones, as well as yellow color expression, which was due to an increase in the absorption at 400-450 nm of the flavonols under the higher pH conditions. Furthermore, we found that the petal extract obtaining using 50% acetone containing chlorophyll showed the same absorption spectrum as that observed for the raw petal. These results indicate that the green-blue color of P. alpestris flowers is developed via an intermolecular co-pigmentation of the anthocyanin (delphinidin 3,3',5'-tri-O-β-glucopyranoside) with flavones, such as luteolin 4'-O-glucoside, the yellow color expression of flavonols, such as myricetin 3,3',5'-tri-O-glucoside under relatively high pH conditions in the cell sap, and the presence of chlorophyll.
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Affiliation(s)
- Takayuki Mizuno
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan.
| | - Kohtaro Sugahara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Soraku-gun, Kyoto, 619-0284, Japan
| | - Chie Tsutsumi
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Moritoshi Iino
- Botanical Gardens, Graduate School of Science, Osaka City University, Katano, Osaka, Japan
| | - Satoshi Koi
- Botanical Gardens, Graduate School of Science, Osaka City University, Katano, Osaka, Japan
| | - Naonobu Noda
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, 305-0852, Japan
| | - Tsukasa Iwashina
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
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de Souza LP, Borghi M, Fernie A. Plant Single-Cell Metabolomics-Challenges and Perspectives. Int J Mol Sci 2020; 21:E8987. [PMID: 33256100 PMCID: PMC7730874 DOI: 10.3390/ijms21238987] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Omics approaches for investigating biological systems were introduced in the mid-1990s and quickly consolidated to become a fundamental pillar of modern biology. The idea of measuring the whole complement of genes, transcripts, proteins, and metabolites has since become widespread and routinely adopted in the pursuit of an infinity of scientific questions. Incremental improvements over technical aspects such as sampling, sensitivity, cost, and throughput pushed even further the boundaries of what these techniques can achieve. In this context, single-cell genomics and transcriptomics quickly became a well-established tool to answer fundamental questions challenging to assess at a whole tissue level. Following a similar trend as the original development of these techniques, proteomics alternatives for single-cell exploration have become more accessible and reliable, whilst metabolomics lag behind the rest. This review summarizes state-of-the-art technologies for spatially resolved metabolomics analysis, as well as the challenges hindering the achievement of sensu stricto metabolome coverage at the single-cell level. Furthermore, we discuss several essential contributions to understanding plant single-cell metabolism, finishing with our opinion on near-future developments and relevant scientific questions that will hopefully be tackled by incorporating these new exciting technologies.
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Affiliation(s)
- Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
| | - Monica Borghi
- Department of Biology, Utah State University, 1435 Old Main Hill, Logan, UT 84322, USA;
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
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Kim J, Pälijärvi M, Karonen M, Salminen JP. Distribution of enzymatic and alkaline oxidative activities of phenolic compounds in plants. PHYTOCHEMISTRY 2020; 179:112501. [PMID: 32877871 DOI: 10.1016/j.phytochem.2020.112501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
In this study, we screened 287 plant tissue samples from 175 plant species for their phenolic profiles. The samples were oxidized enzymatically in planta or at high pH in vitro to determine how these two oxidative conditions would alter the initial polyphenol profiles of the plant. Compounds that contained a pyrogallol or dihydroxyphenethyl group were highly active at pH 10. Enzymatic oxidation favored compounds that contained a catechol group, whereas compounds containing a pyrogallol group or monohydroxysubstituted phenolic moieties at most were oxidized less frequently. This study gives a broad overview of the distribution and alkaline oxidative activities of water-soluble phenolic compounds in plants as well as the enzymatic oxidative activities of various plant tissues.
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Affiliation(s)
- Jorma Kim
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014, Turku, Finland.
| | - Maija Pälijärvi
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014, Turku, Finland.
| | - Maarit Karonen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014, Turku, Finland.
| | - Juha-Pekka Salminen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, FI-20014, Turku, Finland.
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