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Horn PJ, Chapman KD. Imaging plant metabolism in situ. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1654-1670. [PMID: 37889862 PMCID: PMC10938046 DOI: 10.1093/jxb/erad423] [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: 07/13/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023]
Abstract
Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.
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Affiliation(s)
- Patrick J Horn
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
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Ma X, Fernández FM. Advances in mass spectrometry imaging for spatial cancer metabolomics. MASS SPECTROMETRY REVIEWS 2024; 43:235-268. [PMID: 36065601 PMCID: PMC9986357 DOI: 10.1002/mas.21804] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 05/09/2023]
Abstract
Mass spectrometry (MS) has become a central technique in cancer research. The ability to analyze various types of biomolecules in complex biological matrices makes it well suited for understanding biochemical alterations associated with disease progression. Different biological samples, including serum, urine, saliva, and tissues have been successfully analyzed using mass spectrometry. In particular, spatial metabolomics using MS imaging (MSI) allows the direct visualization of metabolite distributions in tissues, thus enabling in-depth understanding of cancer-associated biochemical changes within specific structures. In recent years, MSI studies have been increasingly used to uncover metabolic reprogramming associated with cancer development, enabling the discovery of key biomarkers with potential for cancer diagnostics. In this review, we aim to cover the basic principles of MSI experiments for the nonspecialists, including fundamentals, the sample preparation process, the evolution of the mass spectrometry techniques used, and data analysis strategies. We also review MSI advances associated with cancer research in the last 5 years, including spatial lipidomics and glycomics, the adoption of three-dimensional and multimodal imaging MSI approaches, and the implementation of artificial intelligence/machine learning in MSI-based cancer studies. The adoption of MSI in clinical research and for single-cell metabolomics is also discussed. Spatially resolved studies on other small molecule metabolites such as amino acids, polyamines, and nucleotides/nucleosides will not be discussed in the context.
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Affiliation(s)
- Xin Ma
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
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3
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Liang Q, Mondal P, Li Q, Maqbool T, Zhao C, Jiang D, Szulczewski GJ, Wijeratne GB. Nitro Indole Derivatives as Novel Dual-Polarity Matrices for MALDI Mass Spectrometry and Imaging with Broad Applications. Anal Chem 2024; 96:1668-1677. [PMID: 38226847 DOI: 10.1021/acs.analchem.3c04684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
A new matrix framework is presented in this study for the improved ionization efficiency of complex mixtures by matrix-assisted laser desorption ionization (MALDI) mass spectrometry/imaging. Five nitro indole (NI) derivatives [3-methyl-4-nitro-1H-indole (3,4-MNI), 3-methyl-6-nitro-1H-indole (3,6-MNI), 2,3-dimethyl-4-nitro-1H-indole (2,3,4-DMNI), 2,3-dimethyl-6-nitro-1H-indole (2,3,6-DMNI), and 4-nitro-1H-indole (4-NI)] were synthesized and shown to produce both positive and negative ions with a broad class of analytes as MALDI matrices. NI matrices were compared to several common matrices, such as 2,5-dihydroxybenzoic acid (DHB), alpha-cyano-4-hydroxylcinnamic acid (CHCA), sinapinic acid (SA), 1,5-diaminonaphthelene (1,5-DAN), and 9-aminoacridine (9-AA), for the analysis of lipid, peptide, protein, glycan, and perfluorooctanesulfonic acid (PFOS) compounds. 3,4-MNI demonstrated the best performance among the NI matrices. This matrix resulted in reduced ion suppression and better detection sensitivity for complex mixtures, for example, egg lipids/milk proteins/PFOS in tap water, while 2,3,6-DMNI was the best matrix for blueberry tissue imaging. Several important aspects of this work are reported: (1) dual-polarity ion production with NI matrices and complex mixtures; (2) quantitative analysis of PFOS with a LOQ of 0.5 ppb in tap water and 0.05 ppb in MQ water (without solid phase extraction enrichment), with accuracy and precision within 5%; (3) MALDI imaging with 2,3,6-DMNI as a matrix for plant metabolite/lipid identification with ionization enhancement in the negative ion mode m/z 600-900 region; and (4) development of a thin film deposition under/above tissue method for MALDI imaging with a vacuum sublimation matrix on a high-vacuum MALDI instrument.
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Affiliation(s)
- Qiaoli Liang
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Pritam Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Qi Li
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Tahir Maqbool
- Department of Civil, Construction and Environmental Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Chao Zhao
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Daqian Jiang
- Department of Civil, Construction and Environmental Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Greg J Szulczewski
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Gayan B Wijeratne
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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Li H, Zhang S, Zhao Y, He J, Chen X. Identification of raffinose family oligosaccharides in processed Rehmannia glutinosa Libosch using matrix-assisted laser desorption/ionization mass spectrometry image combined with machine learning. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9635. [PMID: 37817339 DOI: 10.1002/rcm.9635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/07/2023] [Accepted: 08/20/2023] [Indexed: 10/12/2023]
Abstract
RATIONALE Currently, research on oligosaccharides primarily focuses on the physiological activity and function, with a few studies elaborating on the spatial distribution characterization and variation in the processing of Rehmannia glutinosa Libosch. Thus, imaging the spatial distributions and dynamic changes in oligosaccharides during the steaming process is significant for characterizing the metabolic networks of R. glutinosa. It will be beneficial to characterize the impact of steaming on the active ingredients and distribution patterns in different parts of the plant. METHODS A highly sensitive matrix-assisted laser desorption/ionization mass spectrometry image (MALDI-MSI) method was used to visualize the spatial distribution of oligosaccharides in processed R. glutinosa. Furthermore, machine learning was used to distinguish the processed R. glutinosa samples obtained under different steaming conditions. RESULTS Imaging results showed that the oligosaccharides in the fresh R. glutinosa were mainly distributed in the cortex and xylem. As steaming progressed, the tetra- and pentasaccharides were hydrolyzed and diffused gradually into the tissue section. MALDI-MS profiling combined with machine learning was used to identify the processed R. glutinosa samples accurately at different steaming intervals. Eight algorithms were used to build classification machine learning models, which were evaluated for accuracy, precision, recall, and F1 score. The linear discriminant analysis and random forest models performed the best, with prediction accuracies of 0.98 and 0.97, respectively, and thus can be considered for identifying the steaming durations of R. glutinosa. CONCLUSIONS MALDI-MSI combined with machine learning can be used to visualize the distribution of oligosaccharides and identify the processed samples after steaming for different durations. This can enhance our understanding of the metabolic changes that occur during the steaming process of R. glutinosa; meanwhile, it is expected to provide a theoretical reference for the standardization and modernization of processing in the field of medicinal plants.
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Affiliation(s)
- Huizhi Li
- Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences, Shandong University of Traditional Chinese Medicine, Jinan, China
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Shishan Zhang
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yanfang Zhao
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Jixiang He
- Department of Pharmaceutical Analysis, School of Pharmaceutical Sciences, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiangfeng Chen
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
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Chen Y, Liu Y, Li X, He Y, Li W, Peng Y, Zheng J. Recent Advances in Mass Spectrometry-Based Spatially Resolved Molecular Imaging of Drug Disposition and Metabolomics. Drug Metab Dispos 2023; 51:1273-1283. [PMID: 37295949 DOI: 10.1124/dmd.122.001069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/04/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Mass spectrometric imaging is a nontargeted, tag-free, high-throughput, and highly responsive analytical approach. The highly accurate molecular visualization detection technology enables qualitative and quantitative analyses of biologic tissues or cells scanned by mass spectrometry in situ, extracting known and unknown multiple compounds, and simultaneously assessing relative contents of targeting molecules by monitoring their molecular ions and pinpointing the spatial locations of those molecules distributed. Five mass spectrometric imaging techniques and their characteristics are introduced in the review, including matrix-assisted laser desorption ionization mass spectrometry, secondary ion mass spectrometry, desorption electrospray ionization mass spectrometry, laser ablation electrospray ionization mass spectrometry, and laser ablation inductively coupled plasma mass spectrometry. The mass spectrometry-based techniques provide the possibility for spatial metabolomics with the capability of high throughput and precision detection. The approaches have been widely employed to spatially image not only metabolome of endogenous amino acids, peptides, proteins, neurotransmitters, and lipids but also the disposition of exogenous chemicals, such as pharmaceutical agents, environmental pollutants, toxicants, natural products, and heavy metals. The techniques also provide us with spatial distribution imaging of analytes in single cells, tissue microregions, organs, and whole animals. SIGNIFICANCE STATEMENT: The review article includes an overview of five commonly used mass spectrometers for spatial imaging and describes the advantages and disadvantages of each. Examples of the technology applications cover drug disposition, diseases, and omics. Technical aspects of relative and absolute quantification by mass spectrometric imaging and challenges for future new applications are discussed as well. The reviewed knowledge may benefit the development of new drugs and provide a better understanding of biochemical processes related to physiology and diseases.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ximei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Yan He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Weiwei Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Ying Peng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
| | - Jiang Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Key Laboratory of Pharmaceutics of Guizhou Province, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); School of Basic Medicine, School of Pharmacy, Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C., Y.L., X.L., Y.H., W.L.); Division of Pain Management, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China (Y.C.); and Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, P.R. China (Y.P., J.Z.)
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Göldner V, Quach L, Adhitama E, Behrens A, Junk L, Winter M, Placke T, Glorius F, Karst U. Laser desorption/ionization-mass spectrometry for the analysis of interphases in lithium ion batteries. iScience 2023; 26:107517. [PMID: 37636078 PMCID: PMC10448071 DOI: 10.1016/j.isci.2023.107517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/17/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
Laser desorption/ionization-mass spectrometry (LDI-MS) is introduced as a complementary technique for the analysis of interphases formed at electrode|electrolyte interfaces in lithium ion batteries (LIBs). An understanding of these interphases is crucial for designing interphase-forming electrolyte formulations and increasing battery lifetime. Especially organic species are analyzed more effectively using LDI-MS than with established methodologies. The combination with trapped ion mobility spectrometry and tandem mass spectrometry yields additional structural information of interphase components. Furthermore, LDI-MS imaging reveals the lateral distribution of compounds on the electrode surface. Using the introduced methods, a deeper understanding of the mechanism of action of the established solid electrolyte interphase-forming electrolyte additive 3,4-dimethyloxazolidine-2,5-dione (Ala-N-CA) for silicon/graphite anodes is obtained, and active electrochemical transformation products are unambiguously identified. In the future, LDI-MS will help to provide a deeper understanding of interfacial processes in LIBs by using it in a multimodal approach with other surface analysis methods to obtain complementary information.
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Affiliation(s)
- Valentin Göldner
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
- International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Linda Quach
- International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstraße 40, 48149 Münster, Germany
- Institute of Organic Chemistry, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Egy Adhitama
- International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstraße 40, 48149 Münster, Germany
- MEET Battery Research Center, Institute of Physical Chemistry, University of Münster, Corrensstaße 46, 48149 Münster, Germany
| | - Arne Behrens
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
- Bruker Daltonics GmbH & Co. KG, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Luisa Junk
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Martin Winter
- International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstraße 40, 48149 Münster, Germany
- MEET Battery Research Center, Institute of Physical Chemistry, University of Münster, Corrensstaße 46, 48149 Münster, Germany
- Helmholtz Institute Münster, IEK-12, Forschungszentrum Jülich GmbH, Corrensstraße 46, 48149 Münster, Germany
| | - Tobias Placke
- International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstraße 40, 48149 Münster, Germany
- MEET Battery Research Center, Institute of Physical Chemistry, University of Münster, Corrensstaße 46, 48149 Münster, Germany
| | - Frank Glorius
- International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstraße 40, 48149 Münster, Germany
- Institute of Organic Chemistry, University of Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
- International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstraße 40, 48149 Münster, Germany
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Borisjuk L, Horn P, Chapman K, Jakob PM, Gündel A, Rolletschek H. Seeing plants as never before. THE NEW PHYTOLOGIST 2023; 238:1775-1794. [PMID: 36895109 DOI: 10.1111/nph.18871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/06/2023] [Indexed: 05/04/2023]
Abstract
Imaging has long supported our ability to understand the inner life of plants, their development, and response to a dynamic environment. While optical microscopy remains the core tool for imaging, a suite of novel technologies is now beginning to make a significant contribution to visualize plant metabolism. The purpose of this review was to provide the scientific community with an overview of current imaging methods, which rely variously on either nuclear magnetic resonance (NMR), mass spectrometry (MS) or infrared (IR) spectroscopy, and to present some examples of their application in order to illustrate their utility. In addition to providing a description of the basic principles underlying these technologies, the review discusses their various advantages and limitations, reveals the current state of the art, and suggests their potential application to experimental practice. Finally, a view is presented as to how the technologies will likely develop, how these developments may encourage the formulation of novel experimental strategies, and how the enormous potential of these technologies can contribute to progress in plant science.
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Affiliation(s)
- Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Patrick Horn
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Kent Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Peter M Jakob
- Institute of Experimental Physics 5, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Andre Gündel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
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Guo L, Chao H, Yin Y, Li H, Wang H, Zhao W, Hou D, Zhang L, Zhang C, Li M. New insight into the genetic basis of oil content based on noninvasive three-dimensional phenotyping and tissue-specific transcriptome in Brassica napus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:88. [PMID: 37221547 DOI: 10.1186/s13068-023-02324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
BACKGROUND Increasing seed oil content is the most important breeding goal in Brassica napus, and phenotyping is crucial to dissect its genetic basis in crops. To date, QTL mapping for oil content has been based on whole seeds, and the lipid distribution is far from uniform in different tissues of seeds in B. napus. In this case, the phenotype based on whole seeds was unable to sufficiently reveal the complex genetic characteristics of seed oil content. RESULTS Here, the three-dimensional (3D) distribution of lipid was determined for B. napus seeds by magnetic resonance imaging (MRI) and 3D quantitative analysis, and ten novel oil content-related traits were obtained by subdividing the seeds. Based on a high-density genetic linkage map, 35 QTLs were identified for 4 tissues, the outer cotyledon (OC), inner cotyledon (IC), radicle (R) and seed coat (SC), which explained up to 13.76% of the phenotypic variation. Notably, 14 tissue-specific QTLs were reported for the first time, 7 of which were novel. Moreover, haplotype analysis showed that the favorable alleles for different seed tissues exhibited cumulative effects on oil content. Furthermore, tissue-specific transcriptomes revealed that more active energy and pyruvate metabolism influenced carbon flow in the IC, OC and R than in the SC at the early and middle seed development stages, thus affecting the distribution difference in oil content. Combining tissue-specific QTL mapping and transcriptomics, 86 important candidate genes associated with lipid metabolism were identified that underlie 19 unique QTLs, including the fatty acid synthesis rate-limiting enzyme-related gene CAC2, in the QTLs for OC and IC. CONCLUSIONS The present study provides further insight into the genetic basis of seed oil content at the tissue-specific level.
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Affiliation(s)
- Liangxing Guo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongbo Chao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yongtai Yin
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Huaixin Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Weiguo Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Yangling, 712100, China
| | - Dalin Hou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Chunyu Zhang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Lin J, Yang S, Ji J, Xiang P, Wu L, Chen H. Natural or artificial: An example of topographic spatial distribution analysis of mescaline in cactus plants by matrix-assisted laser desorption/ionization mass spectrometry imaging. FRONTIERS IN PLANT SCIENCE 2023; 14:1066595. [PMID: 36844095 PMCID: PMC9950628 DOI: 10.3389/fpls.2023.1066595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Differentiating whether plant products are natural or artificial is of great importance in many practical fields, including forensic science, food safety, cosmetics, and fast-moving consumer goods. Information about the topographic distribution of compounds is an important criterion for answering this question. However, of equal importance is the likelihood that topographic spatial distribution information may provide important and valuable information for molecular mechanism study. METHODS In this study, we took mescaline, a substance with hallucinogenic properties in cacti of the species Trichocereus pachanoi and Lophophora williamsii, as an example to characterize the spatial distribution of mescaline in plants and flowers by liquid chromatograph-mass spectrometry-matrix-assisted laser desorption/ionization mass spectrometry imaging at the macroscopic, tissue structure, and even cellular levels. RESULTS According to our results, the distribution of mescaline in natural plant was concentrated on the active meristems, epidermal tissues, and protruding parts of Trichocereus pachanoi and Lophophora williamsii, while artificially spiked Lophophora diffusa products showed no such difference in their topographic spatial distribution. DISCUSSION This difference in distribution pattern allowed us to distinguish between flowers that could synthesize mescaline on their own and those that had been artificially spiked with mescaline. The interesting topographic spatial distribution results, such as the overlap of the mescaline distribution map and micrographs of the vascular bundles, were consistent with the synthesis and transport theory of mescaline, indicating the potential for applying matrix-assisted laser desorption/ionization mass spectrometry imaging in botanical research.
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10
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Zhang YX, Zhang YD, Shi YP. Tracking Spatial Distribution Alterations of Multiple Endogenous Molecules during Lentil Germination by MALDI Mass Spectrometry Imaging. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2124-2133. [PMID: 36652673 DOI: 10.1021/acs.jafc.2c07513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Exploring the spatial distribution alterations of metabolites during lentil germination is essential to reveal the nutritional value, physiological function, and metabolic pathway in lentils. Hence, an effective matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) method was established for the first time to visualize the spatial localization changes of 53 metabolites in lentils during germination for 12-72 h. The results of MALDI-MSI analysis showed that phosphatidylinositols, phosphatidylethanolamines, phosphatidylglycerols, and phosphatidic acids were mainly located in the cotyledons of lentils throughout the germination process, while triacylglycerols, phosphatidylcholines, diacylglycerols, amino acids, choline, and spermine spread throughout the lentil tissue at the initial stage of germination and gradually presented obvious distribution characteristics in the radicle with increasing germination time. Heat map analysis was used to visualize the correlations between lipid content changes and germination time, which supported the use of germinated lentils as nutraceutical or functional food.
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Affiliation(s)
- Yan-Xia Zhang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Chinese Academy of Sciences, Lanzhou Institute of Chemical Physics, Lanzhou 730000, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yi-Da Zhang
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Chinese Academy of Sciences, Lanzhou Institute of Chemical Physics, Lanzhou 730000, P. R. China
| | - Yan-Ping Shi
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Chinese Academy of Sciences, Lanzhou Institute of Chemical Physics, Lanzhou 730000, P. R. China
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11
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Differential distribution of phytochemicals in Scutellariae Radix and Scutellariae Amoenae Radix using microscopic mass spectrometry imaging. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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12
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Zhao B, Luo Z, Zhang H, Zhang H. Imaging tools for plant nanobiotechnology. Front Genome Ed 2022; 4:1029944. [PMID: 36569338 PMCID: PMC9772283 DOI: 10.3389/fgeed.2022.1029944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The successful application of nanobiotechnology in biomedicine has greatly changed the traditional way of diagnosis and treating of disease, and is promising for revolutionizing the traditional plant nanobiotechnology. Over the past few years, nanobiotechnology has increasingly expanded into plant research area. Nanomaterials can be designed as vectors for targeted delivery and controlled release of fertilizers, pesticides, herbicides, nucleotides, proteins, etc. Interestingly, nanomaterials with unique physical and chemical properties can directly affect plant growth and development; improve plant resistance to disease and stress; design as sensors in plant biology; and even be used for plant genetic engineering. Similarly, there have been concerns about the potential biological toxicity of nanomaterials. Selecting appropriate characterization methods will help understand how nanomaterials interact with plants and promote advances in plant nanobiotechnology. However, there are relatively few reviews of tools for characterizing nanomaterials in plant nanobiotechnology. In this review, we present relevant imaging tools that have been used in plant nanobiotechnology to monitor nanomaterial migration, interaction with and internalization into plants at three-dimensional lengths. Including: 1) Migration of nanomaterial into plant organs 2) Penetration of nanomaterial into plant tissues (iii)Internalization of nanomaterials by plant cells and interactions with plant subcellular structures. We compare the advantages and disadvantages of current characterization tools and propose future optimal characterization methods for plant nanobiotechnology.
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Affiliation(s)
- Bin Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
| | - Zhongxu Luo
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,Department of Chemistry, College of Chemistry and Materials Science, Jinan University, Guangzhou, China
| | - Honglu Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China,*Correspondence: Honglu Zhang, ; Huan Zhang,
| | - Huan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China,*Correspondence: Honglu Zhang, ; Huan Zhang,
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Ma T, Sun C, Han Y, Guo L, Huang L, Wang X. Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Reveals “Spatial-Temporal-Content” Changes of Parishins in Gastrodiae Rhizoma during the Steaming Process. Food Res Int 2022; 162:112092. [DOI: 10.1016/j.foodres.2022.112092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/18/2022] [Accepted: 10/28/2022] [Indexed: 11/05/2022]
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14
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Walton CL, Khalid M, Bible AN, Kertesz V, Retterer ST, Morrell-Falvey J, Cahill JF. In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1615-1625. [PMID: 35904879 DOI: 10.1021/jasms.2c00081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The plant rhizosphere is a complex and dynamic chemical environment where the exchange of molecular signals between plants, microbes, and fungi drives the development of the entire biological system. Exogenous compounds in the rhizosphere are known to affect plant-microbe organization, interactions between organisms, and ultimately, growth and survivability. The function of exogenous compounds in the rhizosphere is still under much investigation, specifically with respect to their roles in plant growth and development, the assembly of the associated microbial community, and the spatiotemporal distribution of molecular components. A major challenge for spatiotemporal measurements is developing a nondisruptive and nondestructive technique capable of analyzing the exogenous compounds contained within the environment. A methodology using liquid microjunction-surface sampling probe-mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes was developed for in situ, spatiotemporal measurement of amino acids (AAs) from bacterial biofilms and plant roots. Exuded arginine was measured from a living Pantoea YR343 biofilm, which resulted in a chemical image indicative of biofilm growth within the device. Spot sampling along the roots of Populus trichocarpa with the LMJ-SSP-MS resulted in the detection of 15 AAs. Variation in AA concentrations across the root system was observed, indicating that exudation is not homogeneous and may be linked to local rhizosphere architecture and different biological processes along the root.
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Affiliation(s)
- Courtney L Walton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Muneeba Khalid
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Amber N Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Vilmos Kertesz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Scott T Retterer
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Jennifer Morrell-Falvey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
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Jayapal PK, Joshi R, Sathasivam R, Van Nguyen B, Faqeerzada MA, Park SU, Sandanam D, Cho BK. Non-destructive measurement of total phenolic compounds in Arabidopsis under various stress conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:982247. [PMID: 36119609 PMCID: PMC9478847 DOI: 10.3389/fpls.2022.982247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Quantifying the phenolic compounds in plants is essential for maintaining the beneficial effects of plants on human health. Existing measurement methods are destructive and/or time consuming. To overcome these issues, research was conducted to develop a non-destructive and rapid measurement of phenolic compounds using hyperspectral imaging (HSI) and machine learning. In this study, the Arabidopsis was used since it is a model plant. They were grown in controlled and various stress conditions (LED lights and drought). Images were captured using HSI in the range of 400-1,000 nm (VIS/NIR) and 900-2,500 nm (SWIR). Initially, the plant region was segmented, and the spectra were extracted from the segmented region. These spectra were synchronized with plants' total phenolic content reference value, which was obtained from high-performance liquid chromatography (HPLC). The partial least square regression (PLSR) model was applied for total phenolic compound prediction. The best prediction values were achieved with SWIR spectra in comparison with VIS/NIR. Hence, SWIR spectra were further used. Spectral dimensionality reduction was performed based on discrete cosine transform (DCT) coefficients and the prediction was performed. The results were better than that of obtained with original spectra. The proposed model performance yielded R 2-values of 0.97 and 0.96 for calibration and validation, respectively. The lowest standard errors of predictions (SEP) were 0.05 and 0.07 mg/g. The proposed model out-performed different state-of-the-art methods. These demonstrate the efficiency of the model in quantifying the total phenolic compounds that are present in plants and opens a way to develop a rapid measurement system.
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Affiliation(s)
- Praveen Kumar Jayapal
- Department of Biosystems Machinery Engineering, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
- Disruptive and Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology (SMART), Singapore, Singapore
| | - Rahul Joshi
- Department of Biosystems Machinery Engineering, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
| | - Ramaraj Sathasivam
- Department of Crop Science, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
| | - Bao Van Nguyen
- Department of Crop Science, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
| | - Mohammad Akbar Faqeerzada
- Department of Biosystems Machinery Engineering, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
| | - Sang Un Park
- Department of Crop Science, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon, South Korea
| | - Domnic Sandanam
- Department of Computer Applications, National Institute of Technology, Tiruchirappalli, India
| | - Byoung-Kwan Cho
- Department of Biosystems Machinery Engineering, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon, South Korea
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Dong S, Zhang Y, Guo X, Zhang C, Wang Z, Yu J, Liu Y, Li C, Hu Y, Sun B, Sun M, Zhang H, Ouyang D, He Z, Wang Y. Glutathione Pulse Therapy: Promote Spatiotemporal Delivery of Reduction-Sensitive Nanoparticles at the "Cellular Level" and Synergize PD-1 Blockade Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202744. [PMID: 35896947 PMCID: PMC9507359 DOI: 10.1002/advs.202202744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Spatiotemporal delivery of nanoparticles (NPs) at the "cellular level" is critical for nanomedicine, which is expected to deliver as much cytotoxic drug into cancer cells as possible when NPs accumulate in tumors. However, macrophages and cancer-associated fibroblasts (CAFs) that are present within tumors limit the efficiency of spatiotemporal delivery. To overcome this limitation, glutathion pulse therapy is designed to promote reduction-sensitive Larotaxel (LTX) prodrug NPs to escape the phagocytosis of macrophages and penetrate through the stromal barrier established by CAFs in the murine triple negative breast cancer model. This therapy improves the penetration of NPs in tumor tissues as well as the accumulation of LTX in cancer cells, and remodels the immunosuppressive microenvironment to synergize PD-1 blockade therapy. More importantly, a method is established that can directly observe the biodistribution of NPs between different cells in vivo to accurately quantify the target drugs accumulated in these cells, thereby advancing the spatiotemporal delivery research of NPs at the "cellular level."
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Affiliation(s)
- Songtao Dong
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Yuan Zhang
- School of PharmacyChina Medical UniversityShenyang110122China
| | - Xiangnan Guo
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Chuang Zhang
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Zhaomeng Wang
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Jiang Yu
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Yubo Liu
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Chang Li
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Yuting Hu
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Bingjun Sun
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Mengchi Sun
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Haotian Zhang
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Defang Ouyang
- State Key Laboratory of Quality Research in Chinese MedicineInstitute of Chinese Medical Sciences (ICMS)University of MacauMacau999078China
| | - Zhonggui He
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
| | - Yongjun Wang
- Department of PharmaceuticsWuya College of InnovationShenyang Pharmaceutical UniversityShenyang110016China
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Mugume Y, Ding G, Dueñas ME, Liu M, Lee YJ, Nikolau BJ, Bassham DC. Complex Changes in Membrane Lipids Associated with the Modification of Autophagy in Arabidopsis. Metabolites 2022; 12:metabo12020190. [PMID: 35208263 PMCID: PMC8876039 DOI: 10.3390/metabo12020190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/26/2022] [Accepted: 02/11/2022] [Indexed: 12/28/2022] Open
Abstract
Autophagy is a conserved mechanism among eukaryotes that degrades and recycles cytoplasmic components. Autophagy is known to influence the plant metabolome, including lipid content; however, its impact on the plant lipidome is not fully understood, and most studies have analyzed a single or few mutants defective in autophagy. To gain more insight into the effect of autophagy on lipid concentrations and composition, we quantitatively profiled glycerolipids from multiple Arabidopsis thaliana mutants altered in autophagy and compared them with wild-type seedlings under nitrogen replete (+N; normal growth) and nitrogen starvation (−N; autophagy inducing) conditions. Mutants include those in genes of the core autophagy pathway, together with other genes that have been reported to affect autophagy. Using Matrix-Assisted Laser Desorption/Ionization—Mass Spectrometry (MALDI-MS), we imaged the cellular distribution of specific lipids in situ and demonstrated that autophagy and nitrogen treatment did not affect their spatial distribution within Arabidopsis seedling leaves. We observed changes, both increases and decreases, in the relative amounts of different lipid species in the mutants compared to WT both in +N and −N conditions, although more changes were seen in −N conditions. The relative amounts of polyunsaturated and very long chain lipids were significantly reduced in autophagy-disrupted mutants compared to WT plants. Collectively, our results provide additional evidence that autophagy affects plant lipid content and that autophagy likely affects lipid properties such as chain length and unsaturation.
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Affiliation(s)
- Yosia Mugume
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA;
| | - Geng Ding
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (G.D.); (B.J.N.)
| | - Maria Emilia Dueñas
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA; (M.E.D.); (Y.-J.L.)
| | - Meiling Liu
- Department of Statistics, Iowa State University, Ames, IA 50011, USA;
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Young-Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA; (M.E.D.); (Y.-J.L.)
| | - Basil J. Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (G.D.); (B.J.N.)
- Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA;
- Correspondence: ; Tel.: +1-515-294-7461
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18
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Jiang H, Zhang Y, Liu Z, Wang X, He J, Jin H. Advanced applications of mass spectrometry imaging technology in quality control and safety assessments of traditional Chinese medicines. JOURNAL OF ETHNOPHARMACOLOGY 2022; 284:114760. [PMID: 34678417 PMCID: PMC9715987 DOI: 10.1016/j.jep.2021.114760] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 05/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional Chinese medicines (TCMs) have made great contributions to the prevention and treatment of human diseases in China, and especially in cases of COVID-19. However, due to quality problems, the lack of standards, and the diversity of dosage forms, adverse reactions to TCMs often occur. Moreover, the composition of TCMs makes them extremely challenging to extract and isolate, complicating studies of toxicity mechanisms. AIM OF THE REVIEW The aim of this paper is therefore to summarize the advanced applications of mass spectrometry imaging (MSI) technology in the quality control, safety evaluations, and determination of toxicity mechanisms of TCMs. MATERIALS AND METHODS Relevant studies from the literature have been collected from scientific databases, such as "PubMed", "Scifinder", "Elsevier", "Google Scholar" using the keywords "MSI", "traditional Chinese medicines", "quality control", "metabolomics", and "mechanism". RESULTS MSI is a new analytical imaging technology that can detect and image the metabolic changes of multiple components of TCMs in plants and animals in a high throughput manner. Compared to other chemical analysis methods, such as liquid chromatography-mass spectrometry (LC-MS), this method does not require the complex extraction and separation of TCMs, and is fast, has high sensitivity, is label-free, and can be performed in high-throughput. Combined with chemometrics methods, MSI can be quickly and easily used for quality screening of TCMs. In addition, this technology can be used to further focus on potential biomarkers and explore the therapeutic/toxic mechanisms of TCMs. CONCLUSIONS As a new type of analysis method, MSI has unique advantages to metabolic analysis, quality control, and mechanisms of action explorations of TCMs, and contributes to the establishment of quality standards to explore the safety and toxicology of TCMs.
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Affiliation(s)
- Haiyan Jiang
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yaxin Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhigang Liu
- School of Biological Science and Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xiangyi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing 100050, China.
| | - Hongtao Jin
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China; Beijing Union-Genius Pharmaceutical Technology Development Co., Ltd., Beijing 100176, China; NMPA Key Laboratory for Safety Research and Evaluation of Innovative Drug, Beijing 100050, China.
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Hu C, Luo W, Xu J, Han X. RECOGNITION AND AVOIDANCE OF ION SOURCE-GENERATED ARTIFACTS IN LIPIDOMICS ANALYSIS. MASS SPECTROMETRY REVIEWS 2022; 41:15-31. [PMID: 32997818 PMCID: PMC8287896 DOI: 10.1002/mas.21659] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/24/2020] [Accepted: 08/31/2020] [Indexed: 05/04/2023]
Abstract
Lipid research is attracting more and more attention as various key roles and novel biological functions of lipids have been demonstrated and discovered in the organism. Mass spectrometry (MS)-based lipidomics approaches are the most powerful and effective tools for analysis of cellular lipidomes with very high sensitivity and specificity. However, the artifacts generated from in-source fragmentation are always present in all kinds of ion sources, even soft ionization techniques (i.e., electrospray ionization and matrix-assisted laser desorption/ionization [MALDI]). These artifacts can cause many problems for lipidomics, especially when the fragment ions correspond to/are isomeric species of other endogenous lipid species in complex biological samples. These commonly observed artifacts could lead to misannotation, false identification, and consequently, incorrect attribution of phenotypes, and will have negative impact on any MS-based lipidomics research including but not limited to biomarker discovery, drug development, etc. Liquid chromatography-MS, shotgun lipidomics, and MALDI-MS imaging are three representative lipidomics approaches in which ion source-generated artifacts are all manifested and are comprehensively summarized in this article. The strategies on how to avoid/reduce the artifacts of in-source fragmentation on lipidomics analysis are also discussed in detail. We believe that with the recognition and avoidance of ion source-generated artifacts, MS-based lipidomics approaches will provide better accuracy on comprehensive analysis of biological samples and will make greater contribution to the research on metabolism and translational/precision medicine (collectively termed functional lipidomics). © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Changfeng Hu
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Wenqing Luo
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Jie Xu
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003 China
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 USA
- Department of Medicine – Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 USA
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Lohse M, Haag R, Lippold E, Vetterlein D, Reemtsma T, Lechtenfeld OJ. Direct Imaging of Plant Metabolites in the Rhizosphere Using Laser Desorption Ionization Ultra-High Resolution Mass Spectrometry. FRONTIERS IN PLANT SCIENCE 2021; 12:753812. [PMID: 34925405 PMCID: PMC8678481 DOI: 10.3389/fpls.2021.753812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
The interplay of rhizosphere components such as root exudates, microbes, and minerals results in small-scale gradients of organic molecules in the soil around roots. The current methods for the direct chemical imaging of plant metabolites in the rhizosphere often lack molecular information or require labeling with fluorescent tags or isotopes. Here, we present a novel workflow using laser desorption ionization (LDI) combined with mass spectrometric imaging (MSI) to directly analyze plant metabolites in a complex soil matrix. Undisturbed samples of the roots and the surrounding soil of Zea mays L. plants from either field- or laboratory-scale experiments were embedded and cryosectioned to 100 μm thin sections. The target metabolites were detected with a spatial resolution of 25 μm in the root and the surrounding soil based on accurate masses using ultra-high mass resolution laser desorption ionization Fourier-transform ion cyclotron resonance mass spectrometry (LDI-FT-ICR-MS). Using this workflow, we could determine the rhizosphere gradients of a dihexose (e.g., sucrose) and other plant metabolites (e.g., coumaric acid, vanillic acid). The molecular gradients for the dihexose showed a high abundance of this metabolite in the root and a strong depletion of the signal intensity within 150 μm from the root surface. Analyzing several sections from the same undisturbed soil sample allowed us to follow molecular gradients along the root axis. Benefiting from the ultra-high mass resolution, isotopologues of the dihexose could be readily resolved to enable the detection of stable isotope labels on the compound level. Overall, the direct molecular imaging via LDI-FT-ICR-MS allows for the first time a non-targeted or targeted analysis of plant metabolites in undisturbed soil samples, paving the way to study the turnover of root-derived organic carbon in the rhizosphere with high chemical and spatial resolution.
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Affiliation(s)
- Martin Lohse
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
| | - Rebecca Haag
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Ansbach University of Applied Sciences, Ansbach, Germany
| | - Eva Lippold
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
- Soil Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thorsten Reemtsma
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- Institute of Analytical Chemistry, University of Leipzig, Leipzig, Germany
| | - Oliver J. Lechtenfeld
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
- ProVIS – Centre for Chemical Microscopy, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
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21
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Johnson AR, Moghe GD, Frank MH. Growing a glue factory: Open questions in laticifer development. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102096. [PMID: 34461600 DOI: 10.1016/j.pbi.2021.102096] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/25/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Latex-containing cells called laticifers are present in at least 41 flowering plant families and are thought to have convergently evolved at least 12 times. These cells are known to function in defense, but little is known about the molecular genetic mechanisms of their development. The expansion of laticifers into their distinctive tube shape can occur through two distinct mechanisms, cell fusion and intrusive growth. The mechanism and extent of intrusive laticifer growth are still being investigated. Hormonal regulation by jasmonic acid and ethylene is important for both laticifer differentiation and latex biosynthesis. Current evidence suggests that laticifers can be specified independently of latex production, but extensive latex production requires specified laticifers. Laticifers are an emerging system for studying the intersection of cell identity specification and specialized metabolism.
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Affiliation(s)
- Arielle R Johnson
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Margaret H Frank
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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22
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Matrix-Free High-Resolution Atmospheric-Pressure SALDI Mass Spectrometry Imaging of Biological Samples Using Nanostructured DIUTHAME Membranes. Metabolites 2021; 11:metabo11090624. [PMID: 34564440 PMCID: PMC8468348 DOI: 10.3390/metabo11090624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 01/06/2023] Open
Abstract
Applications of mass spectrometry imaging (MSI), especially matrix-assisted laser desorption/ionization (MALDI) in the life sciences are becoming increasingly focused on single cell analysis. With the latest instrumental developments, pixel sizes in the micrometer range can be obtained, leading to challenges in matrix application, where imperfections or inhomogeneities in the matrix layer can lead to misinterpretation of MS images. Thereby, the application of premanufactured, homogeneous ionization-assisting devices is a promising approach. Tissue sections were investigated using a matrix-free imaging technique (Desorption Ionization Using Through-Hole Alumina Membrane, DIUTHAME) based on premanufactured nanostructured membranes to be deposited on top of a tissue section, in comparison to the spray-coating of an organic matrix in a MALDI MSI approach. Atmospheric pressure MALDI MSI ion sources were coupled to orbital trapping mass spectrometers. MS signals obtained by the different ionization techniques were annotated using accurate-mass-based database research. Compared to MALDI MSI, DIUTHAME MS images captivated with higher signal homogeneities, higher contrast and reduced background signals, while signal intensities were reduced by about one order of magnitude, independent of analyte class. DIUTHAME membranes, being applicable only on tissue sections thicker than 50 µm, were successfully used for mammal, insect and plant tissue with a high lateral resolution down to 5 µm.
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23
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Wang Y, Hummon AB. MS imaging of multicellular tumor spheroids and organoids as an emerging tool for personalized medicine and drug discovery. J Biol Chem 2021; 297:101139. [PMID: 34461098 PMCID: PMC8463860 DOI: 10.1016/j.jbc.2021.101139] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
MS imaging (MSI) is a powerful tool in drug discovery because of its ability to interrogate a wide range of endogenous and exogenous molecules in a broad variety of samples. The impressive versatility of the approach, where almost any ionizable biomolecule can be analyzed, including peptides, proteins, lipids, carbohydrates, and nucleic acids, has been applied to numerous types of complex biological samples. While originally demonstrated with harvested organs from animal models and biopsies from humans, these models are time consuming and expensive, which makes it necessary to extend the approach to 3D cell culture systems. These systems, which include spheroid models, prepared from immortalized cell lines, and organoid cultures, grown from patient biopsies, can provide insight on the intersection of molecular information on a spatial scale. In particular, the investigation of drug compounds, their metabolism, and the subsequent distribution of their metabolites in 3D cell culture systems by MSI has been a promising area of study. This review summarizes the different ionization methods, sample preparation steps, and data analysis methods of MSI and focuses on several of the latest applications of MALDI-MSI for drug studies in spheroids and organoids. Finally, the application of this approach in patient-derived organoids to evaluate personalized medicine options is discussed.
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Affiliation(s)
- Yijia Wang
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA.
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24
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Righetti L, Bhandari DR, Rolli E, Tortorella S, Bruni R, Dall’Asta C, Spengler B. Mycotoxin Uptake in Wheat - Eavesdropping Fusarium Presence for Priming Plant Defenses or a Trojan Horse to Weaken Them? FRONTIERS IN PLANT SCIENCE 2021; 12:711389. [PMID: 34381485 PMCID: PMC8350570 DOI: 10.3389/fpls.2021.711389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Fusarium mycotoxins represent a major threat for cereal crops and food safety. While previous investigations have described plant biotransforming properties on mycotoxins or metabolic relapses of fungal infections in plants, so far, the potential consequences of radical exposure in healthy crops are mostly unknown. Therefore, we aimed at evaluating whether the exposure to mycotoxins, deoxynivalenol (DON) and zearalenone (ZEN), at the plant-soil interface may be considered a form of biotic stress capable of inducing priming or a potential initiation of fungal attack. To address this, we used atmospheric-pressure scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging to investigate the activation or the inhibition of specific biosynthetic pathways and in situ localization of primary and secondary metabolites in wheat. According to our untargeted metabolomics investigation, the translocation of plant defense metabolites (i.e., hydroxycinnamic acid amide and flavones) follows the mycotoxin accumulation organs, which is the root for ZEN-treated plantlet and culm for DON-treated sample, suggesting a local "defense-on-demand response." Therefore, it can be hypothesized that DON and ZEN are involved in the eavesdropping of Fusarium presence in soil and that wheat response based on secondary metabolites may operate on multiple organs with a potential interplay that involves masked mycotoxins.
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Affiliation(s)
- Laura Righetti
- Department of Food and Drug, University of Parma, Parma, Italy
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Dhaka Ram Bhandari
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Enrico Rolli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Renato Bruni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Giessen, Germany
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25
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Medeiros DB, Brotman Y, Fernie AR. The utility of metabolomics as a tool to inform maize biology. PLANT COMMUNICATIONS 2021; 2:100187. [PMID: 34327322 PMCID: PMC8299083 DOI: 10.1016/j.xplc.2021.100187] [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: 01/12/2021] [Revised: 03/26/2021] [Accepted: 04/19/2021] [Indexed: 05/04/2023]
Abstract
With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).
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Affiliation(s)
- David B. Medeiros
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
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26
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Komkleow S, Niyomploy P, Sangvanich P. Maldi-mass Spectrometry Imaging for Phytoalexins Detection in RD6 Thai Rice. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821040074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth 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 2016. 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. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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28
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In Situ Localization of Plant Lipid Metabolites by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI). Methods Mol Biol 2021. [PMID: 34047991 DOI: 10.1007/978-1-0716-1362-7_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has emerged as a major analytical platform for the determination and localization of lipid metabolites directly from tissue sections. Unlike analysis of lipid extracts, where lipid localizations are lost due to homogenization and/ or solvent extraction, MALDI-MSI analysis is capable of revealing spatial localization of metabolites while simultaneously collecting high chemical resolution mass spectra. Important considerations for obtaining high quality MALDI-MS images include tissue preservation, section preparation, MS data collection and data processing. Errors in any of these steps can lead to poor quality metabolite images and increases the chance for metabolite misidentification and/ or incorrect localization. Here, we present detailed methods and recommendations for specimen preparation, MALDI-MS instrument parameters, software analysis platforms for data processing, and practical considerations for each of these steps to ensure acquisition of high-quality chemical and spatial resolution data for reconstructing MALDI-MS images of plant tissues.
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29
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Dokwal D, Romsdahl TB, Kunz DA, Alonso AP, Dickstein R. Phosphorus deprivation affects composition and spatial distribution of membrane lipids in legume nodules. PLANT PHYSIOLOGY 2021; 185:1847-1859. [PMID: 33793933 PMCID: PMC8133537 DOI: 10.1093/plphys/kiaa115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/13/2020] [Indexed: 05/12/2023]
Abstract
In legumes, symbiotic nitrogen (N) fixation (SNF) occurs in specialized organs called nodules after successful interactions between legume hosts and rhizobia. In a nodule, N-fixing rhizobia are surrounded by symbiosome membranes, through which the exchange of nutrients and ammonium occurs between bacteria and the host legume. Phosphorus (P) is an essential macronutrient, and N2-fixing legumes have a higher requirement for P than legumes grown on mineral N. As in the previous studies, in P deficiency, barrel medic (Medicago truncatula) plants had impaired SNF activity, reduced growth, and accumulated less phosphate in leaves, roots, and nodules compared with the plants grown in P sufficient conditions. Membrane lipids in M. truncatula tissues were assessed using electrospray ionization-mass spectrometry. Galactolipids were found to increase in P deficiency, with declines in phospholipids (PL), especially in leaves. Lower PL losses were found in roots and nodules. Subsequently, matrix-assisted laser desorption/ionization-mass spectrometry imaging was used to spatially map the distribution of the positively charged phosphatidylcholine (PC) species in nodules in both P-replete and P-deficient conditions. Our results reveal heterogeneous distribution of several PC species in nodules, with homogeneous distribution of other PC classes. In P poor conditions, some PC species distributions were observed to change. The results suggest that specific PC species may be differentially important in diverse nodule zones and cell types, and that membrane lipid remodeling during P stress is not uniform across the nodule.
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Affiliation(s)
- Dhiraj Dokwal
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 USA
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203 USA
| | - Trevor B Romsdahl
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 USA
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203 USA
| | - Daniel A Kunz
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 USA
| | - Ana Paula Alonso
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 USA
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203 USA
| | - Rebecca Dickstein
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203 USA
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203 USA
- Author for communication:
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30
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Taylor M, Lukowski JK, Anderton CR. Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:872-894. [PMID: 33656885 PMCID: PMC8033567 DOI: 10.1021/jasms.0c00439] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 05/02/2023]
Abstract
Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.
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Affiliation(s)
- Michael
J. Taylor
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jessica K. Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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31
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Zhang JJ, Yang H. Advance in Methodology and Strategies To Unveil Metabolic Mechanisms of Pesticide Residues in Food Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2658-2667. [PMID: 33645212 DOI: 10.1021/acs.jafc.0c08122] [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] [Indexed: 06/12/2023]
Abstract
Pesticide residues are a food safety concern. A good detection method is critical for rapid and accurate determination of pesticide metabolites in crops and studying metabolism. The pretreatment methods have mainly been ultrasonic extraction-solid-phase extraction and QuEChERS, while detection methods have been radio-chromatography, nuclear magnetic resonance, and mass spectrometry. This perspective briefed the progress of analytical methods used for studying pesticide transformation in crops over the past decade. With the combination of the characteristics of the pesticide molecular structure and the transformation principles of pesticides in crops, we presented specific methods for elucidating new metabolites and the approaches to identify metabolites using multi-high-resolution mass spectrometry.
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Affiliation(s)
- Jing Jing Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan 450002, People's Republic of China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China
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32
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Romsdahl TB, Kambhampati S, Koley S, Yadav UP, Alonso AP, Allen DK, Chapman KD. Analyzing Mass Spectrometry Imaging Data of 13C-Labeled Phospholipids in Camelina sativa and Thlaspi arvense (Pennycress) Embryos. Metabolites 2021; 11:metabo11030148. [PMID: 33806402 PMCID: PMC7999836 DOI: 10.3390/metabo11030148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
The combination of 13C-isotopic labeling and mass spectrometry imaging (MSI) offers an approach to analyze metabolic flux in situ. However, combining isotopic labeling and MSI presents technical challenges ranging from sample preparation, label incorporation, data collection, and analysis. Isotopic labeling and MSI individually create large, complex data sets, and this is compounded when both methods are combined. Therefore, analyzing isotopically labeled MSI data requires streamlined procedures to support biologically meaningful interpretations. Using currently available software and techniques, here we describe a workflow to analyze 13C-labeled isotopologues of the membrane lipid and storage oil lipid intermediate―phosphatidylcholine (PC). Our results with embryos of the oilseed crops, Camelina sativa and Thlaspi arvense (pennycress), demonstrated greater 13C-isotopic labeling in the cotyledons of developing embryos compared with the embryonic axis. Greater isotopic enrichment in PC molecular species with more saturated and longer chain fatty acids suggest different flux patterns related to fatty acid desaturation and elongation pathways. The ability to evaluate MSI data of isotopically labeled plant embryos will facilitate the potential to investigate spatial aspects of metabolic flux in situ.
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Affiliation(s)
- Trevor B. Romsdahl
- Department of Biological Sciences & BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; (T.B.R.); (U.P.Y.); (A.P.A.)
| | | | - Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (S.K.); (S.K.)
| | - Umesh P. Yadav
- Department of Biological Sciences & BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; (T.B.R.); (U.P.Y.); (A.P.A.)
| | - Ana Paula Alonso
- Department of Biological Sciences & BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; (T.B.R.); (U.P.Y.); (A.P.A.)
| | - Doug K. Allen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (S.K.); (S.K.)
- United States Department of Agriculture, Agriculture Research Service, St. Louis, MO 63132, USA
- Correspondence: (D.K.A.); or (K.D.C.); Tel.: +1-940-565-2969 (K.D.C.)
| | - Kent D. Chapman
- Department of Biological Sciences & BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; (T.B.R.); (U.P.Y.); (A.P.A.)
- Correspondence: (D.K.A.); or (K.D.C.); Tel.: +1-940-565-2969 (K.D.C.)
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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Müller MA, Kompauer M, Strupat K, Heiles S, Spengler B. Implementation of a High-Repetition-Rate Laser in an AP-SMALDI MSI System for Enhanced Measurement Performance. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:465-472. [PMID: 33370109 DOI: 10.1021/jasms.0c00368] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging is a promising tool in the life sciences for obtaining spatial and chemical information from complex biological samples. State-of-the-art setups combine high mass resolution and high mass accuracy with high lateral resolution, offering untargeted insights into biochemical processes on the single-cell length scale. Despite recent technological breakthroughs, the sensitivity and acquisition speed of many setups are often in competition with achievable pixel resolutions below 25 μm. New measurement modes were developed by implementing a high-repetition-rate laser into an AP-SMALDI10 ion source, coupled to an orbital trapping mass spectrometer. These new MSI modes allow for a modular use of the new setup. We demonstrate that the system allows single cell features to be visualized in mouse brain tissue sections at a pixel resolution of 5 μm and an imaging speed of 18 pixels/s. Furthermore, the analytical sensitivity was improved in another measurement mode by applying multiple pulses of a highly focused laser beam over larger square pixels ≥25 μm edge length, increasing ion signal intensities up to 20-fold on tissue and decreasing the limit of detection by 1 order of magnitude.
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Affiliation(s)
- Max A Müller
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Mario Kompauer
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Kerstin Strupat
- Thermo Fisher Scientific (Bremen) GmbH, 28199 Bremen, Germany
| | - Sven Heiles
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
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Villate A, San Nicolas M, Gallastegi M, Aulas PA, Olivares M, Usobiaga A, Etxebarria N, Aizpurua-Olaizola O. Review: Metabolomics as a prediction tool for plants performance under environmental stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110789. [PMID: 33487364 DOI: 10.1016/j.plantsci.2020.110789] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/30/2020] [Accepted: 12/05/2020] [Indexed: 05/05/2023]
Abstract
Metabolomics as a diagnosis tool for plant performance has shown good features for breeding and crop improvement. Additionally, due to limitations in land area and the increasing climate changes, breeding projects focusing on abiotic stress tolerance are becoming essential. Nowadays no universal method is available to identify predictive metabolic markers. As a result, research aims must dictate the best method or combination of methods. To this end, we will introduce the key aspects to consider regarding growth scenarios and sampling strategies and discuss major analytical and data treatment approaches that are available to find metabolic markers of plant performance.
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Affiliation(s)
- Aitor Villate
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
| | - Markel San Nicolas
- Dinafem Seeds (Pot Sistemak S.L.), 20018, San Sebastian, Basque Country, Spain; Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Sovereign Fields S.L., 20006, San Sebastian, Basque Country, Spain
| | - Mara Gallastegi
- Dinafem Seeds (Pot Sistemak S.L.), 20018, San Sebastian, Basque Country, Spain; Sovereign Fields S.L., 20006, San Sebastian, Basque Country, Spain
| | - Pierre-Antoine Aulas
- Dinafem Seeds (Pot Sistemak S.L.), 20018, San Sebastian, Basque Country, Spain; Sovereign Fields S.L., 20006, San Sebastian, Basque Country, Spain
| | - Maitane Olivares
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Aresatz Usobiaga
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Nestor Etxebarria
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain; Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Oier Aizpurua-Olaizola
- Dinafem Seeds (Pot Sistemak S.L.), 20018, San Sebastian, Basque Country, Spain; Sovereign Fields S.L., 20006, San Sebastian, Basque Country, Spain.
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Hayashi Y, Ohuchi M, Ryu S, Yagishita S, Hamada A. A procedure for method development and protein binding ratio as the indicator of sensitivity with anticancer agents on MALDI mass spectrometry imaging. Drug Metab Pharmacokinet 2021; 38:100385. [PMID: 33878680 DOI: 10.1016/j.dmpk.2021.100385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/21/2020] [Accepted: 01/20/2021] [Indexed: 01/02/2023]
Abstract
The concentration and distribution of a drug and its metabolites in tissues are key factors for elucidating both drug efficacy and toxicity in drug development. In this study we developed a pharamaco-imaging procedure for 12 agents and investigated the relationship between the properties of target compounds and the sensitivities of detection in matrix-assisted laser desorption/ionization-mass spectrometer imaging (MALDI-MSI). We prepared mock samples with mouse liver homogenates diluted with gelatin solution, limit of detection concentrations of each compound was confirmed. The correlation was evaluated between the intensities of mass signals obtained in MALDI-MSI with each test compound (the intensities of the test compounds) at a consistent concentration and the properties of each test compound. The liver homogenate diluted with gelatin solution showed easier handling and lower coefficients of variation than did liver homogenate only, and can be used as a good surrogate matrix. Based on the analysis of 12 agents, the protein binding ratios showed significant correlation to the detection sensitivities. We presented a procedure for standardization of pharmaco-imaging method development with an in-tissue method using MALDI-MS. Our results indicated the correlation between test compound's sensitivity and their protein binding ratios in plasma or serum.
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Affiliation(s)
- Yoshiharu Hayashi
- Division of Molecular Pharmacology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan; Department of Medical Oncology and Translational Research, Graduate School of Medical and Pharmaceutical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan; Bioanalysis Research Department, CMIC Pharma Science Co., Ltd., 17-18 Nakahata-cho,Nishiwaki, Hyogo, 677-0032, Japan
| | - Mayu Ohuchi
- Division of Molecular Pharmacology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan; Department of Medical Oncology and Translational Research, Graduate School of Medical and Pharmaceutical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Shoraku Ryu
- Division of Molecular Pharmacology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shigehiro Yagishita
- Division of Molecular Pharmacology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akinobu Hamada
- Division of Molecular Pharmacology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan; Department of Medical Oncology and Translational Research, Graduate School of Medical and Pharmaceutical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan.
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Wang T, Lee HK, Yue GGL, Chung ACK, Lau CBS, Cai Z. A novel binary matrix consisting of graphene oxide and caffeic acid for the analysis of scutellarin and its metabolites in mouse kidney by MALDI imaging. Analyst 2021; 146:289-295. [PMID: 33140762 DOI: 10.1039/d0an01539c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although the in vivo metabolic pathways of scutellarin, a traditional Chinese medicine, have been investigated via different liquid chromatography techniques, studies on the distribution and location of scutellarin within organ tissue sections have not been reported. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can generate in situ spatial distribution profiles for scutellarin and its metabolites in a kidney section. However, the direct detection of a small molecule (m/z < 600) using conventional matrices often results in ion suppression and matrix interferences. In this study, we demonstrated a novel methodology using MALDI-MSI for the in situ spatial localization of scutellarin and its metabolites in kidney tissues by applying a binary matrix of graphene oxide (GO) and caffeic acid (CA). The results indicated that the binary matrix (GO/CA) significantly improved the detection efficiency of scutellarin and its metabolites with relatively high sensitivity, selectivity and reproducibility on tissue sections. This methodology was successfully applied to map scutellarin and its metabolites with MALDI-MSI in mouse kidney tissues. Specifically, scutellarin and scutellarein were found to be located in the cortex and medulla regions of the kidney with relatively high abundance, whereas the remaining metabolites appeared in the cortex with low abundance. We believe that the novel imaging methodology may also be used for the studies of cancerous tissues and inform the development of the future therapies of kidney tumors.
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Affiliation(s)
- Tao Wang
- Department of Chemistry and State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China.
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Jarvis BA, Romsdahl TB, McGinn MG, Nazarenus TJ, Cahoon EB, Chapman KD, Sedbrook JC. CRISPR/Cas9-Induced fad2 and rod1 Mutations Stacked With fae1 Confer High Oleic Acid Seed Oil in Pennycress ( Thlaspi arvense L.). FRONTIERS IN PLANT SCIENCE 2021; 12:652319. [PMID: 33968108 PMCID: PMC8100250 DOI: 10.3389/fpls.2021.652319] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/23/2021] [Indexed: 05/05/2023]
Abstract
Pennycress (Thlaspi arvense L.) is being domesticated as an oilseed cash cover crop to be grown in the off-season throughout temperate regions of the world. With its diploid genome and ease of directed mutagenesis using molecular approaches, pennycress seed oil composition can be rapidly tailored for a plethora of food, feed, oleochemical and fuel uses. Here, we utilized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology to produce knockout mutations in the FATTY ACID DESATURASE2 (FAD2) and REDUCED OLEATE DESATURATION1 (ROD1) genes to increase oleic acid content. High oleic acid (18:1) oil is valued for its oxidative stability that is superior to the polyunsaturated fatty acids (PUFAs) linoleic (18:2) and linolenic (18:3), and better cold flow properties than the very long chain fatty acid (VLCFA) erucic (22:1). When combined with a FATTY ACID ELONGATION1 (fae1) knockout mutation, fad2 fae1 and rod1 fae1 double mutants produced ∼90% and ∼60% oleic acid in seed oil, respectively, with PUFAs in fad2 fae1 as well as fad2 single mutants reduced to less than 5%. MALDI-MS spatial imaging analyses of phosphatidylcholine (PC) and triacylglycerol (TAG) molecular species in wild-type pennycress embryo sections from mature seeds revealed that erucic acid is highly enriched in cotyledons which serve as storage organs, suggestive of a role in providing energy for the germinating seedling. In contrast, PUFA-containing TAGs are enriched in the embryonic axis, which may be utilized for cellular membrane expansion during seed germination and seedling emergence. Under standard growth chamber conditions, rod1 fae1 plants grew like wild type whereas fad2 single and fad2 fae1 double mutant plants exhibited delayed growth and overall reduced heights and seed yields, suggesting that reducing PUFAs below a threshold in pennycress had negative physiological effects. Taken together, our results suggest that combinatorial knockout of ROD1 and FAE1 may be a viable route to commercially increase oleic acid content in pennycress seed oil whereas mutations in FAD2 will likely require at least partial function to avoid fitness trade-offs.
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Affiliation(s)
- Brice A. Jarvis
- School of Biological Sciences, Illinois State University, Normal, IL, United States
| | - Trevor B. Romsdahl
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Michaela G. McGinn
- School of Biological Sciences, Illinois State University, Normal, IL, United States
| | - Tara J. Nazarenus
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Edgar B. Cahoon
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kent D. Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - John C. Sedbrook
- School of Biological Sciences, Illinois State University, Normal, IL, United States
- *Correspondence: John C. Sedbrook,
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Dong Y, Sonawane P, Cohen H, Polturak G, Feldberg L, Avivi SH, Rogachev I, Aharoni A. High mass resolution, spatial metabolite mapping enhances the current plant gene and pathway discovery toolbox. THE NEW PHYTOLOGIST 2020; 228:1986-2002. [PMID: 32654288 DOI: 10.1111/nph.16809] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/06/2020] [Indexed: 05/21/2023]
Abstract
Understanding when and where metabolites accumulate provides important cues to the gene function. Mass spectrometry imaging (MSI) enables in situ temporal and spatial measurement of a large assortment of metabolites, providing mapping information regarding their cellular distribution. To describe the current state and technical advances using MSI in plant sciences, we employed MSI to demonstrate its significant contribution to the study of plant specialised metabolism. We show that coupling MSI with: (1) RNA interference (RNAi), (2) virus induced gene silencing (VIGS), (3) agroinfiltration or (4) samples derived from plant natural variation provides great opportunities to understand the accurate gene-metabolite relationship and discover novel gene-associated metabolites. This was exemplified in three plant species (i.e. tomato, tobacco and wheat) by mapping the distribution of metabolites possessing a range of polarities. In particular, we demonstrated that MSI is able to spatially map an entire metabolic pathway, including intermediates and final products, in the intricate biosynthetic route to tomato fruit steroidal glycoalkaloids. We therefore envisage MSI as a key component of the metabolome analysis arsenal employed in plant gene discovery strategies.
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Affiliation(s)
- Yonghui Dong
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Prashant Sonawane
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Hagai Cohen
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Guy Polturak
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Liron Feldberg
- Department of Analytical Chemistry, Israel Institute for Biological Research, Ness Ziona, 7410001, Israel
| | - Shelly Hen Avivi
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Ilana Rogachev
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 761001, Israel
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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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Fangmeyer J, Behrens A, Gleede B, Waldvogel SR, Karst U. Mass-Spectrometric Imaging of Electrode Surfaces-a View on Electrochemical Side Reactions. Angew Chem Int Ed Engl 2020; 59:20428-20433. [PMID: 33448566 PMCID: PMC7693111 DOI: 10.1002/anie.202010134] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Indexed: 12/18/2022]
Abstract
Electrochemical side reactions, often referred to as "electrode fouling", are known to be a major challenge in electro-organic synthesis and the functionality of modern batteries. Often, polymerization of one or more components is observed. When reaching their limit of solubility, those polymers tend to adsorb on the surface of the electrode, resulting in a passivation of the respective electrode area, which may impact electrochemical performance. Here, matrix-assisted laser-desorption/ionization mass spectrometry (MALDI-MS) is presented as valuable imaging technique to visualize polymer deposition on electrode surfaces. Oligomer size distribution and its dependency on the contact time were imaged on a boron-doped diamond (BDD) anode of an electrochemical flow-through cell. The approach allows to detect weak spots, where electrode fouling may take place and provides insight into the identity of side-product pathways.
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Affiliation(s)
- Jens Fangmeyer
- Institute of Inorganic and Analytical ChemistryUniversity of MünsterCorrensstrasse 3048149MünsterGermany
| | - Arne Behrens
- Institute of Inorganic and Analytical ChemistryUniversity of MünsterCorrensstrasse 3048149MünsterGermany
| | - Barbara Gleede
- Department of ChemistryJohannes Gutenberg University MainzDuesbergweg 10–1455128MainzGermany
| | - Siegfried R. Waldvogel
- Department of ChemistryJohannes Gutenberg University MainzDuesbergweg 10–1455128MainzGermany
| | - Uwe Karst
- Institute of Inorganic and Analytical ChemistryUniversity of MünsterCorrensstrasse 3048149MünsterGermany
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Understanding the Fate of Almond ( Prunus dulcis (Mill.) D.A. Webb) Oleosomes during Simulated Digestion. Nutrients 2020; 12:nu12113397. [PMID: 33167391 PMCID: PMC7694400 DOI: 10.3390/nu12113397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Almond kernels contain phytochemicals with positive health effects in relation to heart disease, diabetes and obesity. Several studies have previously highlighted that almond cell wall encapsulation during digestion and particle size are factors associated with these benefits. In the present study, we have characterized almond oleosomes, natural oil droplets abundant in plants, and we have investigated their integrity during simulated gastrointestinal digestion. Methods: Oleosomes were visualized on the almond seed surface by imaging mass spectrometry analysis, and then characterized in terms of droplet size distribution by dynamic light scattering and protein profile by liquid chromatography high-resolution tandem mass spectrometry analysis. Results: The almond oleosomes’ distribution remained monomodal after in vitro mastication, whereas gastric and duodenal digestion led to a bimodal distribution, albeit characterized mainly by a prevalent population with a droplet size decrease related to a rearrangement of the protein profile. Oleosins, structural proteins found in plant oil bodies, persisted unchanged during simulated mastication, with the appearance of new prunin isoforms after gastric and duodenal digestion. Conclusions: The rearrangement of the protein profile could limit lipid bioaccessibility. The data improve our understanding of the behavior of almond lipids during gastrointestinal digestion, and may have implications for energy intake and satiety imparted by almonds.
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Treu A, Kokesch-Himmelreich J, Walter K, Hölscher C, Römpp A. Integrating High-Resolution MALDI Imaging into the Development Pipeline of Anti-Tuberculosis Drugs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2277-2286. [PMID: 32965115 DOI: 10.1021/jasms.0c00235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Successful treatment of tuberculosis (TB) requires antibiotics to reach their intended point of action, i.e., necrotizing granulomas in the lung. MALDI mass spectrometry imaging (MSI) is able to visualize the distribution of antibiotics in tissue, but resolving the small histological structures in mice, which are most commonly used in preclinical trials, requires high spatial resolution. We developed a MALDI MSI method to image antibiotics in the mouse lung with high mass resolution (240k @ m/z 200 fwhm) and high spatial resolution (10 μm pixel size). A crucial step was to develop a cryosectioning protocol that retains the distribution of water-soluble drugs in small and fragile murine lung lobes without inflation or embedding. Choice and application of matrices were optimized to detect human-equivalent drug concentrations in tissue, and measurement parameters were optimized to detect multiple drugs in a single tissue section. We succeeded in visualizing the distribution of all current first-line anti-TB drugs (pyrazinamide, rifampicin, ethambutol, isoniazid) and the second-line drugs moxifloxacin and clofazimine. Four of these compounds were imaged for the first time in the mouse lung. Accurate mass identification was confirmed by on-tissue MS/MS. Evaluation of fragmentation pathways revealed the structure of the double-protonated molecular ion of pyrazinamide. Clofazimine was imaged for the first time with 10 μm pixel size revealing clofazimine accumulation in lipid deposits around airways. In summary, we developed a platform to resolve the detailed histology in the murine lung and to reliably detect a range of anti-TB drugs at human-equivalent doses. Our workflow is currently being employed in preclinical mouse studies to evaluate the efficacy of novel anti-TB drugs.
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Affiliation(s)
- Axel Treu
- Chair of Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Julia Kokesch-Himmelreich
- Chair of Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Kerstin Walter
- Infection Immunology, Leibniz Lung Center, Research Center Borstel, Parkallee 1-40, 23845 Borstel, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Christoph Hölscher
- Infection Immunology, Leibniz Lung Center, Research Center Borstel, Parkallee 1-40, 23845 Borstel, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Andreas Römpp
- Chair of Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
- German Center for Infection Research (DZIF), Inhoffenstraße 7, 38124 Braunschweig, Germany
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Chemical characterization, antioxidant and antimicrobial activities of açaí seed (Euterpe oleracea Mart.) extracts containing A- and B-type procyanidins. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109830] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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45
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Fangmeyer J, Behrens A, Gleede B, Waldvogel SR, Karst U. Mass‐Spectrometric Imaging of Electrode Surfaces—a View on Electrochemical Side Reactions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jens Fangmeyer
- Institute of Inorganic and Analytical Chemistry University of Münster Corrensstrasse 30 48149 Münster Germany
| | - Arne Behrens
- Institute of Inorganic and Analytical Chemistry University of Münster Corrensstrasse 30 48149 Münster Germany
| | - Barbara Gleede
- Department of Chemistry Johannes Gutenberg University Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Siegfried R. Waldvogel
- Department of Chemistry Johannes Gutenberg University Mainz Duesbergweg 10–14 55128 Mainz Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry University of Münster Corrensstrasse 30 48149 Münster Germany
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Sytar O, Zivcak M, Neugart S, Brestic M. Assessment of hyperspectral indicators related to the content of phenolic compounds and multispectral fluorescence records in chicory leaves exposed to various light environments. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:429-438. [PMID: 32912483 DOI: 10.1016/j.plaphy.2020.06.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 05/20/2023]
Abstract
Hyperspectral analysis represents a powerful technique for diagnostics of morphological and chemical information from aboveground parts of the plants, but the real potential of the method in pre-screening of phenolics in leaves is still insufficiently explored. In this study, assessment of the sensitivity and reliability of non-invasive methods of various phenolic compounds, also analyzed by HPLC in chicory plants (Cichorium intybus L.) exposed to various color light pretreatments was done. The hyperspectral records in visible and near infrared (VNIR) spectra were recorded using a handheld spectrometer and relationships between the specific hyperspectral parameters and the contents of tested phenolic compounds in chicory leaves were analyzed. Moreover, the correlations between the hyperspectral parameters and related parameters derived from the multispectral fluorescence records were assessed to compare the sensitivity of both techniques. The results indicated a relatively high correlation of anthocyanin-related parameters (ARI, mARI, mACI indices) with the content of some of tested phenolic compounds (quercetin-3-gluconuride, isorhamnetine-3-gluconuride, etc.), as well as with fluorescence ANTH index. Similar trends were observed in flavonoid parameter based on the near infra-red spectral bands (700, 760 nm), which expressed a high correlation with chlorogenic acid. On the other hand, the most frequently used flavonoid (FLAVI) indices based on UV-to-blue band reflectance showed very weak correlations with phenolic compounds, as well as with fluorescence FLAV index. The detailed analysis of the correlation between reflectance and fluorescence flavonoid parameters has shown that the parameters based on spectral reflectance are sensitive to increase of UV-absorbing compounds from low to moderate values, but, unlike the fluorescence parameter, they are not useful to recognize a further increase from middle to high or very high contents. Thus, our results outlined the possibilities, but also the limits of the use of hyperspectral analysis for rapid screening phenolic content, providing a practical evidence towards more efficient production of bioactive compounds for pharmaceutical or nutraceutical use.
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Affiliation(s)
- Oksana Sytar
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, A. Hlinku 2, 94976, Nitra, Slovak Republic; Plant Physiology and Ecology Department, Taras Shevchenko National University of Kyiv, Institute of Biology, Volodymyrskya Str., 64, Kyiv, 01033, Ukraine.
| | - Marek Zivcak
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, A. Hlinku 2, 94976, Nitra, Slovak Republic.
| | - Susanne Neugart
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany; Quality and Sensory of Plant Products, Georg-August-Universität Göttingen, Wilhelmsplatz 1, 37073, Göttingen, Germany
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, A. Hlinku 2, 94976, Nitra, Slovak Republic
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Zhou M, Gao D, Yang Z, Zhou C, Tan Y, Wang W, Jiang Y. Streaming-enhanced, chip-based biosensor with acoustically active, biomarker-functionalized micropillars: A case study of thrombin detection. Talanta 2020; 222:121480. [PMID: 33167205 DOI: 10.1016/j.talanta.2020.121480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 06/10/2020] [Accepted: 07/27/2020] [Indexed: 10/23/2022]
Abstract
Enzyme-linked immunosorbent assay is a widely used analytical technique for detecting and quantifying disease-specific protein biomarkers. Despite recent progresses in disease-specific protein biomarkers detection with microfluidic chips, many devices still suffer from the limited mass transport of target molecules, and consequently low detection efficiency or long incubation time. In this work, we present a novel strategy to significantly enhance the sensing efficiency of a chip-based biosensor by exploiting micro-streaming in an acoustofluidic device, which boosts intermolecular interactions and a hybridization chain reaction to increase the fluorescent signals. This device was made of a microfluidic chip that contains an array of PDMS micropillars in a ship-shaped microchannel. And the inner surface of the channel was functionalized with capture aptamers that bind with thrombin, chosen as a model target molecule. An ultrasonic transducer underneath the chip operating at 150 kHz generates circular micro-streaming flows around the pillars that significantly improves the binding efficiency of thrombin with capture aptamers by 1) increasing the retention time and 2) enhancing mass transport via local convection versus diffusion. The effects of ultrasound parameters, such as operating frequencies and voltages, on the distribution and magnitude of flows were optimized to obtain a better performance of the sensor chip. Under the optimized conditions, the detection limit was increased by one order of magnitude. Although this work has focused on the detection of thrombin as a model molecule, this streaming-enhanced, microstructure-based sensing strategy can be applied to detect a wide range of molecules or even cells.
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Affiliation(s)
- Min Zhou
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, 518055, China
| | - Dan Gao
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, 518055, China.
| | - Zhou Yang
- School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China
| | - Chao Zhou
- School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, 518055, China
| | - Wei Wang
- School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China.
| | - Yuyang Jiang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong, 518055, China
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Li N, Nie H, Jiang L, Ruan G, Du F, Liu H. Recent advances of ambient ionization mass spectrometry imaging in clinical research. J Sep Sci 2020; 43:3146-3163. [PMID: 32573988 DOI: 10.1002/jssc.202000273] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/03/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023]
Abstract
The structural information and spatial distribution of molecules in biological tissues are closely related to the potential molecular mechanisms of disease origin, transfer, and classification. Ambient ionization mass spectrometry imaging is an effective tool that provides molecular images while describing in situ information of biomolecules in complex samples, in which ionization occurs at atmospheric pressure with the samples being analyzed in the native state. Ambient ionization mass spectrometry imaging can directly analyze tissue samples at a fairly high resolution to obtain molecules in situ information on the tissue surface to identify pathological features associated with a disease, resulting in the wide applications in pharmacy, food science, botanical research, and especially clinical research. Herein, novel ambient ionization techniques, such as techniques based on spray and solid-liquid extraction, techniques based on plasma desorption, techniques based on laser desorption ablation, and techniques based on acoustic desorption were introduced, and the data processing of ambient ionization mass spectrometry imaging was briefly reviewed. Besides, we also highlight recent applications of this imaging technology in clinical researches and discuss the challenges in this imaging technology and the perspectives on the future of the clinical research.
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Affiliation(s)
- Na Li
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, P. R. China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Honggang Nie
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Liping Jiang
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, P. R. China
| | - Guihua Ruan
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, P. R. China
| | - Fuyou Du
- Guangxi Key Laboratory of Electrochemical and Magnetochemical Functional Materials, College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, P. R. China
- College of Biological and Environmental Engineering, Changsha University, Changsha, P. R. China
| | - Huwei Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
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Fraser PD, Aharoni A, Hall RD, Huang S, Giovannoni JJ, Sonnewald U, Fernie AR. Metabolomics should be deployed in the identification and characterization of gene-edited crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:897-902. [PMID: 31923321 DOI: 10.1111/tpj.14679] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/17/2019] [Accepted: 01/07/2020] [Indexed: 05/23/2023]
Abstract
Gene-editing techniques are currently revolutionizing biology, allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits, including disease resistance, abiotic stress tolerance, yield, nutritional quality and additional consumer traits. Unlike transgenic approaches, however, it is not facile to forensically detect gene-editing events at the molecular level, as no foreign DNA exists in the elite line. These limitations in molecular detection approaches are likely to focus more attention on the products generated from the technology than on the process in itself. Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencing as a means of characterizing new varieties generated by gene-editing techniques. Nevertheless, subtle edits such as single base changes or small deletions may be difficult to distinguish from normal variation within a genotype. Given these emerging scenarios, downstream 'omics' technologies reflective of edited affects, such as metabolomics, need to be used in a more prominent manner to fully assess compositional changes in novel foodstuffs. To achieve this goal, metabolomics or 'non-targeted metabolite analysis' needs to make significant advances to deliver greater representation across the metabolome. With the emergence of new edited crop varieties, we advocate: (i) concerted efforts in the advancement of 'omics' technologies, such as metabolomics, and (ii) an effort to redress the use of the technology in the regulatory assessment for metabolically engineered biotech crops.
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Affiliation(s)
- Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Robert D Hall
- Wageningen Research, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, the Netherlands
- Laboratory of Plant Physiology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, the Netherlands
- Netherlands Metabolomics Centre, Einsteinweg 55, Leiden, the Netherlands
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100084, China
| | - James J Giovannoni
- USDA-ARS, Robert W. Holley Center and Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Uwe Sonnewald
- Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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50
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Yang FY, Chen JH, Ruan QQ, Saqib HSA, He WY, You MS. Mass spectrometry imaging: An emerging technology for the analysis of metabolites in insects. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 103:e21643. [PMID: 31667894 DOI: 10.1002/arch.21643] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/29/2019] [Accepted: 10/14/2019] [Indexed: 05/18/2023]
Abstract
Mass spectrometry imaging (MSI) can visualize the composition, abundance, and spatial distribution of molecules in tissues or cells, which has been widely used in the research of life science. Insects, especially the agricultural pests, have received a great deal of interests from the scientists in biodiversity and food security. This review introduces the major characteristics of MSI, summarizes its application to the investigation of insect endogenous metabolites, exogenous metabolites, and the spatiotemporal changes of metabolites between insects and plants, and discusses its shortfalls and perspectives. The significance of these concerns is beneficial for future insect research such as physiology and metabolism.
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Affiliation(s)
- Fei-Ying Yang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun-Hui Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian-Qian Ruan
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hafiz S A Saqib
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Yi He
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Min-Sheng You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
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