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Vats M, Cillero-Pastor B, Cuypers E, Heeren RMA. Mass spectrometry imaging in plants, microbes, and food: a review. Analyst 2024; 149:4553-4582. [PMID: 39196541 DOI: 10.1039/d4an00644e] [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: 08/29/2024]
Abstract
Plant health, which affects the nutritional quality and safety of derivative food products, is influenced by symbiotic interactions with microorganisms. These interactions influence the local molecular profile at the tissue level. Therefore, studying the distribution of molecules within plants, microbes, and plant-based food is crucial to assess plant health, ensure the safety and quality of the agricultural products that become part of our food supply, and plan agricultural management practices. Within this framework, the molecular distribution within plant-based samples can be visualized with mass spectrometry imaging (MSI). This review describes key MSI methodologies, highlighting the role they play in unraveling the localization of metabolites, lipids, proteins, pigments, and elemental components across plants, microbes, and food products. Furthermore, investigations that involve multimodal molecular imaging approaches combining MSI with other imaging techniques are described. The advantages and limitations of the different MSI techniques that influence their applicability in diverse agro-food studies are described to enable informed choices for tailored analyses. For example, some MSI technologies involve meticulous sample preparation while others compromise spatial resolution to gain throughput. Key parameters such as sensitivity, ionization bias and fragmentation, reference database and compound class specificity are described and discussed in this review. With the ongoing refinements in instrumentation, data analysis, and integration of complementary techniques, MSI deepens our insight into the molecular biology of the agricultural ecosystem. This in turn empowers the quest for sustainable and productive agricultural practices.
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Affiliation(s)
- Mudita Vats
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
| | - Berta Cillero-Pastor
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
- MERLN Institute for Technology-inspired Regenerative Medicine, Department of Cell Biology-Inspired Tissue Engineering (cBITE), Maastricht University, Maastricht, the Netherlands
| | - Eva Cuypers
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
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2
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García-Rojas NS, Sierra-Álvarez CD, Ramos-Aboites HE, Moreno-Pedraza A, Winkler R. Identification of Plant Compounds with Mass Spectrometry Imaging (MSI). Metabolites 2024; 14:419. [PMID: 39195515 DOI: 10.3390/metabo14080419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/17/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024] Open
Abstract
The presence and localization of plant metabolites are indicative of physiological processes, e.g., under biotic and abiotic stress conditions. Further, the chemical composition of plant parts is related to their quality as food or for medicinal applications. Mass spectrometry imaging (MSI) has become a popular analytical technique for exploring and visualizing the spatial distribution of plant molecules within a tissue. This review provides a summary of mass spectrometry methods used for mapping and identifying metabolites in plant tissues. We present the benefits and the disadvantages of both vacuum and ambient ionization methods, considering direct and indirect approaches. Finally, we discuss the current limitations in annotating and identifying molecules and perspectives for future investigations.
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Affiliation(s)
- Nancy Shyrley García-Rojas
- Unidad de Genómica Avanzada, Cinvestav, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Mexico
| | | | - Hilda E Ramos-Aboites
- Unidad de Genómica Avanzada, Cinvestav, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Mexico
| | - Abigail Moreno-Pedraza
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany
| | - Robert Winkler
- Unidad de Genómica Avanzada, Cinvestav, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Mexico
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3
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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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4
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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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Choe K, Sweedler JV. Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies. Bio Protoc 2023; 13:e4862. [PMID: 37969752 PMCID: PMC10632168 DOI: 10.21769/bioprotoc.4862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 11/17/2023] Open
Abstract
High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries. Key features • Mass spectrometry analyzes a range of compounds from E. coli colonies as a proxy for liquid culture testing enzyme mutant libraries. • Colonies are transferred to a MALDI target plate by a simple imprinting method. • The screen compares the ratio among several products or searches for the qualitative presence of specific compounds. • The protocol requires a MALDI mass spectrometer.
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Affiliation(s)
- Kisurb Choe
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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6
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Van Dingenen J, De Keyser A, Desmet S, Clarysse A, Beullens S, Michiels J, Planque M, Goormachtig S. Strigolactones repress nodule development and senescence in pea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:7-22. [PMID: 37608631 DOI: 10.1111/tpj.16421] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/21/2023] [Accepted: 08/02/2023] [Indexed: 08/24/2023]
Abstract
Strigolactones are a class of phytohormones that are involved in many different plant developmental processes, including the rhizobium-legume nodule symbiosis. Although both positive and negative effects of strigolactones on the number of nodules have been reported, the influence of strigolactones on nodule development is still unknown. Here, by means of the ramosus (rms) mutants of Pisum sativum (pea) cv Terese, we investigated the impact of strigolactone biosynthesis (rms1 and rms5) and signaling (rms3 and rms4) mutants on nodule growth. The rms mutants had more red, that is, functional, and larger nodules than the wild-type plants. Additionally, the increased nitrogen fixation and senescence zones with consequently reduced meristematic and infection zones indicated that the rms nodules developed faster than the wild-type nodules. An enhanced expression of the nodule zone-specific molecular markers for meristem activity and senescence supported the enlarged, fast maturing nodules. Interestingly, the master nodulation regulator, NODULE INCEPTION, NIN, was strongly induced in nodules of all rms mutants but not prior to inoculation. Determination of sugar levels with both bulk and spatial metabolomics in roots and nodules, respectively, hints at slightly increased malic acid levels early during nodule primordia formation and reduced sugar levels at later stages, possibly the consequence of an increased carbon usage of the enlarged nodules, contributing to the enhanced senescence. Taken together, these results suggest that strigolactones regulate the development of nodules, which is probably mediated through NIN, and available plant sugars.
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Affiliation(s)
- Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Sandrien Desmet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- VIB Metabolomics Core, VIB, Technologiepark 71, 9052, Ghent, Belgium
| | - Alexander Clarysse
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Serge Beullens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Mélanie Planque
- Spatial Metabolomics Expertise Center, VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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7
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Zemaitis KJ, Lin VS, Ahkami AH, Winkler TE, Anderton CR, Veličković D. Expanded Coverage of Phytocompounds by Mass Spectrometry Imaging Using On-Tissue Chemical Derivatization by 4-APEBA. Anal Chem 2023; 95:12701-12709. [PMID: 37594382 DOI: 10.1021/acs.analchem.3c01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Probing the entirety of any species metabolome is an analytical grand challenge, especially on a cellular scale. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a common spatial metabolomics assay, but this technique has limited molecular coverage for several reasons. To expand the application space of spatial metabolomics, we developed an on-tissue chemical derivatization (OTCD) workflow using 4-APEBA for the confident identification of several dozen elusive phytocompounds. Overall, this new OTCD method enabled the annotation of roughly 280 metabolites, with only a 10% overlap in metabolic coverage when compared to analog negative ion mode MALDI-MSI on serial sections. We demonstrate that 4-APEBA outperforms other derivatization agents by providing: (1) broad specificity toward carbonyls, (2) low background, and (3) introduction of bromine isotopes. Notably, the latter two attributes also facilitate more confidence in our bioinformatics for data processing. The workflow detailed here trailblazes a path toward spatial hormonomics within plant samples, enhancing the detection of carboxylates, aldehydes, and plausibly other carbonyls. As such, several phytohormones, which have various roles within stress responses and cellular communication, can now be spatially profiled, as demonstrated in poplar root and soybean root nodule.
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Affiliation(s)
- Kevin J Zemaitis
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vivian S Lin
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Amir H Ahkami
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tanya E Winkler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher R Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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Li W, He Q, Li J, Zhou X, Hu Q, Ma C, Wang X. In Situ Self-Assembled Formation of Nitrogen-Rich Ag@Ti 3C 2 Film for Sensitive Detection and Spatial Imaging of Pesticides with Laser Desorption/Ionization Mass Spectrometry (LDI-MS). ACS APPLIED MATERIALS & INTERFACES 2023; 15:18402-18413. [PMID: 37009649 DOI: 10.1021/acsami.2c22347] [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: 06/19/2023]
Abstract
Pesticide residues are hazardous to human health; thus, developing a rapid and sensitive method for pesticide detection is an urgent need. Herein, novel nitrogen-rich Ag@Ti3C2 (Ag@N-Ti3C2) was synthesized via an ecofriendly, ultraviolet-assisted strategy, followed by in situ formation of a highly homogeneous film on target carriers via a facile water evaporation-induced self-assembly process. Ag@N-Ti3C2 shows greater surface area, electrical conductivity, and thermal conductivity than Ti3C2. This Ag@N-Ti3C2 film overcomes the limitations of conventional matrixes and allows laser desorption/ionization mass spectrometry (LDI-MS) to provide fast and high-throughput analysis of pesticides (e.g., carbendazim, thiamethoxam, propoxur, dimethoate, malathion, and cypermethrin) with ultrahigh sensitivity (detection limits of 0.5-200 ng/L), enhanced reproducibility, extremely low background, and good salt tolerance. Furthermore, the levels of pesticides were quantified with a linear range of 0-4 μg/L (R2 > 0.99). This Ag@N-Ti3C2 film was used for high-throughput analysis of pesticides spiked in traditional Chinese herbs and soft drink samples. Meanwhile, high-resolution Ag@N-Ti3C2 film-assisted LDI-MS imaging (LDI MSI) was used to successfully explore spatial distributions of xenobiotic pesticides and other endogenous small molecules (e.g., amino acids, saccharides, hormones, and saponin) in the roots of plants. This study presents the new Ag@N-Ti3C2 self-assembled film equably deposits on the ITO slides and provides a dual platform for pesticide monitoring and has the advantages of high conductivity, accuracy, simplicity, rapid analysis, minimal sample volume requirement, and an imaging function.
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Affiliation(s)
- Wenhan Li
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250014, China
| | - Qing He
- Collaborative Innovation Center of Steel Technology, University of Science and Technology Beijing, Beijing 100083, China
| | - Jingchao Li
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250014, China
| | - Xiuteng Zhou
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Qiongzheng Hu
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250014, China
| | - Chunxia Ma
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250014, China
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Xiao Wang
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong 250014, China
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Makhumbila P, Rauwane ME, Muedi HH, Madala NE, Figlan S. Metabolome profile variations in common bean (Phaseolus vulgaris L.) resistant and susceptible genotypes incited by rust (Uromyces appendiculatus). Front Genet 2023; 14:1141201. [PMID: 37007949 PMCID: PMC10060544 DOI: 10.3389/fgene.2023.1141201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 03/18/2023] Open
Abstract
The causal agent of rust, Uromyces appendiculatus is a major constraint for common bean (Phaseolus vulgaris) production. This pathogen causes substantial yield losses in many common bean production areas worldwide. U. appendiculatus is widely distributed and although there have been numerous breakthroughs in breeding for resistance, its ability to mutate and evolve still poses a major threat to common bean production. An understanding of plant phytochemical properties can aid in accelerating breeding for rust resistance. In this study, metabolome profiles of two common bean genotypes Teebus-RR-1 (resistant) and Golden Gate Wax (susceptible) were investigated for their response to U. appendiculatus races (1 and 3) at 14- and 21-days post-infection (dpi) using liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (LC-qTOF-MS). Non-targeted data analysis revealed 71 known metabolites that were putatively annotated, and a total of 33 were statistically significant. Key metabolites including flavonoids, terpenoids, alkaloids and lipids were found to be incited by rust infections in both genotypes. Resistant genotype as compared to the susceptible genotype differentially enriched metabolites including aconifine, D-sucrose, galangin, rutarin and others as a defence mechanism against the rust pathogen. The results suggest that timely response to pathogen attack by signalling the production of specific metabolites can be used as a strategy to understand plant defence. This is the first study to illustrate the utilization of metabolomics to understand the interaction of common bean with rust.
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Affiliation(s)
- Penny Makhumbila
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodeport, South Africa
- *Correspondence: Penny Makhumbila,
| | - Molemi E. Rauwane
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodeport, South Africa
- Department of Botany, Nelson Mandela University, Port Elizabeth, South Africa
| | - Hangwani H. Muedi
- Research Support Services, North-West Provincial Department of Agriculture and Rural Development, Potchefstroom, South Africa
| | - Ntakadzeni E. Madala
- Department of Biochemistry, School of Mathematical and Natural Sciences, University of Venda, Thohoyandou, South Africa
| | - Sandiswa Figlan
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodeport, South Africa
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10
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Xiang L, Wang F, Bian Y, Harindintwali JD, Wang Z, Wang Y, Dong J, Chen H, Schaeffer A, Jiang X, Cai Z. Visualizing the Distribution of Phthalate Esters and Plant Metabolites in Carrot by Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15311-15320. [PMID: 36442135 DOI: 10.1021/acs.jafc.2c06995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The accumulation of organic pollutants in vegetables is a major global food safety issue. The concentrations of pollutants in vegetables usually differ across different tissues because of different transport and accumulation pathways. However, owing to the limitations of conventional methods, in situ localization of typical organic pollutants such as phthalate esters (PAEs) in plant tissues has not yet been studied. Here, we developed a quick and efficient method for in situ detection and imaging of the spatial distribution of PAEs in a typical root vegetable, carrot, using matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS). The use of a 2,5-dihydroxybenzoic acid matrix with a spray-sublimation coating method led to the successful identification of PAEs ion signals. The IMS results showed that a typical PAE-di-(2-ethylhexyl)phthalate (DEHP) was broadly distributed in the cortex, phloem, and metaxylem, but was barely detectable in the cambium and protoxylem. Interestingly, MALDI-IMS data also revealed for the first time the spatial distribution of sugars and β-carotene in carrots. In summary, the developed method offers a new and practical methodology for the in situ analysis of PAEs and plant metabolites in plant tissues. As a result, it could provide a more intuitive understanding of the movement and transformation of organic pollutants in soil-plant systems.
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Affiliation(s)
- Leilei Xiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Environmental Research, RWTH Aachen University, WorringerWeg 1, Aachen 52074, Germany
| | - Yongrong Bian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jean Damascene Harindintwali
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziquan Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yu Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jing Dong
- Shimadzu China Innovation Center, Beijing 100000, China
| | - Hong Chen
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Andreas Schaeffer
- Institute for Environmental Research, RWTH Aachen University, WorringerWeg 1, Aachen 52074, Germany
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong, China
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Liu H, Pan Y, Xiong C, Han J, Wang X, Chen J, Nie Z. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) for in situ analysis of endogenous small molecules in biological samples. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Baquer G, Sementé L, Mahamdi T, Correig X, Ràfols P, García-Altares M. What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2022:e21794. [PMID: 35822576 DOI: 10.1002/mas.21794] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) has become a widespread analytical technique to perform nonlabeled spatial molecular identification. The Achilles' heel of MSI is the annotation and identification of molecular species due to intrinsic limitations of the technique (lack of chromatographic separation and the difficulty to apply tandem MS). Successful strategies to perform annotation and identification combine extra analytical steps, like using orthogonal analytical techniques to identify compounds; with algorithms that integrate the spectral and spatial information. In this review, we discuss different experimental strategies and bioinformatics tools to annotate and identify compounds in MSI experiments. We target strategies and tools for small molecule applications, such as lipidomics and metabolomics. First, we explain how sample preparation and the acquisition process influences annotation and identification, from sample preservation to the use of orthogonal techniques. Then, we review twelve software tools for annotation and identification in MSI. Finally, we offer perspectives on two current needs of the MSI community: the adaptation of guidelines for communicating confidence levels in identifications; and the creation of a standard format to store and exchange annotations and identifications in MSI.
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Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Toufik Mahamdi
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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13
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Fujii H, Hibi M, Shimizu S, Yokozeki K, Ogawa J. Three enzymes of Rhizobium radiobacter involved in the novel metabolism of two naturally occurring bioactive oxidative derivatives of L-isoleucine. Biosci Biotechnol Biochem 2022; 86:1247-1254. [PMID: 35793557 DOI: 10.1093/bbb/zbac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022]
Abstract
Rhizobium radiobacter C58 was found to convert 4-hydroxyisoleucine (HIL) and 2-amino-3-methyl-4-ketopentanoate (AMKP), bioactive oxidative derivatives of L-isoleucine, in both cases producing 2-aminobutyrate. Three native enzymes involved in these metabolisms were purified by column chromatography and successfully identified. In this strain, HIL was converted to acetaldehyde and 2-aminobutyrate by coupling action of the transaminase rrIlvE and the aldolase HkpA. AMKP was also converted to acetate and 2-aminobutyrate by coupling action of rrIlvE and a hydrolase DkhA. In the multi-enzymatic reactions, HkpA catalyzes the retro-aldol reaction of 4-hydroxy-3-methyl-2-ketopentanoate into acetaldehyde and 2-ketobutyrate, and DkhA catalyzes hydrolytic cleavage of the carbon-carbon bond of 2,4-diketo-3-methylpentanoate into acetate and 2-ketobutyrate. And rrIlvE catalyzes reversible transamination between HIL and 4-hydroxy-3-methyl-2-ketopentanoate, AMKP and 2,4-diketo-3-methylpentanoate, and 2-ketobutyrate and 2-aminobutyrate. The results suggested that the conversion activity of Rhizobium bacteria play an important role in the complex biological metabolic networks associated with HIL and AMKP.
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Affiliation(s)
- Hidemi Fujii
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, Japan
| | - Makoto Hibi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, Japan
| | - Sakayu Shimizu
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, Japan
| | - Kenzo Yokozeki
- Laboratory of Industrial Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, Japan.,Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Suzuki-cho, Kawasaki-ku, Kawasaki, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, Japan
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14
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Ajith A, Milnes PJ, Johnson GN, Lockyer NP. Mass Spectrometry Imaging for Spatial Chemical Profiling of Vegetative Parts of Plants. PLANTS 2022; 11:plants11091234. [PMID: 35567235 PMCID: PMC9102225 DOI: 10.3390/plants11091234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 11/23/2022]
Abstract
The detection of chemical species and understanding their respective localisations in tissues have important implications in plant science. The conventional methods for imaging spatial localisation of chemical species are often restricted by the number of species that can be identified and is mostly done in a targeted manner. Mass spectrometry imaging combines the ability of traditional mass spectrometry to detect numerous chemical species in a sample with their spatial localisation information by analysing the specimen in a 2D manner. This article details the popular mass spectrometry imaging methodologies which are widely pursued along with their respective sample preparation and the data analysis methods that are commonly used. We also review the advancements through the years in the usage of the technique for the spatial profiling of endogenous metabolites, detection of xenobiotic agrochemicals and disease detection in plants. As an actively pursued area of research, we also address the hurdles in the analysis of plant tissues, the future scopes and an integrated approach to analyse samples combining different mass spectrometry imaging methods to obtain the most information from a sample of interest.
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Affiliation(s)
- Akhila Ajith
- Department of Chemistry, Photon Science Institute, University of Manchester, Manchester M13 9PL, UK;
| | - Phillip J. Milnes
- Syngenta, Jeolott’s Hill International Research Centre, Bracknell RG42 6EY, UK;
| | - Giles N. Johnson
- Department of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PY, UK;
| | - Nicholas P. Lockyer
- Department of Chemistry, Photon Science Institute, University of Manchester, Manchester M13 9PL, UK;
- Correspondence:
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15
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Meng L, Han J, Chen J, Wang X, Huang X, Liu H, Nie Z. Development of an Automatic Ultrasonic Matrix Sprayer for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. Anal Chem 2022; 94:6457-6462. [PMID: 35438954 DOI: 10.1021/acs.analchem.2c00403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) has emerged as a powerful tool for studying the spatial distribution of various types of molecules. Matrix deposition is a critical step for obtaining high-quality imaging data. An automatic device named SoniCoat was fabricated based on an ultrasonic nozzle driven by a pizeoelectric ceramic for matrix coating in the present study. Compared with the minihumidifier developed previously by our group for matrix deposition, SoniCoat realized automation, and the ultrasonic nozzle of this device is easy to clean and less likely to get clogged, indicating a longer life. Compared with commercial and homemade instruments such as the TM-Sprayer and electrospray matrix coating device, our newly developed device achieved a good nebulization effect without the need for high-pressure gas flow and high voltage. Matrix deposition by SoniCoat generated more homogeneous matrix crystals with diameters of about 10 μm and reduced the occurrence of molecular diffusion to a greater extent, compared with the results by TM-Sprayer. Repeatable high-spatial-resolution MS imaging data were obtained with the help of SoniCoat. Furthermore, the newly developed device can also be successfully applied for in situ derivatization.
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Affiliation(s)
- Lingwei Meng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Han
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Junyu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Gupta S, Schillaci M, Roessner U. Metabolomics as an emerging tool to study plant-microbe interactions. Emerg Top Life Sci 2022; 6:175-183. [PMID: 35191478 PMCID: PMC9023012 DOI: 10.1042/etls20210262] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 01/14/2023]
Abstract
In natural environments, interaction between plant roots and microorganisms are common. These interactions between microbial species and plants inhabited by them are being studied using various techniques. Metabolomics research based on mass spectrometric techniques is one of the crucial approaches that underpins system biology and relies on precision instrument analysis. In the last decade, this emerging field has received extensive attention. It provides a qualitative and quantitative approach for determining the mechanisms of symbiosis of bacteria and fungi with plants and also helps to elucidate the tolerance mechanisms of host plants against various abiotic stresses. However, this -omics application and its tools in plant-microbe interaction studies is still underutilized compared with genomic and transcriptomic methods. Therefore, it is crucial to bring this field forward to bear on the study of plant resistance and susceptibility. This review describes the current status of methods and progress in metabolomics applications for plant-microbe interaction studies discussing current challenges and future prospects.
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Affiliation(s)
- Sneha Gupta
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Martino Schillaci
- Consiglio Nazionale Delle Ricerche-Istituto per la Protezione Sostenibile Delle Piante, Strada delle Cacce 73, 10135 Torino, Italy
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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17
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Chi DH, Kahyo T, Islam A, Hasan MM, Waliullah ASM, Mamun MA, Nakajima M, Ikoma T, Akita K, Maekawa Y, Sato T, Setou M. NAD + Levels Are Augmented in Aortic Tissue of ApoE -/- Mice by Dietary Omega-3 Fatty Acids. Arterioscler Thromb Vasc Biol 2022; 42:395-406. [PMID: 35139656 DOI: 10.1161/atvbaha.121.317166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Maintaining bioenergetic homeostasis provides a means to reduce the risk of cardiovascular events during chronological aging. Nicotinamide adenine dinucleotide (NAD+) acts as a signaling molecule, and its levels were used to govern several biological pathways, for example, promoting angiogenesis by SIRT1 (sirtuin 1)-mediated inhibition of Notch signaling to rejuvenate capillary density of old-aged mice. NAD+ modulation shows promise in the vascular remodeling of endothelial cells. However, NAD+ distribution in atherosclerotic regions remains uncharacterized. Omega-3 polyunsaturated fatty acids consumption, such as docosahexaenoic acid and eicosapentaenoic acid, might increase the abundance of cofactors in blood vessels due to omega-3 polyunsaturated fatty acids metabolism. METHODS Apolipoprotein E-deficient (ApoE-/-) mice were fed a Western diet, and the omega-3 polyunsaturated fatty acids-treated groups were supplemented with docosahexaenoic acid (1%, w/w) or eicosapentaenoic acid (1%, w/w) for 3 weeks. Desorption electrospray ionization mass spectrometry imaging was exploited to detect exogenous and endogenous NAD+ imaging. RESULTS NAD+, NADH, NADP+, NADPH, FAD+, FADH, and nicotinic acid adenine dinucleotide of the aortic arches were detected higher in the omega-3 polyunsaturated fatty acids-treated mice than the nontreated control. Comparing the distribution in the outer and inner layers of the arterial walls, only NADPH was detected slightly higher in the outer part in eicosapentaenoic acid-treated mice. CONCLUSIONS Supplementation of adding docosahexaenoic acid or eicosapentaenoic acid to the Western diet led to a higher NAD+, FAD+, and their metabolites in the aortic arch. Considering the pleiotropic roles of NAD+ in biology, this result serves as a beneficial therapeutic strategy in the animal model counter to pathological conditions.
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Affiliation(s)
- Do Huu Chi
- Department of Cellular and Molecular Anatomy (D.H.C., T.K., A.I., M.M.H., A.S.M.W., M.A.M., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Tomoaki Kahyo
- Department of Cellular and Molecular Anatomy (D.H.C., T.K., A.I., M.M.H., A.S.M.W., M.A.M., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan.,International Mass Imaging Center (T.K., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Ariful Islam
- Department of Cellular and Molecular Anatomy (D.H.C., T.K., A.I., M.M.H., A.S.M.W., M.A.M., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Md Mahmudul Hasan
- Department of Cellular and Molecular Anatomy (D.H.C., T.K., A.I., M.M.H., A.S.M.W., M.A.M., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - A S M Waliullah
- Department of Cellular and Molecular Anatomy (D.H.C., T.K., A.I., M.M.H., A.S.M.W., M.A.M., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Md Al Mamun
- Department of Cellular and Molecular Anatomy (D.H.C., T.K., A.I., M.M.H., A.S.M.W., M.A.M., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Madoka Nakajima
- Department of Cellular and Molecular Anatomy (D.H.C., T.K., A.I., M.M.H., A.S.M.W., M.A.M., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan.,International Mass Imaging Center (T.K., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Takenori Ikoma
- Department of Internal Medicine (T.I., K.A., Y.M.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Keitaro Akita
- Department of Internal Medicine (T.I., K.A., Y.M.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Yuichiro Maekawa
- Department of Internal Medicine (T.I., K.A., Y.M.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Tomohito Sato
- Department of Cellular and Molecular Anatomy (D.H.C., T.K., A.I., M.M.H., A.S.M.W., M.A.M., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan.,International Mass Imaging Center (T.K., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy (D.H.C., T.K., A.I., M.M.H., A.S.M.W., M.A.M., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan.,International Mass Imaging Center (T.K., M.N., T.S., M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan.,Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education and Research Center (M.S.), Hamamatsu University School of Medicine, Shizuoka, Japan
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18
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Ma C, Wang X, Zhang H, Liu W, Wang D, Liu F, Lu H, Huang L. High-throughput screening and spatial profiling of low-mass pesticides using a novel Ti 3C 2 MXene nanowire (TMN) as MALDI MS matrix. CHEMOSPHERE 2022; 286:131826. [PMID: 34426141 DOI: 10.1016/j.chemosphere.2021.131826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/19/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Pesticides play critical roles in agricultural fields; however, pesticide residues can cause serious damage to human health and the ecological environment; therefore, developing a rapid and sensitive method for pesticide detection is urgently needed. Nanostructure-assisted matrix laser desorption/ionization (MALDI) mass spectrometry (MS) has great potential for the detection of low-mass pesticides. In this study, a novel Ti3C2 MXene nanowire (TMN) was prepared by a facile sol-gel method and served as a matrix to enhance MALDI MS performance in the analysis of pesticides in positive ion mode. The TMN showed superior performance in the high-throughput detection of six kinds of pesticides (organophosphorus, organochlorine, carbamate, neonicotinoids, triazole, and oxadiazines), with ultrahigh sensitivity (detection limits at sub-ppt levels), remarkable repeatability, excellent salt tolerance, and extremely low background compared to traditional organic matrices due to the specific polyaromatic structure and the doping of nitrogen. Furthermore, this matrix was successfully employed for the analysis of residual pesticides in traditional Chinese herbs, and the level of diniconazole was quantified with a linear range of 0-50 ng/mL (R2 > 0.99). More importantly, the spatial distribution of various endogenous compounds (e.g., amino acids and saccharides, fatty acids, alkaloids, and plant hormones) and xenobiotic pesticides from the intact root of the medicinal plant P. quinquefolium was clearly visualized using the TMN self-assembly film as a matrix for MALDI imaging mass spectrometry (IMS). With superior advantages such as sensitivity, simplicity, rapidness, and minimal sample requirement, TMN as a matrix-assisted MALDI MS shows great promise for various applications.
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Affiliation(s)
- Chunxia Ma
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 1007002, China; Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250014, China; Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 1007002, China; Post Doctoral Management Office, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiao Wang
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250014, China.
| | - Huamin Zhang
- Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 1007002, China
| | - Wei Liu
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250014, China
| | - Daijie Wang
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250014, China
| | - Feng Liu
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250014, China
| | - Heng Lu
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250014, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 1007002, China.
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19
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Borisov RS, Matveeva MD, Zaikin VG. Reactive Matrices for Analytical Matrix-Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry. Crit Rev Anal Chem 2021; 53:1027-1043. [PMID: 34969337 DOI: 10.1080/10408347.2021.2001309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
In recent years, a special focus is placed on the usage of reactive matrices for analytical matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). Since 2003, when the term "reactive matrices" was suggested and the dignity of compounds, possessing dualistic properties as matrices and derivatization agents was demonstrated, corresponding approach has found application in various fields and, in particular, in bioanalysis (metabolomics, lipidomics, etc.). The main advantage of this methodology is that it reduces sample treatment time, simplifies the procedure of sample handling, improves the sensitivity of analysis, enhances the molecular identification and profiling. Within the framework of this review, the main attention is paid to "true" reactive matrices that interact with analyte molecules through an exchange or addition reactions. A special section discusses practical application of reactive matrices in the determination of the distribution of targeted and non-targeted organic substances on the surface of biological tissue sections by MALDI-MS imaging. In this critical review, a controversial proposal is made to consider protonating and deprotonating matrices as reactive, because they can undergo a chemical reaction such as proton transfer that occurs in both target solution and MALDI plume. In this respect, special attention is paid to "proton sponge" matrices that have found a wide application in the analysis of various acidic compounds by MALDI-MS in the negative mode. Historical data on the formation of ions and the fate of matrices in MALDI are considered at the beginning of this article.
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Affiliation(s)
- Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Mariya D Matveeva
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
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20
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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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Unravel the Local Complexity of Biological Environments by MALDI Mass Spectrometry Imaging. Int J Mol Sci 2021; 22:ijms222212393. [PMID: 34830273 PMCID: PMC8623934 DOI: 10.3390/ijms222212393] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/07/2021] [Accepted: 11/14/2021] [Indexed: 11/30/2022] Open
Abstract
Classic metabolomic methods have proven to be very useful to study functional biology and variation in the chemical composition of different tissues. However, they do not provide any information in terms of spatial localization within fine structures. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) does and reaches at best a spatial resolution of 0.25 μm depending on the laser setup, making it a very powerful tool to analyze the local complexity of biological samples at the cellular level. Here, we intend to give an overview of the diversity of the molecules and localizations analyzed using this method as well as to update on the latest adaptations made to circumvent the complexity of samples. MALDI MSI has been widely used in medical sciences and is now developing in research areas as diverse as entomology, microbiology, plant biology, and plant–microbe interactions, the rhizobia symbiosis being the most exhaustively described so far. Those are the fields of interest on which we will focus to demonstrate MALDI MSI strengths in characterizing the spatial distributions of metabolites, lipids, and peptides in relation to biological questions.
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22
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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: 17] [Impact Index Per Article: 5.7] [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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Khatib M, Pouzet C, Lafitte C, Chervin J, Bonzon-Ponnet V, Jauneau A, Esquerré-Tugayé MT. Phenolic profile of a Parma violet unveiled by chemical and fluorescence imaging. AOB PLANTS 2021; 13:plab041. [PMID: 34316339 PMCID: PMC8300547 DOI: 10.1093/aobpla/plab041] [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: 04/12/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
The ability of phenolic compounds to autofluoresce upon illumination by UV or blue light was exploited to explore the nature and distribution of these metabolites within the flower petals, leaves and roots of the violet, Viola alba subsp. dehnhardtii. This was achieved through a dual complementary approach that combined fluorescence microscopy imaging of living intact tissues and chemical extraction of pulverized material. The blue to red fluorescence displayed by living tissues upon illumination was indicative of their richness in phenolic compounds. Phenolic acids were found in all tissues, while flavonoids characterized the aerial part of the plant, anthocyanidins being restricted to the petals. The chemical quantification of phenolics in plant extracts confirmed their tissue-specific distribution and abundance. A key finding was that the spectral signatures obtained through confocal microscopy of endogenous fluorophores in living tissues and their counterpart extracts share the same fluorescence patterns, pointing out the potential of fluorescence imaging of intact organs for a proper estimation of their phenolic content. In addition, this study highlighted a few distinct morphology cell types, in particular foliar-glandular-like structures, and jagged petal cell walls. Altogether, these data provide a comprehensive histochemical localization of phenolics in living tissues of a violet. Converting fluorescence imaging into a chemical imprint indicated that one can rely on fluorescence microscopy of intact living tissues as a rapid, non-destructive means to follow their phenolic imprint under various environmental conditions.
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Affiliation(s)
- Moustafa Khatib
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
| | - Cécile Pouzet
- Plateforme Imagerie FRAIB-TRI, Université de Toulouse, CNRS, 31326 Castanet-Tolosan, France
| | - Claude Lafitte
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 31326 Castanet-Tolosan, France
| | - Justine Chervin
- Plateforme MetaToul-AgromiX, Université de Toulouse, CNRS, 31326 Castanet-Tolosan, France
| | | | - Alain Jauneau
- Plateforme Imagerie FRAIB-TRI, Université de Toulouse, CNRS, 31326 Castanet-Tolosan, France
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Allouche M, Nasri A, Harrath AH, Mansour L, Alwasel S, Beyrem H, Plăvan G, Rohal-Lupher M, Boufahja F. Meiobenthic nematode Oncholaimus campylocercoides as a model in laboratory studies: selection, culture, and fluorescence microscopy after exposure to phenanthrene and chrysene. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:29484-29497. [PMID: 33560507 DOI: 10.1007/s11356-021-12688-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Numerous studies have focused on the response of meiofauna after exposure to polycyclic aromatic hydrocarbons (PAHs), but none has been devoted to their uptake into nematode body compartments. The present study monitored PAH uptake by Oncholaimus campylocercoides which was selected after 40 days in the laboratory through original protocols from natural sediments collected in the Old Harbor of Bizerte, Tunisia. To achieve the mono-species level, a grain size magnification was applied by gradually adding a biosubstrate made from either the crushed shells of Mytilus galloprovincialis or minced leaves of Posidonia oceanica. After selection, O. campylocercoides was cultured and fed with earthworm powder (560 mg.l-1). Thereafter, it was exposed for 3 weeks to phenanthrene and chrysene (38, 116, and 348 ppb). Fluorescence microscopy revealed higher intensities of PAHs at the spicules, mouths, and pharynges compared with the other organs considered. Moreover, the buccal fluorescence showed a significant correlation with that measured in the biosubstrate made with shells of M. galloprovincialis.
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Affiliation(s)
- Mohamed Allouche
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia
| | - Ahmed Nasri
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia
| | - Abdel Halim Harrath
- Zoology Department, College of Science, King Saud University, Box 2455, Riyadh, 11451, Saudi Arabia
| | - Lamjed Mansour
- Zoology Department, College of Science, King Saud University, Box 2455, Riyadh, 11451, Saudi Arabia
| | - Saleh Alwasel
- Zoology Department, College of Science, King Saud University, Box 2455, Riyadh, 11451, Saudi Arabia
| | - Hamouda Beyrem
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia
| | - Gabriel Plăvan
- Faculty of Biology, Alexandru Ioan Cuza University of Iasi, Iasi, Romania
| | - Melissa Rohal-Lupher
- Texas Water Development Board, 1700 North Congress Avenue, Austin, TX, 78701, USA
| | - Fehmi Boufahja
- Faculty of Sciences of Bizerte, Laboratory of Environment Biomonitoring, Coastal Ecology and Ecotoxicology Unit, University of Carthage, 7021, Zarzouna, Tunisia.
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Gomez-Zepeda D, Frausto M, Nájera-González HR, Herrera-Estrella L, Ordaz-Ortiz JJ. Mass spectrometry-based quantification and spatial localization of small organic acid exudates in plant roots under phosphorus deficiency and aluminum toxicity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1791-1806. [PMID: 33797826 DOI: 10.1111/tpj.15261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Low-molecular-weight organic acid (OA) extrusion by plant roots is critical for plant nutrition, tolerance to cations toxicity, and plant-microbe interactions. Therefore, methodologies for the rapid and precise quantification of OAs are necessary to be incorporated in the analysis of roots and their exudates. The spatial location of root exudates is also important to understand the molecular mechanisms directing OA production and release into the rhizosphere. Here, we report the development of two complementary methodologies for OA determination, which were employed to evaluate the effect of inorganic ortho-phosphate (Pi) deficiency and aluminum toxicity on OA excretion by Arabidopsis roots. OA exudation by roots is considered a core response to different types of abiotic stress and for the interaction of roots with soil microbes, and for decades has been a target trait to produce plant varieties with increased capacities of Pi uptake and Al tolerance. Using targeted ultra-performance liquid chromatography coupled with high-resolution tandem mass spectrometry (UPLC-HRMS/MS), we achieved the quantification of six OAs in root exudates at sub-micromolar detection limits with an analysis time of less than 5 min per sample. We also employed targeted (MS/MS) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to detect the spatial location of citric and malic acid with high specificity in roots and exudates. Using these methods, we studied OA exudation in response to Al toxicity and Pi deficiency in Arabidopsis seedlings overexpressing genes involved in OA excretion. Finally, we show the transferability of the MALDI-MSI method by analyzing OA excretion in Marchantia polymorpha gemmalings subjected to Pi deficiency.
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Affiliation(s)
- David Gomez-Zepeda
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
| | - Moises Frausto
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Héctor-Rogelio Nájera-González
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
| | - Luis Herrera-Estrella
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - José-Juan Ordaz-Ortiz
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, 36824, Mexico
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McGuiness PN, Reid JB, Foo E. The influence of ethylene, gibberellins and brassinosteroids on energy and nitrogen-fixation metabolites in nodule tissue. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110846. [PMID: 33691972 DOI: 10.1016/j.plantsci.2021.110846] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/03/2021] [Accepted: 02/06/2021] [Indexed: 05/12/2023]
Abstract
Legume nodules are a unique plant organ that contain nitrogen-fixing rhizobial bacteria. For this interaction to be mutually beneficial, plant and bacterial metabolism must be precisely co-ordinated. Plant hormones are known to play essential roles during the establishment of legume-rhizobial symbioses but their role in subsequent nodule metabolism has not been explored in any depth. The plant hormones brassinosteroids, ethylene and gibberellins influence legume infection, nodule number and in some cases nodule function. In this paper, the influence of these hormones on nodule metabolism was examined in a series of well characterised pea mutants with altered hormone biosynthesis or response. A targeted set of metabolites involved in nutrient exchange and nitrogen fixation was examined in nodule tissue of mutant and wild type plants. Gibberellin-deficiency had a major negative impact on the level of several major dicarboxylates supplied to rhizobia by the plant and also led to a significant deficit in the amino acids involved in glutamine-aspartate transamination, consistent with the limited bacteroid development and low fixation rate of gibberellin-deficient na mutant nodules. In contrast, no major effects of brassinosteroid-deficiency or ethylene-insensitivity on the key metabolites in these pathways were found. Therefore, although all three hormones influence infection and nodule number, only gibberellin is important for the establishment of a functional nodule metabolome.
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Affiliation(s)
- Peter N McGuiness
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - James B Reid
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - Eloise Foo
- School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia.
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27
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Enomoto H. Adhesive film applications help to prepare strawberry fruit sections for desorption electrospray ionization-mass spectrometry imaging. Biosci Biotechnol Biochem 2021; 85:1341-1347. [DOI: 10.1093/bbb/zbab033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/01/2021] [Indexed: 12/31/2022]
Abstract
ABSTRACT
Desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) is a powerful tool to analyze the distribution of metabolites in biological tissues. Cryosectioning of biological tissues is usually required prior to DESI-MSI, but it can be difficult for tissues that are fragile, hard, and have a high-water content. The Kawamoto method uses transparent adhesive films to prepare cryosections; however, its application for plant tissues, such as strawberry tissues, in DESI-MSI has not been verified. In this study, strawberry cryosections maintained original structures were prepared using adhesive film. Subsequently, numerous peaks were detected for the sections using the positive and negative ion modes of DESI-MSI. Several primary and specialized metabolites, such as amino acids, sugars, organic acids, and flavonoids, were identified and visualized. These results suggest the use of adhesive films when cryosectioning could improve DESI-MSI analysis of the metabolites in strawberry fruits and various tissues of other plant species.
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Affiliation(s)
- Hirofumi Enomoto
- Department of Biosciences, Faculty of Science and Engineering, Teikyo University, Utsunomiya, Japan
- Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University, Utsunomiya, Japan
- Advanced Instrumental Analysis Center, Teikyo University, Utsunomiya, Japan
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28
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Krivosheina MS, Borisov RS, Zhilyaev DI, Matveeva MD, Zaikin VG. New suitable deprotonating matrices for the analysis of carboxylic acids and some acidic compounds by matrix-assisted laser desorption/ionization mass spectrometry in negative ion mode. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e8954. [PMID: 32979299 DOI: 10.1002/rcm.8954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Direct non-derivatization analysis of organic acids and acidic compounds by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) in positive ion mode is not always possible due to the low ionization efficiency of analytes. Some new efficient deprotonating matrices were suggested that allowed the production of negative ions from acidic compounds during MALDI-MS experiments. METHODS Various tested carboxyl-containing compounds as well as compounds with acidic properties were mixed with the suggested deprotonating matrices [4-dimethylaminobenzaldehyde (DMABA), N,N-dimethylamino-p-phenylenediamine or 3-aminoquinoline] and applied on a standard MALDI target followed by recording MALDI mass spectra in negative ion mode. RESULTS All the tested acidic compounds mixed with the suggested deprotonating matrices produced abundant [M - H]- ions under MALDI conditions. DMABA produced the strongest signals reflecting greater sensitivity of analysis. CONCLUSIONS The suggested deprotonating matrices are commercially available compounds and are good alternatives to well-known matrices of this kind and, in particular, the often used 9-aminoacridine. DMABA is the best of the tested potential matrices and is suitable for the detection of low molecular weight carboxyl-containing compounds, substituted phenols, and mixtures of naphthenic acids by (-)MALDI-MS.
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Affiliation(s)
- Mariya S Krivosheina
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
- People's Friendship University of Russia, ul. Miklukho-Maklay 6, Moscow, 117198, Russian Federation
| | - Dmitry I Zhilyaev
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
- People's Friendship University of Russia, ul. Miklukho-Maklay 6, Moscow, 117198, Russian Federation
| | - Mariya D Matveeva
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
| | - Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky pr. 29, Moscow, 119991, Russian Federation
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29
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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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30
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Liu A, Ku YS, Contador CA, Lam HM. The Impacts of Domestication and Agricultural Practices on Legume Nutrient Acquisition Through Symbiosis With Rhizobia and Arbuscular Mycorrhizal Fungi. Front Genet 2020; 11:583954. [PMID: 33193716 PMCID: PMC7554533 DOI: 10.3389/fgene.2020.583954] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/08/2020] [Indexed: 12/03/2022] Open
Abstract
Legumes are unique among plants as they can obtain nitrogen through symbiosis with nitrogen-fixing rhizobia that form root nodules in the host plants. Therefore they are valuable crops for sustainable agriculture. Increasing nitrogen fixation efficiency is not only important for achieving better plant growth and yield, but it is also crucial for reducing the use of nitrogen fertilizer. Arbuscular mycorrhizal fungi (AMF) are another group of important beneficial microorganisms that form symbiotic relationships with legumes. AMF can promote host plant growth by providing mineral nutrients and improving the soil ecosystem. The trilateral legume-rhizobia-AMF symbiotic relationships also enhance plant development and tolerance against biotic and abiotic stresses. It is known that domestication and agricultural activities have led to the reduced genetic diversity of cultivated germplasms and higher sensitivity to nutrient deficiencies in crop plants, but how domestication has impacted the capability of legumes to establish beneficial associations with rhizospheric microbes (including rhizobia and fungi) is not well-studied. In this review, we will discuss the impacts of domestication and agricultural practices on the interactions between legumes and soil microbes, focusing on the effects on AMF and rhizobial symbioses and hence nutrient acquisition by host legumes. In addition, we will summarize the genes involved in legume-microbe interactions and studies that have contributed to a better understanding of legume symbiotic associations using metabolic modeling.
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Affiliation(s)
| | | | | | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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31
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Zhan L, Huang X, Xue J, Liu H, Xiong C, Wang J, Nie Z. MALDI-TOF/TOF tandem mass spectrometry imaging reveals non-uniform distribution of disaccharide isomers in plant tissues. Food Chem 2020; 338:127984. [PMID: 33092001 DOI: 10.1016/j.foodchem.2020.127984] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/20/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022]
Abstract
Mass spectrometry imaging (MSI) is a powerful technique for investigating the biomolecular locations within tissues. However, the isomeric compounds are rarely distinguished due to inability of MSI to differentiate isomers in the probing area. Coupling tandem mass spectrometry with MSI can facilitate differentiating isomeric compounds. Here MALDI-TOF/TOF tandem mass spectrometry imaging approach was applied to probing the spatial distributions of isomeric disaccharides in plant tissues. First, MS/MS imaging analysis of disaccharide-matrix droplet spots demonstrated the feasibility of distinguishing isomeric species in tissues, by measuring the relative intensity of specific fragments. Then, tandem MS imaging of disaccharides in onion bulb tissues indicated that sucrose and other unknown non-sucrose disaccharides exhibit heterogeneous locations throughout the tissues. This method enables us to image disaccharide isomers differentially in biological tissues, and to discover new saccharide species in plant. This work also emphasizes the necessity of considering isobaric compounds when interpreting MSI results.
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Affiliation(s)
- Lingpeng Zhan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xi Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jinjuan Xue
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jiyun Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; National Center for Mass Spectrometry in Beijing, Beijing 100190, China.
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32
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Agtuca BJ, Stopka SA, Evans S, Samarah L, Liu Y, Xu D, Stacey MG, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. Metabolomic profiling of wild-type and mutant soybean root nodules using laser-ablation electrospray ionization mass spectrometry reveals altered metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1937-1958. [PMID: 32410239 DOI: 10.1111/tpj.14815] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 05/18/2023]
Abstract
The establishment of the nitrogen-fixing symbiosis between soybean and Bradyrhizobium japonicum is a complex process. To document the changes in plant metabolism as a result of symbiosis, we utilized laser ablation electrospray ionization-mass spectrometry (LAESI-MS) for in situ metabolic profiling of wild-type nodules, nodules infected with a B. japonicum nifH mutant unable to fix nitrogen, nodules doubly infected by both strains, and nodules formed on plants mutated in the stearoyl-acyl carrier protein desaturase (sacpd-c) gene, which were previously shown to have an altered nodule ultrastructure. The results showed that the relative abundance of fatty acids, purines, and lipids was significantly changed in response to the symbiosis. The nifH mutant nodules had elevated levels of jasmonic acid, correlating with signs of nitrogen deprivation. Nodules resulting from the mixed inoculant displayed similar, overlapping metabolic distributions within the sectors of effective (fix+ ) and ineffective (nifH mutant, fix- ) endosymbionts. These data are inconsistent with the notion that plant sanctioning is cell autonomous. Nodules lacking sacpd-c displayed an elevation of soyasaponins and organic acids in the central necrotic regions. The present study demonstrates the utility of LAESI-MS for high-throughput screening of plant phenotypes. Overall, nodules disrupted in the symbiosis were elevated in metabolites related to plant defense.
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Affiliation(s)
- Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Sterling Evans
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Laith Samarah
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Yang Liu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Minviluz G Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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33
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Enomoto H, Kotani M, Ohmura T. Novel Blotting Method for Mass Spectrometry Imaging of Metabolites in Strawberry Fruit by Desorption/Ionization Using Through Hole Alumina Membrane. Foods 2020; 9:foods9040408. [PMID: 32244711 PMCID: PMC7230831 DOI: 10.3390/foods9040408] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 01/21/2023] Open
Abstract
Mass spectrometry imaging (MSI) using matrix-assisted laser desorption/ionization (MALDI) is a powerful technique for visualizing metabolites in the strawberry fruit. During sample preparation for MALDI-MSI, sectioning of the samples is usually required. In general, MALDI-MSI analysis of strawberry fruits that are larger than a single glass slide is difficult because thin sections cannot be prepared. In this study, we attempted to visualize metabolites in large strawberry fruits by MSI, employing a blotting method that uses desorption ionization using a through-hole alumina membrane (DIUTHAME) chip. Large strawberry fruits were cut and a DIUTHAME chip was set on the cross-section to blot the metabolites. After drying the DIUTHAME chip, the metabolites were measured in positive and negative ion modes using a commercial MALDI-type mass spectrometer. Several peaks were detected in both the ion modes. Various metabolites related to food quality, such as sugars, organic acids, and anthocyanins, were detected and successfully visualized by blotting on a DIUTHAME chip in MSI. These results suggest that blotting using a DIUTHAME chip in MSI is useful for visualizing the metabolites present in the strawberry fruit.
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Affiliation(s)
- Hirofumi Enomoto
- Department of Biosciences, Faculty of Science and Engineering, Teikyo University, Utsunomiya 320-8551, Japan
- Division of Integrated Science and Engineering, Graduate School of Science and Engineering, Teikyo University, Utsunomiya 320-8551, Japan
- Advanced Instrumental Analysis Center, Teikyo University, Utsunomiya 320-8551, Japan
- Correspondence: ; Tel.: +81-28-627-7312
| | - Masahiro Kotani
- Hamamatsu Photonics K.K., 314-5 Shimokanzo, Iwata 438-0193, Japan; (M.K.); (T.O.)
| | - Takayuki Ohmura
- Hamamatsu Photonics K.K., 314-5 Shimokanzo, Iwata 438-0193, Japan; (M.K.); (T.O.)
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34
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Veličković D, Chu RK, Myers GL, Ahkami AH, Anderton CR. An approach for visualizing the spatial metabolome of an entire plant root system inspired by the Swiss-rolling technique. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4363. [PMID: 31018010 DOI: 10.1002/jms.4363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 05/11/2023]
Abstract
The spatial configuration and morphology of roots are commonly monitored for a better understanding of plant health and development. However, this approach provides minimal details about the biochemistry regulating the observable traits. Therefore, the ability to metabolically map the entire root structure would be of major value. Here, we developed a sample preparation approach that enables imaging of the entire root within a restricted space (width of microscope slide), which was influenced by the Swiss-rolling technique. We were able to image and confidently identify molecules along the entire root structure from rolled-root tissue sections using multiple spatially resolved mass spectrometry approaches.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Gabriel L Myers
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
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35
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Hay AE, Herrera-Belaroussi A, Rey M, Fournier P, Normand P, Boubakri H. Feedback Regulation of N Fixation in Frankia-Alnus Symbiosis Through Amino Acids Profiling in Field and Greenhouse Nodules. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:499-508. [PMID: 31916486 DOI: 10.1094/mpmi-10-19-0289-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Symbiosis established between actinorhizal plants and Frankia spp., which are nitrogen-fixing actinobacteria, promotes nodule organogenesis, the site of metabolic exchange. The present study aimed to identify amino acid markers involved in Frankia-Alnus interactions by comparing nodules and associated roots from field and greenhouse samples. Our results revealed a high level of citrulline in all samples, followed by arginine (Arg), aspartate (Asp), glutamate (Glu), γ-amino-n-butyric acid (GABA), and alanine (Ala). Interestingly, the field metabolome approach highlighted more contrasted amino acid patterns between nodules and roots compared with greenhouse samples. Indeed, 12 amino acids had a mean relative abundance significantly different between field nodule and root samples, against only four amino acids in greenhouse samples, underlining the importance of developing "ecometabolome" approaches. In order to monitor the effects on Frankia cells (respiration and nitrogen fixation activities) of amino acid with an abundance pattern evocative of a role in symbiosis, in-vitro assays were performed by supplementing them in nitrogen-free cultures. Amino acids had three types of effects: i) those used by Frankia as nitrogen source (Glu, Gln, Asp), ii) amino acids stimulating both nitrogen fixation and respiration (e.g., Cit, GABA, Ala, valine, Asn), and iii) amino acids triggering a toxic effect (Arg, histidine). In this paper, a N-metabolic model was proposed to discuss how the host plant and bacteria modulate amino acids contents in nodules, leading to a fine regulation sustaining high bacterial nitrogen fixation.
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Affiliation(s)
- Anne-Emmanuelle Hay
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
- Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, Centre d'Etude des Substances Naturelles
| | - Aude Herrera-Belaroussi
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Marjolaine Rey
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
- Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, Centre d'Etude des Substances Naturelles
| | - Pascale Fournier
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Philippe Normand
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, F-69361, Lyon, France, Université Claude Bernard Lyon 1, CNRS, UMR 5557, INRA UMR1418, Ecologie Microbienne, F-69622, Villeurbanne, France
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36
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van Schadewijk R, Krug JR, Shen D, Sankar Gupta KBS, Vergeldt FJ, Bisseling T, Webb AG, Van As H, Velders AH, de Groot HJM, Alia A. Magnetic Resonance Microscopy at Cellular Resolution and Localised Spectroscopy of Medicago truncatula at 22.3 Tesla. Sci Rep 2020; 10:971. [PMID: 31969628 PMCID: PMC6976659 DOI: 10.1038/s41598-020-57861-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/18/2019] [Indexed: 01/30/2023] Open
Abstract
Interactions between plants and the soil’s microbial & fungal flora are crucial for the health of soil ecosystems and food production. Microbe-plant interactions are difficult to investigate in situ due to their intertwined relationship involving morphology and metabolism. Here, we describe an approach to overcome this challenge by elucidating morphology and the metabolic profile of Medicago truncatula root nodules using Magnetic Resonance (MR) Microscopy, at the highest magnetic field strength (22.3 T) currently available for imaging. A home-built solenoid RF coil with an inner diameter of 1.5 mm was used to study individual root nodules. A 3D imaging sequence with an isotropic resolution of (7 μm)3 was able to resolve individual cells, and distinguish between cells infected with rhizobia and uninfected cells. Furthermore, we studied the metabolic profile of cells in different sections of the root nodule using localised MR spectroscopy and showed that several metabolites, including betaine, asparagine/aspartate and choline, have different concentrations across nodule zones. The metabolite spatial distribution was visualised using chemical shift imaging. Finally, we describe the technical challenges and outlook towards future in vivo MR microscopy of nodules and the plant root system.
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Affiliation(s)
- Remco van Schadewijk
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Julia R Krug
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands.,Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, Wageningen, 6708 WG, The Netherlands
| | - Defeng Shen
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Karthick B S Sankar Gupta
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - Frank J Vergeldt
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Ton Bisseling
- Laboratory of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Andrew G Webb
- C.J. Gorter Center for High Field MRI, Radiology department, Leiden University Medical Centre, Leiden University, Leiden, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Henk Van As
- Laboratory of Biophysics, Wageningen University & Research, Stippeneng 4, Wageningen, 6708 WE, The Netherlands
| | - Aldrik H Velders
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, Wageningen, 6708 WG, The Netherlands
| | - Huub J M de Groot
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
| | - A Alia
- Solid-state NMR, Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands. .,Institute for Medical Physics and Biophysics, Leipzig University, Härtelstraße 16/18, Leipzig, 04107, Germany.
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37
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Keller C, Gemperline E, Li L. MALDI Mass Spectrometry Imaging of Peptides in Medicago truncatula Root Nodules. Methods Mol Biol 2020; 2139:341-351. [PMID: 32462598 PMCID: PMC7430052 DOI: 10.1007/978-1-0716-0528-8_25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mass spectrometry imaging is routinely used to visualize the distributions of biomolecules in tissue sections. In plants, mass spectrometry imaging of metabolites is more often conducted, but the imaging of larger molecules is less frequently performed despite the importance of proteins and endogenous peptides to the plant. Here, we describe a matrix-assisted laser desorption/ionization mass spectrometry imaging method for the imaging of peptides in Medicago truncatula root nodules. Sample preparation steps including embedding in gelatin, sectioning, and matrix application are described. The method described is employed to determine the spatial distribution of hundreds of peptide peaks.
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Affiliation(s)
- Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Erin Gemperline
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA. .,School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.
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38
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Gupta S, Rupasinghe T, Callahan DL, Natera SHA, Smith PMC, Hill CB, Roessner U, Boughton BA. Spatio-Temporal Metabolite and Elemental Profiling of Salt Stressed Barley Seeds During Initial Stages of Germination by MALDI-MSI and µ-XRF Spectrometry. FRONTIERS IN PLANT SCIENCE 2019; 10:1139. [PMID: 31608088 PMCID: PMC6774343 DOI: 10.3389/fpls.2019.01139] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/21/2019] [Indexed: 05/05/2023]
Abstract
Seed germination is the essential first step in crop establishment, and can be severely affected by salinity stress which can inhibit essential metabolic processes during the germination process. Salt stress during seed germination can trigger lipid-dependent signalling cascades that activate plant adaptation processes, lead to changes in membrane fluidity to help resist the stress, and cause secondary metabolite responses due to increased oxidative stress. In germinating barley (Hordeum vulgare), knowledge of the changes in spatial distribution of lipids and other small molecules at a cellular level in response to salt stress is limited. In this study, mass spectrometry imaging (MSI), liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS), inductively coupled plasma mass spectrometry (ICP-MS), and X-ray fluorescence (XRF) were used to determine the spatial distribution of metabolites, lipids and a range of elements, such as K+ and Na+, in seeds of two barley genotypes with contrasting germination phenology (Australian barley varieties Mundah and Keel). We detected and tentatively identified more than 200 lipid species belonging to seven major lipid classes (fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, prenol lipids, sterol lipids, and polyketides) that differed in their spatial distribution based on genotype (Mundah or Keel), time post-imbibition (0 to 72 h), or treatment (control or salt). We found a tentative flavonoid was discriminant in post-imbibed Mundah embryos under saline conditions, and a delayed flavonoid response in Keel relative to Mundah. We further employed MSI-MS/MS and LC-QToF-MS/MS to explore the identity of the discriminant flavonoid and study the temporal pattern in five additional barley genotypes. ICP-MS was used to quantify the elemental composition of both Mundah and Keel seeds, showing a significant increase in Na+ in salt treated samples. Spatial mapping of elements using µ-XRF localized the elements within the seeds. This study integrates data obtained from three mass spectrometry platforms together with µ-XRF to yield information on the localization of lipids, metabolites and elements improving our understanding of the germination process under salt stress at a molecular level.
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Affiliation(s)
- Sneha Gupta
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Thusitha Rupasinghe
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Damien L. Callahan
- School of Life and Environmental Sciences, Deakin University, Burwood, VIC, Australia
| | - Siria H. A. Natera
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Penelope M. C. Smith
- AgriBio, Centre for AgriBiosciences, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Camilla B. Hill
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Berin A. Boughton
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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39
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Li B, Sun R, Gordon A, Ge J, Zhang Y, Li P, Yang H. 3-Aminophthalhydrazide (Luminol) As a Matrix for Dual-Polarity MALDI MS Imaging. Anal Chem 2019; 91:8221-8228. [PMID: 31149814 DOI: 10.1021/acs.analchem.9b00803] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In many aspects of the matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) technique, the discovery of new MALDI matrixes has been a major task for the improvement of ionization efficiency, signal intensity, and molecular coverage. In this work, five analog compounds, including phthalhydrazide, 3-aminophthalhydrazide (3-APH or luminol) and its sodium salt, 4-aminophthalhydrazide (4-APH), and 3-nitrophthalhydrazide (3-NPH) were evaluated as potential matrixes for MALDI Fourier-transform ion cyclotron resonance (FTICR) MSI of metabolites in mouse brain tissue. The five candidate MALDI matrixes were mainly evaluated according to the solid-state ultraviolet absorption, the ion yields and species, and the dual-polarity detection. Among the five candidate matrixes, 3-APH and its sodium salt enabled the detection of endogenous metabolites better than the three other candidates in dual polarities. The best results were observed with 3-APH. Compared with commonly used MALDI matrixes such as 2,5-dihydroxybenzoic acid, α-cyano-4-hydroxycinnamic acid, and 9-aminoacridine, 3-APH exhibited superior performance in dual polarity MALDI MSI, higher sensitivity, broader molecular coverage, and lower background noise. The use of 3-APH led to on-tissue MALDI FTICR MSI of 159 and 207 mouse brain metabolites in the positive and negative ion modes, respectively. Among these metabolites, nucleotides, fatty acids, glycerolipids, glycerophospholipids, sphingolipids, and saccharolipids are included. 3-APH was further used for MALDI FTICR MSI of metabolic responses to ischemia-induced disturbances in mouse brain subjected to middle cerebral artery occlusion (MCAO), thus revealing the alteration of 105 metabolites in the ipsilateral hemispheres. This further emphasizes the great potential of 3-APH as a matrix for the localization of biomarkers in brain diseases.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , Jiangsu 210009 , China.,School of Traditional Chinese Pharmacy , China Pharmaceutical University , Nanjing , Jiangsu 211198 , China
| | - Ruiyang Sun
- State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , Jiangsu 210009 , China.,School of Traditional Chinese Pharmacy , China Pharmaceutical University , Nanjing , Jiangsu 211198 , China
| | - Andrew Gordon
- State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , Jiangsu 210009 , China.,School of Traditional Chinese Pharmacy , China Pharmaceutical University , Nanjing , Jiangsu 211198 , China
| | - Junyue Ge
- State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , Jiangsu 210009 , China.,School of Traditional Chinese Pharmacy , China Pharmaceutical University , Nanjing , Jiangsu 211198 , China
| | - Ying Zhang
- State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , Jiangsu 210009 , China.,School of Traditional Chinese Pharmacy , China Pharmaceutical University , Nanjing , Jiangsu 211198 , China
| | - Ping Li
- State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , Jiangsu 210009 , China.,School of Traditional Chinese Pharmacy , China Pharmaceutical University , Nanjing , Jiangsu 211198 , China
| | - Hua Yang
- State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing , Jiangsu 210009 , China.,School of Traditional Chinese Pharmacy , China Pharmaceutical University , Nanjing , Jiangsu 211198 , China
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40
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‘What did I do wrong?’ An empirical evaluation of sample preparation methodologies in matrix-assisted laser desorption/ionization-mass spectrometry imaging. Future Sci OA 2019. [DOI: 10.4155/fsoa-2018-0095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: This guide aims to broaden the uptake of MALDI-MSI biomedical research by removing the initial ‘lag phase’ associated with empirical determination in sample preparation and data analysis. Methods: Samples from several tissue types were prepared for lipid, protein and peptide MSI analysis. Broadly, samples were cryo sectioned, mounted onto conductive MALDI slides and sublimed with an analyte specific matrix, recrystallised and analyzed in a Bruker UltrafleXtreme MALDI TOF/TOF. Results/conclusion: Here we present a general guide that serves as the first comprehensive, explanatory index for curation and verification of both sample preparation and data generation during the MALDI-MSI process.
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41
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Cao Q, Wang Y, Chen B, Ma F, Hao L, Li G, Ouyang C, Li L. Visualization and Identification of Neurotransmitters in Crustacean Brain via Multifaceted Mass Spectrometric Approaches. ACS Chem Neurosci 2019; 10:1222-1229. [PMID: 30721026 PMCID: PMC6436947 DOI: 10.1021/acschemneuro.8b00730] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has emerged as a label-free analytical tool for fast biomolecule profiling on tissue sections. Among various functional molecules, mapping neurotransmitters and related metabolites is of tremendous significance, as these compounds are critical to signaling in the central nervous system. Here, we demonstrated the use of both derivatization and reaction-free approaches that greatly reduced signal complexity and thus enabled complementary signaling molecule visualization on crab brain sections via MALDI-LTQ-Orbitrap XL platform. Pyrylium salt served as a primary amine derivatization reagent and produced prominent signal enhancement of multiple neurotransmitters, including dopamine, serotonin, γ-aminobutyric acid, and histamine that were not detected in underivatized tissues. Molecules with other functional groups, such as acetylcholine and phosphocholine, were directly imaged after matrix application. The identities of discovered neurotransmitters were verified by standards using LC-MS/MS. This study broadens our understanding of metabolic signaling in the crustacean nervous system and highlights potential of multifaceted MS techniques for unambiguous neurotransmitter characterization.
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Affiliation(s)
- Qinjingwen Cao
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yijia Wang
- Department of Chemical Physics, School of Chemistry and Materials Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Bingming Chen
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Fengfei Ma
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Ling Hao
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Gongyu Li
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Chuanzi Ouyang
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- School of Pharmacy, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
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42
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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43
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Glycosylamines-based reactive matrix designed for imaging acidity in Ponkan fruit using matrix assisted laser desorption/ionization mass spectrometry imaging. Anal Chim Acta 2018; 1041:78-86. [DOI: 10.1016/j.aca.2018.09.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 11/22/2022]
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44
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Barbosa EA, Bonfim MF, Bloch C, Engler G, Rocha T, de Almeida Engler J. Imaging Mass Spectrometry of Endogenous Polypeptides and Secondary Metabolites from Galls Induced by Root-Knot Nematodes in Tomato Roots. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1048-1059. [PMID: 29663868 DOI: 10.1094/mpmi-02-18-0049-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nematodes are devastating pests that infect most cultivated plant species and cause considerable agricultural losses worldwide. The understanding of metabolic adjustments induced during plant-nematode interaction is crucial to generate resistant plants or to select more efficient molecules to fight against this pest. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has been used herein for in situ detection and mapping endogenous polypeptides and secondary metabolites from nematode-induced gall tissue. One of the major critical features of this technique is sample preparation; mainly, the generation of intact sections of plant cells with their rigid cell walls and vacuolated cytoplasm. Our experimental settings allowed us to obtain sections without contamination of exogenous ions or diffusion of molecules and to map the differential presence of low and high molecular weight ions in uninfected roots compared with nematode-induced galls. We predict the presence of lipids in both uninfected roots and galls, which was validated by MALDI time-of-flight tandem mass spectrometry and high-resolution mass spectrometry analysis of lipid extracts. Based on the isotopic ion distribution profile, both esters and glycerophospholipids were predicted compounds and may be playing an important role in gall development. Our results indicate that the MALDI-MSI technology is a promising tool to identify secondary metabolites as well as peptides and proteins in complex plant tissues like galls to decipher molecular processes responsible for infection and maintenance of these feeding sites during nematode parasitism.
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Affiliation(s)
- Eder Alves Barbosa
- 1 Laboratório de espectrometria de massa, Embrapa Recursos Genéticos e Biotecnologia, PqEB, 70770-900, Brasília-DF, Brazil
- 2 Laboratório de Síntese e Análise de Biomoléculas, Instituto de Química, Universidade de Brasília, 70910-900, Brasília-DF, Brazil
| | - Mauro Ferreira Bonfim
- 2 Laboratório de Síntese e Análise de Biomoléculas, Instituto de Química, Universidade de Brasília, 70910-900, Brasília-DF, Brazil
- 3 Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB; and
| | - Carlos Bloch
- 1 Laboratório de espectrometria de massa, Embrapa Recursos Genéticos e Biotecnologia, PqEB, 70770-900, Brasília-DF, Brazil
| | - Gilbert Engler
- 4 INRA, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Thales Rocha
- 3 Laboratório de Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, PqEB; and
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Veličković D, Agtuca BJ, Stopka SA, Vertes A, Koppenaal DW, Paša-Tolić L, Stacey G, Anderton CR. Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange. THE ISME JOURNAL 2018. [PMID: 29899508 DOI: 10.1038/s41396-018-0188-188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
In this study, the three-dimensional spatial distributions of a number of metabolites involved in regulating symbiosis and biological nitrogen fixation (BNF) within soybean root nodules were revealed using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). While many metabolites exhibited distinct spatial compartmentalization, some metabolites were asymmetrically distributed throughout the nodule (e.g., S-adenosylmethionine). These results establish a more complex metabolic view of plant-bacteria symbiosis (and BNF) within soybean nodules than previously hypothesized. Collectively these findings suggest that spatial perspectives in metabolic regulation should be considered to unravel the overall complexity of interacting organisms, like those relating to associations of nitrogen-fixing bacteria with host plants.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA.
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Veličković D, Agtuca BJ, Stopka SA, Vertes A, Koppenaal DW, Paša-Tolić L, Stacey G, Anderton CR. Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange. THE ISME JOURNAL 2018; 12:2335-2338. [PMID: 29899508 PMCID: PMC6092352 DOI: 10.1038/s41396-018-0188-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/02/2018] [Accepted: 02/26/2018] [Indexed: 11/30/2022]
Abstract
In this study, the three-dimensional spatial distributions of a number of metabolites involved in regulating symbiosis and biological nitrogen fixation (BNF) within soybean root nodules were revealed using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). While many metabolites exhibited distinct spatial compartmentalization, some metabolites were asymmetrically distributed throughout the nodule (e.g., S-adenosylmethionine). These results establish a more complex metabolic view of plant-bacteria symbiosis (and BNF) within soybean nodules than previously hypothesized. Collectively these findings suggest that spatial perspectives in metabolic regulation should be considered to unravel the overall complexity of interacting organisms, like those relating to associations of nitrogen-fixing bacteria with host plants.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA.
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Qin L, Zhang Y, Liu Y, He H, Han M, Li Y, Zeng M, Wang X. Recent advances in matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) for in situ analysis of endogenous molecules in plants. PHYTOCHEMICAL ANALYSIS : PCA 2018; 29:351-364. [PMID: 29667236 DOI: 10.1002/pca.2759] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/01/2018] [Accepted: 02/04/2018] [Indexed: 05/27/2023]
Abstract
INTRODUCTION Mass spectrometry imaging (MSI) as a label-free and powerful imaging technique enables in situ evaluation of a tissue metabolome and/or proteome, becoming increasingly popular in the detection of plant endogenous molecules. OBJECTIVE The characterisation of structure and spatial information of endogenous molecules in plants are both very important aspects to better understand the physiological mechanism of plant organism. METHODS Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a commonly-used tissue imaging technique, which requires matrix to assist in situ detection of a variety of molecules on the surface of a tissue section. In previous studies, MALDI-MSI was mostly used for the detection of molecules from animal tissue sections, compared to plant samples due to cell structural limitations, such as plant cuticles, epicuticular waxes, and cell walls. Despite the enormous progress that has been made in tissue imaging, there is still a challenge for MALDI-MSI suitable for the imaging of endogenous compounds in plants. RESULTS This review summarises the recent advances in MALDI-MSI, focusing on the application of in situ detection of endogenous molecules in different plant organs, i.e. root, stem, leaf, flower, fruit, and seed. CONCLUSION Further improvements on instrumentation sensitivity, matrix selection, image processing and sample preparation will expand the application of MALDI-MSI in plant research.
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Affiliation(s)
- Liang Qin
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Yawen Zhang
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Yaqin Liu
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Huixin He
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Manman Han
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
| | - Yanyan Li
- The Hospital of Minzu University of China, Minzu University of China, Beijing, P. R. China
| | - Maomao Zeng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- Collaborative Innovation Centre of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, P. R. China
| | - Xiaodong Wang
- Centre for Imaging & Systems Biology, Minzu University of China, Beijing, P. R. China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, P. R. China
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Separation and characterization of homopipecolic acid isoflavonoid ester derivatives isolated from Ononis spinosa L. root. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1091:21-28. [PMID: 29803686 DOI: 10.1016/j.jchromb.2018.05.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/09/2018] [Accepted: 05/15/2018] [Indexed: 11/21/2022]
Abstract
Spiny restharrow root (Ononis spinosa L.) and its preparations are mainly used for the treatment of urinary infections or bladder stones in numerous countries. Spiny restharrow root is rich in isoflavonoids (formononetin, calycosin and pseudobaptigenin), pterocarpans (medicarpin and maackiain) and dihydroisoflavonoids (onogenin and sativanone), which metabolites are present as glucosides, glucoside malonates, glucoside acetates and free aglycones in the root. The in-depth analysis of tandem mass spectrometric (MS) and high-resolution MS (HR-MS) data revealed the presence of nitrogen-containing compounds in the root extracts. An ion-exchange-based purification and a preparative-scale reversed phase chromatographic isolation procedure was developed for the characterization of these new natural products. For the unambiguous identification of the isolated compounds NMR experiments were carried out. The thorough characterization confirmed the presence of six piperidin-2-yl-acetic acid (homopipecolic acid) esters of isoflavonoid glucosides. This is the first report of homopipecolic acid esters isolated from higher plants.
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O'Rourke MB, Padula MP, Smith C, Youssef P, Cordwell S, Witting P, Sutherland G, Crossett B. Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows. J Vis Exp 2018. [PMID: 29364257 DOI: 10.3791/56778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The use of matrix-assisted laser desorption/ionization, mass spectrometry imaging (MALDI MSI) has rapidly expanded, since this technique analyzes a host of biomolecules from drugs and lipids to N-glycans. Although various sample preparation techniques exist, detecting peptides from formaldehyde preserved tissues remains one of the most difficult challenges for this type of mass spectrometric analysis. For this reason, we have created and optimized a robust methodology that preserves the spatial information contained within the sample, while eliciting the greatest number of ionizable peptides. We have also aimed to achieve this in a cost effective and simple way, thereby eliminating potential bias or preparation error, which can occur when using automated instrumentation. The end result is a reproducible and inexpensive protocol.
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Affiliation(s)
- Matthew B O'Rourke
- Mass Spectrometry Core Facility, University of Sydney; Proteomics Core Facility, University of Technology Sydney;
| | | | - Caine Smith
- Neuropathology Group, Discipline of Pathology, School of Medical Sciences, University of Sydney
| | - Priscilla Youssef
- Redox Biology Group, Discipline of Pathology, School of Medical Sciences, University of Sydney
| | | | - Paul Witting
- Redox Biology Group, Discipline of Pathology, School of Medical Sciences, University of Sydney
| | - Greg Sutherland
- Neuropathology Group, Discipline of Pathology, School of Medical Sciences, University of Sydney
| | - Ben Crossett
- Mass Spectrometry Core Facility, University of Sydney
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50
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Stasulli NM, Shank EA. Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry. FEMS Microbiol Rev 2018; 40:807-813. [PMID: 28204504 DOI: 10.1093/femsre/fuw032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/11/2016] [Accepted: 07/22/2016] [Indexed: 02/07/2023] Open
Abstract
The ability of microbes to secrete bioactive chemical signals into their environment has been known for over a century. However, it is only in the last decade that imaging mass spectrometry has provided us with the ability to directly visualize the spatial distributions of these microbial metabolites. This technology involves collecting mass spectra from multiple discrete locations across a biological sample, yielding chemical ‘maps’ that simultaneously reveal the distributions of hundreds of metabolites in two dimensions. Advances in microbial imaging mass spectrometry summarized here have included the identification of novel strain- or coculture-specific compounds, the visualization of biotransformation events (where one metabolite is converted into another by a neighboring microbe), and the implementation of a method to reconstruct the 3D subsurface distributions of metabolites, among others. Here we review the recent literature and discuss how imaging mass spectrometry has spurred novel insights regarding the chemical consequences of microbial interactions.
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Affiliation(s)
- Nikolas M Stasulli
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Elizabeth A Shank
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, NC, USA.,Curriculum of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, NC, USA
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