1
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Khadem H, Mangini M, Farazpour S, De Luca AC. Correlative Raman Imaging: Development and Cancer Applications. BIOSENSORS 2024; 14:324. [PMID: 39056600 PMCID: PMC11274409 DOI: 10.3390/bios14070324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024]
Abstract
Despite extensive research efforts, cancer continues to stand as one of the leading causes of death on a global scale. To gain profound insights into the intricate mechanisms underlying cancer onset and progression, it is imperative to possess methodologies that allow the study of cancer cells at the single-cell level, focusing on critical parameters such as cell morphology, metabolism, and molecular characteristics. These insights are essential for effectively discerning between healthy and cancerous cells and comprehending tumoral progression. Recent advancements in microscopy techniques have significantly advanced the study of cancer cells, with Raman microspectroscopy (RM) emerging as a particularly powerful tool. Indeed, RM can provide both biochemical and spatial details at the single-cell level without the need for labels or causing disruptions to cell integrity. Moreover, RM can be correlated with other microscopy techniques, creating a synergy that offers a spectrum of complementary insights into cancer cell morphology and biology. This review aims to explore the correlation between RM and other microscopy techniques such as confocal fluoresce microscopy (CFM), atomic force microscopy (AFM), digital holography microscopy (DHM), and mass spectrometry imaging (MSI). Each of these techniques has their own strengths, providing different perspectives and parameters about cancer cell features. The correlation between information from these various analysis methods is a valuable tool for physicians and researchers, aiding in the comprehension of cancer cell morphology and biology, unraveling mechanisms underlying cancer progression, and facilitating the development of early diagnosis and/or monitoring cancer progression.
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Affiliation(s)
- Hossein Khadem
- Institute for Experimental Endocrinology and Oncology 'G. Salvatore', IEOS-Second Unit, National Research Council, 80131 Naples, Italy
| | - Maria Mangini
- Institute for Experimental Endocrinology and Oncology 'G. Salvatore', IEOS-Second Unit, National Research Council, 80131 Naples, Italy
| | - Somayeh Farazpour
- Institute for Experimental Endocrinology and Oncology 'G. Salvatore', IEOS-Second Unit, National Research Council, 80131 Naples, Italy
| | - Anna Chiara De Luca
- Institute for Experimental Endocrinology and Oncology 'G. Salvatore', IEOS-Second Unit, National Research Council, 80131 Naples, Italy
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2
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Parmar D, Rosado-Rosa JM, Shrout JD, Sweedler JV. Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms. Methods 2024; 224:21-34. [PMID: 38295894 PMCID: PMC11149699 DOI: 10.1016/j.ymeth.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/17/2023] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.
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Affiliation(s)
- Dharmeshkumar Parmar
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joenisse M Rosado-Rosa
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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3
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Jensen M, Liu S, Stepula E, Martella D, Birjandi AA, Farrell‐Dillon K, Chan KLA, Parsons M, Chiappini C, Chapple SJ, Mann GE, Vercauteren T, Abbate V, Bergholt MS. Opto-Lipidomics of Tissues. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302962. [PMID: 38145965 PMCID: PMC11005704 DOI: 10.1002/advs.202302962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/30/2023] [Indexed: 12/27/2023]
Abstract
Lipid metabolism and signaling play pivotal functions in biology and disease development. Despite this, currently available optical techniques are limited in their ability to directly visualize the lipidome in tissues. In this study, opto-lipidomics, a new approach to optical molecular tissue imaging is introduced. The capability of vibrational Raman spectroscopy is expanded to identify individual lipids in complex tissue matrices through correlation with desorption electrospray ionization (DESI) - mass spectrometry (MS) imaging in an integrated instrument. A computational pipeline of inter-modality analysis is established to infer lipidomic information from optical vibrational spectra. Opto-lipidomic imaging of transient cerebral ischemia-reperfusion injury in a murine model of ischemic stroke demonstrates the visualization and identification of lipids in disease with high molecular specificity using Raman scattered light. Furthermore, opto-lipidomics in a handheld fiber-optic Raman probe is deployed and demonstrates real-time classification of bulk brain tissues based on specific lipid abundances. Opto-lipidomics opens a host of new opportunities to study lipid biomarkers for diagnostics, prognostics, and novel therapeutic targets.
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Affiliation(s)
- Magnus Jensen
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
| | - Shiyue Liu
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
- Institute of Pharmaceutical ScienceKing's College LondonLondonSE1 9NHUK
| | - Elzbieta Stepula
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
| | - Davide Martella
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
| | - Anahid A. Birjandi
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
| | - Keith Farrell‐Dillon
- King's British Heart Foundation Centre of Research ExcellenceSchool of Cardiovascular and Metabolic Medicine & SciencesFaculty of Life Sciences & MedicineKing's College London150 Stamford StreetLondonSE1 9NHUK
| | | | - Maddy Parsons
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonSE1 1ULUK
| | - Ciro Chiappini
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
| | - Sarah J. Chapple
- Institute of Pharmaceutical ScienceKing's College LondonLondonSE1 9NHUK
- King's British Heart Foundation Centre of Research ExcellenceSchool of Cardiovascular and Metabolic Medicine & SciencesFaculty of Life Sciences & MedicineKing's College London150 Stamford StreetLondonSE1 9NHUK
| | - Giovanni E. Mann
- Institute of Pharmaceutical ScienceKing's College LondonLondonSE1 9NHUK
- King's British Heart Foundation Centre of Research ExcellenceSchool of Cardiovascular and Metabolic Medicine & SciencesFaculty of Life Sciences & MedicineKing's College London150 Stamford StreetLondonSE1 9NHUK
| | - Tom Vercauteren
- School of Biomedical Engineering and Imaging SciencesKing's College LondonLondonWC2R 2LSUK
| | - Vincenzo Abbate
- Department of AnalyticalEnvironmental and Forensic SciencesKing's College London150 Stamford StreetLondonSE1 9NHUK
| | - Mads S. Bergholt
- Centre for Craniofacial and Regenerative BiologyKing's College LondonLondonSE1 9RTUK
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4
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Barut I, Fletcher JS. Cell and tissue imaging by secondary ion mass spectrometry. Biointerphases 2023; 18:061202. [PMID: 38108477 DOI: 10.1116/6.0003140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023] Open
Abstract
This Tutorial focuses on the use of secondary ion mass spectrometry for the analysis of cellular and tissue samples. The Tutorial aims to cover the considerations in sample preparation analytical set up and some specific aspects of data interpretation associated with such analysis.
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Affiliation(s)
- Inci Barut
- Department of Pharmacy, Basic Pharmaceutical Sciences, Gazi University, Ankara 06330, Turkey
| | - John S Fletcher
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 413 90, Sweden
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5
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Fu B, Mao X, Park Y, Zhao Z, Yan T, Jung W, Francis DH, Li W, Pian B, Salimijazi F, Suri M, Hanrath T, Barstow B, Chen P. Single-cell multimodal imaging uncovers energy conversion pathways in biohybrids. Nat Chem 2023; 15:1400-1407. [PMID: 37500951 DOI: 10.1038/s41557-023-01285-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Microbe-semiconductor biohybrids, which integrate microbial enzymatic synthesis with the light-harvesting capabilities of inorganic semiconductors, have emerged as promising solar-to-chemical conversion systems. Improving the electron transport at the nano-bio interface and inside cells is important for boosting conversion efficiencies, yet the underlying mechanism is challenging to study by bulk measurements owing to the heterogeneities of both constituents. Here we develop a generalizable, quantitative multimodal microscopy platform that combines multi-channel optical imaging and photocurrent mapping to probe such biohybrids down to single- to sub-cell/particle levels. We uncover and differentiate the critical roles of different hydrogenases in the lithoautotrophic bacterium Ralstonia eutropha for bioplastic formation, discover this bacterium's surprisingly large nanoampere-level electron-uptake capability, and dissect the cross-membrane electron-transport pathways. This imaging platform, and the associated analytical framework, can uncover electron-transport mechanisms in various types of biohybrid, and potentially offers a means to use and engineer R. eutropha for efficient chemical production coupled with photocatalytic materials.
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Affiliation(s)
- Bing Fu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Xianwen Mao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Materials Science and Engineering, Institute of Functional Intelligent Materials, and Centre for Advanced 2D Materials, National University of Singapore, Singapore, Singapore
| | - Youngchan Park
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Zhiheng Zhao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Tianlei Yan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Won Jung
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Danielle H Francis
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Friends School of Baltimore, Baltimore, MD, USA
| | - Wenjie Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Brooke Pian
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Farshid Salimijazi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Mokshin Suri
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, USA
| | - Tobias Hanrath
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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6
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van Hoogstraten SWG, Kuik C, Arts JJC, Cillero-Pastor B. Molecular imaging of bacterial biofilms-a systematic review. Crit Rev Microbiol 2023:1-22. [PMID: 37452571 DOI: 10.1080/1040841x.2023.2223704] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023]
Abstract
The formation of bacterial biofilms in the human body and on medical devices is a serious human health concern. Infections related to bacterial biofilms are often chronic and difficult to treat. Detailed information on biofilm formation and composition over time is essential for a fundamental understanding of the underlying mechanisms of biofilm formation and its response to anti-biofilm therapy. However, information on the chemical composition, structural components of biofilms, and molecular interactions regarding metabolism- and communication pathways within the biofilm, such as uptake of administered drugs or inter-bacteria communication, remains elusive. Imaging these molecules and their distribution in the biofilm increases insight into biofilm development, growth, and response to environmental factors or drugs. This systematic review provides an overview of molecular imaging techniques used for bacterial biofilm imaging. The techniques included mass spectrometry-based techniques, fluorescence-labelling techniques, spectroscopic techniques, nuclear magnetic resonance spectroscopy (NMR), micro-computed tomography (µCT), and several multimodal approaches. Many molecules were imaged, such as proteins, lipids, metabolites, and quorum-sensing (QS) molecules, which are crucial in intercellular communication pathways. Advantages and disadvantages of each technique, including multimodal approaches, to study molecular processes in bacterial biofilms are discussed, and recommendations on which technique best suits specific research aims are provided.
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Affiliation(s)
- S W G van Hoogstraten
- Laboratory for Experimental Orthopaedics, Department of Orthopaedic Surgery, CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - C Kuik
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, the Netherlands
| | - J J C Arts
- Laboratory for Experimental Orthopaedics, Department of Orthopaedic Surgery, CAPHRI, Maastricht University Medical Centre, Maastricht, the Netherlands
- Department of Biomedical Engineering, Orthopaedic Biomechanics, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - B Cillero-Pastor
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, the Netherlands
- Department of Cell Biology-Inspired Tissue Engineering, The MERLN Institute for Technology-Inspired Regenerative Medicine, University of Maastricht, Maastricht, the Netherlands
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7
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Burzio C, Mohammadi AS, Malmberg P, Modin O, Persson F, Wilén BM. Chemical Imaging of Pharmaceuticals in Biofilms for Wastewater Treatment Using Secondary Ion Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7431-7441. [PMID: 37130040 DOI: 10.1021/acs.est.2c05027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The occurrence of pharmaceuticals in the aquatic environment is a global water quality challenge for several reasons, such as deleterious effects on ecological and human health, antibiotic resistance development, and endocrine-disrupting effects on aquatic organisms. To optimize their removal from the water cycle, understanding the processes during biological wastewater treatment is crucial. Time-of-flight secondary ion mass spectrometry imaging was successfully applied to investigate and analyze the distribution of pharmaceuticals as well as endogenous molecules in the complex biological matrix of biofilms for wastewater treatment. Several compounds and their localization were identified in the biofilm section, including citalopram, ketoconazole, ketoconazole transformation products, and sertraline. The images revealed the pharmaceuticals gathered in distinct sites of the biofilm matrix. While citalopram penetrated the biofilm deeply, sertraline remained confined in its outer layer. Both pharmaceuticals seemed to mainly colocalize with phosphocholine lipids. Ketoconazole concentrated in small areas with high signal intensity. The approach outlined here presents a powerful strategy for visualizing the chemical composition of biofilms for wastewater treatment and demonstrates its promising utility for elucidating the mechanisms behind pharmaceutical and antimicrobial removal in biological wastewater treatment.
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Affiliation(s)
- Cecilia Burzio
- Department of Architecture and Civil Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Amir Saeid Mohammadi
- Department of Architecture and Civil Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Per Malmberg
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Oskar Modin
- Department of Architecture and Civil Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Frank Persson
- Department of Architecture and Civil Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Britt-Marie Wilén
- Department of Architecture and Civil Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
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8
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Robertson SN, Soukarieh F, White TM, Camara M, Romero M, Griffiths RL. Probing Interkingdom Signaling Molecules via Liquid Extraction Surface Analysis-Mass Spectrometry. Anal Chem 2023; 95:5079-5086. [PMID: 36881460 PMCID: PMC10034741 DOI: 10.1021/acs.analchem.2c05703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Previously, metabolites diffused or secreted from microbial samples have been analyzed via liquid chromatography-mass spectrometry (LC-MS) approaches following lengthy extraction protocols. Here, we present a model system for growing biofilms on discs before utilizing rapid and direct surface sampling MS, namely, liquid extraction surface analysis, to study the microbial exometabolome. One of the benefits of this approach is its surface-specific nature, enabling mimicking biofilm formation in a way that the study of planktonic liquid cultures cannot imitate. Even though Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Candida albicans (C. albicans) have been studied previously in isolation, very few studies consider the complexity of the interplay between these pathogens, which are commonly combined causative agents of infection. Our model system provides a route to investigate changes in the exometabolome, such as metabolites that become circulatory in the presence of multiple pathogens. Our results agree with previous reports showing that 2-alkyl-4(1H)-quinolone signal molecules produced by P. aeruginosa are important markers of infection and suggest that methods for monitoring levels of 2-heptyl-4-hydroxyquinoline and 2,4-dihydroxyquinoline, as well as pyocyanin, could be beneficial in the determination of causative agents in interkingdom infection including P. aeruginosa. Furthermore, studying changes in exometabolome metabolites between pqs quorum sensing antagonists in treated and nontreated samples suggests suppression of phenazine production by P. aeruginosa. Hence, our model provides a rapid analytical approach to gaining a mechanistic understanding of bacterial signaling.
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Affiliation(s)
- Shaun N Robertson
- U.K. National Biofilm Innovation Centre (NBIC), Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD Nottingham, U.K
| | - Fadi Soukarieh
- U.K. National Biofilm Innovation Centre (NBIC), Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD Nottingham, U.K
| | - Thomas M White
- Faculty of Science, School of Pharmacy, University of Nottingham, NG7 2RD Nottingham, U.K
| | - Miguel Camara
- U.K. National Biofilm Innovation Centre (NBIC), Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD Nottingham, U.K
| | - Manuel Romero
- U.K. National Biofilm Innovation Centre (NBIC), Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD Nottingham, U.K
- Department of Microbiology and Parasitology, Faculty of Biology-CIBUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Rian L Griffiths
- Faculty of Science, School of Pharmacy, University of Nottingham, NG7 2RD Nottingham, U.K
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9
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Abouleila Y, Ali A, Masuda K, Mashaghi A, Shimizu Y. Capillary microsampling-based single-cell metabolomics by mass spectrometry and its applications in medicine and drug discovery. Cancer Biomark 2022; 33:437-447. [DOI: 10.3233/cbm-210184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Characterization of cellular metabolic states is a technical challenge in biomedicine. Cellular heterogeneity caused by inherent diversity in expression of metabolic enzymes or due to sensitivity of metabolic reactions to perturbations, necessitates single cell analysis of metabolism. Heterogeneity is typically seen in cancer and thus, single-cell metabolomics is expectedly useful in studying cancer progression, metastasis, and variations in cancer drug response. However, low sample volumes and analyte concentrations limit detection of critically important metabolites. Capillary microsampling-based mass spectrometry approaches are emerging as a promising solution for achieving single-cell omics. Herein, we focus on the recent advances in capillary microsampling-based mass spectrometry techniques for single-cell metabolomics. We discuss recent technical developments and applications to cancer medicine and drug discovery.
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Affiliation(s)
- Yasmine Abouleila
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- Research Center, Misr International University, Cairo, Egypt
| | - Ahmed Ali
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- Research Center, Misr International University, Cairo, Egypt
| | - Keiko Masuda
- RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Alireza Mashaghi
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
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11
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Mass spectrometry imaging and its potential in food microbiology. Int J Food Microbiol 2022; 371:109675. [DOI: 10.1016/j.ijfoodmicro.2022.109675] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022]
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12
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González-Cabrera M, Wieland K, Eitenberger E, Bleier A, Brunnbauer L, Limbeck A, Hutter H, Haisch C, Lendl B, Domínguez-Vidal A, Ayora-Cañada MJ. Multisensor hyperspectral imaging approach for the microchemical analysis of ultramarine blue pigments. Sci Rep 2022; 12:707. [PMID: 35027601 PMCID: PMC8758711 DOI: 10.1038/s41598-021-04597-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/28/2021] [Indexed: 12/27/2022] Open
Abstract
This work presents a multisensor hyperspectral approach for the characterization of ultramarine blue, a valuable historical pigment, at the microscopic scale combining the information of four analytical techniques at the elemental and molecular levels. The hyperspectral images collected were combined in a single hypercube, where the pixels of the various spectral components are aligned on top of each other. Selected spectral descriptors have been defined to reduce data dimensionality before applying unsupervised chemometric data analysis approaches. Lazurite, responsible for the blue color of the pigment, was detected as the major mineral phase present in synthetic and good quality pigments. Impurities like pyrite were detected in lower quality samples, although the clear identification of other mineral phases with silicate basis was more difficult. There is no correlation between the spatial distribution of the bands arising in the Raman spectra of natural samples in the region 1200-1850 cm-1 and any of the transition metals or rare earth elements (REE). With this information, the previous hypothesis (based on bulk analysis) attributing these bands to luminescence emissions due to impurities of these elements must be revised. We propose the consideration of CO2 molecules trapped in the cages of the aluminosilicate structure of sodalite-type. Additionally, correlation between certain Raman features and the combined presence of Ca, P, and REE, in particular Nd, was detected for the lowest quality pigment. Our results highlight the usefulness of fusing chemical images obtained via different imaging techniques to obtain relevant information on chemical structure and properties.
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Affiliation(s)
- M González-Cabrera
- Department of Physical and Analytical Chemistry, Universidad de Jaén, Campus Las Lagunillas, s/n, 23071, Jaén, Spain
| | - K Wieland
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
- Chair of Analytical Chemistry, Technical University of Munich, Elisabeth-Winterhalter-Weg 6, 81377, Munich, Germany
| | - E Eitenberger
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - A Bleier
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - L Brunnbauer
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - A Limbeck
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - H Hutter
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - C Haisch
- Chair of Analytical Chemistry, Technical University of Munich, Elisabeth-Winterhalter-Weg 6, 81377, Munich, Germany
| | - B Lendl
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164, 1060, Vienna, Austria
| | - A Domínguez-Vidal
- Department of Physical and Analytical Chemistry, Universidad de Jaén, Campus Las Lagunillas, s/n, 23071, Jaén, Spain
| | - M J Ayora-Cañada
- Department of Physical and Analytical Chemistry, Universidad de Jaén, Campus Las Lagunillas, s/n, 23071, Jaén, Spain.
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13
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Iakab S, Ràfols P, Correig-Blanchar X, García-Altares M. Perspective on Multimodal Imaging Techniques Coupling Mass Spectrometry and Vibrational Spectroscopy: Picturing the Best of Both Worlds. Anal Chem 2021; 93:6301-6310. [PMID: 33856207 PMCID: PMC8491157 DOI: 10.1021/acs.analchem.0c04986] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/07/2021] [Indexed: 01/19/2023]
Abstract
Studies on complex biological phenomena often combine two or more imaging techniques to collect high-quality comprehensive data directly in situ, preserving the biological context. Mass spectrometry imaging (MSI) and vibrational spectroscopy imaging (VSI) complement each other in terms of spatial resolution and molecular information. In the past decade, several combinations of such multimodal strategies arose in research fields as diverse as microbiology, cancer, and forensics, overcoming many challenges toward the unification of these techniques. Here we focus on presenting the advantages and challenges of multimodal imaging from the point of view of studying biological samples as well as giving a perspective on the upcoming trends regarding this topic. The latest efforts in the field are discussed, highlighting the purpose of the technique for clinical applications.
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Affiliation(s)
- Stefania
Alexandra Iakab
- Rovira
i Virgili University, Department of Electronic
Engineering, IISPV, 43007 Tarragona, Spain
- Spanish
Biomedical Research Centre in Diabetes and Associated Metabolic Disorders
(CIBERDEM), 28029 Madrid, Spain
| | - Pere Ràfols
- Rovira
i Virgili University, Department of Electronic
Engineering, IISPV, 43007 Tarragona, Spain
- Spanish
Biomedical Research Centre in Diabetes and Associated Metabolic Disorders
(CIBERDEM), 28029 Madrid, Spain
| | - Xavier Correig-Blanchar
- Rovira
i Virgili University, Department of Electronic
Engineering, IISPV, 43007 Tarragona, Spain
- Spanish
Biomedical Research Centre in Diabetes and Associated Metabolic Disorders
(CIBERDEM), 28029 Madrid, Spain
| | - María García-Altares
- Rovira
i Virgili University, Department of Electronic
Engineering, IISPV, 43007 Tarragona, Spain
- Spanish
Biomedical Research Centre in Diabetes and Associated Metabolic Disorders
(CIBERDEM), 28029 Madrid, Spain
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14
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Jia J, Ellis JF, Cao T, Fu K, Morales-Soto N, Shrout JD, Sweedler JV, Bohn PW. Biopolymer Patterning-Directed Secretion in Mucoid and Nonmucoid Strains of Pseudomonas aeruginosa Revealed by Multimodal Chemical Imaging. ACS Infect Dis 2021; 7:598-607. [PMID: 33620198 DOI: 10.1021/acsinfecdis.0c00765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quinolone, pyocyanin, and rhamnolipid production were studied in Pseudomonas aeruginosa by spatially patterning mucin, a glycoprotein important to infection of lung epithelia. Mass spectrometric imaging and confocal Raman microscopy are combined to probe P. aeruginosa biofilms from mucoid and nonmucoid strains grown on lithographically defined patterns. Quinolone signatures from biofilms on patterned vs unpatterned and mucin vs mercaptoundecanoic acid (MUA) surfaces were compared. Microbial attachment is accompanied by secretion of 2-alkyl-4-quinolones as well as rhamnolipids from the mucoid and nonmucoid strains. Pyocyanin was also detected both in the biofilm and in the supernatant in the mucoid strain only. Significant differences in the spatiotemporal distributions of secreted factors are observed between strains and among different surface patterning conditions. The mucoid strain is sensitive to composition and patterning while the nonmucoid strain is not, and in promoting community development in the mucoid strain, nonpatterned surfaces are better than patterned, and mucin is better than MUA. Also, the mucoid strain secretes the virulence factor pyocyanin in a way that correlates with distress. A change in the relative abundance for two rhamnolipids is observed in the mucoid strain during exposure to mucin, whereas minimal variation is observed in the nonmucoid strain. Differences between mucoid and nonmucoid strains are consistent with their strain-specific phenology, in which the mucoid strain develops highly protected and withdrawn biofilms that achieve Pseudomonas quinolone signal production under limited conditions.
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Affiliation(s)
- Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Joanna F. Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,United States
| | - Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kaiyu Fu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556,United States
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556,United States
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801,United States
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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15
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Lorenz M, Wagner R, Jesse S, Marsh JM, Mamak M, Proksch R, Ovchinnikova OS. Nanoscale Mass Spectrometry Multimodal Imaging via Tip-Enhanced Photothermal Desorption. ACS NANO 2020; 14:16791-16802. [PMID: 33232114 DOI: 10.1021/acsnano.0c05019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Materials ranging from adhesives, pharmaceuticals, lubricants, and personal care products are traditionally studied using macroscopic characterization techniques. However, their functionality is in reality defined by details of chemical organization on often noncrystalline matter with characteristic length scales on the order of microns to nanometers. Additionally, these materials are traditionally difficult to analyze using standard vacuum-based approaches that provide nanoscale chemical characterization due to their volatile and beam-sensitive nature. Therefore, approaches that operate under ambient conditions need to be developed that allow probing of nanoscale chemical phenomena and correlated functionality. Here, we demonstrate a tool for probing and visualizing local chemical environments and correlating them to material structure and functionality using advanced multimodal chemical imaging on a combined atomic force microscopy (AFM) and mass spectrometry (MS) system using tip-enhanced photothermal desorption with atmospheric pressure chemical ionization (APCI). We demonstrate enhanced performance metrics of the technique for correlated imaging and point sampling and illustrate the applicability for the analysis of trace chemicals on a human hair, additives in adhesives on paper, and pharmaceuticals samples notoriously difficult to analyze in a vacuum environment. Overall, this approach of correlating local chemical environments to structure and functionality is key to advancing research in many fields ranging from biology, to medicine, to material science.
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Affiliation(s)
- Matthias Lorenz
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Ryan Wagner
- Asylum Research an Oxford Instruments Company, Santa Barbara, California 93117, United States
| | - Stephen Jesse
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | | | - Marc Mamak
- Procter & Gamble Company, Cincinnati, Ohio 45202, United States
| | - Roger Proksch
- Asylum Research an Oxford Instruments Company, Santa Barbara, California 93117, United States
| | - Olga S Ovchinnikova
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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16
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Tuck M, Blanc L, Touti R, Patterson NH, Van Nuffel S, Villette S, Taveau JC, Römpp A, Brunelle A, Lecomte S, Desbenoit N. Multimodal Imaging Based on Vibrational Spectroscopies and Mass Spectrometry Imaging Applied to Biological Tissue: A Multiscale and Multiomics Review. Anal Chem 2020; 93:445-477. [PMID: 33253546 DOI: 10.1021/acs.analchem.0c04595] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tuck
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Landry Blanc
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Rita Touti
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232-8575, United States
| | - Sebastiaan Van Nuffel
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sandrine Villette
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Jean-Christophe Taveau
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Andreas Römpp
- Bioanalytical Sciences and Food Analysis, University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
| | - Alain Brunelle
- Laboratoire d'Archéologie Moléculaire et Structurale, LAMS UMR 8220, CNRS, Sorbonne Université, 4 Place Jussieu, 75005 Paris, France
| | - Sophie Lecomte
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Nicolas Desbenoit
- Institut de Chimie & Biologie des Membranes & des Nano-objets, CBMN UMR 5248, CNRS, Université de Bordeaux, 1 Allée Geoffroy Saint-Hilaire, 33600 Pessac, France
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17
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Griffiths RL. Surface‐sampling mass spectrometry and imaging: Direct analysis of bacterial species. SURF INTERFACE ANAL 2020. [DOI: 10.1002/sia.6907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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18
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Do H, Kwon SR, Fu K, Morales-Soto N, Shrout JD, Bohn PW. Electrochemical Surface-Enhanced Raman Spectroscopy of Pyocyanin Secreted by Pseudomonas aeruginosa Communities. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7043-7049. [PMID: 31042392 PMCID: PMC8006532 DOI: 10.1021/acs.langmuir.9b00184] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Pyocyanin (PYO) is one of many toxins secreted by the opportunistic human pathogenic bacterium Pseudomonas aeruginosa. Direct detection of PYO in biofilms is crucial because PYO can provide important information about infection-related virulence mechanisms in P. aeruginosa. Because PYO is both redox-active and Raman-active, we seek to simultaneously acquire both spectroscopic and redox state information about PYO. The combination of surface-enhanced Raman spectroscopy (SERS) and voltammetry is used here to provide insights into the molecular redox behavior of PYO while controlling the SERS and electrochemical (EC) response of PYO with external stimuli, such as pH and applied potential. Furthermore, PYO secretion from biofilms of different P. aeruginosa strains is compared. Both SERS spectra and EC behavior are observed to change with pH, and several pH-dependent bands are identified in the SERS spectra, which can potentially be used to probe the local environment. Comparison of the voltammetric behavior of wild-type and a PYO-deficient mutant unequivocally identifies PYO as a major component of the secretome. Spectroelectrochemical studies of the PYO standard reveal decreasing SERS intensities of PYO bands under reducing conditions. Extending these experiments to pellicle biofilms shows similar behavior with applied potential, and SERS imaging indicates that secreted PYO is localized in regions approximately the size of P. aeruginosa cells. The in situ spectroelectrochemical biofilm characterization approach developed here suggests that EC-SERS monitoring of secreted molecules can be used diagnostically and correlated with the progress of infection.
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Affiliation(s)
- Hyein Do
- Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Seung-Ryong Kwon
- Department of Chemical and Biomolecular
Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United
States
| | - Kaiyu Fu
- Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Nydia Morales-Soto
- Department of Civil and Environmental
Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana
46556, United States
| | - Joshua D. Shrout
- Department of Civil and Environmental
Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana
46556, United States
- Department of Biological Sciences, University of
Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry,
University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Chemical and Biomolecular
Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United
States
- Corresponding Author
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19
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Lasch P, Noda I. Two-Dimensional Correlation Spectroscopy (2D-COS) for Analysis of Spatially Resolved Vibrational Spectra. APPLIED SPECTROSCOPY 2019; 73:359-379. [PMID: 30488717 DOI: 10.1177/0003702818819880] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The last two decades have seen tremendous progress in the application of two-dimensional correlation spectroscopy (2D-COS) as a versatile analysis method for data series obtained using a large variety of different spectroscopic modalities, including infrared (IR) and Raman spectroscopy. The analysis technique is applicable to a series of spectra recorded under the influence of an external sample perturbation. Two-dimensional COS analysis is not only helpful to decipher correlations, which may exist between distinct spectral features, but can also be utilized to obtain the sequence of individual spectral changes. The focus of this review article is on the application of 2D-COS for analyzing spatially resolved data with special emphasis on hyperspectral imaging (HSI) study. In this review, we briefly introduce the fundamentals of the generalized 2D-COS analysis approach, discuss specific points of 2D-COS application to spatially resolved spectra and demonstrate essential aspects of data pre-processing for 2D-COS analysis of spatially resolved spectra. Based on illustrative examples, we show that 2D-COS is useful for spectral band assignment in HSI applications and demonstrate its utility for detecting subtle correlations between spectra features, or between features from different imaging modalities in the case of heterospectral (multimodal) HSI. Furthermore, a short overview on existing 2D-COS software tools is provided. It is hoped that this article represents not only a useful guideline for 2D-COS analyses of spatially resolved hyperspectral data but supports also further dissemination of the 2D-COS analysis method as a whole.
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Affiliation(s)
- Peter Lasch
- 1 Robert Koch-Institute, ZBS6-Proteomics and Spectroscopy, Berlin, Germany
| | - Isao Noda
- 2 Department of Materials Science and Engineering, University of Delaware, Newark, DE, USA
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20
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Ali A, Abouleila Y, Shimizu Y, Hiyama E, Watanabe TM, Yanagida T, Germond A. Single-Cell Screening of Tamoxifen Abundance and Effect Using Mass Spectrometry and Raman-Spectroscopy. Anal Chem 2019; 91:2710-2718. [PMID: 30664349 DOI: 10.1021/acs.analchem.8b04393] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Monitoring drug uptake, its metabolism, and response on the single-cell level is invaluable for sustaining drug discovery efforts. In this study, we show the possibility of accessing the information about the aforementioned processes at the single-cell level by monitoring the anticancer drug tamoxifen using live single-cell mass spectrometry (LSC-MS) and Raman spectroscopy. First, we explored whether Raman spectroscopy could be used as a label-free and nondestructive screening technique to identify and predict the drug response at the single-cell level. Then, a subset of the screened cells was isolated and analyzed by LSC-MS to measure tamoxifen and its metabolite, 4-Hydroxytamoxifen (4-OHT) in a highly selective, sensitive, and semiquantitative manner. Our results show the Raman spectral signature changed in response to tamoxifen treatment which allowed us to identify and predict the drug response. Tamoxifen and 4-OHT abundances quantified by LSC-MS suggested some heterogeneity among single-cells. A similar phenomenon was observed in the ratio of metabolized to unmetabolized tamoxifen across single-cells. Moreover, a correlation was found between tamoxifen and its metabolite, suggesting that the drug was up taken and metabolized by the cell. Finally, we found some potential correlations between Raman spectral intensities and tamoxifen abundance, or its metabolism, suggesting a possible relationship between the two signals. This study demonstrates for the first time the potential of using Raman spectroscopy and LSC-MS to investigate pharmacokinetics at the single-cell level.
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Affiliation(s)
- Ahmed Ali
- Riken Biodynamics Research Center (BDR) , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan.,Research Center , Misr International University , Cairo 19648 , Egypt
| | - Yasmine Abouleila
- Riken Biodynamics Research Center (BDR) , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan.,Research Center , Misr International University , Cairo 19648 , Egypt
| | - Yoshihiro Shimizu
- Riken Biodynamics Research Center (BDR) , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan
| | - Eiso Hiyama
- Graduate School of Biomedical and Health Sciences , 1-2-3 Kasumi , Hiroshima , 734-0037 , Japan
| | - Tomonobu M Watanabe
- Riken Biodynamics Research Center (BDR) , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan
| | - Toshio Yanagida
- Riken Biodynamics Research Center (BDR) , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan
| | - Arno Germond
- Riken Biodynamics Research Center (BDR) , 6-2-3 Furuedai , Suita , Osaka 565-0874 , Japan
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21
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Cao T, Morales-Soto N, Jia J, Baig NF, Dunham SJB, Ellis J, Sweedler JV, Shrout JD, Bohn PW. Spatiotemporal Dynamics of Molecular Messaging in Bacterial Co-Cultures Studied by Multimodal Chemical Imaging. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2019; 10863:108630A. [PMID: 33790492 PMCID: PMC8009051 DOI: 10.1117/12.2501349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Microbial community behavior is coupled to a set of genetically-regulated chemical signals that correlate with cell density - the quorum sensing (QS) system - and there is growing appreciation that the QS-regulated behavior of bacteria is chemically, spatially, and temporally complex. In addition, while it has been known for some time that different species use different QS networks, we are beginning to appreciate that different strains of the same bacterial species also differ in their QS networks. Here we combine mass spectrometric imaging (MSI) and confocal Raman microscopy (CRM) approaches to investigate co-cultures involving different strains (FRD1 and PAO1C) of the same species (Pseudomonas aeruginosa) as well as those involving different species (P. aeruginosa and E. coli). Combining MSI and CRM makes it possible to supersede the limits imposed by individual imaging approaches and enables the spatial mapping of individual bacterial species and their microbial products within a mixed bacterial community growing in situ on surfaces. MSI is used to delineate the secretion of a specific rhamnolipid surfactant as well as alkyl quinolone (AQ) messengers between FRD1 and PAO1C strains of P. aeruginosa, showing that the spatial distribution and production rate of AQ messengers in PAO1C far outstrips that of FRD1. In the case of multiple species, CRM is used to show that the prolific secretion of AQs by the PAO1C strain of P. aeruginosa is used to mediate its interaction with co-cultured E. coli.
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Affiliation(s)
- Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Nameera F Baig
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720
| | - Sage J B Dunham
- Entech Instruments, 2207 Agate Court, Simi Valley, CA 93065
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Joseph Ellis
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
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22
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Belianinov A, Ievlev AV, Lorenz M, Borodinov N, Doughty B, Kalinin SV, Fernández FM, Ovchinnikova OS. Correlated Materials Characterization via Multimodal Chemical and Functional Imaging. ACS NANO 2018; 12:11798-11818. [PMID: 30422627 PMCID: PMC9850281 DOI: 10.1021/acsnano.8b07292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Multimodal chemical imaging simultaneously offers high-resolution chemical and physical information with nanoscale and, in select cases, atomic resolution. By coupling modalities that collect physical and chemical information, we can address scientific problems in biological systems, battery and fuel cell research, catalysis, pharmaceuticals, photovoltaics, medicine, and many others. The combined systems enable the local correlation of material properties with chemical makeup, making fundamental questions of how chemistry and structure drive functionality approachable. In this Review, we present recent progress and offer a perspective for chemical imaging used to characterize a variety of samples by a number of platforms. Specifically, we present cases of infrared and Raman spectroscopies combined with scanning probe microscopy; optical microscopy and mass spectrometry; nonlinear optical microscopy; and, finally, ion, electron, and probe microscopies with mass spectrometry. We also discuss the challenges associated with the use of data originated by the combinatorial hardware, analysis, and machine learning as well as processing tools necessary for the interpretation of multidimensional data acquired from multimodal studies.
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Affiliation(s)
- Alex Belianinov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Anton V. Ievlev
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Matthias Lorenz
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nikolay Borodinov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Benjamin Doughty
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sergei V. Kalinin
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Facundo M. Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology and Petit Institute for Biochemistry and Bioscience, Atlanta, Georgia 30332, United States
| | - Olga S. Ovchinnikova
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Corresponding Author:
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23
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Neumann EK, Comi TJ, Spegazzini N, Mitchell JW, Rubakhin SS, Gillette MU, Bhargava R, Sweedler JV. Multimodal Chemical Analysis of the Brain by High Mass Resolution Mass Spectrometry and Infrared Spectroscopic Imaging. Anal Chem 2018; 90:11572-11580. [PMID: 30188687 DOI: 10.1021/acs.analchem.8b02913] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The brain functions through chemical interactions between many different cell types, including neurons and glia. Acquiring comprehensive information on complex, heterogeneous systems requires multiple analytical tools, each of which have unique chemical specificity and spatial resolution. Multimodal imaging generates complementary chemical information via spatially localized molecular maps, ideally from the same sample, but requires method enhancements that span from data acquisition to interpretation. We devised a protocol for performing matrix-assisted laser desorption/ionization (MALDI)-Fourier transform ion cyclotron resonance-mass spectrometry imaging (MSI), followed by infrared (IR) spectroscopic imaging on the same specimen. Multimodal measurements from the same tissue provide precise spatial alignment between modalities, enabling more advanced image processing such as image fusion and sharpening. Performing MSI first produces higher quality data from each technique compared to performing IR imaging before MSI. The difference is likely due to fixing the tissue section during MALDI matrix removal, thereby preventing analyte degradation occurring during IR imaging from an unfixed specimen. Leveraging the unique capabilities of each modality, we utilized pan sharpening of MS (mass spectrometry) ion images with selected bands from IR spectroscopy and midlevel data fusion. In comparison to sharpening with histological images, pan sharpening can employ a plethora of IR bands, producing sharpened MS images while retaining the fidelity of the initial ion images. Using Laplacian pyramid sharpening, we determine the localization of several lipids present within the hippocampus with high mass accuracy at 5 μm pixel widths. Further, through midlevel data fusion of the imaging data sets combined with k-means clustering, the combined data set discriminates between additional anatomical structures unrecognized by the individual imaging approaches. Significant differences between molecular ion abundances are detected between relevant structures within the hippocampus, such as the CA1 and CA3 regions. Our methodology provides high quality multiplex and multimodal chemical imaging of the same tissue sample, enabling more advanced data processing and analysis routines.
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24
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Ryabchykov O, Popp J, Bocklitz T. Fusion of MALDI Spectrometric Imaging and Raman Spectroscopic Data for the Analysis of Biological Samples. Front Chem 2018; 6:257. [PMID: 30062092 PMCID: PMC6055053 DOI: 10.3389/fchem.2018.00257] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 06/08/2018] [Indexed: 01/03/2023] Open
Abstract
Despite of a large number of imaging techniques for the characterization of biological samples, no universal one has been reported yet. In this work, a data fusion approach was investigated for combining Raman spectroscopic data with matrix-assisted laser desorption/ionization (MALDI) mass spectrometric data. It betters the image analysis of biological samples because Raman and MALDI information can be complementary to each other. While MALDI spectrometry yields detailed information regarding the lipid content, Raman spectroscopy provides valuable information about the overall chemical composition of the sample. The combination of Raman spectroscopic and MALDI spectrometric imaging data helps distinguishing different regions within the sample with a higher precision than would be possible by using either technique. We demonstrate that a data weighting step within the data fusion is necessary to reveal additional spectral features. The selected weighting approach was evaluated by examining the proportions of variance within the data explained by the first principal components of a principal component analysis (PCA) and visualizing the PCA results for each data type and combined data. In summary, the presented data fusion approach provides a concrete guideline on how to combine Raman spectroscopic and MALDI spectrometric imaging data for biological analysis.
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Affiliation(s)
- Oleg Ryabchykov
- Spectroscopy and Imaging Research Department, Leibniz Institute of Photonic Technology, Member of Leibniz Health Technology, Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Juergen Popp
- Spectroscopy and Imaging Research Department, Leibniz Institute of Photonic Technology, Member of Leibniz Health Technology, Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Bocklitz
- Spectroscopy and Imaging Research Department, Leibniz Institute of Photonic Technology, Member of Leibniz Health Technology, Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Jena, Germany
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25
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Magana M, Sereti C, Ioannidis A, Mitchell CA, Ball AR, Magiorkinis E, Chatzipanagiotou S, Hamblin MR, Hadjifrangiskou M, Tegos GP. Options and Limitations in Clinical Investigation of Bacterial Biofilms. Clin Microbiol Rev 2018; 31:e00084-16. [PMID: 29618576 PMCID: PMC6056845 DOI: 10.1128/cmr.00084-16] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteria can form single- and multispecies biofilms exhibiting diverse features based upon the microbial composition of their community and microenvironment. The study of bacterial biofilm development has received great interest in the past 20 years and is motivated by the elegant complexity characteristic of these multicellular communities and their role in infectious diseases. Biofilms can thrive on virtually any surface and can be beneficial or detrimental based upon the community's interplay and the surface. Advances in the understanding of structural and functional variations and the roles that biofilms play in disease and host-pathogen interactions have been addressed through comprehensive literature searches. In this review article, a synopsis of the methodological landscape of biofilm analysis is provided, including an evaluation of the current trends in methodological research. We deem this worthwhile because a keyword-oriented bibliographical search reveals that less than 5% of the biofilm literature is devoted to methodology. In this report, we (i) summarize current methodologies for biofilm characterization, monitoring, and quantification; (ii) discuss advances in the discovery of effective imaging and sensing tools and modalities; (iii) provide an overview of tailored animal models that assess features of biofilm infections; and (iv) make recommendations defining the most appropriate methodological tools for clinical settings.
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Affiliation(s)
- Maria Magana
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
| | - Christina Sereti
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
- Department of Microbiology, Thriassio General Hospital, Attiki, Greece
| | - Anastasios Ioannidis
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese, Sparta, Greece
| | - Courtney A Mitchell
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Anthony R Ball
- Gliese 623b, Mendon, Massachusetts, USA
- GAMA Therapeutics LLC, Pepperell, Massachusetts, USA
| | - Emmanouil Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, University of Athens, Athens-Goudi, Greece
| | | | - Michael R Hamblin
- Harvard-MIT Division of Health Science and Technology, Cambridge, Massachusetts, USA
- Department of Dermatology, Harvard Medical School, Boston, Massachusetts, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Maria Hadjifrangiskou
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - George P Tegos
- Gliese 623b, Mendon, Massachusetts, USA
- GAMA Therapeutics LLC, Pepperell, Massachusetts, USA
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26
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Li B, Dunham SJB, Ellis JF, Lange JD, Smith JR, Yang N, King TL, Amaya KR, Arnett CM, Sweedler JV. A Versatile Strategy for Characterization and Imaging of Drip Flow Microbial Biofilms. Anal Chem 2018; 90:6725-6734. [PMID: 29723465 DOI: 10.1021/acs.analchem.8b00560] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The inherent architectural and chemical complexities of microbial biofilms mask our understanding of how these communities form, survive, propagate, and influence their surrounding environment. Here we describe a simple and versatile workflow for the cultivation and characterization of model flow-cell-based microbial ecosystems. A customized low-shear drip flow reactor was designed and employed to cultivate single and coculture flow-cell biofilms at the air-liquid interface of several metal surfaces. Pseudomonas putida F1 and Shewanella oneidensis MR-1 were selected as model organisms for this study. The utility and versatility of this platform was demonstrated via the application of several chemical and morphological imaging techniques-including matrix-assisted laser desorption/ionization mass spectrometry imaging, secondary ion mass spectrometry imaging, and scanning electron microscopy-and through the examination of model systems grown on iron substrates of varying compositions. Implementation of these techniques in combination with tandem mass spectrometry and a two-step imaging principal component analysis strategy resulted in the identification and characterization of 23 lipids and 3 oligosaccharides in P. putida F1 biofilms, the discovery of interaction-specific analytes, and the observation of several variations in cell and substrate morphology present during microbially influenced corrosion. The presented workflow is well-suited for examination of both single and multispecies drip flow biofilms and offers a platform for fundamental inquiries into biofilm formation, microbe-microbe interactions, and microbially influenced corrosion.
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Affiliation(s)
- Bin Li
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Sage J B Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Joanna F Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Justin D Lange
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Justin R Smith
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Ning Yang
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Travis L King
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Kensey R Amaya
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Clint M Arnett
- Engineer Research and Development Center-Construction Engineering Research Laboratory (ERDC-CERL) , Champaign , Illinois 61822 , United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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27
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Bodelón G, Montes-García V, Pérez-Juste J, Pastoriza-Santos I. Surface-Enhanced Raman Scattering Spectroscopy for Label-Free Analysis of P. aeruginosa Quorum Sensing. Front Cell Infect Microbiol 2018; 8:143. [PMID: 29868499 PMCID: PMC5958199 DOI: 10.3389/fcimb.2018.00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/20/2018] [Indexed: 12/20/2022] Open
Abstract
Bacterial quorum sensing systems regulate the production of an ample variety of bioactive extracellular compounds that are involved in interspecies microbial interactions and in the interplay between the microbes and their hosts. The development of new approaches for enabling chemical detection of such cellular activities is important in order to gain new insight into their function and biological significance. In recent years, surface-enhanced Raman scattering (SERS) spectroscopy has emerged as an ultrasensitive analytical tool employing rationally designed plasmonic nanostructured substrates. This review highlights recent advances of SERS spectroscopy for label-free detection and imaging of quorum sensing-regulated processes in the human opportunistic pathogen Pseudomonas aeruginosa. We also briefly describe the challenges and limitations of the technique and conclude with a summary of future prospects for the field.
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Affiliation(s)
- Gustavo Bodelón
- Departamento de Química Física y Centro Singular de Investigaciones Biomédicas (CINBIO), Universidad de Vigo, Vigo, Spain
| | - Verónica Montes-García
- Departamento de Química Física y Centro Singular de Investigaciones Biomédicas (CINBIO), Universidad de Vigo, Vigo, Spain
| | - Jorge Pérez-Juste
- Departamento de Química Física y Centro Singular de Investigaciones Biomédicas (CINBIO), Universidad de Vigo, Vigo, Spain
| | - Isabel Pastoriza-Santos
- Departamento de Química Física y Centro Singular de Investigaciones Biomédicas (CINBIO), Universidad de Vigo, Vigo, Spain
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28
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Dunham SJB, Ellis JF, Baig NF, Morales-Soto N, Cao T, Shrout JD, Bohn PW, Sweedler JV. Quantitative SIMS Imaging of Agar-Based Microbial Communities. Anal Chem 2018; 90:5654-5663. [PMID: 29623707 PMCID: PMC5930052 DOI: 10.1021/acs.analchem.7b05180] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.
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Affiliation(s)
- Sage J. B. Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
| | - Joseph F. Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
| | - Nameera F. Baig
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Nydia Morales-Soto
- Department of Civil and Environmental Engineering and Earth Sciences, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Tianyuan Cao
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Joshua D. Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Paul W. Bohn
- Department of Chemistry and Biochemistry, and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign, Urbana, IL 61801
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29
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Abstract
Biofilms are a communal way of living for microorganisms in which microorganism cells are surrounded by extracellular polymeric substances (EPS). Most microorganisms can live in biofilm form. Since microorganisms are everywhere, understanding biofilm structure and composition is crucial for making the world a better place to live, not only for humans but also for other living creatures. Raman spectroscopy is a nondestructive technique and provides fingerprint information about an analyte of interest. Surface-enhanced Raman spectroscopy is a form of this technique and provides enhanced scattering of the analyte that is in close vicinity of a nanostructured noble metal surface such as silver or gold. In this review, the applications of both techniques and their combination with other biofilm analysis techniques for characterization of composition and structure of biofilms are discussed.
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30
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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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31
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Chen B, OuYang C, Tian Z, Xu M, Li L. A high resolution atmospheric pressure matrix-assisted laser desorption/ionization-quadrupole-orbitrap MS platform enables in situ analysis of biomolecules by multi-mode ionization and acquisition. Anal Chim Acta 2018; 1007:16-25. [PMID: 29405984 DOI: 10.1016/j.aca.2017.12.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 12/25/2017] [Accepted: 12/29/2017] [Indexed: 11/28/2022]
Abstract
Introduced in 2000, atmospheric pressure (AP)/matrix-assisted laser desorption/ionization (MALDI) has attracted substantial attention in the mass spectrometry community due to its ease of sample introduction and handling, interchangeability with ESI source and capability of analyzing volatile species. In this study, an AP/MALDI source with ultra-high spatial resolution was coupled to a Q Exactive HF orbitrap mass spectrometer for high resolution in situ analysis by MALDI, laserspray ionization (LSI) and matrix assisted ionization (MAI) without instrument modification. LSI and MAI generated multiply charged ions, which expanded the mass detection range and improved fragmentation efficiency. Full MS, targeted MS/MS, data dependent acquisition (DDA) and parallel reaction monitoring (PRM) acquisitions were performed on peptide and protein standards, tissue extracts and tissue sections for in depth characterization of various biomolecules. High resolution full MS and MS/MS images were obtained from crustacean and rat tissues with pixel size less than 30 μm. Overall, AP/MALDI-Q-Orbitrap is a fast scanning instrument that is capable of performing multiple types of ionization and multiple acquisition modes without instrument modification. This instrument platform provides an attractive alternative to other high resolution MALDI instruments.
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Affiliation(s)
- Bingming Chen
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Chuanzi OuYang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Zichuan Tian
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Meng Xu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States; Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, United States.
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32
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Rae Buchberger A, DeLaney K, Johnson J, Li L. Mass Spectrometry Imaging: A Review of Emerging Advancements and Future Insights. Anal Chem 2018; 90:240-265. [PMID: 29155564 PMCID: PMC5959842 DOI: 10.1021/acs.analchem.7b04733] [Citation(s) in RCA: 569] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Amanda Rae Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, 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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33
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Ofner J, Brenner F, Wieland K, Eitenberger E, Kirschner J, Eisenmenger-Sittner C, Török S, Döme B, Konegger T, Kasper-Giebl A, Hutter H, Friedbacher G, Lendl B, Lohninger H. Image-Based Chemical Structure Determination. Sci Rep 2017; 7:6832. [PMID: 28754996 PMCID: PMC5533744 DOI: 10.1038/s41598-017-07041-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/21/2017] [Indexed: 11/09/2022] Open
Abstract
Chemical imaging is a powerful tool for understanding the chemical composition and nature of heterogeneous samples. Recent developments in elemental, vibrational, and mass-spectrometric chemical imaging with high spatial resolution (50–200 nm) and reasonable timescale (a few hours) are capable of providing complementary chemical information about various samples. However, a single technique is insufficient to provide a comprehensive understanding of chemically complex materials. For bulk samples, the combination of different analytical methods and the application of statistical methods for extracting correlated information across different techniques is a well-established and powerful concept. However, combined multivariate analytics of chemical images obtained via different imaging techniques is still in its infancy, hampered by a lack of analytical methodologies for data fusion and analysis. This study demonstrates the application of multivariate statistics to chemical images taken from the same sample via various methods to assist in chemical structure determination.
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Affiliation(s)
- Johannes Ofner
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria.
| | - Florian Brenner
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Karin Wieland
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Elisabeth Eitenberger
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Johannes Kirschner
- Institute of Solide State Physics, TU Wien, Wiedner Hauptstrasse 8, 1040, Vienna, Austria
| | | | - Szilvia Török
- National Korányi Institute of Pulmonology, Budapest, Hungary
| | - Balazs Döme
- National Korányi Institute of Pulmonology, Budapest, Hungary.,Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Medical University of Vienna, Vienna, Austria
| | - Thomas Konegger
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Anne Kasper-Giebl
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Herbert Hutter
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Gernot Friedbacher
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Bernhard Lendl
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Hans Lohninger
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
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34
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Huang D, Hua X, Xiu GL, Zheng YJ, Yu XY, Long YT. Secondary ion mass spectrometry: The application in the analysis of atmospheric particulate matter. Anal Chim Acta 2017; 989:1-14. [PMID: 28915935 DOI: 10.1016/j.aca.2017.07.042] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 07/12/2017] [Accepted: 07/18/2017] [Indexed: 12/13/2022]
Abstract
Currently, considerable attention has been paid to atmospheric particulate matter (PM) investigation due to its importance in human health and global climate change. Surface characterization, single particle analysis and depth profiling of PM is important for a better understanding of its formation processes and predicting its impact on the environment and human being. Secondary ion mass spectrometry (SIMS) is a surface technique with high surface sensitivity, high spatial resolution chemical imaging and unique depth profiling capabilities. Recent research shows that SIMS has great potential in analyzing both surface and bulk chemical information of PM. In this review, we give a brief introduction of SIMS working principle and survey recent applications of SIMS in PM characterization. Particularly, analyses from different types of PM sources by various SIMS techniques were discussed concerning their advantages and limitations. The future development and needs of SIMS in atmospheric aerosol measurement are proposed with a perspective in broader environmental sciences.
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Affiliation(s)
- Di Huang
- State Environmental Protection Key Lab of Environmental Risk Assessment and Control on Chemical Processes, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Xin Hua
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China.
| | - Guang-Li Xiu
- State Environmental Protection Key Lab of Environmental Risk Assessment and Control on Chemical Processes, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, PR China.
| | - Yong-Jie Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China
| | - Xiao-Ying Yu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China
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35
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Visualizing Antimicrobials in Bacterial Biofilms: Three-Dimensional Biochemical Imaging Using TOF-SIMS. mSphere 2017; 2:mSphere00211-17. [PMID: 28744481 PMCID: PMC5518269 DOI: 10.1128/msphere.00211-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/25/2017] [Indexed: 11/20/2022] Open
Abstract
Modern analytical techniques are becoming increasingly important in the life sciences; imaging mass spectrometry offers the opportunity to gain unprecedented amounts of information on the distribution of chemicals in samples—both xenobiotics and endogenous compounds. In particular, simultaneous imaging of antibiotics (and other antimicrobial compounds) and bacterium-derived metabolites in complex biological samples could be very important in the future for helping to understand how sample matrices impact the survival of bacteria under antibiotic challenge. We have shown that an imaging mass spectrometric technique, TOF-SIMS, will be potentially extremely valuable for this kind of research in the future. Bacterial biofilms are groups of bacteria that exist within a self-produced extracellular matrix, adhering to each other and usually to a surface. They grow on medical equipment and inserts such as catheters and are responsible for many persistent infections throughout the body, as they can have high resistance to many antimicrobials. Pseudomonas aeruginosa is an opportunistic pathogen that can cause both acute and chronic infections and is used as a model for research into biofilms. Direct biochemical methods of imaging of molecules in bacterial biofilms are of high value in gaining a better understanding of the fundamental biology of biofilms and biochemical gradients within them. Time of flight–secondary-ion mass spectrometry (TOF-SIMS) is one approach, which combines relatively high spatial resolution and sensitivity and can perform depth profiling analysis. It has been used to analyze bacterial biofilms but has not yet been used to study the distribution of antimicrobials (including antibiotics and the antimicrobial metal gallium) within biofilms. Here we compared two methods of imaging of the interior structure of P. aeruginosa in biological samples using TOF-SIMS, looking at both antimicrobials and endogenous biochemicals: cryosectioning of tissue samples and depth profiling to give pseudo-three-dimensional (pseudo-3D) images. The sample types included both simple biofilms grown on glass slides and bacteria growing in tissues in an ex vivo pig lung model. The two techniques for the 3D imaging of biofilms are potentially valuable complementary tools for analyzing bacterial infection. IMPORTANCE Modern analytical techniques are becoming increasingly important in the life sciences; imaging mass spectrometry offers the opportunity to gain unprecedented amounts of information on the distribution of chemicals in samples—both xenobiotics and endogenous compounds. In particular, simultaneous imaging of antibiotics (and other antimicrobial compounds) and bacterium-derived metabolites in complex biological samples could be very important in the future for helping to understand how sample matrices impact the survival of bacteria under antibiotic challenge. We have shown that an imaging mass spectrometric technique, TOF-SIMS, will be potentially extremely valuable for this kind of research in the future.
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36
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Yung YP, Wickramasinghe R, Vaikkinen A, Kauppila TJ, Veryovkin IV, Hanley L. Solid Sampling with a Diode Laser for Portable Ambient Mass Spectrometry. Anal Chem 2017. [PMID: 28632988 PMCID: PMC5518277 DOI: 10.1021/acs.analchem.7b01745] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
A hand-held diode
laser is implemented for solid sampling in portable
ambient mass spectrometry (MS). Specifically, a pseudocontinuous wave
battery-powered surgical laser diode is employed for portable laser
diode thermal desorption (LDTD) at 940 nm and compared with nanosecond
pulsed laser ablation at 2940 nm. Postionization is achieved in both
cases using atmospheric pressure photoionization (APPI). The laser
ablation atmospheric pressure photoionization (LAAPPI) and LDTD-APPI
mass spectra of sage leaves (Salvia officinalis) using a field-deployable quadrupole ion trap MS display many similar
ion peaks, as do the mass spectra of membrane grown biofilms of Pseudomonas aeruginosa. These results indicate that
LDTD-APPI method should be useful for in-field sampling of plant and
microbial communities, for example, by portable ambient MS. The feasibility
of many portable MS applications is facilitated by the availability
of relatively low cost, portable, battery-powered diode lasers. LDTD
could also be coupled with plasma- or electrospray-based ionization
for the analysis of a variety of solid samples.
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Affiliation(s)
- Yeni P Yung
- Department of Chemistry, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Raveendra Wickramasinghe
- Department of Chemistry, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Anu Vaikkinen
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki , Helsinki, Finland
| | - Tiina J Kauppila
- Division of Pharmaceutical Chemistry and Technology, University of Helsinki , Helsinki, Finland
| | - Igor V Veryovkin
- Department of Chemistry, University of Illinois at Chicago , Chicago, Illinois 60607, United States
| | - Luke Hanley
- Department of Chemistry, University of Illinois at Chicago , Chicago, Illinois 60607, United States
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37
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Ho YN, Shu LJ, Yang YL. Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28488813 DOI: 10.1002/wsbm.1387] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/24/2017] [Accepted: 02/28/2017] [Indexed: 12/19/2022]
Abstract
Imaging mass spectrometry (IMS) allows the study of the spatial distribution of small molecules in biological samples. IMS is able to identify and quantify chemicals in situ from whole tissue sections to single cells. Both vacuum mass spectrometry (MS) and ambient MS systems have advanced considerably over the last decade; however, some limitations are still hard to surmount. Sample pretreatment, matrix or solvent choices, and instrument improvement are the key factors that determine the successful application of IMS to different samples and analytes. IMS with innovative MS analyzers, powerful MS spectrum databases, and analysis tools can efficiently dereplicate, identify, and quantify natural products. Moreover, multimodal imaging systems and multiple MS-based systems provide additional structural, chemical, and morphological information and are applied as complementary tools to explore new fields. IMS has been applied to reveal interactions between living organisms at molecular level. Recently, IMS has helped solve many previously unidentifiable relations between bacteria, fungi, plants, animals, and insects. Other significant interactions on the chemical level can also be resolved using expanding IMS techniques. WIREs Syst Biol Med 2017, 9:e1387. doi: 10.1002/wsbm.1387 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ying-Ning Ho
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Lin-Jie Shu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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Raman microspectroscopy, surface-enhanced Raman scattering microspectroscopy, and stable-isotope Raman microspectroscopy for biofilm characterization. Anal Bioanal Chem 2017; 409:4353-4375. [DOI: 10.1007/s00216-017-0303-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/31/2017] [Accepted: 03/08/2017] [Indexed: 12/27/2022]
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39
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Comi TJ, Do TD, Rubakhin SS, Sweedler JV. Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry. J Am Chem Soc 2017; 139:3920-3929. [PMID: 28135079 PMCID: PMC5364434 DOI: 10.1021/jacs.6b12822] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Indexed: 02/06/2023]
Abstract
The chemical differences between individual cells within large cellular populations provide unique information on organisms' homeostasis and the development of diseased states. Even genetically identical cell lineages diverge due to local microenvironments and stochastic processes. The minute sample volumes and low abundance of some constituents in cells hinder our understanding of cellular heterogeneity. Although amplification methods facilitate single-cell genomics and transcriptomics, the characterization of metabolites and proteins remains challenging both because of the lack of effective amplification approaches and the wide diversity in cellular constituents. Mass spectrometry has become an enabling technology for the investigation of individual cellular metabolite profiles with its exquisite sensitivity, large dynamic range, and ability to characterize hundreds to thousands of compounds. While advances in instrumentation have improved figures of merit, acquiring measurements at high throughput and sampling from large populations of cells are still not routine. In this Perspective, we highlight the current trends and progress in mass-spectrometry-based analysis of single cells, with a focus on the technologies that will enable the next generation of single-cell measurements.
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Affiliation(s)
- Troy J. Comi
- Department of Chemistry and
the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Thanh D. Do
- Department of Chemistry and
the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S. Rubakhin
- Department of Chemistry and
the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and
the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Abstract
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In the two decades since mass spectrometry imaging (MSI) was first
applied to visualize the distribution of peptides across biological
tissues and cells, the technique has become increasingly effective
and reliable. MSI excels at providing complementary information to
existing methods for molecular analysis—such as genomics, transcriptomics,
and metabolomics—and stands apart from other chemical imaging
modalities through its capability to generate information that is
simultaneously multiplexed and chemically specific. Today a diverse
family of MSI approaches are applied throughout the scientific community
to study the distribution of proteins, peptides, and small-molecule
metabolites across many biological models. The inherent strengths
of MSI make the technique valuable for studying
microbial systems. Many microbes reside in surface-attached multicellular
and multispecies communities, such as biofilms and motile colonies,
where they work together to harness surrounding nutrients, fend off
hostile organisms, and shield one another from adverse environmental
conditions. These processes, as well as many others essential for
microbial survival, are mediated through the production and utilization
of a diverse assortment of chemicals. Although bacterial cells are
generally only a few microns in diameter, the ecologies they influence
can encompass entire ecosystems, and the chemical changes that they
bring about can occur over time scales ranging from milliseconds to
decades. Because of their incredible complexity, our understanding
of and influence over microbial systems requires detailed scientific
evaluations that yield both chemical and spatial information. MSI
is well-positioned to fulfill these requirements. With small adaptations
to existing methods, the technique can be applied to study a wide
variety of chemical interactions, including those that occur inside
single-species microbial communities, between cohabitating microbes,
and between microbes and their hosts. In recognition of this
potential for scientific advancement, researchers
have adapted MSI methodologies for the specific needs of the microbiology
research community. As a result, workflows exist for imaging microbial
systems with many of the common MSI ionization methods. Despite this
progress, there is substantial room for improvements in instrumentation,
sample preparation, and data interpretation. This Account provides
a brief overview of the state of technology in microbial MSI, illuminates
selected applications that demonstrate the potential of the technique,
and highlights a series of development challenges that are needed
to move the field forward. In the coming years, as microbial MSI becomes
easier to use and more universally applicable, the technique will
evolve into a fundamental tool widely applied throughout many divisions
of science, medicine, and industry.
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Affiliation(s)
- Sage J. B. Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joanna F. Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Bin Li
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Ofner J, Kirschner J, Eitenberger E, Friedbacher G, Kasper-Giebl A, Lohninger H, Eisenmenger-Sittner C, Lendl B. A novel substrate for multisensor hyperspectral imaging. J Microsc 2016; 265:341-348. [PMID: 27892598 DOI: 10.1111/jmi.12506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 10/28/2016] [Accepted: 10/30/2016] [Indexed: 12/28/2022]
Abstract
The quality of chemical imaging, especially multisensor hyperspectral imaging, strongly depends on sample preparation techniques and instrumental infrastructure but also on the choice of an appropriate imaging substrate. To optimize the combined imaging of Raman microspectroscopy, scanning-electron microscopy and energy-dispersive X-ray spectroscopy, a novel substrate was developed based on sputtering of highly purified aluminium onto classical microscope slides. The novel aluminium substrate overcomes several disadvantages of classical substrates like impurities of the substrate material and contamination of the surface as well as surface roughness and homogeneity. Therefore, it provides excellent conditions for various hyperspectral imaging techniques and enables high-quality multisensor hyperspectral chemical imaging at submicron lateral resolutions.
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Affiliation(s)
- J Ofner
- TU Wien, Institute of Chemical Technologies and Analytics, Vienna, Austria
| | - J Kirschner
- TU Wien, Institute of Solide State Physics, Vienna, Austria
| | - E Eitenberger
- TU Wien, Institute of Chemical Technologies and Analytics, Vienna, Austria
| | - G Friedbacher
- TU Wien, Institute of Chemical Technologies and Analytics, Vienna, Austria
| | - A Kasper-Giebl
- TU Wien, Institute of Chemical Technologies and Analytics, Vienna, Austria
| | - H Lohninger
- TU Wien, Institute of Chemical Technologies and Analytics, Vienna, Austria
| | | | - B Lendl
- TU Wien, Institute of Chemical Technologies and Analytics, Vienna, Austria
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Li B, Comi TJ, Si T, Dunham SJB, Sweedler JV. A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1030-1035. [PMID: 27476992 PMCID: PMC5297451 DOI: 10.1002/jms.3827] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/19/2016] [Accepted: 07/26/2016] [Indexed: 05/03/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging of biofilms cultured on agar plates is challenging because of problems related to matrix deposition onto agar. We describe a one-step, spray-based application of a 2,5-dihydroxybenzoic acid solution for direct matrix-assisted laser desorption/ionization imaging of hydrated Bacillus subtilis biofilms on agar. Using both an optimized airbrush and a home-built automatic sprayer, region-specific distributions of signaling metabolites and cannibalistic factors were visualized from B. subtilis cells cultivated on biofilm-promoting medium. The approach provides a homogeneous, relatively dry coating on hydrated samples, improving spot to spot signal repeatability compared with sieved matrix application, and is easily adapted for imaging a range of agar-based biofilms. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Bin Li
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Troy J Comi
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tong Si
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sage J B Dunham
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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43
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Si T, Li B, Zhang K, Xu Y, Zhao H, Sweedler JV. Characterization of Bacillus subtilis Colony Biofilms via Mass Spectrometry and Fluorescence Imaging. J Proteome Res 2016; 15:1955-62. [PMID: 27136705 PMCID: PMC4895246 DOI: 10.1021/acs.jproteome.6b00127] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Colony
biofilms of Bacillus subtilis are a widely
used model for studying cellular differentiation. Here, we applied
matrix-assisted laser desorption/ionization (MALDI) mass spectrometry
imaging (MSI) to examine cellular and molecular heterogeneity in B. subtilis colony biofilms. From B. subtilis cells cultivated on a biofilm-promoting medium, we detected two
cannibalistic factors not found in previous MALDI MSI studies of the
same strain under different culturing conditions. Given the importance
of cannibalism in matrix formation of B. subtilis biofilms, we employed a transcriptional reporter to monitor matrix-producing
cell subpopulations using fluorescence imaging. These two complementary
imaging approaches were used to characterize three B. subtilis strains, the wild type isolate NCIB3610, and two mutants, Δspo0A and ΔabrB, with defective and
enhanced biofilm phenotypes, respectively. Upon deletion of key transcriptional
factors, correlated changes were observed in biofilm morphology, signaling,
cannibalistic factor distribution, and matrix-related gene expression,
providing new insights on cannibalism in biofilm development. This
work underscores the advantages of using multimodal imaging to compare
spatial patterns of selected molecules with the associated protein
expression patterns, obtaining information on cellular heterogeneity
and function not obtainable when using a single method to characterize
biofilm formation.
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Affiliation(s)
- Tong Si
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Bin Li
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Ke Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Yiran Xu
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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Polisetti S, Bible AN, Morrell-Falvey JL, Bohn PW. Raman chemical imaging of the rhizosphere bacterium Pantoea sp. YR343 and its co-culture with Arabidopsis thaliana. Analyst 2016; 141:2175-82. [PMID: 26948490 DOI: 10.1039/c6an00080k] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Chemical imaging of plant-bacteria co-cultures makes it possible to characterize bacterial populations and behaviors and their interactions with proximal organisms, under conditions closest to the environment in the rhizosphere. Here Raman micro-spectroscopy and confocal Raman imaging are used as minimally invasive probes to study the rhizosphere bacterial isolate, Pantoea sp. YR343, and its co-culture with model plant Arabidopsis thaliana by combining enhanced Raman spectroscopies with electron microscopy and principal component analysis (PCA). The presence of carotenoid pigments in the wild type Pantoea sp. YR343 was characterized using resonance Raman scattering, which was also used to confirm successful disruption of the crtB gene in an engineered carotenoid mutant strain. Other components of the Pantoea sp. YR343 cells were imaged in the presence of resonantly enhanced pigments using a combination of surface enhanced Raman imaging and PCA. Pantoea sp. YR343 cells decorated with Ag colloid synthesized ex situ gave spectra dominated by carotenoid scattering, whereas colloids synthesized in situ produced spectral signatures characteristic of flavins in the cell membrane. Scanning electron microscopy (SEM) of whole cells and transmission electron microscopy (TEM) images of thinly sliced cross-sections were used to assess structural integrity of the coated cells and to establish the origin of spectral signatures based on the position of Ag nanoparticles in the cells. Raman imaging was also used to characterize senescent green Arabidopsis thaliana plant roots inoculated with Pantoea sp. YR343, and PCA was used to distinguish spectral contributions from plant and bacterial cells, thereby establishing the potential of Raman imaging to visualize the distribution of rhizobacteria on plant roots.
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Affiliation(s)
- Sneha Polisetti
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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45
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Li B, Dunham SJ, Dong Y, Yoon S, Zeng M, Sweedler JV. Analytical capabilities of mass spectrometry imaging and its potential applications in food science. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2015.10.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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46
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Abstract
The label-free detection of microbial cells attached to a surface is an active field of research. The field is driven by the need to understand and control the growth of biofilms in a number of applications, including basic research in natural environments, industrial facilities, and clinical devices, to name a few. Despite significant progress in the ability to monitor the growth of biofilms and related living cells, the sensitivity and selectivity of such sensors are still a challenge. We believe that among the many different technologies available for monitoring biofilm growth, optical techniques are the most promising, as they afford direct imaging and offer high sensitivity and specificity. Furthermore, as each technique offers different insights into the biofilm growth mechanism, our analysis allows us to provide an overview of the biological processes at play. In addition, we use a set of key parameters to compare state-of-the-art techniques in the field, including a critical assessment of each method, to identify the most promising types of sensors. We highlight the challenges that need to be overcome to improve the characteristics of current biofilm sensor technologies and indicate where further developments are required. In addition, we provide guidelines for selecting a suitable sensor for detecting microbial cells on a surface.
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Baig NF, Dunham SJB, Morales-Soto N, Shrout JD, Sweedler JV, Bohn PW. Multimodal chemical imaging of molecular messengers in emerging Pseudomonas aeruginosa bacterial communities. Analyst 2015; 140:6544-52. [PMID: 26331158 DOI: 10.1039/c5an01149c] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Two label-free molecular imaging techniques, confocal Raman microscopy (CRM) and secondary ion mass spectrometry (SIMS), are combined for in situ characterization of the spatiotemporal distributions of quinolone metabolites and signaling molecules in communities of the pathogenic bacterium Pseudomonas aeruginosa. Dramatic molecular differences are observed between planktonic and biofilm modes of growth for these bacteria. We observe patterned aggregation and a high abundance of N-oxide quinolines in early biofilms and swarm zones of P. aeruginosa, while the concentrations of these secreted components in planktonic cells and agar plate colonies are below CRM and SIMS detection limits. CRM, in conjunction with principal component analysis (PCA) is used to distinguish between the two co-localized isomeric analyte pairs 4-hydroxy-2-heptylquinoline-N-oxide (HQNO)/2-heptyl-3-hydroxyquinolone (PQS) and 4-hydroxy-2-nonylquinoline-N-oxide (NQNO)/2-nonyl-hydroxyquinolone (C9-PQS) based on differences in their vibrational fingerprints, illustrating how the technique can be used to guide tandem-MS and tandem-MS imaging analysis. Because N-oxide quinolines are ubiquitous and expressed early in biofilms, these analytes may be fundamentally important for early biofilm formation and the growth and organization of P. aeruginosa microbial communities. This study underscores the advantages of using multimodal molecular imaging to study complex biological systems.
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Affiliation(s)
- Nameera F Baig
- Department of Chemistry and Biochemistry and Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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Polisetti S, Baig N, Bible A, Morrell-Falvey J, Doktycz M, Bohn PW. Using Raman Spectroscopy and SERS for in-situ studies of rhizosphere bacteria. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9550:95500D. [PMID: 34539030 PMCID: PMC8444273 DOI: 10.1117/12.2188647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacteria colonize plant roots to form a symbiotic relationship with the plant and can play in important role in promoting plant growth. Raman spectroscopy is a useful technique to study these bacterial systems and the chemical signals they utilize to interact with the plant. We present a Raman study of Pantoea YR343 that was isolated from the rhizosphere of Populus deltoides (Eastern Cottonwood). Pantoea sp. YR343 produce yellowish carotenoid pigment that play a role in protection against UV radiation, in the anti-oxidative pathways and in membrane fluidity. Raman spectroscopy is used to non-invasively characterize the membrane bound carotenoids. The spectra collected from a mutant strain created by knocking out the crtB gene that encodes a phytoene synthase responsible for early stage of carotenoid biosynthesis, lack the carotenoid peaks. Surface Enhanced Raman Spectroscopy is being employed to detect the plant phytoharmone indoleacetic acid that is synthesized by the bacteria. This work describes our recent progress towards utilizing Raman spectroscopy as a label free, non-destructive method of studying plant-bacteria interactions in the rhizosphere.
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Affiliation(s)
- Sneha Polisetti
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Nameera Baig
- Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556
| | - Amber Bible
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | | | - Mitchel Doktycz
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Paul W. Bohn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
- Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556
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