1
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Li W, Shao C, Li C, Zhou H, Yu L, Yang J, Wan H, He Y. Metabolomics: A useful tool for ischemic stroke research. J Pharm Anal 2023; 13:968-983. [PMID: 37842657 PMCID: PMC10568109 DOI: 10.1016/j.jpha.2023.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/14/2023] [Accepted: 05/29/2023] [Indexed: 10/17/2023] Open
Abstract
Ischemic stroke (IS) is a multifactorial and heterogeneous disease. Despite years of studies, effective strategies for the diagnosis, management and treatment of stroke are still lacking in clinical practice. Metabolomics is a growing field in systems biology. It is starting to show promise in the identification of biomarkers and in the use of pharmacometabolomics to help patients with certain disorders choose their course of treatment. The development of metabolomics has enabled further and more biological applications. Particularly, metabolomics is increasingly being used to diagnose diseases, discover new drug targets, elucidate mechanisms, and monitor therapeutic outcomes and its potential effect on precision medicine. In this review, we reviewed some recent advances in the study of metabolomics as well as how metabolomics might be used to identify novel biomarkers and understand the mechanisms of IS. Then, the use of metabolomics approaches to investigate the molecular processes and active ingredients of Chinese herbal formulations with anti-IS capabilities is summarized. We finally summarized recent developments in single cell metabolomics for exploring the metabolic profiles of single cells. Although the field is relatively young, the development of single cell metabolomics promises to provide a powerful tool for unraveling the pathogenesis of IS.
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Affiliation(s)
- Wentao Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chongyu Shao
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chang Li
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Huifen Zhou
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Li Yu
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiehong Yang
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Haitong Wan
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yu He
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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2
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Mellinger AL, Muddiman DC, Gamcsik MP. Highlighting Functional Mass Spectrometry Imaging Methods in Bioanalysis. J Proteome Res 2022; 21:1800-1807. [PMID: 35749637 DOI: 10.1021/acs.jproteome.2c00220] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most mass spectrometry imaging (MSI) methods provide a molecular map of tissue content but little information on tissue function. Mapping tissue function is possible using several well-known examples of "functional imaging" such as positron emission tomography and functional magnetic resonance imaging that can provide the spatial distribution of time-dependent biological processes. These functional imaging methods represent the net output of molecular networks influenced by local tissue environments that are difficult to predict from molecular/cellular content alone. However, for decades, MSI methods have also been demonstrated to provide functional imaging data on a variety of biological processes. In fact, MSI exceeds some of the classic functional imaging methods, demonstrating the ability to provide functional data from the nanoscale (subcellular) to whole tissue or organ level. This Perspective highlights several examples of how different MSI ionization and detection technologies can provide unprecedented detailed spatial maps of time-dependent biological processes, namely, nucleic acid synthesis, lipid metabolism, bioenergetics, and protein metabolism. By classifying various MSI methods under the umbrella of "functional MSI", we hope to draw attention to both the unique capabilities and accessibility with the aim of expanding this underappreciated field to include new approaches and applications.
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Affiliation(s)
- Allyson L Mellinger
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - David C Muddiman
- FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Michael P Gamcsik
- UNC/NCSU Joint Department of Biomedical Engineering, Raleigh, North Carolina 27695, United States
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3
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Nguyen TD, Mellander L, Lork A, Thomen A, Philipsen M, Kurczy ME, Phan NT, Ewing AG. Visualization of Partial Exocytotic Content Release and Chemical Transport into Nanovesicles in Cells. ACS NANO 2022; 16:4831-4842. [PMID: 35189057 PMCID: PMC8945366 DOI: 10.1021/acsnano.2c00344] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
For decades, "all-or-none" and "kiss-and-run" were thought to be the only major exocytotic release modes in cell-to-cell communication, while the significance of partial release has not yet been widely recognized and accepted owing to the lack of direct evidence for exocytotic partial release. Correlative imaging with transmission electron microscopy and NanoSIMS imaging and a dual stable isotope labeling approach was used to study the cargo status of vesicles before and after exocytosis; demonstrating a measurable loss of transmitter in individual vesicles following stimulation due to partial release. Model secretory cells were incubated with 13C-labeled l-3,4-dihydroxyphenylalanine, resulting in the loading of 13C-labeled dopamine into their vesicles. A second label, di-N-desethylamiodarone, having the stable isotope 127I, was introduced during stimulation. A significant drop in the level of 13C-labeled dopamine and a reduction in vesicle size, with an increasing level of 127I-, was observed in vesicles of stimulated cells. Colocalization of 13C and 127I- in several vesicles was observed after stimulation. Thus, chemical visualization shows transient opening of vesicles to the exterior of the cell without full release the dopamine cargo. We present a direct calculation for the fraction of neurotransmitter release from combined imaging data. The average vesicular release is 60% of the total catecholamine. An important observation is that extracellular molecules can be introduced to cells during the partial exocytotic release process. This nonendocytic transport process appears to be a general route of entry that might be exploited pharmacologically.
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Affiliation(s)
- Tho Duc
Khanh Nguyen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Lisa Mellander
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Alicia Lork
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Aurélien Thomen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Mai Philipsen
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg SE-412 96, Sweden
| | - Michael E. Kurczy
- DMPK,
Research and Early Development, Cardiovascular, Renal and Metabolism
(CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg S-431 83, Sweden
| | - Nhu T.N. Phan
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Andrew G. Ewing
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg SE-412 96, Sweden
- E-mail:
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4
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Chen Y, Liu Y, Gao X. The Application of Single-Cell Technologies in Cardiovascular Research. Front Cell Dev Biol 2021; 9:751371. [PMID: 34708045 PMCID: PMC8542723 DOI: 10.3389/fcell.2021.751371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/21/2021] [Indexed: 12/21/2022] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of deaths in the world. The intricacies of the cellular composition and tissue microenvironment in heart and vasculature complicate the dissection of molecular mechanisms of CVDs. Over the past decade, the rapid development of single-cell omics technologies generated vast quantities of information at various biological levels, which have shed light on the cellular and molecular dynamics in cardiovascular development, homeostasis and diseases. Here, we summarize the latest single-cell omics techniques, and show how they have facilitated our understanding of cardiovascular biology. We also briefly discuss the clinical value and future outlook of single-cell applications in the field.
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Affiliation(s)
- Yinan Chen
- Fuwai Hospital, Chinese Academy of Medical Sciences, Shenzhen, China.,State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Liu
- Department of Vascular Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiang Gao
- Department of Vascular Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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5
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Audinot JN, Philipp P, De Castro O, Biesemeier A, Hoang QH, Wirtz T. Highest resolution chemical imaging based on secondary ion mass spectrometry performed on the helium ion microscope. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:105901. [PMID: 34404033 DOI: 10.1088/1361-6633/ac1e32] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
This paper is a review on the combination between Helium Ion Microscopy (HIM) and Secondary Ion Mass Spectrometry (SIMS), which is a recently developed technique that is of particular relevance in the context of the quest for high-resolution high-sensitivity nano-analytical solutions. We start by giving an overview on the HIM-SIMS concept and the underlying fundamental principles of both HIM and SIMS. We then present and discuss instrumental aspects of the HIM and SIMS techniques, highlighting the advantage of the integrated HIM-SIMS instrument. We give an overview on the performance characteristics of the HIM-SIMS technique, which is capable of producing elemental SIMS maps with lateral resolution below 20 nm, approaching the physical resolution limits, while maintaining a sub-nanometric resolution in the secondary electron microscopy mode. In addition, we showcase different strategies and methods allowing to take profit of both capabilities of the HIM-SIMS instrument (high-resolution imaging using secondary electrons and mass filtered secondary sons) in a correlative approach. Since its development HIM-SIMS has been successfully applied to a large variety of scientific and technological topics. Here, we will present and summarise recent applications of nanoscale imaging in materials research, life sciences and geology.
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Affiliation(s)
- Jean-Nicolas Audinot
- Advanced Instrumentation for Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Patrick Philipp
- Advanced Instrumentation for Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Olivier De Castro
- Advanced Instrumentation for Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Antje Biesemeier
- Advanced Instrumentation for Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Quang Hung Hoang
- Advanced Instrumentation for Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
| | - Tom Wirtz
- Advanced Instrumentation for Nano-Analytics (AINA), MRT Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxembourg
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6
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Yester JW, Liu H, Gyngard F, Ammanamanchi N, Little KC, Thomas D, Sullivan MLG, Lal S, Steinhauser ML, Kühn B. Use of stable isotope-tagged thymidine and multi-isotope imaging mass spectrometry (MIMS) for quantification of human cardiomyocyte division. Nat Protoc 2021; 16:1995-2022. [PMID: 33627842 PMCID: PMC8221415 DOI: 10.1038/s41596-020-00477-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022]
Abstract
Quantification of cellular proliferation in humans is important for understanding biology and responses to injury and disease. However, existing methods require administration of tracers that cannot be ethically administered in humans. We present a protocol for the direct quantification of cellular proliferation in human hearts. The protocol involves administration of non-radioactive, non-toxic stable isotope 15Nitrogen-enriched thymidine (15N-thymidine), which is incorporated into DNA during S-phase, in infants with tetralogy of Fallot, a common form of congenital heart disease. Infants with tetralogy of Fallot undergo surgical repair, which requires the removal of pieces of myocardium that would otherwise be discarded. This protocol allows for the quantification of cardiomyocyte proliferation in this discarded tissue. We quantitatively analyzed the incorporation of 15N-thymidine with multi-isotope imaging spectrometry (MIMS) at a sub-nuclear resolution, which we combined with correlative confocal microscopy to quantify formation of binucleated cardiomyocytes and cardiomyocytes with polyploid nuclei. The entire protocol spans 3-8 months, which is dependent on the timing of surgical repair, and 3-4.5 researcher days. This protocol could be adapted to study cellular proliferation in a variety of human tissues.
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Affiliation(s)
- Jessie W Yester
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Honghai Liu
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Frank Gyngard
- Center for NanoImaging, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Niyatie Ammanamanchi
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Kathryn C Little
- Clinical Research Support Services (CRSS), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
- UPMC Shadyside Hospital, Pittsburgh, PA, USA
| | - Dawn Thomas
- Clinical Research Support Services (CRSS), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
| | - Mara L G Sullivan
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Department of Cell Biology, Pittsburgh, PA, USA
| | - Sean Lal
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA
- Center for NanoImaging, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
- Division of Cardiology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Matthew L Steinhauser
- Center for NanoImaging, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, USA.
- UPMC Heart and Vascular Institute, UPMC Presbyterian, Pittsburgh, PA, USA.
- Aging Institute, University of Pittsburgh, Bridgeside Point 1, Pittsburgh, PA, USA.
| | - Bernhard Kühn
- Division of Cardiology, Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), UPMC Children's Hospital of Pittsburgh and Department of Pediatrics, Pittsburgh, PA, USA.
- McGowan Institute of Regenerative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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7
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Liu R, Yang Z. Single cell metabolomics using mass spectrometry: Techniques and data analysis. Anal Chim Acta 2021; 1143:124-134. [PMID: 33384110 PMCID: PMC7775990 DOI: 10.1016/j.aca.2020.11.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023]
Abstract
Mass spectrometry (MS) based techniques are gaining popularity for metabolomics research due to their high sensitivity, wide detection range, and capability of molecular identification. Utilizing such powerful technique to explore the cellular metabolism at the single cell level not only appreciates the subtle cell-to-cell difference (i.e., cell heterogeneity), but also gains biological merits corresponding to individual cells or small cell subpopulations. In this review article, we first briefly summarize recent advances in single cell MS experimental techniques, and then emphasize on the single cell metabolomics data analysis approaches. Through implementation of statistical analysis and more advanced data analysis methods, single cell metabolomics is expected to find more potential applications in the translational and clinical fields in the future.
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Affiliation(s)
- Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA; Alliance Pharma. Inc., Malvern, PA, 19355, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
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8
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Affiliation(s)
- Keke Hu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Tho D. K. Nguyen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Pieter E. Oomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
- ParaMedir B.V., 1e Energieweg 13, 9301 LK Roden, The Netherlands
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
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9
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Thomen A, Najafinobar N, Penen F, Kay E, Upadhyay PP, Li X, Phan NTN, Malmberg P, Klarqvist M, Andersson S, Kurczy ME, Ewing AG. Subcellular Mass Spectrometry Imaging and Absolute Quantitative Analysis across Organelles. ACS NANO 2020; 14:4316-4325. [PMID: 32239916 PMCID: PMC7199216 DOI: 10.1021/acsnano.9b09804] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/02/2020] [Indexed: 05/22/2023]
Abstract
Mass spectrometry imaging is a field that promises to become a mainstream bioanalysis technology by allowing the combination of single-cell imaging and subcellular quantitative analysis. The frontier of single-cell imaging has advanced to the point where it is now possible to compare the chemical contents of individual organelles in terms of raw or normalized ion signal. However, to realize the full potential of this technology, it is necessary to move beyond this concept of relative quantification. Here we present a nanoSIMS imaging method that directly measures the absolute concentration of an organelle-associated, isotopically labeled, pro-drug directly from a mass spectrometry image. This is validated with a recently developed nanoelectrochemistry method for single organelles. We establish a limit of detection based on the number of isotopic labels used and the volume of the organelle of interest, also offering this calculation as a web application. This approach allows subcellular quantification of drugs and metabolites, an overarching and previously unmet goal in cell science and pharmaceutical development.
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Affiliation(s)
- Aurélien Thomen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg, 412 96, Sweden
| | - Neda Najafinobar
- Medicinal
Chemistry, Research and Early Development, Respiratory, Inflammation,
and Autoimmune, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Florent Penen
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg, 412 96, Sweden
| | - Emma Kay
- Bioscience,
Research and Early Development, Cardiovascular, Renal and Metabolism,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Pratik P. Upadhyay
- Pharmaceutical
Technolgy and Development, AstraZeneca R&D, Gothenburg, 430 52, Sweden
| | - Xianchan Li
- Center
for Imaging and Systems Biology, College of Life and Environmental
Sciences, Minzu University of China, Beijing, 100081, China
| | - Nhu T. N. Phan
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg, 412 96, Sweden
| | - Per Malmberg
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg, 412 96, Sweden
| | - Magnus Klarqvist
- Early
Product Development, Pharmaceutical Science, R&D, AstraZeneca, Gothenburg, 431 50, Sweden
| | - Shalini Andersson
- New Modalities,
Discovery Sciences, R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Michael E. Kurczy
- DMPK,
Research and Early Development, Cardiovascular, Renal and Metabolism,
BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 430 51, Sweden
| | - Andrew G. Ewing
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg, 412 96, Sweden
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10
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Ievlev AV, Belianinov A, Jesse S, Allison DP, Doktycz MJ, Retterer ST, Kalinin SV, Ovchinnikova OS. Automated Interpretation and Extraction of Topographic Information from Time of Flight Secondary Ion Mass Spectrometry Data. Sci Rep 2017; 7:17099. [PMID: 29213083 PMCID: PMC5719033 DOI: 10.1038/s41598-017-17049-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 11/07/2017] [Indexed: 11/26/2022] Open
Abstract
Time of flight secondary ion mass spectrometry (ToF-SIMS) is a powerful surface-sensitive characterization tool allowing the imaging of chemical properties over a wide range of organic and inorganic material systems. This technique allows precise studies of chemical composition with sub-100-nm lateral and nanometer depth spatial resolution. However, comprehensive interpretation of ToF-SIMS results is challenging because of the very large data volume and high dimensionality. Furthermore, investigation of samples with pronounced topographical features is complicated by systematic and measureable shifts in the mass spectrum. In this work we developed an approach for the interpretation of the ToF-SIMS data, based on the advanced data analytics. Along with characterization of the chemical composition, our approach allows extraction of the sample surface morphology from a time of flight registration technique. This approach allows one to perform correlated investigations of surface morphology, biological function, and chemical composition of Arabidopsis roots.
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Affiliation(s)
- Anton V Ievlev
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA.
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA.
| | - Alexei Belianinov
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
| | - Stephen Jesse
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
| | - David P Allison
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
- Department Biochemistry & Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Mitchel J Doktycz
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
| | - Scott T Retterer
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
| | - Sergei V Kalinin
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
| | - Olga S Ovchinnikova
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
- Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN, 37831, USA
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11
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Abstract
Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, the authors provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analyses, and current outlooks. Specifically, the authors offer an overview of SIMS and development of the NanoSIMS. The authors describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, the authors provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, the authors present a perspective on the future of this technology and where they think it will have the greatest impact in near future.
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12
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Nookala AR, Mitra J, Chaudhari NS, Hegde ML, Kumar A. An Overview of Human Immunodeficiency Virus Type 1-Associated Common Neurological Complications: Does Aging Pose a Challenge? J Alzheimers Dis 2017; 60:S169-S193. [PMID: 28800335 PMCID: PMC6152920 DOI: 10.3233/jad-170473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
With increasing survival of patients infected with human immunodeficiency virus type 1 (HIV-1), the manifestation of heterogeneous neurological complications is also increasing alarmingly in these patients. Currently, more than 30% of about 40 million HIV-1 infected people worldwide develop central nervous system (CNS)-associated dysfunction, including dementia, sensory, and motor neuropathy. Furthermore, the highly effective antiretroviral therapy has been shown to increase the prevalence of mild cognitive functions while reducing other HIV-1-associated neurological complications. On the contrary, the presence of neurological disorder frequently affects the outcome of conventional HIV-1 therapy. Although, both the children and adults suffer from the post-HIV treatment-associated cognitive impairment, adults, especially depending on the age of disease onset, are more prone to CNS dysfunction. Thus, addressing neurological complications in an HIV-1-infected patient is a delicate balance of several factors and requires characterization of the molecular signature of associated CNS disorders involving intricate cross-talk with HIV-1-derived neurotoxins and other cellular factors. In this review, we summarize some of the current data supporting both the direct and indirect mechanisms, including neuro-inflammation and genome instability in association with aging, leading to CNS dysfunction after HIV-1 infection, and discuss the potential strategies addressing the treatment or prevention of HIV-1-mediated neurotoxicity.
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Affiliation(s)
- Anantha Ram Nookala
- Division of Pharmacology and Toxicology, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Joy Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
| | - Nitish S. Chaudhari
- Division of Pharmacology and Toxicology, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Muralidhar L. Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, USA
- Weill Cornell Medical College of Cornell University, NY, USA
| | - Anil Kumar
- Division of Pharmacology and Toxicology, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO, USA
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13
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He C, Fong LG, Young SG, Jiang H. NanoSIMS imaging: an approach for visualizing and quantifying lipids in cells and tissues. J Investig Med 2016; 65:669-672. [PMID: 27793974 DOI: 10.1136/jim-2016-000239] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2016] [Indexed: 12/22/2022]
Abstract
Over the past few decades, several approaches have been used to image lipids in cells and tissues, but most have limited spatial resolution and sensitivity. Here, we discuss a relatively new approach, nanoscale secondary ion mass spectrometry imaging, that makes it possible to visualize lipids in cells and tissues in a quantitative fashion and with high spatial resolution and high sensitivity.
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Affiliation(s)
- Cuiwen He
- Departments of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Loren G Fong
- Departments of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Stephen G Young
- Departments of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA.,Departments of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Haibo Jiang
- Centre for Microscopy, Characterisation, and Analysis, The University of Western Australia, Perth, Western Australia, Australia
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14
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NanoSIMS chemical imaging combined with correlative microscopy for biological sample analysis. Curr Opin Biotechnol 2016; 41:130-135. [PMID: 27506876 DOI: 10.1016/j.copbio.2016.06.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/17/2016] [Accepted: 06/23/2016] [Indexed: 12/18/2022]
Abstract
Nano-scale Secondary Ion Mass Spectrometry (NanoSIMS) is one of the most powerful in situ elemental and isotopic analysis techniques available to biologists. The combination of stable isotope probing with NanoSIMS (nanoSIP) has opened up new avenues for biological studies over the past decade. However, due to limitations inherent with any analytical methodology, additional information from correlative techniques is usually required to address real biological questions. Here we review recent developments in correlative analysis applied to complex biological systems: first, high-resolution tracking of molecules (e.g. peptides, lipids) by correlation with electron microscopy and atomic force microscopy; second, identification of a specific microbial taxon with fluorescence in situ hybridization and quantification of its metabolic capacities; and, third, molecular specific imaging with new probes.
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15
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Musat N, Musat F, Weber PK, Pett-Ridge J. Tracking microbial interactions with NanoSIMS. Curr Opin Biotechnol 2016; 41:114-121. [PMID: 27419912 DOI: 10.1016/j.copbio.2016.06.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/09/2016] [Accepted: 06/23/2016] [Indexed: 12/29/2022]
Abstract
The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where used to track exchanges of isotopically labelled molecules between organisms. We highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont-host nutrient sharing.
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Affiliation(s)
- Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
| | - Florin Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Peter Kilian Weber
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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16
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Three-dimensional imaging of cholesterol and sphingolipids within a Madin-Darby canine kidney cell. Biointerphases 2016; 11:02A309. [PMID: 26746168 DOI: 10.1116/1.4939681] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Metabolic stable isotope incorporation and secondary ion mass spectrometry (SIMS) depth profiling performed on a Cameca NanoSIMS 50 were used to image the (18)O-cholesterol and (15)N-sphingolipid distributions within a portion of a Madin-Darby canine kidney (MDCK) cell. Three-dimensional representations of the component-specific isotope distributions show clearly defined regions of (18)O-cholesterol and (15)N-sphingolipid enrichment that seem to be separate subcellular compartments. The low levels of nitrogen-containing secondary ions detected at the (18)O-enriched regions suggest that these (18)O-cholesterol-rich structures may be lipid droplets, which have a core consisting of cholesterol esters and triacylglycerides.
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Abstract
Obesity and its major comorbidities, including type 2 diabetes mellitus, nonalcoholic fatty liver disease (NAFLD), obesity cardiomyopathy, and certain cancers, have caused life expectancy in the United States to decline in recent years. Obesity is the increased accumulation of triglycerides (TG), which are synthesized from glycerol and long-chain fatty acids (LCFA) throughout the body. LCFA enter adipocytes, hepatocytes, and cardiomyocytes via specific, facilitated transport processes. Metabolism of increased cellular TG content in obesity may lead to comorbidities such as NAFLD and cardiomyopathy. Better understanding of LCFA transport processes may lead to successful treatment of obesity and NAFLD.
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Affiliation(s)
- Paul D Berk
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia College of Physicians and Surgeons, Columbia University Medical Center, 650 West 168 Street, New York, NY 10032, USA; Division of Preventive Medicine, Department of Medicine, Columbia College of Physicians and Surgeons, Columbia University Medical Center, William Black Building, 650 West 168 Street, Room 1006, Box 57A, New York, NY 10032, USA.
| | - Elizabeth C Verna
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia College of Physicians and Surgeons, Columbia University Medical Center, 650 West 168 Street, New York, NY 10032, USA
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18
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Daemen S, van Zandvoort MAMJ, Parekh SH, Hesselink MKC. Microscopy tools for the investigation of intracellular lipid storage and dynamics. Mol Metab 2015; 5:153-163. [PMID: 26977387 PMCID: PMC4770264 DOI: 10.1016/j.molmet.2015.12.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 12/19/2015] [Accepted: 12/27/2015] [Indexed: 12/01/2022] Open
Abstract
Background Excess storage of lipids in ectopic tissues, such as skeletal muscle, liver, and heart, seems to associate closely with metabolic abnormalities and cardiac disease. Intracellular lipid storage occurs in lipid droplets, which have gained attention as active organelles in cellular metabolism. Recent developments in high-resolution microscopy and microscopic spectroscopy have opened up new avenues to examine the physiology and biochemistry of intracellular lipids. Scope of review The aim of this review is to give an overview of recent technical advances in microscopy, and its application for the visualization, identification, and quantification of intracellular lipids, with special focus to lipid droplets. In addition, we attempt to summarize the probes currently available for the visualization of lipids. Major conclusions The continuous development of lipid probes in combination with the rapid development of microscopic techniques can provide new insights in the role and dynamics of intracellular lipids. Moreover, in situ identification of intracellular lipids is now possible and promises to add a new dimensionality to analysis of lipid biochemistry, and its relation to (patho)physiology.
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Key Words
- BODIPY, Boron-dipyrromethene
- CARS, coherent anti-stokes Raman scattering
- CLEM, correlative light electron microscopy
- CLSM, confocal laser scanning microscopy
- DIC, differential interference microscopy
- FA, fatty acid
- FIB-SEM, focused ion beam scanning electron microscopy
- FLIP, fluorescence loss in photobleaching
- FRAP, fluorescent recovery after photobleaching
- FRET, fluorescence resonance energy transfer
- Fluorescent lipid probes
- GFP, green fluorescent protein
- HCV, hepatitis C virus
- LD, lipid droplet
- Lipid droplets
- Live-cell imaging
- Metabolic disease
- NBD, nitro-benzoxadiazolyl
- PALM, photoactivation localization microscopy
- SBEM, serial block face scanning electron microscopy
- SIMS, Secondary Ion Mass Spectrometry
- SRS, Stimulated Raman Scattering
- STED, stimulated emission depletion
- STORM, stochastic optical reconstruction microscopy
- Super-resolution
- TAG, triacylglycerol
- TEM, transmission electron microscopy
- TOF-SIMS, time-of-flight SIMS
- TPLSM, two-photon laser scanning microscopy
- Vibrational microscopy
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Affiliation(s)
- Sabine Daemen
- Department of Human Movement Sciences and Human Biology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands.
| | - Marc A M J van Zandvoort
- Department of Genetics and Molecular Cell Biology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands; Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, Aachen, Germany.
| | - Sapun H Parekh
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Matthijs K C Hesselink
- Department of Human Movement Sciences and Human Biology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands.
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Kraft ML, Klitzing HA. Imaging lipids with secondary ion mass spectrometry. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1108-19. [PMID: 24657337 DOI: 10.1016/j.bbalip.2014.03.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 10/25/2022]
Abstract
This review discusses the application of time-of-flight secondary ion mass spectrometry (TOF-SIMS) and magnetic sector SIMS with high lateral resolution performed on a Cameca NanoSIMS 50(L) to imaging lipids. The similarities between the two SIMS approaches and the differences that impart them with complementary strengths are described, and various strategies for sample preparation and to optimize the quality of the SIMS data are presented. Recent reports that demonstrate the new insight into lipid biochemistry that can be acquired with SIMS are also highlighted. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Mary L Kraft
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Haley A Klitzing
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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20
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Passarelli MK, Ewing AG. Single-cell imaging mass spectrometry. Curr Opin Chem Biol 2013; 17:854-9. [PMID: 23948695 DOI: 10.1016/j.cbpa.2013.07.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 07/03/2013] [Accepted: 07/03/2013] [Indexed: 10/26/2022]
Abstract
Single-cell imaging mass spectrometry (IMS) is a powerful technique used to map the distributions of endogenous biomolecules with subcellular resolution. Currently, secondary ion mass spectrometry is the predominant technique for single-cell IMS, thanks to its submicron lateral resolution and surface sensitivity. However, recent methodological and technological developments aimed at improving the spatial resolution of matrix assisted laser desorption ionization (MALDI) have made this technique a potential platform of single-cell IMS. MALDI opens the field of single-cell IMS to new possibilities, including single cell proteomic imaging and atmospheric pressure analyses; however, sensitivity is a challenge. In this report, we estimate the availability of proteins and lipids in a single cell and discuss strategies employed to improve sensitivity at the single-cell level.
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21
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Previs SF, McLaren DG, Wang SP, Stout SJ, Zhou H, Herath K, Shah V, Miller PL, Wilsie L, Castro-Perez J, Johns DG, Cleary MA, Roddy TP. New methodologies for studying lipid synthesis and turnover: looking backwards to enable moving forwards. Biochim Biophys Acta Mol Basis Dis 2013; 1842:402-13. [PMID: 23707557 DOI: 10.1016/j.bbadis.2013.05.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 05/11/2013] [Accepted: 05/13/2013] [Indexed: 12/26/2022]
Abstract
Our ability to understand the pathogenesis of problems surrounding lipid accretion requires attention towards quantifying lipid kinetics. In addition, studies of metabolic flux should also help unravel mechanisms that lead to imbalances in inter-organ lipid trafficking which contribute to dyslipidemia and/or peripheral lipid accumulation (e.g. hepatic fat deposits). This review aims to outline the development and use of novel methods for studying lipid kinetics in vivo. Although our focus is directed towards some of the approaches that are currently reported in the literature, we include a discussion of the older literature in order to put "new" methods in better perspective and inform readers of valuable historical research. Presumably, future advances in understanding lipid dynamics will benefit from a careful consideration of the past efforts, where possible we have tried to identify seminal papers or those that provide clear data to emphasize essential points. This article is part of a Special Issue entitled: Modulation of Adipose Tissue in Health and Disease.
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Affiliation(s)
- Stephen F Previs
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | - David G McLaren
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Sheng-Ping Wang
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Steven J Stout
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Haihong Zhou
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Kithsiri Herath
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Vinit Shah
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Paul L Miller
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Larissa Wilsie
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Jose Castro-Perez
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Douglas G Johns
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Michele A Cleary
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Thomas P Roddy
- Molecular Biomarkers, Merck, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
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22
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Steinhauser ML, Lechene CP. Quantitative imaging of subcellular metabolism with stable isotopes and multi-isotope imaging mass spectrometry. Semin Cell Dev Biol 2013; 24:661-7. [PMID: 23660233 DOI: 10.1016/j.semcdb.2013.05.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multi-isotope imaging mass spectrometry (MIMS) is the quantitative imaging of stable isotope labels in cells with a new type of secondary ion mass spectrometer (NanoSIMS). The power of the methodology is attributable to (i) the immense advantage of using non-toxic stable isotope labels, (ii) high resolution imaging that approaches the resolution of usual transmission electron microscopy and (iii) the precise quantification of label down to 1 part-per-million and spanning several orders of magnitude. Here we review the basic elements of MIMS and describe new applications of MIMS to the quantitative study of metabolic processes including protein and nucleic acid synthesis in model organisms ranging from microbes to humans.
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Affiliation(s)
- Matthew L Steinhauser
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, United States; Division of Genetics, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, United States; Division of Cardiovascular Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, United States
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23
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Passarelli MK, Ewing AG, Winograd N. Single-cell lipidomics: characterizing and imaging lipids on the surface of individual Aplysia californica neurons with cluster secondary ion mass spectrometry. Anal Chem 2013; 85:2231-8. [PMID: 23323749 PMCID: PMC3867296 DOI: 10.1021/ac303038j] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neurons isolated from Aplysia californica , an organism with a well-defined neural network, were imaged with secondary ion mass spectrometry, C(60)-SIMS. A major lipid component of the neuronal membrane was identified as 1-hexadecyl-2-octadecenoyl-sn-glycero-3-phosphocholine [PC(16:0e/18:1)] using tandem mass spectrometry (MS/MS). The assignment was made directly off the sample surface using a C(60)-QSTAR instrument, a prototype instrument that combines an ion source with a commercial electrospray ionization/matrix-assisted laser desorption ionization (ESI/MALDI) mass spectrometer. Normal phase liquid chromatography mass spectrometry (NP-LC-MS) was used to confirm the assignment. Cholesterol and vitamin E were also identified with in situ tandem MS analyses that were compared to reference spectra obtained from purified compounds. In order to improve sensitivity on the single-cell level, the tandem MS spectrum of vitamin E reference material was used to extract and compile all the vitamin E related peaks from the cell image. The mass spectrometry images reveal heterogeneous distributions of intact lipid species, PC(16:0e/18:1), vitamin E, and cholesterol on the surface of a single neuron. The ability to detect these molecules and determine their relative distribution on the single-cell level shows that the C(60)-QSTAR is a potential platform for studying important biochemical processes, such as neuron degeneration.
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Affiliation(s)
- Melissa K. Passarelli
- Department of Chemistry, University Park, PA 16802, USA
- Department of Chemistry and Molecular Biology, The University of Gothenburg, SE-41296 Göteborg, Sweden
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, The University of Gothenburg, SE-41296 Göteborg, Sweden
- Department of Chemical and Biological Engineering, Chalmers University of Technology, S-41296 Göteborg, Sweden
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24
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Abstract
Imaging technologies developed in the early 20th century achieved contrast solely by relying on macroscopic and morphological differences between the tissues of interest and the surrounding tissues. Since then, there has been a movement toward imaging at the cellular and molecular level in order to visualize biological processes. This rapidly growing field is known as molecular imaging. In the last decade, many methodologies for imaging proteins have emerged. However, most of these approaches cannot be extended to imaging beyond the proteome. Here, we highlight some of the recently developed technologies that enable imaging of non-proteinaceous molecules in the cell: lipids, signalling molecules, inorganic ions, glycans, nucleic acids, small-molecule metabolites, and protein post-translational modifications such as phosphorylation and methylation.
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Affiliation(s)
- Pamela V. Chang
- Department of Chemistry, University of California, Berkeley, 94720, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, U.S.A
- Howard Hughes Medical Institute, University of California, Berkeley, U.S.A
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25
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Lanni EJ, Rubakhin SS, Sweedler JV. Mass spectrometry imaging and profiling of single cells. J Proteomics 2012; 75:5036-5051. [PMID: 22498881 DOI: 10.1016/j.jprot.2012.03.017] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/08/2012] [Accepted: 03/13/2012] [Indexed: 11/25/2022]
Abstract
Mass spectrometry imaging and profiling of individual cells and subcellular structures provide unique analytical capabilities for biological and biomedical research, including determination of the biochemical heterogeneity of cellular populations and intracellular localization of pharmaceuticals. Two mass spectrometry technologies-secondary ion mass spectrometry (SIMS) and matrix assisted laser desorption/ionization mass spectrometry (MALDI MS)-are most often used in micro-bioanalytical investigations. Recent advances in ion probe technologies have increased the dynamic range and sensitivity of analyte detection by SIMS, allowing two- and three-dimensional localization of analytes in a variety of cells. SIMS operating in the mass spectrometry imaging (MSI) mode can routinely reach spatial resolutions at the submicron level; therefore, it is frequently used in studies of the chemical composition of subcellular structures. MALDI MS offers a large mass range and high sensitivity of analyte detection. It has been successfully applied in a variety of single-cell and organelle profiling studies. Innovative instrumentation such as scanning microprobe MALDI and mass microscope spectrometers enables new subcellular MSI measurements. Other approaches for MS-based chemical imaging and profiling include those based on near-field laser ablation and inductively-coupled plasma MS analysis, which offer complementary capabilities for subcellular chemical imaging and profiling.
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Affiliation(s)
- Eric J Lanni
- Department of Chemistry and the Beckman Institute of Science and Technology, University of Illinois, Urbana IL 61801, USA
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute of Science and Technology, University of Illinois, Urbana IL 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute of Science and Technology, University of Illinois, Urbana IL 61801, USA.
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26
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Abstract
Recent advances in high-resolution imaging secondary ion mass spectrometry (SIMS) (J Biol 5: 20, 2006) have made isotopic tracing at the single-cell level a standard technique for microbial ecology and systems biology; elemental and metal cofactor analyses are also showing significant promise. For example, with the NanoSIMS, metabolic activities of single microbial cells can be tracked by imaging natural isotopic/elemental composition or isotope distribution after stable isotope probing. When linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. We broadly call this combination of methods nanoSIP, for nanometer-scale stable isotope probing. Here we present the primary materials and methods used for nanoSIP, with an emphasis on key steps and potential pitfalls. Applications to pure cultures, cocultures, and complex communities are discussed.
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Affiliation(s)
- Jennifer Pett-Ridge
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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27
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Passarelli MK, Winograd N. Lipid imaging with time-of-flight secondary ion mass spectrometry (ToF-SIMS). BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1811:976-90. [PMID: 21664291 PMCID: PMC3199347 DOI: 10.1016/j.bbalip.2011.05.007] [Citation(s) in RCA: 210] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 05/13/2011] [Accepted: 05/18/2011] [Indexed: 02/07/2023]
Abstract
Fundamental advances in secondary ion mass spectrometry (SIMS) now allow for the examination and characterization of lipids directly from biological materials. The successful application of SIMS-based imaging in the investigation of lipids directly from tissue and cells are demonstrated. Common complications and technical pitfalls are discussed. In this review, we examine the use of cluster ion sources and cryogenically compatible sample handling for improved ion yields and to expand the application potential of SIMS. Methodological improvements, including pre-treating the sample to improve ion yields and protocol development for 3-dimensional analyses (i.e. molecular depth profiling), are also included in this discussion. New high performance SIMS instruments showcasing the most advanced instrumental developments, including tandem MS capabilities and continuous ion beam compatibility, are described and the future direction for SIMS in lipid imaging is evaluated.
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Affiliation(s)
- Melissa K Passarelli
- Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park
| | - Nicholas Winograd
- Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park
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28
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Lafontan M. Historical perspectives in fat cell biology: the fat cell as a model for the investigation of hormonal and metabolic pathways. Am J Physiol Cell Physiol 2011; 302:C327-59. [PMID: 21900692 DOI: 10.1152/ajpcell.00168.2011] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
For many years, there was little interest in the biochemistry or physiology of adipose tissue. It is now well recognized that adipocytes play an important dynamic role in metabolic regulation. They are able to sense metabolic states via their ability to perceive a large number of nervous and hormonal signals. They are also able to produce hormones, called adipokines, that affect nutrient intake, metabolism and energy expenditure. The report by Rodbell in 1964 that intact fat cells can be obtained by collagenase digestion of adipose tissue revolutionized studies on the hormonal regulation and metabolism of the fat cell. In the context of the advent of systems biology in the field of cell biology, the present seems an appropriate time to look back at the global contribution of the fat cell to cell biology knowledge. This review focuses on the very early approaches that used the fat cell as a tool to discover and understand various cellular mechanisms. Attention essentially focuses on the early investigations revealing the major contribution of mature fat cells and also fat cells originating from adipose cell lines to the discovery of major events related to hormone action (hormone receptors and transduction pathways involved in hormonal signaling) and mechanisms involved in metabolite processing (hexose uptake and uptake, storage, and efflux of fatty acids). Dormant preadipocytes exist in the stroma-vascular fraction of the adipose tissue of rodents and humans; cell culture systems have proven to be valuable models for the study of the processes involved in the formation of new fat cells. Finally, more recent insights into adipocyte secretion, a completely new role with major metabolic impact, are also briefly summarized.
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Affiliation(s)
- Max Lafontan
- Institut National de la Santé et de la Recherche Médicale, UMR, Hôpital Rangueil, Toulouse, France.
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29
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Careri M, Mangia A. Trends in analytical atomic and molecular mass spectrometry in biology and the life sciences. Anal Bioanal Chem 2010; 399:2585-95. [DOI: 10.1007/s00216-010-4585-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 12/06/2010] [Indexed: 12/30/2022]
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30
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Carley AN, Kleinfeld AM. Fatty acid (FFA) transport in cardiomyocytes revealed by imaging unbound FFA is mediated by an FFA pump modulated by the CD36 protein. J Biol Chem 2010; 286:4589-97. [PMID: 21147770 DOI: 10.1074/jbc.m110.182162] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Free fatty acid (FFA) transport across the cardiomyocyte plasma membrane is essential to proper cardiac function, but the role of membrane proteins and FFA metabolism in FFA transport remains unclear. Metabolism is thought to maintain intracellular FFA at low levels, providing the driving force for FFA transport, but intracellular FFA levels have not been measured directly. We report the first measurements of the intracellular unbound FFA concentrations (FFA(i)) in cardiomyocytes. The fluorescent indicator of FFA, ADIFAB (acrylodan-labeled rat intestinal fatty acid-binding protein), was microinjected into isolated cardiomyocytes from wild type (WT) and FAT/CD36 null C57B1/6 mice. Quantitative imaging of ADIFAB fluorescence revealed the time courses of FFA influx and efflux. For WT mice, rate constants for efflux (∼0.02 s(-1)) were twice influx, and steady state FFA(i) were more than 3-fold larger than extracellular unbound FFA (FFA(o)). The concentration gradient and the initial rate of FFA influx saturated with increasing FFA(o). Similar characteristics were observed for oleate, palmitate, and arachidonate. FAT/CD36 null cells revealed similar characteristics, except that efflux was 2-3-fold slower than WT cells. Rate constants determined with intracellular ADIFAB were confirmed by measurements of intracellular pH. FFA uptake by suspensions of cardiomyocytes determined by monitoring FFA(o) using extracellular ADIFAB confirmed the influx rate constants determined from FFA(i) measurements and demonstrated that rates of FFA transport and etomoxir-sensitive metabolism are regulated independently. We conclude that FFA influx in cardiac myocytes is mediated by a membrane pump whose transport rate constants may be modulated by FAT/CD36.
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Affiliation(s)
- Andrew N Carley
- Torrey Pines Institute for Molecular Studies, San Diego, California 92121, USA
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Walewski JL, Ge F, Gagner M, Inabnet WB, Pomp A, Branch AD, Berk PD. Adipocyte accumulation of long-chain fatty acids in obesity is multifactorial, resulting from increased fatty acid uptake and decreased activity of genes involved in fat utilization. Obes Surg 2009; 20:93-107. [PMID: 19866242 DOI: 10.1007/s11695-009-0002-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Accepted: 10/06/2009] [Indexed: 12/11/2022]
Abstract
BACKGROUND The obesity epidemic causes significant morbidity and mortality. Knowledge of cellular function and gene expression in obese adipose tissue will yield insights into obesity pathogenesis and suggest therapeutic targets. The aim of this work is to study the processes determining fat accumulation in adipose tissue from obese patients. METHODS Omental fat was collected from two cohorts of obese bariatric surgery patients and sex-matched normal-weight donors. Isolated adipocytes were compared for cell size, volume, and long-chain fatty acid (LCFA) uptake. Omental fat RNAs were screened by 10K microarray (cohort 1: three obese, three normal) or Whole Genome microarray (cohort 2: seven obese, four normal). Statistical differences in gene and pathway expression were identified in cohort 1 using the GeneSifter Software (Geospiza) with key results confirmed in cohort 2 samples by microarray, quantitative real-time polymerase chain reaction, and pathway analysis. RESULTS Obese omental adipocytes had increased surface area, volume, and V (max) for saturable LCFA uptake. Dodecenoyl-coenzyme A delta isomerase, central to LCFA metabolism, was approximately 1.6-fold underexpressed in obese fat in cohorts 1 and 2. Additionally, the Kyoto Encyclopedia of Genes and Genomics pathway analysis identified oxidative phosphorylation and fatty acid metabolism pathways as having coordinate, nonrandom downregulation of gene expression in both cohorts. CONCLUSIONS In obese omental fat, saturable adipocyte LCFA uptake was greater than in controls, and expression of key genes involved in lipolysis, beta-oxidation, and metabolism of fatty acids was reduced. Thus, both increased uptake and reduced metabolism of LCFAs contribute to the accumulation of LCFAs in obese adipocytes.
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Affiliation(s)
- José L Walewski
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
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32
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Boxer SG, Kraft ML, Weber PK. Advances in imaging secondary ion mass spectrometry for biological samples. Annu Rev Biophys 2009; 38:53-74. [PMID: 19086820 DOI: 10.1146/annurev.biophys.050708.133634] [Citation(s) in RCA: 206] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Imaging mass spectrometry combines the power of mass spectrometry to identify complex molecules based on mass with sample imaging. Recent advances in secondary ion mass spectrometry have improved sensitivity and spatial resolution, so that these methods have the potential to bridge between high-resolution structures obtained by X-ray crystallography and cyro-electron microscopy and ultrastructure visualized by conventional light microscopy. Following background information on the method and instrumentation, we address the key issue of sample preparation. Because mass spectrometry is performed in high vacuum, it is essential to preserve the lateral organization of the sample while removing bulk water, and this has been a major barrier for applications to biological systems. Recent applications of imaging mass spectrometry to cell biology, microbial communities, and biosynthetic pathways are summarized briefly, and studies of biological membrane organization are described in greater depth.
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Affiliation(s)
- Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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Berk PD. Regulatable fatty acid transport mechanisms are central to the pathophysiology of obesity, fatty liver, and metabolic syndrome. Hepatology 2008; 48:1362-76. [PMID: 18972439 PMCID: PMC2956590 DOI: 10.1002/hep.22632] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Paul D Berk
- Department of Medicine, Division of Digestive and Liver Diseases, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
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34
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Jones EA, Lockyer NP, Vickerman JC. Depth profiling brain tissue sections with a 40 keV C60+ primary ion beam. Anal Chem 2008; 80:2125-32. [PMID: 18278949 DOI: 10.1021/ac702127q] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, the effect of prolonged C60(+) primary ion bombardment on the chemical information available from a section of rat brain is discussed. Initial attempts demonstrate the rapid loss of molecular signal from the bombarded area with both C60(+) and Au(+) used as a monatomic comparison. However, the nature of this signal disappearance is shown to be different. Analysis of the C60(+) data indicates a correlation between signal loss and the appearance of sodium and potassium adducts of phosphate and protein fragments; this is supported by model systems. By using an ammonium formate wash to reduce the salt levels within the tissue this effect is removed, allowing the chemistry of the tissue section to be better probed. Results collected from multiple sections suggest that at room temperature under vacuum conditions there is a migration of lipids to the surface of the tissue. Three-dimensional (3D) imaging is used to demonstrate that once these lipids are removed other species, such as proteins, are uncovered. By depth profiling the sample in a frozen state, the degree and importance of lipid migration to the observed localization of native compounds is assessed. This investigation into the behavior of biological tissue under high C60(+) fluxes not only allows an evaluation of the potential accuracy of 3D SIMS mapping of important biological molecules but also demonstrates the possibility of using ion doses beyond the traditional "static limit" to provide higher secondary ion yields that could lead to greater detection limits and smaller useful lateral resolution within such analyses.
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Affiliation(s)
- Emrys A Jones
- Surface Analysis Research Centre, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom.
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35
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Differences in adipocyte long chain fatty acid uptake in Osborne-Mendel and S5B/Pl rats in response to high-fat diets. Int J Obes (Lond) 2008; 32:853-62. [PMID: 18197182 DOI: 10.1038/sj.ijo.0803792] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To determine whether strain differences in adipocyte uptake of long chain fatty acids (LCFAs) contribute to differences in weight gain by Osborne-Mendel (OM) and S5B/Pl rats (S) fed a high-fat diet (HFD). SUBJECTS Ninety-four adult (12-14-week old) male OM and S rats. MEASUREMENTS Body weight; epididymal fat pad weight; adipocyte size, number, LCFA uptake kinetics; and plasma insulin and leptin during administration of HFD or chow diets (CDs). RESULTS In both strains, rate of weight gain (RWG) was greater on an HFD than a CD; RWG on an HFD was greater, overall, in OM than S. A significant RWG increase occurred on days 1 and 2 in both strains. It was normalized in S by days 6-9 but persisted at least till day 14 in OM. RWGs were significantly correlated (P<0.001) with the V(max) for saturable adipocyte LCFA uptake (V(max)). In S, an increase in V(max) on day 1 returned to baseline by day 7 and was correlated with both plasma insulin and leptin levels throughout. In OM, a greater increase in V(max) was evident by day 2, and persisted for at least 14 days, during which both insulin and leptin levels remained elevated. Growth in epididymal fat pads on the HFD correlated with body weight, reflecting hypertrophy in OM and both hypertrophy and hyperplasia in S. CONCLUSIONS (a) Changes in V(max) contribute significantly to changes in RWG on HFDs. (b) There are important strain differences in circulating insulin and leptin responses to an HFD. (c) Both insulin and leptin responses to an HFD are closely correlated with V(max) of adipocyte fatty acid uptake in S animals, but suggest early onset of insulin resistance in OM. Thus, differences in hormonal regulation of adipocyte LCFA uptake may underlie the different responses of OM and S to HFD.
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36
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Easy flat embedding of oriented samples in hydrophilic resin (LR White) under controlled atmosphere: application allowing both nucleic acid hybridizations (CARD-FISH) and ultrastructural observations. Acta Histochem 2008; 110:427-31. [PMID: 18187186 DOI: 10.1016/j.acthis.2007.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 10/29/2007] [Accepted: 11/02/2007] [Indexed: 11/22/2022]
Abstract
Hydrophilic resins present the advantage of making possible both hybridization experiments involving either antibodies or oligonucleotide probes and ultrastructural observations. Whereas various embedding protocols are available, only very few concern flat-embedded preparations. In this study we describe an easy protocol for flat embedding of small-oriented biological samples in hydrophilic resins (LR White). The most important constraints are (i) to polymerize the samples under argon-saturated atmosphere (avoiding oxygen which is an inhibitor of LR White polymerization) and (ii) to use transparent flat embedding molds. Two kinds of samples were analyzed: small pieces of large tissue that need to be accurately oriented for a valuable analysis and very small organisms such as free-living nematodes, which are very hard to investigate with conventional paraffin wax embedding techniques. Semi-thin sections strongly reinforce the quality of the observations from oligonucleotidic in situ hybridization experiments by reducing the background usually encountered in oligonucleotide probe hybridization experiments from sections. Such protocols could also permit a cheap alternative to the use of laser scanning confocal microscopes for oligonucleotidic in situ hybridization as in FISH and CARD-FISH experiments from histological sections. The interest of this embedding protocol is reinforced by the fact that molecular in situ hybridization experiments and ultrastructural observations from thin sections can be carried out from a single-small individual (<1mm in length) sample.
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37
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Kampf JP, Parmley D, Kleinfeld AM. Free fatty acid transport across adipocytes is mediated by an unknown membrane protein pump. Am J Physiol Endocrinol Metab 2007; 293:E1207-14. [PMID: 17711989 DOI: 10.1152/ajpendo.00259.2007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The role of cell membranes in regulating the flux of long chain free fatty acids (FFA) into and out of adipocytes is intensely debated. Four different membrane proteins including, FABPpm, CD36/FAT, caveolin-1, and FATP have been identified as facilitating FFA transport. Moreover, CD36 and caveolin-1 are also reported to mediate transport in conjunction with lipid rafts. The principal evidence for these findings is a correlation of the level of FFA uptake with the expression level of these proteins and with the integrity of lipid rafts. The 3T3-L1 and 3T3-F442A cell lines in their preadipocyte states reveal little or no expression of these proteins and correspondingly low levels of uptake. Here we have microinjected the adipocyte and preadipocyte cell lines with ADIFAB, the fluorescent indicator of FFA. The ADIFAB fluorescence allowed us to monitor the intracellular unbound FFA concentration during FFA influx and efflux. We show that these measurements of transport, in contrast to FFA uptake measurements, correlate neither with expression of these proteins nor with lipid raft integrity in preadipocytes and adipocytes. Transport characteristics, including the generation of an ATP-dependent FFA concentration gradient, are virtually identical in adipocytes and preadipocytes. We suggest that the origin of the discrepancy between uptake and our measurements is that most of the FFA transported into the cells is lost during the uptake but not in the transport protocols. We conclude that long chain fatty acid transport in adipocytes is very likely mediated by an as-yet-unidentified membrane protein pump.
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Affiliation(s)
- J Patrick Kampf
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121, USA
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38
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Smith AJ, Thompson BR, Sanders MA, Bernlohr DA. Interaction of the adipocyte fatty acid-binding protein with the hormone-sensitive lipase: regulation by fatty acids and phosphorylation. J Biol Chem 2007; 282:32424-32. [PMID: 17785468 DOI: 10.1074/jbc.m703730200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adipocyte fatty acid-binding protein (AFABP/aP2) forms a physical complex with the hormone-sensitive lipase (HSL) and AFABP/aP2-null mice exhibit reduced basal and hormone-stimulated lipolysis. To identify the determinants affecting the interaction fluorescence resonance energy transfer (FRET) imaging was used in conjunction with a mutagenesis strategy to evaluate the roles AFABP/aP2 fatty acid binding and HSL phosphorylation have in complex formation as well as determine the HSL binding site on AFABP/aP2. The nonfatty acid binding mutant of AFABP/aP2 (R126Q) failed to form a FRET-competent complex with HSL either under basal or forskolin-stimulated conditions, indicating that lipid binding is required for association. Once bound to HSL and on the surface of the lipid droplet, YFP-AFABP/aP2 (but not YFP-HSL) exhibited energy transfer between the fusion protein and BODIPY-C12-labeled triacylglycerol. Serine to alanine mutations at the two PKA phosphorylation sites of HSL (659 and 660), or at the AMPK phosphorylation sites (565), blocked FRET between HSL and AFABP/aP2. Substitution of isoleucine for lysine at position 21 of AFABP/aP2 (K21I), but not 31 (K31I), resulted in a non-HSL-binding protein indicating that residues on helix alphaI of AFABP/aP2 define a component of the HSL binding site. These results indicate that the ligand-bound form of AFABP/aP2.interacts with the activated, phosphorylated HSL and that the association is likely to be regulatory; either delivering FA to inhibit HSL (facilitating feedback inhibition) or affecting multicomponent complex formation on the droplet surface.
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Affiliation(s)
- Anne J Smith
- Department of Biochemistry, Molecular Biology, and Biophysics, Imaging Center, The University of Minnesota, Minneapolis 55455, USA
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39
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Abstract
Imaging mass spectrometry combines the chemical specificity and parallel detection of mass spectrometry with microscopic imaging capabilities. The ability to simultaneously obtain images from all analytes detected, from atomic to macromolecular ions, allows the analyst to probe the chemical organization of a sample and to correlate this with physical features. The sensitivity of the ionization step, sample preparation, the spatial resolution, and the speed of the technique are all important parameters that affect the type of information obtained. Recently, significant progress has been made in each of these steps for both secondary ion mass spectrometry (SIMS) and matrix-assisted laser desorption/ionization (MALDI) imaging of biological samples. Examples demonstrating localization of proteins in tumors, a reduction of lamellar phospholipids in the region binding two single celled organisms, and sub-cellular distributions of several biomolecules have all contributed to an increasing upsurge in interest in imaging mass spectrometry. Here we review many of the instrumental developments and methodological approaches responsible for this increased interest, compare and contrast the information provided by SIMS and MALDI imaging, and discuss future possibilities.
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Affiliation(s)
- Liam A McDonnell
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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40
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Harton SE, Zhu Z, Stevie FA, Aoyama Y, Ade H. Carbon-13 Labeling for Quantitative Analysis of Molecular Movement in Heterogeneous Organic Materials Using Secondary Ion Mass Spectrometry. Anal Chem 2007; 79:5358-63. [PMID: 17555299 DOI: 10.1021/ac070437q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Secondary ion mass spectrometry (SIMS) is used to probe the movement of macromolecules in heterogeneous organic systems. Using 13C tracer labeling and two model systems, polystyrene/poly(2-vinylpyridine) (PS/P2VP) and polystyrene/poly(4-bromostyrene) (PS/P4BrS), the diffusion of 13C-labeled PS has been investigated near the respective heterogeneous interfaces using a CAMECA-IMS-6F magnetic sector mass spectrometer. 13C labeling has been shown to greatly minimize matrix effects (i.e., changes in secondary ion yields due to changing chemical environment) in heterogeneous systems. P2VP is a nitrogen-rich polymer (C7H7N monomer composition), making it an excellent model polymer for exploration of this technique for potential future use in biological applications, and probing the PS/P4BrS interface demonstrates the versatility of this technique for analysis of various heteroatom-containing materials. Results confirm that the 13C-labeling method does indeed allow for quantitative analysis of molecular movement in heterogeneous organic systems containing matrix-enhancing heteroatoms such as nitrogen. Therefore, extension of this method to more complicated biological systems involving multiple heteroatoms (oxygen, nitrogen, etc.), layers, and heterogeneous interfaces, as well as two- and three-dimensional profiling and imaging using SIMS, can be envisaged.
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Affiliation(s)
- Shane E Harton
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA.
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41
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Gazi E, Gardner P, Lockyer NP, Hart CA, Brown MD, Clarke NW. Direct evidence of lipid translocation between adipocytes and prostate cancer cells with imaging FTIR microspectroscopy. J Lipid Res 2007; 48:1846-56. [PMID: 17496269 DOI: 10.1194/jlr.m700131-jlr200] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Various epidemiological studies show a positive correlation between high intake of dietary FAs and metastatic prostate cancer (CaP). Moreover, CaP metastasizes to the bone marrow, which harbors a rich source of lipids stored within adipocytes. Here, we use Fourier transform infrared (FTIR) microspectroscopy to study adipocyte biochemistry and to demonstrate that PC-3 cells uptake isotopically labeled FA [deuterated palmitic acid (D(31)-PA)] from an adipocyte. Using this vibrational spectroscopic technique, we detected subcellular locations in a single adipocyte enriched with D(31)-PA using the upsilon(as+s)(C-D)(2+3) (D(31)-PA): upsilon(as+s)(C-H)(2+3) (lipid hydrocarbon) signal. In addition, larger adipocytes were found to consist of a higher percentage of D(31)-PA of the total lipid found within the adipocyte. Following background subtraction, the upsilon(as)(C-D)(2+3) signal illuminated starved PC-3 cells cocultured with D(31)-PA-loaded adipocytes, indicating translocation of the labeled FA. This study demonstrates lipid-specific translocation between adipocytes and tumor cells and the use of FTIR microspectroscopy to characterize various biomolecular features of a single adipocyte without the requirement for cell isolation and lipid extraction.
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Affiliation(s)
- Ehsan Gazi
- ProMPT Genito Urinary Cancer Research Group, Paterson Institute for Cancer Research, The University of Manchester, Manchester, UK.
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42
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Clode PL, Stern RA, Marshall AT. Subcellular imaging of isotopically labeled carbon compounds in a biological sample by ion microprobe (NanoSIMS). Microsc Res Tech 2007; 70:220-9. [PMID: 17279515 DOI: 10.1002/jemt.20409] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Here we demonstrate the technique of nanoscale secondary ion mass spectrometry, utilizing the Cameca NanoSIMS50 ion microprobe, to detect and image the metabolism of an isotopically labeled compound (NaH(13)CO(3)) in a biological sample. In particular, we have designed and verified protocols for imaging the subcellular distribution and determining the relative abundance of labeled (13)C, within the coral Galaxea fascicularis. Analyses were conducted on 1-mum thick sections of resin-embedded material, using both scanned (mapping) and static (spot analysis) Cs(+) primary ion beam of approximately 100 nm diameter. Using these samples we establish that NanoSIMS has adequate mass resolution to reliably distinguish (13)C from potential isobaric interference by (12)C(1)H and that data extracted from ion maps are comparable to those acquired by spot analyses. Independent of the method of acquisition, ratioing of (13)C to the naturally abundant (12)C is essential if meaningful data, which can be statistically compared to standard and control samples, are to be obtained. These results highlight the potential of NanoSIMS for intracellular tracking of a variety of organic and inorganic compounds labeled with stable isotopes of C, N, O, S, P, and halogens.
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Affiliation(s)
- Peta L Clode
- Centre for Microscopy and Microanalysis, The University of Western Australia, Crawley, Western Australia, Australia.
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43
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Ostrowski SG, Kurczy ME, Roddy TP, Winograd N, Ewing AG. Secondary ion MS imaging to relatively quantify cholesterol in the membranes of individual cells from differentially treated populations. Anal Chem 2007; 79:3554-60. [PMID: 17428032 PMCID: PMC1905852 DOI: 10.1021/ac061825f] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a well-established bioanalytical method for directly imaging the chemical distribution across single cells. Here we report a protocol for the use of SIMS imaging to comparatively quantify the relative difference in cholesterol level between the plasma membranes of two cells. It should be possible to apply this procedure to the study of other selected lipids. This development enables direct comparison of the chemical effects of different drug treatments and incubation conditions in the plasma membrane at the single-cell level. Relative, quantitative TOF-SIMS imaging has been used here to compare macrophage cells treated to contain elevated levels of cholesterol with respect to control cells. In situ fluorescence microscopy with two different membrane dyes was used to discriminate morphologically similar but differentially treated cells prior to SIMS analysis. SIMS images of fluorescently identified cells reveal that the two populations of cells have distinct outer leaflet membrane compositions with the membranes of the cholesterol-treated macrophages containing more than twice the amount of cholesterol of control macrophages. Relative quantification with SIMS to compare the chemical composition of single cells can provide valuable information about normal biological functions, causative agents of diseases, and possible therapies for diseases.
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44
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Lechene C, Hillion F, McMahon G, Benson D, Kleinfeld AM, Kampf JP, Distel D, Luyten Y, Bonventre J, Hentschel D, Park KM, Ito S, Schwartz M, Benichou G, Slodzian G. High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry. J Biol 2007; 5:20. [PMID: 17010211 PMCID: PMC1781526 DOI: 10.1186/jbiol42] [Citation(s) in RCA: 226] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 04/21/2006] [Accepted: 05/11/2006] [Indexed: 11/28/2022] Open
Abstract
Background Secondary-ion mass spectrometry (SIMS) is an important tool for investigating isotopic composition in the chemical and materials sciences, but its use in biology has been limited by technical considerations. Multi-isotope imaging mass spectrometry (MIMS), which combines a new generation of SIMS instrument with sophisticated ion optics, labeling with stable isotopes, and quantitative image-analysis software, was developed to study biological materials. Results The new instrument allows the production of mass images of high lateral resolution (down to 33 nm), as well as the counting or imaging of several isotopes simultaneously. As MIMS can distinguish between ions of very similar mass, such as 12C15N- and 13C14N-, it enables the precise and reproducible measurement of isotope ratios, and thus of the levels of enrichment in specific isotopic labels, within volumes of less than a cubic micrometer. The sensitivity of MIMS is at least 1,000 times that of 14C autoradiography. The depth resolution can be smaller than 1 nm because only a few atomic layers are needed to create an atomic mass image. We illustrate the use of MIMS to image unlabeled mammalian cultured cells and tissue sections; to analyze fatty-acid transport in adipocyte lipid droplets using 13C-oleic acid; to examine nitrogen fixation in bacteria using 15N gaseous nitrogen; to measure levels of protein renewal in the cochlea and in post-ischemic kidney cells using 15N-leucine; to study DNA and RNA co-distribution and uridine incorporation in the nucleolus using 15N-uridine and 81Br of bromodeoxyuridine or 14C-thymidine; to reveal domains in cultured endothelial cells using the native isotopes 12C, 16O, 14N and 31P; and to track a few 15N-labeled donor spleen cells in the lymph nodes of the host mouse. Conclusion MIMS makes it possible for the first time to both image and quantify molecules labeled with stable or radioactive isotopes within subcellular compartments.
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Affiliation(s)
- Claude Lechene
- National Resource for Imaging Mass Spectrometry, Harvard Medical School and Department of Medicine, Brigham and Women's Hospital, Cambridge, MA 02139, USA
| | - Francois Hillion
- Cameca, 29 Quai des Gresillons, 92622 Gennevilliers Cedex, France
| | - Greg McMahon
- National Resource for Imaging Mass Spectrometry, Harvard Medical School and Department of Medicine, Brigham and Women's Hospital, Cambridge, MA 02139, USA
| | | | - Alan M Kleinfeld
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121, USA
| | - J Patrick Kampf
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121, USA
| | - Daniel Distel
- Ocean Genome Legacy Foundation, Ipswich, MA 01938, USA
| | - Yvette Luyten
- Ocean Genome Legacy Foundation, Ipswich, MA 01938, USA
| | - Joseph Bonventre
- Harvard Medical School and Renal Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dirk Hentschel
- Harvard Medical School and Renal Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kwon Moo Park
- Harvard Medical School and Renal Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Susumu Ito
- Harvard Medical School, Boston, MA 02115, USA
| | - Martin Schwartz
- Department of Microbiology, University of Virginia, Charlottesville, VA 22908, USA
| | - Gilles Benichou
- Harvard Medical School and Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Georges Slodzian
- Universite Paris-Sud, Centre de Spectrométrie Nucléaire et de Spectrométrie de Masse, 91406 Orsay, France
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Kampf JP, Kleinfeld AM. Is Membrane Transport of FFA Mediated by Lipid, Protein, or Both? Physiology (Bethesda) 2007; 22:7-14. [PMID: 17289927 DOI: 10.1152/physiol.00011.2006] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- J Patrick Kampf
- Torrey Pines Institute for Molecular Studies, San Diego, CA, USA
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Herrmann AM, Clode PL, Fletcher IR, Nunan N, Stockdale EA, O'Donnell AG, Murphy DV. A novel method for the study of the biophysical interface in soils using nano-scale secondary ion mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:29-34. [PMID: 17131465 DOI: 10.1002/rcm.2811] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The spatial location of microorganisms and their activity within the soil matrix have major impacts on biological processes such as nutrient cycling. However, characterizing the biophysical interface in soils is hampered by a lack of techniques at relevant scales. A novel method for studying the distribution of microorganisms that have incorporated isotopically labelled substrate ('active' microorganisms) in relation to the soil microbial habitat is provided by nano-scale secondary ion mass spectrometry (NanoSIMS). Pseudomonas fluorescens are ubiquitous in soil and were therefore used as a model for 'active' microorganisms in soil. Batch cultures (NCTC 10038) were grown in a minimal salt medium containing 15N-ammonium sulphate (15/14N ratio of 1.174), added to quartz-based white sand or soil (coarse textured sand), embedded in Araldite 502 resin and sectioned for NanoSIMS analysis. The 15N-enriched P. fluorescens could be identified within the soil structure, demonstrating that the NanoSIMS technique enables the study of spatial location of microbial activity in relation to the heterogeneous soil matrix. This technique is complementary to the existing techniques of digital imaging analysis of soil thin sections and scanning electron microscopy. Together with advanced computer-aided tomography of soils and mathematical modelling of soil heterogeneity, NanoSIMS may be a powerful tool for studying physical and biological interactions, thereby furthering our understanding of the biophysical interface in soils.
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Affiliation(s)
- Anke M Herrmann
- School of Earth and Geographical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
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McMahon G, Saint-Cyr HF, Lechene C, Unkefer CJ. CN- secondary ions form by recombination as demonstrated using multi-isotope mass spectrometry of 13C- and 15N-labeled polyglycine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1181-7. [PMID: 16750387 DOI: 10.1016/j.jasms.2006.04.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 04/01/2006] [Accepted: 04/08/2006] [Indexed: 05/10/2023]
Abstract
We have studied the mechanism of formation CN- secondary ions under Cs+ primary ion bombardment. We have synthesized 13C and 15N labeled polyglycine samples with the distance between the two labels and the local atomic environment of the 13C label systematically varied. We have measured four masses in parallel: 12C, 13C, and two of 12C14N, 13C14N, 12C15N, and 13C15N. We have calculated the 13C/12C isotope ratio, and the different combinations of the CN isotope ratios (27CN/26CN, 28CN/27CN, and 28CN/26CN). We have measured a high 13C15N- secondary ion current from the 13C and 15N labeled polyglycines, even when the 13C and 15N labels are separated. By comparing the magnitude of the varied combinations of isotope ratios among the samples with different labeling positions, we conclude the following: CN- formation is in large fraction due to recombination of C and N; the CO double bond decreases the extent of CN- formation compared to the case where carbon is singly bonded to two hydrogen atoms; and double-labeling with 13C and 15N allows us to detect with high sensitivity the molecular ion 13C15N-.
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Affiliation(s)
- G McMahon
- National Resource for Imaging Mass Spectrometry, Harvard Medical School and Brigham and Women's Hospital, Cambridge, Massachusetts 02139, USA
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Kampf JP, Cupp D, Kleinfeld AM. Different Mechanisms of Free Fatty Acid Flip-Flop and Dissociation Revealed by Temperature and Molecular Species Dependence of Transport across Lipid Vesicles. J Biol Chem 2006; 281:21566-21574. [PMID: 16737957 DOI: 10.1074/jbc.m602067200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mechanism of free fatty acid (FFA) transport across membranes is a subject of intense investigation. We have demonstrated recently that flip-flop is the rate-limiting step for transport of oleic acid across phospholipid vesicles (Cupp, D., Kampf, J. P., and Kleinfeld, A. M. (2004) Biochemistry 43, 4473-4481). To better understand the nature of the flip-flop barrier, we measured the temperature dependence of a series of saturated and monounsaturated FFA. We determined the rate constants for flip-flop and dissociation for small (SUV), large (LUV), and giant (GUV) unilamellar vesicles composed of egg phosphatidylcholine. For all FFA and vesicle types, dissociation was faster than flip-flop, and for all FFA, flip-flop and dissociation were faster in SUV than in LUV or GUV. Rate constants for both flip-flop and dissociation decreased exponentially with increasing FFA size. However, only the flip-flop rate constants increased significantly with temperature; the barrier to flip-flop was virtually entirely due to an enthalpic activation free energy. The barrier to dissociation was primarily entropic. Analysis in terms of a simple free volume (V(f)) model revealed V(f) values for flip-flop that ranged between approximately 12 and 15 Angstroms(3), with larger values for SUV than for LUV or GUV. V(f) values increased with temperature, and this temperature dependence generated the enthalpic barrier to flip-flop. The barrier for dissociation and its size dependence primarily reflect the aqueous solubility of FFA. These are the first results to distinguish the energetics of flipflop and dissociation. This should lead to a better understanding of the mechanisms governing FFA transport across biological membranes.
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Affiliation(s)
- J Patrick Kampf
- Torrey Pines Institute for Molecular Studies, San Diego, California 92121
| | - David Cupp
- Torrey Pines Institute for Molecular Studies, San Diego, California 92121
| | - Alan M Kleinfeld
- Torrey Pines Institute for Molecular Studies, San Diego, California 92121.
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Guerquin-Kern JL, Wu TD, Quintana C, Croisy A. Progress in analytical imaging of the cell by dynamic secondary ion mass spectrometry (SIMS microscopy). Biochim Biophys Acta Gen Subj 2005; 1724:228-38. [PMID: 15982822 DOI: 10.1016/j.bbagen.2005.05.013] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Revised: 05/04/2005] [Accepted: 05/09/2005] [Indexed: 10/25/2022]
Abstract
This paper reviews the most recent methodological advances in the field of biological imaging using dynamic secondary ion mass spectrometry (SIMS). After a short reminder of the basic principle of SIMS imaging, the latest high-resolution dynamic SIMS equipment is briefly described. This new ion nanoprobe (CAMECA NanoSIMS 50) has a lateral resolution of less than 50 nm with primary Cs+ ion, the ability to detect simultaneously 5 different ions from the same micro-volume and a very good transmission even at high mass resolution (60% at M/DeltaM=5000). Basic considerations related to sample preparation, mass resolution and primary ion implantation are given. The decisive capability of this new instrument, and more generally of high-resolution dynamic SIMS imaging in biology, are illustrated with the most recent examples of utilization.
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Affiliation(s)
- Jean-Luc Guerquin-Kern
- Laboratoire de Microscopie Ionique, Institut Curie Recherche, Bât 112, Centre Universitaire, 91405 Orsay Cedex, France
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