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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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Toullec G, Lyndby NH, Banc-Prandi G, Pogoreutz C, Martin Olmos C, Meibom A, Rädecker N. Symbiotic nutrient exchange enhances the long-term survival of cassiosomes, the autonomous stinging-cell structures of Cassiopea. mSphere 2024; 9:e0032223. [PMID: 38088556 PMCID: PMC10826341 DOI: 10.1128/msphere.00322-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/17/2023] [Indexed: 01/31/2024] Open
Abstract
Medusae of the widely distributed upside-down jellyfish Cassiopea release autonomous, mobile stinging structures. These so-called cassiosomes play a role in predator defense and prey capture, and are major contributors to "contactless" stinging incidents in (sub-)tropical shallow waters. While the presence of endosymbiotic dinoflagellates in cassiosomes has previously been observed, their potential contribution to the metabolism and long-term survival of cassiosomes is unknown. Combining stable isotope labeling and correlative scanning electron microscopy and nanoscale secondary ion mass spectrometry imaging with a long-term in vitro experiment, our study reveals a mutualistic symbiosis based on nutritional exchanges in dinoflagellate-bearing cassiosomes. We show that organic carbon input from the dinoflagellates fuels the metabolism of the host tissue and enables anabolic nitrogen assimilation. This symbiotic nutrient exchange enhances the life span of cassiosomes for at least one month in vitro. Overall, our study demonstrates that cassiosomes, in analogy with Cassiopea medusae, are photosymbiotic holobionts. Cassiosomes, which are easily accessible under aquarium conditions, promise to be a powerful new miniaturized model system for in-depth ultrastructural and molecular investigation of cnidarian photosymbioses.IMPORTANCEThe upside-down jellyfish Cassiopea releases autonomous tissue structures, which are a major cause of contactless stinging incidents in (sub-) tropical coastal waters. These so-called cassiosomes frequently harbor algal symbionts, yet their role in cassiosome functioning and survival is unknown. Our results show that cassiosomes are metabolically active and supported by algal symbionts. Algal photosynthesis enhances the cassiosomes long-term survival in the light. This functional understanding of cassiosomes thereby contributes to explaining the prevalence of contactless stinging incidents and the ecological success of some Cassiopea species. Finally, we show that cassiosomes are miniaturized symbiotic holobionts that can be used to study host-microbe interactions in a simplified system.
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Affiliation(s)
- Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Niclas Heidelberg Lyndby
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Guilhem Banc-Prandi
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Claudia Pogoreutz
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Cristina Martin Olmos
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Science, University of Lausanne, Lausanne, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Center for Advanced Surface Analysis, Institute of Earth Science, University of Lausanne, Lausanne, Switzerland
| | - Nils Rädecker
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Bonnin EA, Golmohammadi A, Rehm R, Tetzlaff C, Rizzoli SO. High-resolution analysis of bound Ca 2+ in neurons and synapses. Life Sci Alliance 2024; 7:e202302030. [PMID: 37833073 PMCID: PMC10575792 DOI: 10.26508/lsa.202302030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Calcium (Ca2+) is a well-known second messenger in all cells, and is especially relevant for neuronal activity. Neuronal Ca2+ is found in different forms, with a minority being freely soluble in the cell and more than 99% being bound to proteins. Free Ca2+ has received much attention over the last few decades, but protein-bound Ca2+ has been difficult to analyze. Here, we introduce correlative fluorescence and nanoscale secondary ion mass spectrometry imaging as a tool to describe bound Ca2+ As expected, bound Ca2+ is ubiquitous. It does not correlate to free Ca2+ dynamics at the whole-neuron level, but does correlate significantly to the intensity of markers for GABAergic pre-synapse and glutamatergic post-synapses. In contrast, a negative correlation to pre-synaptic activity was observed, with lower levels of bound Ca2+ observed in the more active synapses. We conclude that bound Ca2+ may regulate neuronal activity and should receive more attention in the future.
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Affiliation(s)
- Elisa A Bonnin
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Excellence Cluster Multiscale Bioimaging (MBExC), Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany
| | - Arash Golmohammadi
- Group of Computational Synaptic Physiology, Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Ronja Rehm
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Christian Tetzlaff
- Group of Computational Synaptic Physiology, Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Excellence Cluster Multiscale Bioimaging (MBExC), Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany
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Valdebenito S, Ajasin D, Prideaux B, Eugenin EA. Correlative Imaging to Detect Rare HIV Reservoirs and Associated Damage in Tissues. Methods Mol Biol 2024; 2807:93-110. [PMID: 38743223 DOI: 10.1007/978-1-0716-3862-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Correlative light-electron microscopy (CLEM) has evolved in the last decades, especially after significant developments in sample preparation, imaging acquisition, software, spatial resolution, and equipment, including confocal, live-cell, super-resolution, and electron microscopy (scanning, transmission, focused ion beam, and cryo-electron microscopy). However, the recent evolution of different laser-related techniques, such as mass spectrometry imaging (MSI) and laser capture microdissection, could further expand spatial imaging capabilities into high-resolution OMIC approaches such as proteomic, lipidomics, small molecule, and drug discovery. Here, we will describe a protocol to integrate the detection of rare viral reservoirs with imaging mass spectrometry.
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Affiliation(s)
- Silvana Valdebenito
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - David Ajasin
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Brendan Prideaux
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Eliseo A Eugenin
- Department of Neurobiology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA.
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Li Q, Chang J, Li L, Lin X, Li Y. Research progress of nano-scale secondary ion mass spectrometry (NanoSIMS) in soil science: Evolution, applications, and challenges. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167257. [PMID: 37741415 DOI: 10.1016/j.scitotenv.2023.167257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
Nano-scale secondary ion mass spectrometry (NanoSIMS) has emerged as a powerful analytical tool for investigating various aspects of soils. In recent decades, the widespread adoption of advanced instrumentation and methods has contributed significantly to our understanding of organic-mineral assemblages. However, few literature reviews have comprehensively summarized NanoSIMS and its evolution, applications, limitations, and integration with other analytical techniques. In this review, we addressed this gap by comprehensively overviewing the development of NanoSIMS as an analytical tool in soils. This review covers studies on soil organic matter (SOM) cycling, soil-root interactions, and the behavior of metals, discussing the capability and limitations related to the distribution, composition, and interactions of various soil components that occur at mineral-organic interfaces. Furthermore, we examine recent advancements in high-resolution imaging and mass spectrometry technologies and their impact on the utilization of NanoSIMS in soils, along with potential new applications such as utilizing multiple ion beams and integrating them with other analytical techniques. The review emphasizes the importance of employing advanced techniques and methods to explore micro-interfaces and provide in situ descriptions of organic-mineral assemblages in future research. The ongoing development and refinement of NanoSIMS may yield new insights and breakthroughs in soil science, deepening our understanding of the intricate relationships between soil components and the processes that govern soil health and fertility.
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Affiliation(s)
- Qi Li
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jingjing Chang
- Key Laboratory for New Technology Research of Vegetable, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Linfeng Li
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaoyang Lin
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yichun Li
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation, Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
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