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Zeng M, Wang W, Yin Y, Zheng C. A simple coordinate transformation method for quickly locating the features of interest in TEM samples. Microscopy (Oxf) 2024:dfae009. [PMID: 38421047 DOI: 10.1093/jmicro/dfae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/16/2024] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
We developed a simple coordinate transformation method for quickly locating features of interest (FOIs) of samples in transmission electron microscope (TEM). The method is well suited for conducting sample searches in aberration-corrected scanning/transmission electron microscopes (S/TEM), where the survey can be very time-consuming because of the limited field of view imposed by the highly excited objective lens after fine-tuning the aberration correctors. For implementation, a digital image of the sample and the TEM holder was captured using a simple stereo-optical microscope. Naturally presented geometric patterns on the holder were referenced to construct a projective transformation between the electron and optical coordinate systems. The test results demonstrated that the method was accurate and required no electron microscope or specimen holder modifications. Additionally, it eliminated the need to mount the sample onto specific patterned TEM grids or deposit markers, resulting in universal applications for most TEM samples, holders and electron microscopes for fast FOI identification. Furthermore, we implemented the method into a Gatan script for graphical-user-interface-based step-by-step instructions. Through online communication, the script enabled real-time navigation and tracking of the motion of samples in TEM on enlarged optical images with a panoramic view.
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Affiliation(s)
- Mingzhi Zeng
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Songhu Rd 2005, Yangpu District, Shanghai 200438, China
| | - Wenzhao Wang
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Songhu Rd 2005, Yangpu District, Shanghai 200438, China
| | - Yang Yin
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Songhu Rd 2005, Yangpu District, Shanghai 200438, China
| | - Changlin Zheng
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Songhu Rd 2005, Yangpu District, Shanghai 200438, China
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2
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Jadavi S, Dante S, Civiero L, Sandre M, Bubacco L, Tosatto L, Bianchini P, Canale C, Diaspro A. Fluorescence labeling methods influence the aggregation process of α-syn in vitro differently. NANOSCALE 2023; 15:8270-8277. [PMID: 37073868 DOI: 10.1039/d2nr05487f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In a previous study, the coexistence of different aggregation pathways of insulin and β-amyloid (Aβ) peptides was demonstrated by correlative stimulated emission depletion (STED) microscopy and atomic force microscopy (AFM). This had been explained by suboptimal proteins labeling strategies that generate heterogeneous populations of aggregating species. However, because of the limited number of proteins considered, the failure of the fluorescent labeling that occurs in a large portion of the aggregating fibrils observed for insulin and Aβ peptides, could not be considered a general phenomenon valid for all molecular systems. Here, we investigated the aggregation process of α-synuclein (α-syn), an amyloidogenic peptide involved in Parkinson's disease, which is significantly larger (MW ∼14 kDa) than insulin and Aβ, previously investigated. The results showed that an unspecific labeling procedure, such as that previously adopted for shorter proteins, reproduced the coexistence of labeled/unlabeled fibers. Therefore, a site-specific labeling method was developed to target a domain of the peptide scarcely involved in the aggregation process. Correlative STED-AFM illustrated that all fibrillar aggregates derived from the aggregation of α-syn at the dye-to-protein ratio of 1 : 22 were fluorescent. These results, demonstrated here for the specific case of α-syn, highlight that the labeling artifacts can be avoided by careful designing the labeling strategy for the molecular system under investigation. The use of a label-free correlative microscopy technique would play a crucial role in the control of the setting of these conditions.
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Affiliation(s)
- S Jadavi
- Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genova, Italy
- Department of Physics, University of Genova, Via Dodecaneso 33, 16146 Genova, Italy.
| | - S Dante
- Materials Characterization Facility, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - L Civiero
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
- IRCCS San Camillo Hospital, Via Alberoni 70, 30126 Venice, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, 35131 Padova, Italy
| | - M Sandre
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, 35131 Padova, Italy
- Parkinson and Movement Disorders Unit, Department of Neuroscience, University of Padova, Via Nicolò Giustiniani, 5, 35128 Padova, Italy
| | - L Bubacco
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35131 Padova, Italy
- IRCCS San Camillo Hospital, Via Alberoni 70, 30126 Venice, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, 35131 Padova, Italy
| | - L Tosatto
- Istituti di Biofisica, CNR, Trento, Italy
| | - P Bianchini
- Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genova, Italy
| | - C Canale
- Department of Physics, University of Genova, Via Dodecaneso 33, 16146 Genova, Italy.
| | - A Diaspro
- Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genova, Italy
- Department of Physics, University of Genova, Via Dodecaneso 33, 16146 Genova, Italy.
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3
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Poeta LS, Ordóñez MP, Fournier E, Nelson AJ. Correlative tomography and authentication features of a shrunken head (tsantsa). PLoS One 2022; 17:e0270305. [PMID: 35921270 PMCID: PMC9348654 DOI: 10.1371/journal.pone.0270305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Museum personnel and the general public have become quite familiar with the presence of shrunken heads in museum collections, but the procedures to authenticate the history and origin of these unique cultural items are not yet reliable. These shrunken heads, called tsantsas, are meant to be the cultural material remains of ceremonies conducted by the Shuar and Achuar Peoples of South America. This project seeks to integrate the use of micro-computed tomography (micro-CT) scanning with methods used in previous studies (clinical computed tomography (CT) and visual inspections) to examine authentication procedures of shrunken heads (tsantsas) held in contemporary museum collections. We use a correlative tomographic approach using several scans at successively higher resolutions to determine whether a tsantsa was created from human remains, and if so, what key features can best contribute to its authentication. Conclusively, our correlative tomographic approaches provide new insights into the determination process of whether a tsantsa was created from real human remains or not. Also, this study questions whether the previously conceptualized dichotomy of ceremonial or commercial might be better thought of as a continuum of practice. Investigating and redefining the examination and authentication procedures of tsantsas is crucial for future ethical curation, management, and repatriation efforts of this unique cultural material of the Shuar and Achuar Peoples.
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Affiliation(s)
| | - Maria Patricia Ordóñez
- Colegio de Ciencias Sociales y Humanidades, Universidad San Fransisco de Quito, Quito, Ecuador
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Tracking Bacterial Nanocellulose in Animal Tissues by Fluorescence Microscopy. NANOMATERIALS 2022; 12:nano12152605. [PMID: 35957036 PMCID: PMC9370207 DOI: 10.3390/nano12152605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 02/07/2023]
Abstract
The potential of nanomaterials in food technology is nowadays well-established. However, their commercial use requires a careful risk assessment, in particular concerning the fate of nanomaterials in the human body. Bacterial nanocellulose (BNC), a nanofibrillar polysaccharide, has been used as a food product for many years in Asia. However, given its nano-character, several toxicological studies must be performed, according to the European Food Safety Agency’s guidance. Those should especially answer the question of whether nanoparticulate cellulose is absorbed in the gastrointestinal tract. This raises the need to develop a screening technique capable of detecting isolated nanosized particles in biological tissues. Herein, the potential of a cellulose-binding module fused to a green fluorescent protein (GFP–CBM) to detect single bacterial cellulose nanocrystals (BCNC) obtained by acid hydrolysis was assessed. Adsorption studies were performed to characterize the interaction of GFP–CBM with BNC and BCNC. Correlative electron light microscopy was used to demonstrate that isolated BCNC may be detected by fluorescence microscopy. The uptake of BCNC by macrophages was also assessed. Finally, an exploratory 21-day repeated-dose study was performed, wherein Wistar rats were fed daily with BNC. The presence of BNC or BCNC throughout the GIT was observed only in the intestinal lumen, suggesting that cellulose particles were not absorbed. While a more comprehensive toxicological study is necessary, these results strengthen the idea that BNC can be considered a safe food additive.
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Heiligenstein X, Lucas MS. One for All, All for One: A Close Look at In-Resin Fluorescence Protocols for CLEM. Front Cell Dev Biol 2022; 10:866472. [PMID: 35846358 PMCID: PMC9280628 DOI: 10.3389/fcell.2022.866472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Sample preparation is the novel bottleneck for high throughput correlative light and electron microscopy (CLEM). Protocols suitable for both imaging methods must therefore balance the requirements of each technique. For fluorescence light microscopy, a structure of interest can be targeted using: 1) staining, which is often structure or tissue specific rather than protein specific, 2) dye-coupled proteins or antibodies, or 3) genetically encoded fluorescent proteins. Each of these three methods has its own advantages. For ultrastructural investigation by electron microscopy (EM) resin embedding remains a significant sample preparation approach, as it stabilizes the sample such that it withstands the vacuum conditions of the EM, and enables long-term storage. Traditionally, samples are treated with heavy metal salts prior to resin embedding, in order to increase imaging contrast for EM. This is particularly important for volume EM (vEM) techniques. Yet, commonly used contrasting agents (e.g., osmium tetroxide, uranyl acetate) tend to impair fluorescence. The discovery that fluorescence can be preserved in resin-embedded specimens after mild heavy metal staining was a game changer for CLEM. These so-called in-resin fluorescence protocols present a significant leap forward for CLEM approaches towards high precision localization of a fluorescent signal in (volume) EM data. Integrated microscopy approaches, combining LM and EM detection into a single instrument certainly require such an “all in one” sample preparation. Preserving, or adding, dedicated fluorescence prior to resin embedding requires a compromise, which often comes at the expense of EM imaging contrast and membrane visibility. Especially vEM can be strongly hampered by a lack of heavy metal contrasting. This review critically reflects upon the fundamental aspects of resin embedding with regard to 1) specimen fixation and the physics and chemistry underlying the preservation of protein structure with respect to fluorescence and antigenicity, 2) optimization of EM contrast for transmission or scanning EM, and 3) the choice of embedding resin. On this basis, various existing workflows employing in-resin fluorescence are described, highlighting their common features, discussing advantages and disadvantages of the respective approach, and finally concluding with promising future developments for in-resin CLEM.
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Affiliation(s)
| | - Miriam S. Lucas
- Scientific Center for Light and Electron Microscopy (ScopeM), ETH Zurich, Zurich, Switzerland
- *Correspondence: Miriam S. Lucas,
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Hobson CM, Aaron JS. Combining multiple fluorescence imaging techniques in biology: when one microscope is not enough. Mol Biol Cell 2022; 33:tp1. [PMID: 35549314 PMCID: PMC9265156 DOI: 10.1091/mbc.e21-10-0506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
While fluorescence microscopy has proven to be an exceedingly useful tool in bioscience, it is difficult to offer simultaneous high resolution, fast speed, large volume, and good biocompatibility in a single imaging technique. Thus, when determining the image data required to quantitatively test a complex biological hypothesis, it often becomes evident that multiple imaging techniques are necessary. Recent years have seen an explosion in development of novel fluorescence microscopy techniques, each of which features a unique suite of capabilities. In this Technical Perspective, we highlight recent studies to illustrate the benefits, and often the necessity, of combining multiple fluorescence microscopy modalities. We provide guidance in choosing optimal technique combinations to effectively address a biological question. Ultimately, we aim to promote a more well-rounded approach in designing fluorescence microscopy experiments, leading to more robust quantitative insight.
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Affiliation(s)
- Chad M Hobson
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - Jesse S Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
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Mukhamadiyarov RA, Bogdanov LA, Mishinov SV, Kutikhin AG. A Novel Technique for Preparation, Staining, and Visualization of Tissue with Metal Implants and Extraskeletal Calcification Areas. Sovrem Tekhnologii Med 2021; 12:13-20. [PMID: 34795988 PMCID: PMC8596281 DOI: 10.17691/stm2020.12.4.02] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Indexed: 11/27/2022] Open
Abstract
The aim of the study was to evaluate the efficacy of a novel technique for preparation, staining, and visualization of tissues containing extra-skeletal mineralization areas, all-metal implants or their prototypes for their subsequent examination using scanning electron microscopy in the backscattered electron mode.
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Affiliation(s)
- R A Mukhamadiyarov
- Senior Researcher, Laboratory for Fundamental Aspects of Atherosclerosis, Department of Experimental and Clinical Cardiology; Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Blvd, Kemerovo, 650002, Russia
| | - L A Bogdanov
- Junior Researcher, Laboratory for Fundamental Aspects of Atherosclerosis, Department of Experimental and Clinical Cardiology; Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Blvd, Kemerovo, 650002, Russia
| | - S V Mishinov
- Senior Researcher, Neurosurgeon, Neurosurgery Unit; Novosibirsk Scientific Research Institute of Traumatology and Orthopedics named after Ya.L. Tsivyan of the Ministry of Health of the Russian Federation, 17 Frunze St., Novosibirsk, 630091, Russia
| | - A G Kutikhin
- Head of the Laboratory for Fundamental Aspects of Atherosclerosis, Department of Experimental and Clinical Cardiology Research Institute for Complex Issues of Cardiovascular Diseases, 6 Sosnovy Blvd, Kemerovo, 650002, Russia
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8
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Mukhamadiyarov RA, Bogdanov LA, Glushkova TV, Shishkova DK, Kostyunin AE, Koshelev VA, Shabaev AR, Frolov AV, Stasev AN, Lyapin AA, Kutikhin AG. EMbedding and Backscattered Scanning Electron Microscopy: A Detailed Protocol for the Whole-Specimen, High-Resolution Analysis of Cardiovascular Tissues. Front Cardiovasc Med 2021; 8:739549. [PMID: 34760942 PMCID: PMC8573413 DOI: 10.3389/fcvm.2021.739549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022] Open
Abstract
Currently, an ultrastructural analysis of cardiovascular tissues is significantly complicated. Routine histopathological examinations and immunohistochemical staining suffer from a relatively low resolution of light microscopy, whereas the fluorescence imaging of plaques and bioprosthetic heart valves yields considerable background noise from the convoluted extracellular matrix that often results in a low signal-to-noise ratio. Besides, the sectioning of calcified or stent-expanded blood vessels or mineralised heart valves leads to a critical loss of their integrity, demanding other methods to be developed. Here, we designed a conceptually novel approach that combines conventional formalin fixation, sequential incubation in heavy metal solutions (osmium tetroxide, uranyl acetate or lanthanides, and lead citrate), and the embedding of the whole specimen into epoxy resin to retain its integrity while accessing the region of interest by grinding and polishing. Upon carbon sputtering, the sample is visualised by means of backscattered scanning electron microscopy. The technique fully preserves calcified and stent-expanded tissues, permits a detailed analysis of vascular and valvular composition and architecture, enables discrimination between multiple cell types (including endothelial cells, vascular smooth muscle cells, fibroblasts, adipocytes, mast cells, foam cells, foreign-body giant cells, canonical macrophages, neutrophils, and lymphocytes) and microvascular identities (arterioles, venules, and capillaries), and gives a technical possibility for quantitating the number, area, and density of the blood vessels. Hence, we suggest that our approach is capable of providing a pathophysiological insight into cardiovascular disease development. The protocol does not require specific expertise and can be employed in virtually any laboratory that has a scanning electron microscope.
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Affiliation(s)
- Rinat A Mukhamadiyarov
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Leo A Bogdanov
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Tatiana V Glushkova
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Daria K Shishkova
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Alexander E Kostyunin
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Vladislav A Koshelev
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Amin R Shabaev
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Alexey V Frolov
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Alexander N Stasev
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Anton A Lyapin
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
| | - Anton G Kutikhin
- Department of Experimental Medicine, Research Institute for Complex Issues of Cardiovascular Diseases, Kemerovo, Russia
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Okolo CA, Kounatidis I, Groen J, Nahas KL, Balint S, Fish TM, Koronfel MA, Cortajarena AL, Dobbie IM, Pereiro E, Harkiolaki M. Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures. Nat Protoc 2021; 16:2851-2885. [PMID: 33990802 DOI: 10.1038/s41596-021-00522-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
3D correlative microscopy methods have revolutionized biomedical research, allowing the acquisition of multidimensional information to gain an in-depth understanding of biological systems. With the advent of relevant cryo-preservation methods, correlative imaging of cryogenically preserved samples has led to nanometer resolution imaging (2-50 nm) under harsh imaging regimes such as electron and soft X-ray tomography. These methods have now been combined with conventional and super-resolution fluorescence imaging at cryogenic temperatures to augment information content from a given sample, resulting in the immediate requirement for protocols that facilitate hassle-free, unambiguous cross-correlation between microscopes. We present here sample preparation strategies and a direct comparison of different working fiducialization regimes that facilitate 3D correlation of cryo-structured illumination microscopy and cryo-soft X-ray tomography. Our protocol has been tested at two synchrotron beamlines (B24 at Diamond Light Source in the UK and BL09 Mistral at ALBA in Spain) and has led to the development of a decision aid that facilitates experimental design with the strategic use of markers based on project requirements. This protocol takes between 1.5 h and 3.5 d to complete, depending on the cell populations used (adherent cells may require several days to grow on sample carriers).
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Affiliation(s)
- Chidinma A Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | | | - Kamal L Nahas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stefan Balint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Thomas M Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Mohamed A Koronfel
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ian M Dobbie
- Micron Advanced Imaging Consortium, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Eva Pereiro
- Beamline 09-MISTRAL, ALBA Synchrotron, Barcelona, Spain
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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Kuchenbrod MT, Schubert US, Heintzmann R, Hoeppener S. Revisiting staining of biological samples for electron microscopy: perspectives for recent research. MATERIALS HORIZONS 2021; 8:685-699. [PMID: 34821312 DOI: 10.1039/d0mh01579b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This review revisits essential staining protocols for electron microscopy focussing on the visualization of active sites, i.e. enzymes, metabolites or proteins, in cells and tissues, which have been developed 50 to 60 years ago, however, never were established as standard protocols being used in electron microscopy in a routine fashion. These approaches offer numerous possibilities to expand the knowledge of cellular function and specifically address the localization of active compounds of these systems. It is our conviction, that many of these techniques are still useful, in particular when applied in conjunction with correlative light and electron microscopy. Revisiting specialized classical electron microscopy staining protocols for use in correlative microscopy is particularly promising, as some of these protocols were originally developed as staining methods for light microscopy. To account for this history, rather than summarizing the most recent achievements in literature, we instead first provide an overview of techniques that have been used in the past. While some of these techniques have been successfully implemented into modern microscopy techniques during recent years already, more possibilities are yet to be re-discovered and provide exciting new perspectives for their future use.
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Affiliation(s)
- Maren T Kuchenbrod
- Laboratory of Organic and Macromolecular Chemistry (IOMC) Friedrich Schiller University Jena, Humboldstr. 10, 07743, Germany.
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Vos Y, Lane RI, Peddie CJ, Wolters AHG, Hoogenboom JP. Retarding Field Integrated Fluorescence and Electron Microscope. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:109-120. [PMID: 33349285 DOI: 10.1017/s1431927620024745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The authors present the application of a retarding field between the electron objective lens and sample in an integrated fluorescence and electron microscope. The retarding field enhances signal collection and signal strength in the electron microscope. This is beneficial for samples prepared for integrated fluorescence and electron microscopy as the amount of staining material added to enhance electron microscopy signal is typically lower compared to conventional samples in order to preserve fluorescence. We demonstrate signal enhancement through the applied retarding field for both 80-nm post-embedding immunolabeled sections and 100-nm in-resin preserved fluorescence sections. Moreover, we show that tuning the electron landing energy particularly improves imaging conditions for ultra-thin (50 nm) sections, where optimization of both retarding field and interaction volume contribute to the signal improvement. Finally, we show that our integrated retarding field setup allows landing energies down to a few electron volts with 0.3 eV dispersion, which opens new prospects for assessing electron beam induced damage by in situ quantification of the observed bleaching of the fluorescence following irradiation.
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Affiliation(s)
- Yoram Vos
- Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, Delft2628CJ, The Netherlands
| | - Ryan I Lane
- Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, Delft2628CJ, The Netherlands
| | - Chris J Peddie
- Electron Microscopy STP, The Francis Crick Institute, 1 Midland Road, LondonNW1 1AT, UK
| | - Anouk H G Wolters
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, Groningen9713 AV, The Netherlands
| | - Jacob P Hoogenboom
- Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, Delft2628CJ, The Netherlands
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12
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Thomas CI, Ryan MA, Scholl B, Guerrero-Given D, Fitzpatrick D, Kamasawa N. Targeting Functionally Characterized Synaptic Architecture Using Inherent Fiducials and 3D Correlative Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:156-169. [PMID: 33303051 DOI: 10.1017/s1431927620024757] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Brain circuits are highly interconnected three-dimensional structures fabricated from components ranging vastly in size; from cell bodies to individual synapses. While neuronal activity can be visualized with advanced light microscopy (LM) techniques, the resolution of electron microscopy (EM) is critical for identifying synaptic connections between neurons. Here, we combine these two techniques, affording the advantage of each and allowing for measurements to be made of the same neural features across imaging platforms. We established an EM-label-free workflow utilizing inherent structural features to correlate in vivo two-photon LM and volumetric scanning EM (SEM) in the ferret visual cortex. By optimizing the volume SEM sample preparation protocol, imaging with the OnPoint detector, and utilizing the focal charge compensation device during serial block-face imaging, we achieved sufficient resolution and signal-to-noise ratio to analyze synaptic ultrastructure for hundreds of synapses within sample volumes. Our novel workflow provides a reliable method for quantitatively characterizing synaptic ultrastructure in functionally imaged neurons, providing new insights into neuronal circuit organization.
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Affiliation(s)
- Connon I Thomas
- Electron Microscopy Core Facility, Imaging Center, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL33458, USA
| | - Melissa A Ryan
- Electron Microscopy Core Facility, Imaging Center, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL33458, USA
| | - Benjamin Scholl
- Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL33458, USA
| | - Debbie Guerrero-Given
- Electron Microscopy Core Facility, Imaging Center, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL33458, USA
| | - David Fitzpatrick
- Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL33458, USA
| | - Naomi Kamasawa
- Electron Microscopy Core Facility, Imaging Center, Max Planck Florida Institute for Neuroscience, 1 Max Planck Way, Jupiter, FL33458, USA
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13
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Wu GH, Mitchell PG, Galaz-Montoya JG, Hecksel CW, Sontag EM, Gangadharan V, Marshman J, Mankus D, Bisher ME, Lytton-Jean AKR, Frydman J, Czymmek K, Chiu W. Multi-scale 3D Cryo-Correlative Microscopy for Vitrified Cells. Structure 2020; 28:1231-1237.e3. [PMID: 32814034 PMCID: PMC7642057 DOI: 10.1016/j.str.2020.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/10/2020] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
Three-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging modalities to visualize the same specimen at cryogenic temperature at different scales: cryo-fluorescence confocal microscopy, volume cryo-focused ion beam scanning electron microscopy, and transmission cryo-electron tomography. Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labeled chaperone Hsp104. Since our workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could be used for large-scale phenotypic studies of frozen-hydrated specimens in a variety of healthy and diseased conditions with and without treatments.
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Affiliation(s)
- Gong-Her Wu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Patrick G Mitchell
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jesus G Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Corey W Hecksel
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Emily M Sontag
- Department of Biology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | | | - Jeffrey Marshman
- Zeiss Research Microscopy Solutions, White Plains, NY 10601, USA
| | - David Mankus
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Margaret E Bisher
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abigail K R Lytton-Jean
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Judith Frydman
- Department of Biology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Kirk Czymmek
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA; Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
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14
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Meijering E. A bird's-eye view of deep learning in bioimage analysis. Comput Struct Biotechnol J 2020; 18:2312-2325. [PMID: 32994890 PMCID: PMC7494605 DOI: 10.1016/j.csbj.2020.08.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/26/2020] [Accepted: 08/01/2020] [Indexed: 02/07/2023] Open
Abstract
Deep learning of artificial neural networks has become the de facto standard approach to solving data analysis problems in virtually all fields of science and engineering. Also in biology and medicine, deep learning technologies are fundamentally transforming how we acquire, process, analyze, and interpret data, with potentially far-reaching consequences for healthcare. In this mini-review, we take a bird's-eye view at the past, present, and future developments of deep learning, starting from science at large, to biomedical imaging, and bioimage analysis in particular.
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Affiliation(s)
- Erik Meijering
- School of Computer Science and Engineering & Graduate School of Biomedical Engineering, University of New South Wales, Sydney, Australia
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15
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Mohammadian S, Agronskaia AV, Blab GA, van Donselaar EG, de Heus C, Liv N, Klumperman J, Gerritsen HC. Integrated super resolution fluorescence microscopy and transmission electron microscopy. Ultramicroscopy 2020; 215:113007. [PMID: 32470633 DOI: 10.1016/j.ultramic.2020.113007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/14/2020] [Accepted: 04/19/2020] [Indexed: 10/24/2022]
Abstract
In correlative light and electron microscopy (CLEM), the capabilities of fluorescence microscopy (FM) and electron microscopy (EM) are united. FM combines a large field of view with high sensitivity for detecting fluorescence, which makes it an excellent tool for identifying regions of interest. EM has a much smaller field of view but offers superb resolution that allows studying cellular ultrastructure. In CLEM, the potentials of both techniques are combined but a limiting factor is the large difference in resolution between the two imaging modalities. Adding super resolution FM to CLEM reduces the resolution gap between FM and EM; it offers the possibility of identifying multiple targets within the diffraction limit and can increase correlation accuracy. CLEM is usually carried out in two separate setups, which requires transfer of the sample. This may result in distortion and damage of the specimen, which can complicate finding back regions of interest. By integrating the two imaging modalities, such problems can be avoided. Here, an integrated super resolution correlative microscopy approach is presented based on a wide-field super resolution FM integrated in a Transmission Electron Microscope (TEM). Switching imaging modalities is accomplished by rotation of the TEM sample holder. First imaging experiments are presented on sections of Lowicryl embedded Human Umbilical Vein Endothelial Cells labeled for Caveolin both with Protein A-Gold, and Alexa Fluor®647. TEM and FM images were overlaid using fiducial markers visible in both imaging modalities with an overlay accuracy of 28 ± 11 nm. This is close to the optical resolution of ~50 nm.
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Affiliation(s)
- Sajjad Mohammadian
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Alexandra V Agronskaia
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Gerhard A Blab
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands
| | - Elly G van Donselaar
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Cecilia de Heus
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Nalan Liv
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Judith Klumperman
- Department of Cell Biology, Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Hans C Gerritsen
- Molecular Biophysics, Department of Physics, Faculty of Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, Netherlands.
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16
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Loukanov A, Nikolova S, Filipov C, Nakabayashi S. Metabolic labeling of Escherichia coli
genomic DNA with erythrosine-11-dUTP for functional imaging via correlative microscopy. Microsc Res Tech 2020; 83:937-944. [DOI: 10.1002/jemt.23487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/02/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandre Loukanov
- Division of Strategic Research and Development, Graduate School of Science and Engineering; Saitama University; Saitama Japan
- Laboratory of Engineering NanoBiotechnology, Department of Engineering Geoecology; University of Mining and Geology “St. Ivan Rilski”; Sofia Bulgaria
| | - Svetla Nikolova
- Medical University-Sofia; University Hospital “Maichin Dom”, National Genetic Laboratory; Sofia Bulgaria
| | - Chavdar Filipov
- Faculty of Veterinary Medicine; University of Forestry, Sofia; Sofia Bulgaria
| | - Seiichiro Nakabayashi
- Division of Strategic Research and Development, Graduate School of Science and Engineering; Saitama University; Saitama Japan
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17
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Asam C, Buerger K, Felthaus O, Brébant V, Rachel R, Prantl L, Witzgall R, Haerteis S, Aung T. Subcellular localization of the chemotherapeutic agent doxorubicin in renal epithelial cells and in tumor cells using correlative light and electron microscopy. Clin Hemorheol Microcirc 2019; 73:157-167. [DOI: 10.3233/ch-199212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Claudia Asam
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Korbinian Buerger
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Oliver Felthaus
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
| | - Vanessa Brébant
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
| | - Reinhard Rachel
- Centre for Electron Microscopy, Faculty of Biology and Preclinical Medicine, University of Regensburg, Germany
| | - Lukas Prantl
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
| | - Ralph Witzgall
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Silke Haerteis
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Germany
| | - Thiha Aung
- Centre of Plastic, Aesthetic, Hand and Reconstructive Surgery, University of Regensburg, Regensburg, Germany
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18
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Beekman P, Enciso-Martinez A, Rho HS, Pujari SP, Lenferink A, Zuilhof H, Terstappen LWMM, Otto C, Le Gac S. Immuno-capture of extracellular vesicles for individual multi-modal characterization using AFM, SEM and Raman spectroscopy. LAB ON A CHIP 2019; 19:2526-2536. [PMID: 31292600 DOI: 10.1039/c9lc00081j] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Tumor-derived extracellular vesicles (tdEVs) are promising blood biomarkers for cancer disease management. However, blood is a highly complex fluid that contains multiple objects in the same size range as tdEVs (30 nm-1 μm), which obscures an unimpeded analysis of tdEVs. Here, we report a multi-modal analysis platform for the specific capture of tdEVs on antibody-functionalized stainless steel substrates, followed by their analysis using SEM, Raman spectroscopy and AFM, at the single EV level in terms of size and size distribution, and chemical fingerprint. After covalent attachment of anti-EpCAM (epithelial cell adhesion molecule) antibodies on stainless steel substrates, EV samples derived from a prostate cancer cell line (LnCAP) were flushed into a microfluidic device assembled with this stainless steel substrate for capture. To track the captured objects between the different analytical instruments and subsequent correlative analysis, navigation markers were fabricated onto the substrate from a cyanoacrylate glue. Specific capture of tdEVs on the antibody-functionalized surface was demonstrated using SEM, AFM and Raman imaging, with excellent correlation between the data acquired by the individual techniques. The particle distribution was visualized with SEM. Furthermore, a characteristic lipid-protein band at 2850-2950 cm-1 was observed with Raman spectroscopy, and with AFM the size distribution and surface density of the captured EVs was assessed. Finally, correlation of SEM and Raman images enabled discrimination of tdEVs from cyanoacrylate glue particles, highlighting the capability of this multi-modal analysis platform for distinguishing tdEVs from contamination. The trans-instrumental compatibility of the stainless steel substrate and the possibility to spatially correlate the images of the different modalities with the help of the navigation markers open new avenues to a wide spectrum of combinations of different analytical and imaging techniques for the study of more complex EV samples.
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Affiliation(s)
- Pepijn Beekman
- Laboratory of Organic Chemistry, Wageningen University, The Netherlands and Applied Microfluidics for BioEngineering Research, MESA+ Institute for Nanotechnology and TechMed Center, University of Twente, The Netherlands.
| | | | - Hoon Suk Rho
- Applied Microfluidics for BioEngineering Research, MESA+ Institute for Nanotechnology and TechMed Center, University of Twente, The Netherlands. and Department of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, The Netherlands
| | | | - Aufried Lenferink
- Medical Cell BioPhysics, TechMed Center, University of Twente, The Netherlands.
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, The Netherlands and School of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, Tianjin, China
| | | | - Cees Otto
- Medical Cell BioPhysics, TechMed Center, University of Twente, The Netherlands.
| | - Séverine Le Gac
- Applied Microfluidics for BioEngineering Research, MESA+ Institute for Nanotechnology and TechMed Center, University of Twente, The Netherlands.
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19
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Lami SK, Smith G, Cao E, Hastings JT. The radiation chemistry of focused electron-beam induced etching of copper in liquids. NANOSCALE 2019; 11:11550-11561. [PMID: 31168552 DOI: 10.1039/c9nr01857c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Well-controlled, focused electron-beam induced etching of copper thin films has been successfully conducted on bulk substrates in an environmental scanning electron microscope by controlling liquid-film thickness with an in situ correlative interferometry system. Knowledge of the liquid-film thickness enables a hybrid Monte Carlo/continuum model of the radiation chemistry to accurately predict the copper etch rate using only electron scattering cross-sections, radical yields, and reaction rates from previous studies. Etch rates depended strongly on the thickness of the liquid film and simulations confirmed that this was a result of increased oxidizing radical generation. Etch rates also depended strongly, but non-linearly, on electron beam current, and simulations showed that this effect arises through the dose-rate dependence of reactions of radical species.
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Affiliation(s)
- Sarah K Lami
- Department of Electrical and Computer Engineering, University of Kentucky, Lexington, Kentucky 40506, USA.
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20
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Enciso-Martinez A, Timmermans FJ, Nanou A, Terstappen LWMM, Otto C. SEM-Raman image cytometry of cells. Analyst 2019; 143:4495-4502. [PMID: 30160261 DOI: 10.1039/c8an00955d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Correlative and integrated scanning electron microscopy (SEM) and Raman micro-spectroscopy is presented that enables the characterization and identification of different cancer and non-cancer cells through SEM-Raman image cytometry. The hybrid microscopy system enables the acquisition of high resolution SEM images of uncoated cells and the spatial correlation with chemical information as obtained from Raman micro-spectroscopic imaging. A sample preparation protocol and a workflow are presented that are compatible with the demands of hybrid SEM-Raman microscopy. Stainless steel cell substrates were used that are both conductive and give a low optical response in Raman scattering. Correlative and integrated SEM-Raman micro-spectroscopy is illustrated with cells from blood and cells from a SKBR-3 breast cancer cell line.
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Affiliation(s)
- A Enciso-Martinez
- Medical Cell Biophysics group, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands.
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21
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Ando T, Bhamidimarri SP, Brending N, Colin-York H, Collinson L, De Jonge N, de Pablo PJ, Debroye E, Eggeling C, Franck C, Fritzsche M, Gerritsen H, Giepmans BNG, Grunewald K, Hofkens J, Hoogenboom JP, Janssen KPF, Kaufman R, Klumpermann J, Kurniawan N, Kusch J, Liv N, Parekh V, Peckys DB, Rehfeldt F, Reutens DC, Roeffaers MBJ, Salditt T, Schaap IAT, Schwarz US, Verkade P, Vogel MW, Wagner R, Winterhalter M, Yuan H, Zifarelli G. The 2018 correlative microscopy techniques roadmap. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:443001. [PMID: 30799880 PMCID: PMC6372154 DOI: 10.1088/1361-6463/aad055] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/14/2018] [Accepted: 07/01/2018] [Indexed: 05/19/2023]
Abstract
Developments in microscopy have been instrumental to progress in the life sciences, and many new techniques have been introduced and led to new discoveries throughout the last century. A wide and diverse range of methodologies is now available, including electron microscopy, atomic force microscopy, magnetic resonance imaging, small-angle x-ray scattering and multiple super-resolution fluorescence techniques, and each of these methods provides valuable read-outs to meet the demands set by the samples under study. Yet, the investigation of cell development requires a multi-parametric approach to address both the structure and spatio-temporal organization of organelles, and also the transduction of chemical signals and forces involved in cell-cell interactions. Although the microscopy technologies for observing each of these characteristics are well developed, none of them can offer read-out of all characteristics simultaneously, which limits the information content of a measurement. For example, while electron microscopy is able to disclose the structural layout of cells and the macromolecular arrangement of proteins, it cannot directly follow dynamics in living cells. The latter can be achieved with fluorescence microscopy which, however, requires labelling and lacks spatial resolution. A remedy is to combine and correlate different readouts from the same specimen, which opens new avenues to understand structure-function relations in biomedical research. At the same time, such correlative approaches pose new challenges concerning sample preparation, instrument stability, region of interest retrieval, and data analysis. Because the field of correlative microscopy is relatively young, the capabilities of the various approaches have yet to be fully explored, and uncertainties remain when considering the best choice of strategy and workflow for the correlative experiment. With this in mind, the Journal of Physics D: Applied Physics presents a special roadmap on the correlative microscopy techniques, giving a comprehensive overview from various leading scientists in this field, via a collection of multiple short viewpoints.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | | | | | - H Colin-York
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
| | | | - Niels De Jonge
- INM-Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
- Saarland University, 66123 Saarbrücken, Germany
| | - P J de Pablo
- Dpto. Física de la Materia Condensada Universidad Autónoma de Madrid 28049, Madrid, Spain
- Instituto de Física de la Materia Condensada IFIMAC, Universidad Autónoma de Madrid 28049, Madrid, Spain
| | - Elke Debroye
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Institute of Applied Optics, Friedrich-Schiller University, Jena, Germany
- Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
| | - Christian Franck
- Department of Mechanical Engineering, University of Wisconsin-Madison, 1513 University Ave, Madison, WI 53706, United States of America
| | - Marco Fritzsche
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, OX3 9DS Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Hans Gerritsen
- Debye Institute, Utrecht University, Utrecht, Netherlands
| | - Ben N G Giepmans
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Kay Grunewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Heinrich-Pette-Institute, Leibniz Institute of Virology, Hamburg, Germany
| | - Johan Hofkens
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | | | | | - Rainer Kaufman
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centre of Structural Systems Biology Hamburg and University of Hamburg, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Judith Klumpermann
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Nyoman Kurniawan
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Nalan Liv
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, Netherlands
| | - Viha Parekh
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Diana B Peckys
- Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Florian Rehfeldt
- University of Göttingen, Third Institute of Physics-Biophysics, 37077 Göttingen, Germany
| | - David C Reutens
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Tim Salditt
- University of Göttingen, Institute for X-Ray Physics, 37077 Göttingen, Germany
| | - Iwan A T Schaap
- SmarAct GmbH, Schütte-Lanz-Str. 9, D-26135 Oldenburg, Germany
| | - Ulrich S Schwarz
- Institute for Theoretical Physics and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Michael W Vogel
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard Wagner
- Department of Life Sciences & Chemistry, Jacobs University, Bremen, Germany
| | | | - Haifeng Yuan
- KU Leuven, Department of Chemistry, B-3001 Heverlee, Belgium
| | - Giovanni Zifarelli
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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22
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Ayoub S, Tsai KC, Khalighi AH, Sacks MS. The Three-Dimensional Microenvironment of the Mitral Valve: Insights into the Effects of Physiological Loads. Cell Mol Bioeng 2018; 11:291-306. [PMID: 31719888 PMCID: PMC6816749 DOI: 10.1007/s12195-018-0529-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 05/14/2018] [Indexed: 10/24/2022] Open
Abstract
INTRODUCTION In the mitral valve (MV), numerous pathological factors, especially those resulting from changes in external loading, have been shown to affect MV structure and composition. Such changes are driven by the MV interstitial cell (MVIC) population via protein synthesis and enzymatic degradation of extracellular matrix (ECM) components. METHODS While cell phenotype, ECM composition and regulation, and tissue level changes in MVIC shape under stress have been studied, a detailed understanding of the three-dimensional (3D) microstructural mechanisms are lacking. As a first step in addressing this challenge, we applied focused ion beam scanning electron microscopy (FIB-SEM) to reveal novel details of the MV microenvironment in 3D. RESULTS We demonstrated that collagen is organized into large fibers consisting of an average of 605 ± 113 fibrils, with a mean diameter of 61.2 ± 9.8 nm. In contrast, elastin was organized into two distinct structural subtypes: (1) sheet-like lamellar elastin, and (2) circumferentially oriented elastin struts, based on both the aspect ratio and transmural tilt. MVICs were observed to have a large cytoplasmic volume, as evidenced by the large mean surface area to volume ratio 3.68 ± 0.35, which increased under physiological loading conditions to 4.98 ± 1.17. CONCLUSIONS Our findings suggest that each MVIC mechanically interacted only with the nearest 3-4 collagen fibers. This key observation suggests that in developing multiscale MV models, each MVIC can be considered a mechanically integral part of the local fiber ensemble and is unlikely to be influenced by more distant structures.
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Affiliation(s)
- Salma Ayoub
- Willerson Center for Cardiovascular Modeling and Simulation, Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th Street, POB 5.236, 1 University Station C0200, Austin, TX 78712 USA
| | - Karen C. Tsai
- Willerson Center for Cardiovascular Modeling and Simulation, Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th Street, POB 5.236, 1 University Station C0200, Austin, TX 78712 USA
| | - Amir H. Khalighi
- Willerson Center for Cardiovascular Modeling and Simulation, Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th Street, POB 5.236, 1 University Station C0200, Austin, TX 78712 USA
| | - Michael S. Sacks
- Willerson Center for Cardiovascular Modeling and Simulation, Institute for Computational Engineering and Sciences and the Department of Biomedical Engineering, The University of Texas at Austin, 201 East 24th Street, POB 5.236, 1 University Station C0200, Austin, TX 78712 USA
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23
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Single-molecule studies beyond optical imaging: Multi-parameter single-molecule spectroscopy. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2017.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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Mochalov KE, Chistyakov AA, Solovyeva DO, Mezin AV, Oleinikov VA, Vaskan IS, Molinari M, Agapov II, Nabiev I, Efimov AE. An instrumental approach to combining confocal microspectroscopy and 3D scanning probe nanotomography. Ultramicroscopy 2017; 182:118-123. [DOI: 10.1016/j.ultramic.2017.06.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 06/02/2017] [Accepted: 06/19/2017] [Indexed: 01/09/2023]
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25
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Hackley PC, Valentine BJ, Voortman LM, VAN Oosten Slingeland DSB, Hatcherian J. Utilization of integrated correlative light and electron microscopy (iCLEM) for imaging sedimentary organic matter. J Microsc 2017; 267:371-383. [PMID: 28665484 DOI: 10.1111/jmi.12576] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/17/2017] [Accepted: 04/12/2017] [Indexed: 01/13/2023]
Abstract
We report here a new microscopic technique for imaging and identifying sedimentary organic matter in geologic materials that combines inverted fluorescence microscopy with scanning electron microscopy and allows for sequential imaging of the same region of interest without transferring the sample between instruments. This integrated correlative light and electron microscopy technique is demonstrated with observations from an immature lacustrine oil shale from the Eocene Green River Mahogany Zone and mid-oil window paralic shale from the Upper Cretaceous Tuscaloosa Group. This technique has the potential to allow for identification and characterization of organic matter in shale hydrocarbon reservoirs that is not possible using either light or electron microscopy alone, and may be applied to understanding the organic matter type and thermal regime in which organic nanoporosity forms, thereby reducing uncertainty in the estimation of undiscovered hydrocarbon resources.
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Affiliation(s)
- Paul C Hackley
- U.S. Geological Survey, MS 956 National Center, Reston, Virginia, U.S.A
| | - Brett J Valentine
- U.S. Geological Survey, MS 956 National Center, Reston, Virginia, U.S.A
| | | | | | - Javin Hatcherian
- U.S. Geological Survey, MS 956 National Center, Reston, Virginia, U.S.A
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26
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Relocation is the key to successful correlative fluorescence and scanning electron microscopy. Methods Cell Biol 2017; 140:215-244. [PMID: 28528635 DOI: 10.1016/bs.mcb.2017.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this chapter the authors report on an automated hardware and software solution enabling swift correlative sample array mapping of fluorescently stained molecules within cells and tissues across length scales. Samples are first observed utilizing wide-field optical and fluorescence microscopy, followed by scanning electron microscopy, using calibration points on a dedicated sample-relocation holder. We investigated HeLa cells in vitro, fluorescently labeled for monosialoganglioside one (GM-1), across both imaging platforms within tens of minutes of initial sample preparation. This resulted in a high-throughput and high spatially resolved correlative fluorescence and electron microscopy analysis and allowed us to collect complementary nanoscopic information on the molecular and structural composition of two differently distinct HeLa cell populations expressing different levels of GM-1. Furthermore, using the small zebrafish animal model Danio rerio, we showed the versatility and relocation accuracy of the sample-relocation holder to locate fluo-tagged macromolecular complexes within large volumes using long ribbons of serial tissue sections. The subsequent electron microscopy imaging of the tissue arrays of interest enabled the generation of correlated information on the fine distribution of albumin within hepatic and kidney tissue. Our approach underpins the merits that an automated sample-relocation holder solution brings in support of results-driven research, where relevant biological questions can be answered, and high-throughput data can be generated in a rigorous statistical manner.
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Haring MT, Liv N, Zonnevylle AC, Narvaez AC, Voortman LM, Kruit P, Hoogenboom JP. Automated sub-5 nm image registration in integrated correlative fluorescence and electron microscopy using cathodoluminescence pointers. Sci Rep 2017; 7:43621. [PMID: 28252673 PMCID: PMC5333625 DOI: 10.1038/srep43621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/26/2017] [Indexed: 11/09/2022] Open
Abstract
In the biological sciences, data from fluorescence and electron microscopy is correlated to allow fluorescence biomolecule identification within the cellular ultrastructure and/or ultrastructural analysis following live-cell imaging. High-accuracy (sub-100 nm) image overlay requires the addition of fiducial markers, which makes overlay accuracy dependent on the number of fiducials present in the region of interest. Here, we report an automated method for light-electron image overlay at high accuracy, i.e. below 5 nm. Our method relies on direct visualization of the electron beam position in the fluorescence detection channel using cathodoluminescence pointers. We show that image overlay using cathodoluminescence pointers corrects for image distortions, is independent of user interpretation, and does not require fiducials, allowing image correlation with molecular precision anywhere on a sample.
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Affiliation(s)
- Martijn T. Haring
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Nalan Liv
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | | | - Angela C. Narvaez
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | | | - Pieter Kruit
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Jacob P. Hoogenboom
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
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Hauser M, Wojcik M, Kim D, Mahmoudi M, Li W, Xu K. Correlative Super-Resolution Microscopy: New Dimensions and New Opportunities. Chem Rev 2017; 117:7428-7456. [PMID: 28045508 DOI: 10.1021/acs.chemrev.6b00604] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Correlative microscopy, the integration of two or more microscopy techniques performed on the same sample, produces results that emphasize the strengths of each technique while offsetting their individual weaknesses. Light microscopy has historically been a central method in correlative microscopy due to its widespread availability, compatibility with hydrated and live biological samples, and excellent molecular specificity through fluorescence labeling. However, conventional light microscopy can only achieve a resolution of ∼300 nm, undercutting its advantages in correlations with higher-resolution methods. The rise of super-resolution microscopy (SRM) over the past decade has drastically improved the resolution of light microscopy to ∼10 nm, thus creating exciting new opportunities and challenges for correlative microscopy. Here we review how these challenges are addressed to effectively correlate SRM with other microscopy techniques, including light microscopy, electron microscopy, cryomicroscopy, atomic force microscopy, and various forms of spectroscopy. Though we emphasize biological studies, we also discuss the application of correlative SRM to materials characterization and single-molecule reactions. Finally, we point out current limitations and discuss possible future improvements and advances. We thus demonstrate how a correlative approach adds new dimensions of information and provides new opportunities in the fast-growing field of SRM.
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Affiliation(s)
- Meghan Hauser
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Michal Wojcik
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Doory Kim
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Morteza Mahmoudi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Wan Li
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California , Berkeley, California 94720, United States.,Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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Wolff G, Hagen C, Grünewald K, Kaufmann R. Towards correlative super-resolution fluorescence and electron cryo-microscopy. Biol Cell 2016; 108:245-58. [PMID: 27225383 PMCID: PMC5524168 DOI: 10.1111/boc.201600008] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 12/31/2022]
Abstract
Correlative light and electron microscopy (CLEM) has become a powerful tool in life sciences. Particularly cryo-CLEM, the combination of fluorescence cryo-microscopy (cryo-FM) permitting for non-invasive specific multi-colour labelling, with electron cryo-microscopy (cryo-EM) providing the undisturbed structural context at a resolution down to the Ångstrom range, has enabled a broad range of new biological applications. Imaging rare structures or events in crowded environments, such as inside a cell, requires specific fluorescence-based information for guiding cryo-EM data acquisition and/or to verify the identity of the structure of interest. Furthermore, cryo-CLEM can provide information about the arrangement of specific proteins in the wider structural context of their native nano-environment. However, a major obstacle of cryo-CLEM currently hindering many biological applications is the large resolution gap between cryo-FM (typically in the range of ∼400 nm) and cryo-EM (single nanometre to the Ångstrom range). Very recently, first proof of concept experiments demonstrated the feasibility of super-resolution cryo-FM imaging and the correlation with cryo-EM. This opened the door towards super-resolution cryo-CLEM, and thus towards direct correlation of structural details from both imaging modalities.
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Affiliation(s)
- Georg Wolff
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christoph Hagen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rainer Kaufmann
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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Nagarajan S, Pioche-Durieu C, Tizei LHG, Fang CY, Bertrand JR, Le Cam E, Chang HC, Treussart F, Kociak M. Simultaneous cathodoluminescence and electron microscopy cytometry of cellular vesicles labeled with fluorescent nanodiamonds. NANOSCALE 2016; 8:11588-11594. [PMID: 27216436 DOI: 10.1039/c6nr01908k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Light and Transmission Electron Microscopies (LM and TEM) hold potential in bioimaging owing to the advantages of fast imaging of multiple cells with LM and ultrastructure resolution offered by TEM. Integrated or correlated LM and TEM are the current approaches to combine the advantages of both techniques. Here we propose an alternative in which the electron beam of a scanning TEM (STEM) is used to excite concomitantly the luminescence of nanoparticle labels (a process known as cathodoluminescence, CL), and image the cell ultrastructure. This CL-STEM imaging allows obtaining luminescence spectra and imaging ultrastructure simultaneously. We present a proof of principle experiment, showing the potential of this technique in image cytometry of cell vesicular components. To label the vesicles we used fluorescent diamond nanocrystals (nanodiamonds, NDs) of size ≈150 nm coated with different cationic polymers, known to trigger different internalization pathways. Each polymer was associated with a type of ND with a different emission spectrum. With CL-STEM, for each individual vesicle, we were able to measure (i) their size with nanometric resolution, (ii) their content in different ND labels, and realize intracellular component cytometry. In contrast to the recently reported organelle flow cytometry technique that requires cell sonication, CL-STEM-based image cytometry preserves the cell integrity and provides a much higher resolution in size. Although this novel approach is still limited by a low throughput, the automatization of data acquisition and image analysis, combined with improved intracellular targeting, should facilitate applications in cell biology at the subcellular level.
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Affiliation(s)
- Sounderya Nagarajan
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France.
| | - Catherine Pioche-Durieu
- Signalisations, Noyaux et Innovations en Cancérologie, UMR 8126 CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gustave Roussy, 94805 Villejuif, France
| | - Luiz H G Tizei
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France.
| | - Chia-Yi Fang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Jean-Rémi Bertrand
- Laboratoire de Vectorologie et Thérapeutiques Anticancéreuses, UMR8203, CNRS, Univ. Paris-Sud, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Eric Le Cam
- Signalisations, Noyaux et Innovations en Cancérologie, UMR 8126 CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gustave Roussy, 94805 Villejuif, France
| | - Huan-Cheng Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - François Treussart
- Laboratoire Aimé Cotton, CNRS, Univ. Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay, France.
| | - Mathieu Kociak
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France.
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Shahidi R, Williams EA, Conzelmann M, Asadulina A, Verasztó C, Jasek S, Bezares-Calderón LA, Jékely G. A serial multiplex immunogold labeling method for identifying peptidergic neurons in connectomes. eLife 2015; 4. [PMID: 26670546 PMCID: PMC4749568 DOI: 10.7554/elife.11147] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/27/2015] [Indexed: 02/07/2023] Open
Abstract
Electron microscopy-based connectomics aims to comprehensively map synaptic connections in neural tissue. However, current approaches are limited in their capacity to directly assign molecular identities to neurons. Here, we use serial multiplex immunogold labeling (siGOLD) and serial-section transmission electron microscopy (ssTEM) to identify multiple peptidergic neurons in a connectome. The high immunogenicity of neuropeptides and their broad distribution along axons, allowed us to identify distinct neurons by immunolabeling small subsets of sections within larger series. We demonstrate the scalability of siGOLD by using 11 neuropeptide antibodies on a full-body larval ssTEM dataset of the annelid Platynereis. We also reconstruct a peptidergic circuitry comprising the sensory nuchal organs, found by siGOLD to express pigment-dispersing factor, a circadian neuropeptide. Our approach enables the direct overlaying of chemical neuromodulatory maps onto synaptic connectomic maps in the study of nervous systems. DOI:http://dx.doi.org/10.7554/eLife.11147.001 In the nervous system, cells called neurons connect to each other to form large “neural” networks. The most powerful method that is currently available for tracing neurons and mapping the connections between them is called electron microscopy. This requires slicing brain tissue into ultrathin sections, which are then imaged one by one. However, while electron microscopy provides highly detailed information about the structure of the connections between neurons, it does not reveal which molecules the neurons use to communicate with each other. To address this question, Shahidi et al. have developed a new approach called ‘siGOLD’. Unlike previous approaches, siGOLD allows signal molecules inside cells to be labeled with protein tags called antibodies without compromising the ability to examine the tissue with electron microscopy. The technique was developed using the larvae of a marine worm called Platynereis. A single larva was sliced into 5000 sections thin enough to view under an electron microscope, and 150 of these were selected to represent the entire body. Because neurons are typically long and thin, individual neurons usually spanned multiple slices. To identify the neurons, Shahidi et al. then applied an antibody that recognizes a specific signal molecule to a subset of the slices. The antibodies were labeled with gold particles, which show up as black dots under the electron microscope. Because the molecules recognized by the antibodies are present all along the neuron, and because individual neurons extend over multiple slices, it was possible to trace single neurons by labeling only a small number of slices. Repeating this process in different subsets of slices with antibodies that bind to different signal molecules allowed entire neural circuits to be mapped. In the future, Shahidi et al.’s approach could be adapted to study neural networks in other organisms such as flies, fish and mice. DOI:http://dx.doi.org/10.7554/eLife.11147.002
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Affiliation(s)
- Réza Shahidi
- Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | | | | | - Albina Asadulina
- Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Csaba Verasztó
- Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Sanja Jasek
- Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | | | - Gáspár Jékely
- Max-Planck-Institute for Developmental Biology, Tübingen, Germany
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Frankl A, Mari M, Reggiori F. Electron microscopy for ultrastructural analysis and protein localization in Saccharomyces cerevisiae. MICROBIAL CELL 2015; 2:412-428. [PMID: 28357267 PMCID: PMC5349205 DOI: 10.15698/mic2015.11.237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The yeast Saccharomyces cerevisiae is a key model system for studying of a multitude of cellular processes because of its amenability to genetics, molecular biology and biochemical procedures. Ultrastructural examinations of this organism, though, are traditionally difficult because of the presence of a thick cell wall and the high density of cytoplasmic proteins. A series of recent methodological and technical developments, however, has revived interest in morphological analyses of yeast (e.g. 123). Here we present a review of established and new methods, from sample preparation to imaging, for the ultrastructural analysis of S. cerevisiae. We include information for the use of different fixation methods, embedding procedures, approaches for contrast enhancement, and sample visualization techniques, with references to successful examples. The goal of this review is to guide researchers that want to investigate a particular process at the ultrastructural level in yeast by aiding in the selection of the most appropriate approach to visualize a specific structure or subcellular compartment.
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Affiliation(s)
- Andri Frankl
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Muriel Mari
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Fulvio Reggiori
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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