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Pedrazo-Tardajos A, Claes N, Wang D, Sánchez-Iglesias A, Nandi P, Jenkinson K, De Meyer R, Liz-Marzán LM, Bals S. Direct visualization of ligands on gold nanoparticles in a liquid environment. Nat Chem 2024; 16:1278-1285. [PMID: 38937593 DOI: 10.1038/s41557-024-01574-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024]
Abstract
The interactions between gold nanoparticles, their surface ligands and the solvent critically influence the properties of these nanoparticles. Although spectroscopic and scattering techniques have been used to investigate their ensemble structure, a comprehensive understanding of these processes at the nanoscale remains challenging. Electron microscopy makes it possible to characterize the local structure and composition but is limited by insufficient contrast, electron beam sensitivity and the requirement for ultrahigh-vacuum conditions, which prevent the investigation of dynamic aspects. Here we show that, by exploiting high-quality graphene liquid cells, we can overcome these limitations and investigate the structure of the ligand shell around gold nanoparticles and at the ligand-gold interface in a liquid environment. Using this graphene liquid cell, we visualize the anisotropy, composition and dynamics of ligand distribution on gold nanorod surfaces. Our results indicate a micellar model for surfactant organization. This work provides a reliable and direct visualization of ligand distribution around colloidal nanoparticles.
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Affiliation(s)
- Adrián Pedrazo-Tardajos
- EMAT-University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Nathalie Claes
- EMAT-University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Da Wang
- EMAT-University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Ana Sánchez-Iglesias
- CIC biomaGUNE, Donostia-San Sebastián, Spain
- Centro de Investigación Biomédica en Red, Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, Donostia-San Sebastián, Spain
| | - Proloy Nandi
- EMAT-University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Kellie Jenkinson
- EMAT-University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Robin De Meyer
- EMAT-University of Antwerp, Antwerp, Belgium
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Luis M Liz-Marzán
- CIC biomaGUNE, Donostia-San Sebastián, Spain
- Centro de Investigación Biomédica en Red, Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Cinbio, Universidade de Vigo, Vigo, Spain
| | - Sara Bals
- EMAT-University of Antwerp, Antwerp, Belgium.
- NANOlab Center of Excellence, University of Antwerp, Antwerp, Belgium.
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2
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Sasaki Y, Hirayama S, Nakao R. Scanning Electron Microscopy of Escherichia coli Encapsulated in a Spacerized Graphene Sandwich. Microscopy (Oxf) 2022; 71:175-180. [DOI: 10.1093/jmicro/dfac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 02/25/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Electron microscopy of biological materials such as bacteria allows multifaceted analysis to understand their structure and function with high resolution, which is difficult to achieve with optical microscopy. However, the samples are damaged or broken by electron beam irradiation and by the vacuum environment. Here, we observed bacteria in a suspension encapsulated in a graphene sandwich that prevents electron beam damage without the need for fixation. Specifically, we demonstrated in situ scanning electron microscopy observation of Escherichia coli in a graphene sandwich containing a perforated membrane as a spacer, encapsulating non-immobilized E. coli between the graphene layers. However, E. coli activity, such as division, was not observed, although the irradiated cells grew slightly when re-suspended under optimal culture conditions. Our findings suggest that the graphene sandwich methodology enables the observation of wet E. coli cells by electron microscopy but requires refinement to allow the live imaging of biological materials.
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Affiliation(s)
- Yuki Sasaki
- Nanostructures Research Laboratory, Japan Fine Ceramics Center, 2-4-1 Mutsuno, Atsuta-ku, Nagoya 456-8587, Japan
| | - Satoru Hirayama
- Division of Microbiology and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, 2-5274, Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ryoma Nakao
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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Abstract
Abstract
Deep learning is transforming most areas of science and technology, including electron microscopy. This review paper offers a practical perspective aimed at developers with limited familiarity. For context, we review popular applications of deep learning in electron microscopy. Following, we discuss hardware and software needed to get started with deep learning and interface with electron microscopes. We then review neural network components, popular architectures, and their optimization. Finally, we discuss future directions of deep learning in electron microscopy.
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4
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Azim S, Bultema LA, de Kock MB, Osorio-Blanco ER, Calderón M, Gonschior J, Leimkohl JP, Tellkamp F, Bücker R, Schulz EC, Keskin S, de Jonge N, Kassier GH, Miller RJD. Environmental Liquid Cell Technique for Improved Electron Microscopic Imaging of Soft Matter in Solution. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:44-53. [PMID: 33280632 DOI: 10.1017/s1431927620024654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Liquid-phase transmission electron microscopy is a technique for simultaneous imaging of the structure and dynamics of specimens in a liquid environment. The conventional sample geometry consists of a liquid layer tightly sandwiched between two Si3N4 windows with a nominal spacing on the order of 0.5 μm. We describe a variation of the conventional approach, wherein the Si3N4 windows are separated by a 10-μm-thick spacer, thus providing room for gas flow inside the liquid specimen enclosure. Adjusting the pressure and flow speed of humid air inside this environmental liquid cell (ELC) creates a stable liquid layer of controllable thickness on the bottom window, thus facilitating high-resolution observations of low mass-thickness contrast objects at low electron doses. We demonstrate controllable liquid thicknesses in the range 160 ± 34 to 340 ± 71 nm resulting in corresponding edge resolutions of 0.8 ± 0.06 to 1.7 ± 0.8 nm as measured for immersed gold nanoparticles. Liquid layer thickness 40 ± 8 nm allowed imaging of low-contrast polystyrene particles. Hydration effects in the ELC have been studied using poly-N-isopropylacrylamide nanogels with a silica core. Therefore, ELC can be a suitable tool for in situ investigations of liquid specimens.
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Affiliation(s)
- Sana Azim
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
| | - Lindsey A Bultema
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
| | - Michiel B de Kock
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
- Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Notkestraße 85, 22607Hamburg, Germany
| | | | - Marcelo Calderón
- POLYMAT & Applied Chemistry Department, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel de Lardizabal 3, 20018Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48013Bilbao, Spain
| | - Josef Gonschior
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
| | - Jan-Philipp Leimkohl
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
| | - Friedjof Tellkamp
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
| | - Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
| | - Eike C Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
| | - Sercan Keskin
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123Saarbrücken, Germany
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123Saarbrücken, Germany
- Department of Physics, Saarland University, Campus D2 2, 66123Saarbrücken, Germany
| | - Günther H Kassier
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Geb. 99 (CFEL), 22761Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. Georg Street, Toronto, ONM5S 3H6, Canada
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5
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Yoon A, Herzog A, Grosse P, Alsem DH, Chee SW, Roldán Cuenya B. Dynamic Imaging of Nanostructures in an Electrolyte with a Scanning Electron Microscope. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:121-128. [PMID: 33403947 DOI: 10.1017/s1431927620024769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The development of microfabricated liquid cells has enabled dynamic studies of nanostructures within a liquid environment with electron microscopy. While such setups are most commonly found in transmission electron microscope (TEM) holders, their implementation in a scanning electron microscope (SEM) offers intriguing potential for multi-modal studies where the large chamber volume allows for the integration of multiple detectors. Here, we describe an electrochemical liquid cell SEM platform that employs the same cells enclosed by silicon nitride membrane windows found in liquid cell TEM holders and demonstrate the imaging of copper oxide nanoparticles in solution using both backscattered and transmitted electrons. In particular, the transmitted electron images collected at high scattering angles show contrast inversion at liquid layer thicknesses of several hundred nanometers, which can be used to determine the presence of liquid in the cell, while maintaining enough resolution to image nanoparticles that are tens of nanometers in size. Using Monte Carlo simulations, we show that both imaging modes have their advantages for liquid phase imaging and rationalize the contrast inversion observed in the transmitted electron image.
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Affiliation(s)
- Aram Yoon
- Department of Interface Science, Fritz-Haber-Institute of the Max-Planck Society, Berlin, Germany
| | - Antonia Herzog
- Department of Interface Science, Fritz-Haber-Institute of the Max-Planck Society, Berlin, Germany
| | - Philipp Grosse
- Department of Interface Science, Fritz-Haber-Institute of the Max-Planck Society, Berlin, Germany
| | | | - See Wee Chee
- Department of Interface Science, Fritz-Haber-Institute of the Max-Planck Society, Berlin, Germany
| | - Beatriz Roldán Cuenya
- Department of Interface Science, Fritz-Haber-Institute of the Max-Planck Society, Berlin, Germany
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6
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Parent LR, Gnanasekaran K, Korpanty J, Gianneschi NC. 100th Anniversary of Macromolecular Science Viewpoint: Polymeric Materials by In Situ Liquid-Phase Transmission Electron Microscopy. ACS Macro Lett 2021; 10:14-38. [PMID: 35548998 DOI: 10.1021/acsmacrolett.0c00595] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A century ago, Hermann Staudinger proposed the macromolecular theory of polymers, and now, as we enter the second century of polymer science, we face a different set of opportunities and challenges for the development of functional soft matter. Indeed, many fundamental questions remain open, relating to physical structures and mechanisms of phase transformations at the molecular and nanoscale. In this Viewpoint, we describe efforts to develop a dynamic, in situ microscopy tool suited to the study of polymeric materials at the nanoscale that allows for direct observation of discrete structures and processes in solution, as a complement to light, neutron, and X-ray scattering methods. Liquid-phase transmission electron microscopy (LPTEM) is a nascent in situ imaging technique for characterizing and examining solvated nanomaterials in real time. Though still under development, LPTEM has been shown to be capable of several modes of imaging: (1) imaging static solvated materials analogous to cryo-TEM, (2) videography of nanomaterials in motion, (3) observing solutions or nanomaterials undergoing physical and chemical transformations, including synthesis, assembly, and phase transitions, and (4) observing electron beam-induced chemical-materials processes. Herein, we describe opportunities and limitations of LPTEM for polymer science. We review the basic experimental platform of LPTEM and describe the origin of electron beam effects that go hand in hand with the imaging process. These electron beam effects cause perturbation and damage to the sample and solvent that can manifest as artefacts in images and videos. We describe sample-specific experimental guidelines and outline approaches to mitigate, characterize, and quantify beam damaging effects. Altogether, we seek to provide an overview of this nascent field in the context of its potential to contribute to the advancement of polymer science.
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Affiliation(s)
- Lucas R. Parent
- Innovation Partnership Building, The University of Connecticut, Storrs, Connecticut 06269, United States
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7
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Wu H, Friedrich H, Patterson JP, Sommerdijk NAJM, de Jonge N. Liquid-Phase Electron Microscopy for Soft Matter Science and Biology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001582. [PMID: 32419161 DOI: 10.1002/adma.202001582] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 05/20/2023]
Abstract
Innovations in liquid-phase electron microscopy (LP-EM) have made it possible to perform experiments at the optimized conditions needed to examine soft matter. The main obstacle is conducting experiments in such a way that electron beam radiation can be used to obtain answers for scientific questions without changing the structure and (bio)chemical processes in the sample due to the influence of the radiation. By overcoming these experimental difficulties at least partially, LP-EM has evolved into a new microscopy method with nanometer spatial resolution and sub-second temporal resolution for analysis of soft matter in materials science and biology. Both experimental design and applications of LP-EM for soft matter materials science and biological research are reviewed, and a perspective of possible future directions is given.
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Affiliation(s)
- Hanglong Wu
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Heiner Friedrich
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, 5600 MB, The Netherlands
| | - Joseph P Patterson
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Nico A J M Sommerdijk
- Department of Biochemistry, Radboud University Medical Center, Nijmegen, 6500 HB, The Netherlands
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, Saarbrücken, 66123, Germany
- Department of Physics, Saarland University, Saarbrücken, 66123, Germany
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8
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Alansary D, Peckys DB, Niemeyer BA, de Jonge N. Detecting single ORAI1 proteins within the plasma membrane reveals higher-order channel complexes. J Cell Sci 2020; 133:jcs.240358. [PMID: 31822631 DOI: 10.1242/jcs.240358] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/02/2019] [Indexed: 12/22/2022] Open
Abstract
ORAI1 proteins form highly selective Ca2+ channels in the plasma membrane. Crystallographic data point towards a hexameric stoichiometry of ORAI1 channels, whereas optical methods postulated ORAI1 channels to reside as dimers at rest, and other data suggests that they have a tetrameric configuration. Here, liquid-phase scanning transmission electron microscopy (STEM) and quantum dot (QD) labeling was utilized to study the conformation of ORAI1 proteins at rest. To address the question of whether ORAI1 was present as a dimer, experiments were designed using single ORAI1 monomers and covalently linked ORAI1 dimers with either one or two label-binding positions. The microscopic data was statistically analyzed via the pair correlation function. Label pairs were found in all cases, even for concatenated dimers with one label-binding position, which is only possible if a significant fraction of ORAI1 was assembled in larger order oligomers than dimers, binding at least two QDs. This interpretation of the data was consistent with Blue Native PAGE analysis showing that ORAI1 is mainly present as a complex of an apparent molecular mass larger than that calculated for a dimer.
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Affiliation(s)
- Dalia Alansary
- Molecular Biophysics, University of Saarland, Center for Integrative Physiology and Molecular Medicine, 66421 Homburg/Saar, Germany
| | - Diana B Peckys
- Molecular Biophysics, University of Saarland, Center for Integrative Physiology and Molecular Medicine, 66421 Homburg/Saar, Germany
| | - Barbara A Niemeyer
- Molecular Biophysics, University of Saarland, Center for Integrative Physiology and Molecular Medicine, 66421 Homburg/Saar, Germany
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, 66123 Saarbrücken, Germany .,Department of Physics, University of Saarland, 66123 Saarbrücken, Germany
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9
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Pu S, Gong C, Robertson AW. Liquid cell transmission electron microscopy and its applications. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191204. [PMID: 32218950 PMCID: PMC7029903 DOI: 10.1098/rsos.191204] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
Transmission electron microscopy (TEM) has long been an essential tool for understanding the structure of materials. Over the past couple of decades, this venerable technique has undergone a number of revolutions, such as the development of aberration correction for atomic level imaging, the realization of cryogenic TEM for imaging biological specimens, and new instrumentation permitting the observation of dynamic systems in situ. Research in the latter has rapidly accelerated in recent years, based on a silicon-chip architecture that permits a versatile array of experiments to be performed under the high vacuum of the TEM. Of particular interest is using these silicon chips to enclose fluids safely inside the TEM, allowing us to observe liquid dynamics at the nanoscale. In situ imaging of liquid phase reactions under TEM can greatly enhance our understanding of fundamental processes in fields from electrochemistry to cell biology. Here, we review how in situ TEM experiments of liquids can be performed, with a particular focus on microchip-encapsulated liquid cell TEM. We will cover the basics of the technique, and its strengths and weaknesses with respect to related in situ TEM methods for characterizing liquid systems. We will show how this technique has provided unique insights into nanomaterial synthesis and manipulation, battery science and biological cells. A discussion on the main challenges of the technique, and potential means to mitigate and overcome them, will also be presented.
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10
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He K, Shokuhfar T, Shahbazian-Yassar R. Imaging of soft materials using in situ liquid-cell transmission electron microscopy. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:103001. [PMID: 30524096 DOI: 10.1088/1361-648x/aaf616] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This review summarizes the breakthroughs in the field of soft material characterization by in situ liquid-cell transmission electron microscopy (TEM). The focus of this review is mostly on soft biological species such as cells, bacteria, viruses, proteins and polymers. The comparison between the two main liquid-cell systems (silicon nitride membranes liquid cell and graphene liquid cell) is also discussed in terms of their spatial resolution and imaging/analytical capabilities. We have showcased how liquid-cell TEM can reveal the structural details of whole cells, enable the chemical probing of proteins, detect the structural conformation of viruses, and monitor the dynamics of polymerization. In addition, the challenges faced by decoupling electron beam effect on beam-sensitive soft materials are discussed. At the end, future perspectives of in situ liquid-cell TEM studies of soft materials are outlined.
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Affiliation(s)
- Kun He
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, IL 60607, United States of America
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11
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Sato C, Yamazawa T, Ohtani A, Maruyama Y, Memtily N, Sato M, Hatano Y, Shiga T, Ebihara T. Primary cultured neuronal networks and type 2 diabetes model mouse fatty liver tissues in aqueous liquid observed by atmospheric SEM (ASEM): Staining preferences of metal solutions. Micron 2019; 118:9-21. [DOI: 10.1016/j.micron.2018.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/13/2018] [Accepted: 11/22/2018] [Indexed: 01/25/2023]
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12
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Keskin S, de Jonge N. Reduced Radiation Damage in Transmission Electron Microscopy of Proteins in Graphene Liquid Cells. NANO LETTERS 2018; 18:7435-7440. [PMID: 30431282 DOI: 10.1021/acs.nanolett.8b02490] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Liquid-phase electron microscopy (LPEM) is capable of imaging native (unstained) protein structure in liquid, but the achievable spatial resolution is limited by radiation damage. This damaging effect is more pronounced when targeting small molecular features than for larger structures. The matter is even more complicated because the critical dose that a sample can endure before radiation damage not only varies between proteins but also critically depends on the experimental conditions. Here, we examined the effect of the electron beam on the observed protein structure for optimized conditions using a liquid sample enclosure assembled from graphene sheets. It has been shown that graphene can reduce the damaging effect of electrons on biological materials. We used radiation sensitive microtubule proteins and investigated the radiation damage on these structures as a function of the spatial frequencies of the observed features with transmission electron microscopy (TEM). Microtubule samples were also examined using cryo-electron microscopy (cryo-TEM) for comparison. We used an electron flux of 11 ± 1-16 ± 1 e-/Å2s and obtained a series of images from the same sample region. Our results show that graphene-encapsulated microtubules can maintain their structural features of spatial frequencies of up to 0.20 nm-1 (5 nm), reflecting protofilaments for electron densities of up to 7.2 ± 1.4 × 102 e-/Å2, an order of magnitude higher than measured for frozen microtubules in amorphous ice.
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Affiliation(s)
- Sercan Keskin
- Leibniz Institute for New Materials (INM) , Saarbrücken D-66123 , Germany
| | - Niels de Jonge
- Leibniz Institute for New Materials (INM) , Saarbrücken D-66123 , Germany
- Department of Physics , Saarland University , Saarbrücken D-66123 , Germany
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13
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de Jonge N. Theory of the spatial resolution of (scanning) transmission electron microscopy in liquid water or ice layers. Ultramicroscopy 2018; 187:113-125. [DOI: 10.1016/j.ultramic.2018.01.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/02/2018] [Accepted: 01/17/2018] [Indexed: 01/29/2023]
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14
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Dahmke IN, Verch A, Hermannsdörfer J, Peckys DB, Weatherup RS, Hofmann S, de Jonge N. Graphene Liquid Enclosure for Single-Molecule Analysis of Membrane Proteins in Whole Cells Using Electron Microscopy. ACS NANO 2017; 11:11108-11117. [PMID: 29023096 DOI: 10.1021/acsnano.7b05258] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Membrane proteins govern many important functions in cells via dynamic oligomerization into active complexes. However, analytical methods to study their distribution and functional state in relation to the cellular structure are currently limited. Here, we introduce a technique for studying single-membrane proteins within their native context of the intact plasma membrane. SKBR3 breast cancer cells were grown on silicon microchips with thin silicon nitride windows. The cells were fixed, and the epidermal growth factor receptor ErbB2 was specifically labeled with quantum dot (QD) nanoparticles. For correlative fluorescence- and liquid-phase electron microscopy, we enclosed the liquid samples by chemical vapor deposited (CVD) graphene films. Depending on the local cell thickness, QD labels were imaged with a spatial resolution of 2 nm at a low electron dose. The distribution and stoichiometric assembly of ErbB2 receptors were determined at several different cellular locations, including tunneling nanotubes, where we found higher levels of homodimerization at the connecting sites. This experimental approach is applicable to a wide range of cell lines and membrane proteins and particularly suitable for studies involving both inter- and intracellular heterogeneity in protein distribution and expression.
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Affiliation(s)
- Indra N Dahmke
- INM - Leibniz Institute for New Materials , D-66123 Saarbrücken, Germany
| | - Andreas Verch
- INM - Leibniz Institute for New Materials , D-66123 Saarbrücken, Germany
| | | | - Diana B Peckys
- Department of Biophysics, Saarland University , D-66421 Homburg, Germany
| | - Robert S Weatherup
- Engineering Department, University of Cambridge , Cambridge CB3 0FA, United Kingdom
| | - Stephan Hofmann
- Engineering Department, University of Cambridge , Cambridge CB3 0FA, United Kingdom
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials , D-66123 Saarbrücken, Germany
- Department of Physics, Saarland University , D-66123 Saarbrücken, Germany
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15
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Vanhecke D, Kuhn DA, Jimenez de Aberasturi D, Balog S, Milosevic A, Urban D, Peckys D, de Jonge N, Parak WJ, Petri-Fink A, Rothen-Rutishauser B. Involvement of two uptake mechanisms of gold and iron oxide nanoparticles in a co-exposure scenario using mouse macrophages. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2396-2409. [PMID: 29234575 PMCID: PMC5704759 DOI: 10.3762/bjnano.8.239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 10/11/2017] [Indexed: 05/26/2023]
Abstract
Little is known about the simultaneous uptake of different engineered nanoparticle types, as it can be expected in our daily life. In order to test such co-exposure effects, murine macrophages (J774A.1 cell line) were incubated with gold (AuNPs) and iron oxide nanoparticles (FeO x NPs) either alone or combined. Environmental scanning electron microscopy revealed that single NPs of both types bound within minutes on the cell surface but with a distinctive difference between FeO x NPs and AuNPs. Uptake analysis studies based on laser scanning microscopy, transmission electron microscopy, and inductively coupled plasma optical emission spectrometry revealed intracellular appearance of both NP types in all exposure scenarios and a time-dependent increase. This increase was higher for both AuNPs and FeO x NPs during co-exposure. Cells treated with endocytotic inhibitors recovered after co-exposure, which additionally hinted that two uptake mechanisms are involved. Cross-talk between uptake pathways is relevant for toxicological studies: Co-exposure acts as an uptake accelerant. If the goal is to maximize the cellular uptake, e.g., for the delivery of pharmaceutical agents, this can be beneficial. However, co-exposure should also be taken into account in the case of risk assessment of occupational settings. The demonstration of co-exposure-invoked pathway interactions reveals that synergetic nanoparticle effects, either positive or negative, must be considered for nanotechnology and nanomedicine in particular to develop to its full potential.
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Affiliation(s)
- Dimitri Vanhecke
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | - Dagmar A Kuhn
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | | | - Sandor Balog
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | - Ana Milosevic
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | - Dominic Urban
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
| | - Diana Peckys
- Department of Biophysics, CIPMM Geb. 48, Saarland University, 66421 Homburg/Saar, Germany
| | - Niels de Jonge
- Department of Biophysics, CIPMM Geb. 48, Saarland University, 66421 Homburg/Saar, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany
| | - Wolfgang J Parak
- CIC Biomagune, Miramon Ibilbidea 182, 20014 Donostia, Gipuzkoa, San Sebastian, Spain
- Fachbereich Physik, Philipps Universität Marburg, Renthof 7, 35037 Marburg, Germany
| | - Alke Petri-Fink
- Adolphe Merkle Institute, Université de Fribourg, Chemin des Verdiers 4, CH 1700, Fribourg, Switzerland
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16
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Peckys DB, Korf U, Wiemann S, de Jonge N. Liquid-phase electron microscopy of molecular drug response in breast cancer cells reveals irresponsive cell subpopulations related to lack of HER2 homodimers. Mol Biol Cell 2017; 28:mbc.E17-06-0381. [PMID: 28794264 PMCID: PMC5687022 DOI: 10.1091/mbc.e17-06-0381] [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: 06/14/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 12/31/2022] Open
Abstract
The development of drug resistance in cancer poses a major clinical problem. An example is human epidermal growth factor receptor 2 (HER2) overexpressing breast cancer often treated with anti-HER2 antibody therapies, such as trastuzumab. Since drug resistance is rooted mainly in tumor cell heterogeneity, we examined the drug effect in different subpopulations of SKBR3 breast cancer cells, and compared the results with a drug resistant cell line, HCC1954. Correlative light microscopy and liquid-phase scanning transmission electron microscopy (STEM) were used to quantitatively analyze HER2 responses upon drug binding, whereby many tens of whole cells were imaged. Trastuzumab was found to selectively cross-link and down regulate HER2 homodimers from the plasma membranes of bulk cancer cells. In contrast, HER2 resided mainly as monomers in rare subpopulations of resting- and cancer stem cells (CSCs), and these monomers were not internalized after drug binding. The HER2 distribution was hardly influenced by trastuzumab for the HCC1954 cells. These findings show that resting cells and CSCs are irresponsive to the drug, and thus point towards a molecular explanation behind the origin of drug resistance. This analytical method is broadly applicable to study membrane protein interactions in the intact plasma membrane, while accounting for cell heterogeneity.
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Affiliation(s)
- Diana B Peckys
- Department of Biophysics, Saarland University, D-66421 Homburg, Germany
| | - Ulrike Korf
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
- Department of Physics, Saarland University, 66123 Saarbrücken, Germany
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17
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Peckys DB, Stoerger C, Latta L, Wissenbach U, Flockerzi V, de Jonge N. The stoichiometry of the TMEM16A ion channel determined in intact plasma membranes of COS-7 cells using liquid-phase electron microscopy. J Struct Biol 2017; 199:102-113. [PMID: 28559167 DOI: 10.1016/j.jsb.2017.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 11/29/2022]
Abstract
TMEM16A is a membrane protein forming a calcium-activated chloride channel. A homodimeric stoichiometry of the TMEM16 family of proteins has been reported but an important question is whether the protein resides always in a dimeric configuration in the plasma membrane or whether monomers of the protein are also present in its native state within in the intact plasma membrane. We have determined the stoichiometry of the human (h)TMEM16A within whole COS-7 cells in liquid. For the purpose of detecting TMEM16A subunits, single proteins were tagged by the streptavidin-binding peptide within extracellular loops accessible by streptavidin coated quantum dot (QD) nanoparticles. The labeled proteins were then imaged using correlative light microscopy and environmental scanning electron microscopy (ESEM) using scanning transmission electron microscopy (STEM) detection. The locations of 19,583 individual proteins were determined of which a statistical analysis using the pair correlation function revealed the presence of a dimeric conformation of the protein. The amounts of detected label pairs and single labels were compared between experiments in which the TMEM16A SBP-tag position was varied, and experiments in which tagged and non-tagged TMEM16A proteins were present. It followed that hTMEM16A resides in the plasma membrane as dimer only and is not present as monomer. This strategy may help to elucidate the stoichiometry of other membrane protein species within the context of the intact plasma membrane in future.
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Affiliation(s)
- Diana B Peckys
- Department of Biophysics, Saarland University, 66421 Homburg, Germany
| | - Christof Stoerger
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, 66421 Homburg, Germany
| | - Lorenz Latta
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, 66421 Homburg, Germany
| | - Ulrich Wissenbach
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, 66421 Homburg, Germany
| | - Veit Flockerzi
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, 66421 Homburg, Germany
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, Saarland University, 66123 Saarbrücken, Germany; Department of Physics, Saarland University, 66123 Saarbrücken, Germany.
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18
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DE JONGE N. Membrane protein stoichiometry studied in intact mammalian cells using liquid-phase electron microscopy. J Microsc 2017; 269:134-142. [DOI: 10.1111/jmi.12570] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/15/2017] [Accepted: 03/25/2017] [Indexed: 02/02/2023]
Affiliation(s)
- N. DE JONGE
- Leibniz Institute for New Materials; Saarbrücken Germany
- Department of Physics; University of Saarland; Saarbrücken Germany
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19
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Cho H, Jones MR, Nguyen SC, Hauwiller MR, Zettl A, Alivisatos AP. The Use of Graphene and Its Derivatives for Liquid-Phase Transmission Electron Microscopy of Radiation-Sensitive Specimens. NANO LETTERS 2017; 17:414-420. [PMID: 28026186 DOI: 10.1021/acs.nanolett.6b04383] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One of the key challenges facing liquid-phase transmission electron microscopy (TEM) of biological specimens has been the damaging effects of electron beam irradiation. The strongly ionizing electron beam is known to induce radiolysis of surrounding water molecules, leading to the formation of reactive radical species. In this study, we employ DNA-assembled Au nanoparticle superlattices (DNA-AuNP superlattices) as a model system to demonstrate that graphene and its derivatives can be used to mitigate electron beam-induced damage. We can image DNA-AuNP superlattices in their native saline environment when the liquid cell window material is graphene, but not when it is silicon nitride. In the latter case, initial dissociation of assembled AuNPs was followed by their random aggregation and etching. Using graphene-coated silicon nitride windows, we were able to replicate the observation of stable DNA-AuNP superlattices achieved with graphene liquid cells. We then carried out a correlative Raman spectroscopy and TEM study to compare the effect of electron beam irradiation on graphene with and without the presence of water and found that graphene reacts with the products of water radiolysis. We attribute the protective effect of graphene to its ability to efficiently scavenge reactive radical species, especially the hydroxyl radicals which are known to cause DNA strand breaks. We confirmed this by showing that stable DNA-AuNP assemblies can be imaged in silicon nitride liquid cells when graphene oxide and graphene quantum dots, which have also recently been reported as efficient radical scavengers, are added directly to the solution. We anticipate that our study will open up more opportunities for studying biological specimens using liquid-phase TEM with the use of graphene and its derivatives as biocompatible radical scavengers to alleviate the effects of radiation damage.
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Affiliation(s)
- Hoduk Cho
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Matthew R Jones
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Son C Nguyen
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg , Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Matthew R Hauwiller
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Alex Zettl
- Materials Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Department of Physics, University of California , Berkeley, California 94720, United States
- Kavli Energy NanoScience Institute , Berkeley, California 94720, United States
| | - A Paul Alivisatos
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
- Kavli Energy NanoScience Institute , Berkeley, California 94720, United States
- Department of Materials Science and Engineering, University of California , Berkeley, California 94720, United States
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20
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Peckys DB, Alansary D, Niemeyer BA, de Jonge N. Visualizing Quantum Dot Labeled ORAI1 Proteins in Intact Cells Via Correlative Light and Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:902-912. [PMID: 27515473 DOI: 10.1017/s1431927616011491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
ORAI1 proteins are ion channel subunits and the essential pore-forming units of the calcium release-activated calcium channel complex essential for T-cell activation and many other cellular processes. In this study, we used environmental scanning electron microscopy (ESEM) with scanning transmission electron microscopy (STEM) detection to image plasma membrane expressed ORAI1 proteins in whole Jurkat T cells in the liquid state. Utilizing a stably transfected Jurkat T cell clone expressing human ORAI1 with an extracellular human influenza hemagglutinin (HA) tag we investigated if liquid-phase STEM can be applied to detect recombinant surface expressed protein. Streptavidin coated quantum dots were coupled in a one-to-one stoichiometry to ORAI1 proteins detected by biotinylated anti-HA fragmented antibody fragments. High-resolution electron microscopic images revealed the individual label locations from which protein pair distances were determined. These data were analyzed using the pair correlation function and, in addition, an analysis of cluster size and frequency was performed. ORAI1 was found to be present in hexamers in a small fraction only, and ORAI1 resided mostly in monomers and dimers.
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Affiliation(s)
- Diana B Peckys
- 1Department of Molecular Biophysics,Saarland University,CIPMM,66421 Homburg,Germany
| | - Dalia Alansary
- 1Department of Molecular Biophysics,Saarland University,CIPMM,66421 Homburg,Germany
| | - Barbara A Niemeyer
- 1Department of Molecular Biophysics,Saarland University,CIPMM,66421 Homburg,Germany
| | - Niels de Jonge
- 2INM - Leibniz Institute for New Materials,66123 Saarbrücken,Germany
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