1
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Jia D, Cui M, Ding X. Visualizing DNA/RNA, Proteins, and Small Molecule Metabolites within Live Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404482. [PMID: 39096065 DOI: 10.1002/smll.202404482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/15/2024] [Indexed: 08/04/2024]
Abstract
Live cell imaging is essential for obtaining spatial and temporal insights into dynamic molecular events within heterogeneous individual cells, in situ intracellular networks, and in vivo organisms. Molecular tracking in live cells is also a critical and general requirement for studying dynamic physiological processes in cell biology, cancer, developmental biology, and neuroscience. Alongside this context, this review provides a comprehensive overview of recent research progress in live-cell imaging of RNAs, DNAs, proteins, and small-molecule metabolites, as well as their applications in molecular diagnosis, immunodiagnosis, and biochemical diagnosis. A series of advanced live-cell imaging techniques have been introduced and summarized, including high-precision live-cell imaging, high-resolution imaging, low-abundance imaging, multidimensional imaging, multipath imaging, rapid imaging, and computationally driven live-cell imaging methods, all of which offer valuable insights for disease prevention, diagnosis, and treatment. This review article also addresses the current challenges, potential solutions, and future development prospects in this field.
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Affiliation(s)
- Dongling Jia
- School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Minhui Cui
- School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Xianting Ding
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
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2
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Alam MS, Penedo M, Sumikama T, Miyazawa K, Hirahara K, Fukuma T. Revealing the Mechanism Underlying 3D-AFM Imaging of Suspended Structures by Experiments and Simulations. SMALL METHODS 2024:e2400287. [PMID: 39031872 DOI: 10.1002/smtd.202400287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/06/2024] [Indexed: 07/22/2024]
Abstract
The invention of 3D atomic force microscopy (3D-AFM) has enabled visualizing subnanoscale 3D hydration structures. Meanwhile, its applications to imaging flexible molecular chains have started to be experimentally explored. However, the validity and principle of such imaging have yet to be clarified by comparing experiments and simulations or cross-observations with an alternative technique. Such studies are impeded by the lack of an appropriate model. Here, this difficulty is overcome by fabricating 3D carbon nanotube (CNT) structures flexible enough for 3D-AFM, large enough for scanning electron microscopy (SEM), and simple enough for simulations. SEM and 3D-AFM observations of the same model provide unambiguous evidence to support the possibility of imaging overlapped nanostructures, such as suspended CNT and underlying platinum (Pt) nanodots. Langevin dynamics simulations of such 3D-AFM imaging clarify the imaging mechanism, where the flexible CNT is laterally displaced to allow the AFM probe access to the underlying structures. These results consistently show that 3D-AFM images are affected by the friction between the CNT and AFM nanoprobe, yet it can be significantly suppressed by oscillating the cantilever. This study reinforces the theoretical basis of 3D-AFM for imaging various 3D self-organizing systems in diverse fields, from life sciences to interface sciences.
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Affiliation(s)
- Mohammad Shahidul Alam
- Division of Nano Life Science, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Marcos Penedo
- École Polytechnique Fédérale de Lausanne, Institute for Bioengineering, Laboratory for Bio and Nanoinstrumentation, Lausanne, CH 1015, Switzerland
| | - Takashi Sumikama
- WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Keisuke Miyazawa
- WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Kaori Hirahara
- Department of Mechanical Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Fukuma
- Division of Nano Life Science, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- WPI Nano Life Science Institute (WPI-Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
- Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
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3
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Sproncken CCM, Liu P, Monney J, Fall WS, Pierucci C, Scholten PBV, Van Bueren B, Penedo M, Fantner GE, Wensink HH, Steiner U, Weder C, Bruns N, Mayer M, Ianiro A. Large-area, self-healing block copolymer membranes for energy conversion. Nature 2024; 630:866-871. [PMID: 38839964 PMCID: PMC11208134 DOI: 10.1038/s41586-024-07481-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/29/2024] [Indexed: 06/07/2024]
Abstract
Membranes are widely used for separation processes in applications such as water desalination, batteries and dialysis, and are crucial in key sectors of our economy and society1. The majority of technologically exploited membranes are based on solid polymers and function as passive barriers, whose transport characteristics are governed by their chemical composition and nanostructure. Although such membranes are ubiquitous, it has proved challenging to maximize selectivity and permeability independently, leading to trade-offs between these pertinent characteristics2. Self-assembled biological membranes, in which barrier and transport functions are decoupled3,4, provide the inspiration to address this problem5,6. Here we introduce a self-assembly strategy that uses the interface of an aqueous two-phase system to template and stabilize molecularly thin (approximately 35 nm) biomimetic block copolymer bilayers of scalable area that can exceed 10 cm2 without defects. These membranes are self-healing, and their barrier function against the passage of ions (specific resistance of approximately 1 MΩ cm2) approaches that of phospholipid membranes. The fluidity of these membranes enables straightforward functionalization with molecular carriers that shuttle potassium ions down a concentration gradient with exquisite selectivity over sodium ions. This ion selectivity enables the generation of electric power from equimolar solutions of NaCl and KCl in devices that mimic the electric organ of electric rays.
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Affiliation(s)
- Christian C M Sproncken
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
| | - Peng Liu
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Justin Monney
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - William S Fall
- Laboratoire de Physique des Solides - UMR 8502, CNRS, Université Paris-Saclay, Orsay, France
| | - Carolina Pierucci
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
| | - Philip B V Scholten
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
| | - Brian Van Bueren
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Marcos Penedo
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - Georg Ernest Fantner
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - Henricus H Wensink
- Laboratoire de Physique des Solides - UMR 8502, CNRS, Université Paris-Saclay, Orsay, France
| | - Ullrich Steiner
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
| | - Christoph Weder
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
| | - Nico Bruns
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
- Department of Chemistry and Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland.
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland.
| | - Alessandro Ianiro
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland.
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland.
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4
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Chitty C, Kuliga K, Xue WF. Atomic force microscopy 3D structural reconstruction of individual particles in the study of amyloid protein assemblies. Biochem Soc Trans 2024; 52:761-771. [PMID: 38600027 DOI: 10.1042/bst20230857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Recent developments in atomic force microscopy (AFM) image analysis have made three-dimensional (3D) structural reconstruction of individual particles observed on 2D AFM height images a reality. Here, we review the emerging contact point reconstruction AFM (CPR-AFM) methodology and its application in 3D reconstruction of individual helical amyloid filaments in the context of the challenges presented by the structural analysis of highly polymorphous and heterogeneous amyloid protein structures. How individual particle-level structural analysis can contribute to resolving the amyloid polymorph structure-function relationships, the environmental triggers leading to protein misfolding and aggregation into amyloid species, the influences by the conditions or minor fluctuations in the initial monomeric protein structure on the speed of amyloid fibril formation, and the extent of the different types of amyloid species that can be formed, are discussed. Future perspectives in the capabilities of AFM-based 3D structural reconstruction methodology exploiting synergies with other recent AFM technology advances are also discussed to highlight the potential of AFM as an emergent general, accessible and multimodal structural biology tool for the analysis of individual biomolecules.
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Affiliation(s)
- Claudia Chitty
- Division of Natural Sciences, School of Biosciences, University of Kent, CT2 7NJ Canterbury, U.K
| | - Kinga Kuliga
- Division of Natural Sciences, School of Biosciences, University of Kent, CT2 7NJ Canterbury, U.K
| | - Wei-Feng Xue
- Division of Natural Sciences, School of Biosciences, University of Kent, CT2 7NJ Canterbury, U.K
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5
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Li M. Harnessing atomic force microscopy-based single-cell analysis to advance physical oncology. Microsc Res Tech 2024; 87:631-659. [PMID: 38053519 DOI: 10.1002/jemt.24467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023]
Abstract
Single-cell analysis is an emerging and promising frontier in the field of life sciences, which is expected to facilitate the exploration of fundamental laws of physiological and pathological processes. Single-cell analysis allows experimental access to cell-to-cell heterogeneity to reveal the distinctive behaviors of individual cells, offering novel opportunities to dissect the complexity of severe human diseases such as cancers. Among the single-cell analysis tools, atomic force microscopy (AFM) is a powerful and versatile one which is able to nondestructively image the fine topographies and quantitatively measure multiple mechanical properties of single living cancer cells in their native states under aqueous conditions with unprecedented spatiotemporal resolution. Over the past few decades, AFM has been widely utilized to detect the structural and mechanical behaviors of individual cancer cells during the process of tumor formation, invasion, and metastasis, yielding numerous unique insights into tumor pathogenesis from the biomechanical perspective and contributing much to the field of cancer mechanobiology. Here, the achievements of AFM-based analysis of single cancer cells to advance physical oncology are comprehensively summarized, and challenges and future perspectives are also discussed. RESEARCH HIGHLIGHTS: Achievements of AFM in characterizing the structural and mechanical behaviors of single cancer cells are summarized, and future directions are discussed. AFM is not only capable of visualizing cellular fine structures, but can also measure multiple cellular mechanical properties as well as cell-generated mechanical forces. There is still plenty of room for harnessing AFM-based single-cell analysis to advance physical oncology.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
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6
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Qiu Y, Sajidah ES, Kondo S, Narimatsu S, Sandira MI, Higashiguchi Y, Nishide G, Taoka A, Hazawa M, Inaba Y, Inoue H, Matsushima A, Okada Y, Nakada M, Ando T, Lim K, Wong RW. An Efficient Method for Isolating and Purifying Nuclei from Mice Brain for Single-Molecule Imaging Using High-Speed Atomic Force Microscopy. Cells 2024; 13:279. [PMID: 38334671 PMCID: PMC10855070 DOI: 10.3390/cells13030279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
Nuclear pore complexes (NPCs) on the nuclear membrane surface have a crucial function in controlling the movement of small molecules and macromolecules between the cell nucleus and cytoplasm through their intricate core channel resembling a spiderweb with several layers. Currently, there are few methods available to accurately measure the dynamics of nuclear pores on the nuclear membranes at the nanoscale. The limitation of traditional optical imaging is due to diffraction, which prevents achieving the required resolution for observing a diverse array of organelles and proteins within cells. Super-resolution techniques have effectively addressed this constraint by enabling the observation of subcellular components on the nanoscale. Nevertheless, it is crucial to acknowledge that these methods often need the use of fixed samples. This also raises the question of how closely a static image represents the real intracellular dynamic system. High-speed atomic force microscopy (HS-AFM) is a unique technique used in the field of dynamic structural biology, enabling the study of individual molecules in motion close to their native states. Establishing a reliable and repeatable technique for imaging mammalian tissue at the nanoscale using HS-AFM remains challenging due to inadequate sample preparation. This study presents the rapid strainer microfiltration (RSM) protocol for directly preparing high-quality nuclei from the mouse brain. Subsequently, we promptly utilize HS-AFM real-time imaging and cinematography approaches to record the spatiotemporal of nuclear pore nano-dynamics from the mouse brain.
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Affiliation(s)
- Yujia Qiu
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Elma Sakinatus Sajidah
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Sota Kondo
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Shinnosuke Narimatsu
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Muhammad Isman Sandira
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Yoshiki Higashiguchi
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Goro Nishide
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
| | - Azuma Taoka
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Masaharu Hazawa
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
| | - Yuka Inaba
- Metabolism and Nutrition Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-8641, Japan
| | - Hiroshi Inoue
- Metabolism and Nutrition Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-8641, Japan
| | - Ayami Matsushima
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Mitsutoshi Nakada
- Department of Neurosurgery, Graduate School of Medical Science, Kanazawa University, Kanazawa 920-8641, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Keesiang Lim
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
| | - Richard W. Wong
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan; (Y.Q.); (M.I.S.)
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan (M.H.); (T.A.)
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa 920-1192, Japan
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7
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Gisbert VG, Espinosa FM, Sanchez JG, Serrano MC, Garcia R. Nanorheology and Nanoindentation Revealed a Softening and an Increased Viscous Fluidity of Adherent Mammalian Cells upon Increasing the Frequency. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304884. [PMID: 37775942 DOI: 10.1002/smll.202304884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/01/2023] [Indexed: 10/01/2023]
Abstract
The nanomechanical response of a cell depends on the frequency at which the cell is probed. The components of the cell that contribute to this property and their interplay are not well understood. Here, two force microscopy methods are integrated to characterize the frequency and/or the velocity-dependent properties of living cells. It is shown on HeLa and fibroblasts, that cells soften and fluidize upon increasing the frequency or the velocity of the deformation. This property was independent of the type and values (25 or 1000 nm) of the deformation. At low frequencies (2-10 Hz) or velocities (1-10 µm s-1 ), the response is dominated by the mechanical properties of the cell surface. At higher frequencies (>10 Hz) or velocities (>10 µm s-1 ), the response is dominated by the hydrodynamic drag of the cytosol. Softening and fluidization does not seem to involve any structural remodeling. It reflects a redistribution of the applied stress between the solid and liquid-like elements of the cell as the frequency or the velocity is changed. The data indicates that the quasistatic mechanical properties of a cell featuring a cytoskeleton pathology might be mimicked by the response of a non-pathological cell which is probed at a high frequency.
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Affiliation(s)
- Victor G Gisbert
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, Madrid, 28049, Spain
| | - Francsico M Espinosa
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, Madrid, 28049, Spain
| | - Juan G Sanchez
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, Madrid, 28049, Spain
| | - Maria Concepcion Serrano
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, Madrid, 28049, Spain
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/ Sor Juana Inés de la Cruz 3, Madrid, 28049, Spain
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8
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Feng Y, Roos WH. Atomic Force Microscopy: An Introduction. Methods Mol Biol 2024; 2694:295-316. [PMID: 37824010 DOI: 10.1007/978-1-0716-3377-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields, for instance, in biological sciences, where it is paramount to investigate structures at the single particle level. Often, two-dimensional images are not sufficient, and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. New developments in AFM are discussed, and by including approaches such as bimodal AFM and high-speed AFM (HS-AFM), we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
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Affiliation(s)
- Yuzhen Feng
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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9
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Sumikama T. Computation of topographic and three-dimensional atomic force microscopy images of biopolymers by calculating forces. Biophys Rev 2023; 15:2059-2064. [PMID: 38192341 PMCID: PMC10771545 DOI: 10.1007/s12551-023-01167-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024] Open
Abstract
Atomic force microscopy (AFM) is widely utilized to visualize the molecular motions of biomolecules. Comparison of experimentally measured AFM images with simulated AFM images based on known structures of biomolecules is often necessary to elucidate what is actually resolved in the images. Experimental AFM images are generated by force measurements; however, conventional AFM simulation has been based on geometrical considerations rather than calculating forces using molecular dynamics simulations due to limited computation time. This letter summarizes recently developed methods to simulate topographic and three-dimensional AFM (3D-AFM) images of biopolymers such as chromosomes and cytoskeleton fibers. Scanning such biomolecules in AFM measurements usually results in nonequilibrium-type work being performed. As such, the Jarzynski equality was employed to relate the nonequilibrium work to the free energy profiles, and the forces were calculated by differentiating the free energy profiles. The biomolecules and probes were approximated using a supra-coarse-grained model, allowing the simulation of force-distance curves in feasible time. It was found that there is an optimum scanning velocity and that some of polymer structures are resolved in the simulated 3D-AFM images. The theoretical background adopted to rationalize the use of small probe radius in the conventional AFM simulation of biomolecules is clarified.
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Affiliation(s)
- Takashi Sumikama
- PRESTO, JST, Kawaguchi, Saitama 332-0012 Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, 920-1192 Japan
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10
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Wang X, Xu W, Li J, Shi C, Guo Y, Shan J, Qi R. Nano-omics: Frontier fields of fusion of nanotechnology. SMART MEDICINE 2023; 2:e20230039. [PMID: 39188303 PMCID: PMC11236068 DOI: 10.1002/smmd.20230039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/15/2023] [Indexed: 08/28/2024]
Abstract
Nanotechnology, an emerging force, has infiltrated diverse domains like biomedical, materials, and environmental sciences. Nano-omics, an emerging fusion, combines nanotechnology with omics, boasting amplified sensitivity and resolution. This review introduces nanotechnology basics, surveys its recent strides in nano-omics, deliberates present challenges, and envisions future growth.
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Affiliation(s)
- Xuan Wang
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjingChina
- Jiangsu Key Laboratory of Pediatric Respiratory DiseaseInstitute of PediatricsNanjing University of Chinese MedicineNanjingChina
- Medical Metabolomics CenterNanjing University of Chinese MedicineNanjingChina
| | - Weichen Xu
- Jiangsu Key Laboratory of Pediatric Respiratory DiseaseInstitute of PediatricsNanjing University of Chinese MedicineNanjingChina
- Medical Metabolomics CenterNanjing University of Chinese MedicineNanjingChina
| | - Jun Li
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjingChina
| | - Chen Shi
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjingChina
- Jiangsu Key Laboratory of Pediatric Respiratory DiseaseInstitute of PediatricsNanjing University of Chinese MedicineNanjingChina
- Medical Metabolomics CenterNanjing University of Chinese MedicineNanjingChina
| | - Yuanyuan Guo
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjingChina
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory DiseaseInstitute of PediatricsNanjing University of Chinese MedicineNanjingChina
- Medical Metabolomics CenterNanjing University of Chinese MedicineNanjingChina
| | - Ruogu Qi
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicineNanjingChina
- Department of NanomedicineHouston Methodist Research InstituteHoustonTexasUS
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11
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Ichikawa T, Alam MS, Penedo M, Matsumoto K, Fujita S, Miyazawa K, Furusho H, Miyata K, Nakamura C, Fukuma T. Protocol for live imaging of intracellular nanoscale structures using atomic force microscopy with nanoneedle probes. STAR Protoc 2023; 4:102468. [PMID: 37481726 PMCID: PMC10374873 DOI: 10.1016/j.xpro.2023.102468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/18/2023] [Accepted: 06/28/2023] [Indexed: 07/25/2023] Open
Abstract
Atomic force microscopy (AFM) is capable of nanoscale imaging but has so far only been used on cell surfaces when applied to a living cell. Here, we describe a step-by-step protocol for nanoendoscopy-AFM, which enables the imaging of nanoscale structures inside living cells. The protocol consists of cell staining, fabrication of the nanoneedle probes, observation inside living cells using 2D and 3D nanoendoscopy-AFM, and visualization of the 3D data. For complete details on the use and execution of this protocol, please refer to Penedo et al. (2021)1 and Penedo et al. (2021).2.
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Affiliation(s)
- Takehiko Ichikawa
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Mohammad Shahidul Alam
- Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Marcos Penedo
- École Polytechnique Fédérale de Lausanne, Institute for Bioengineering, Laboratory for Bio and Nanoinstrumentation, Lausanne, CH 1015, Switzerland
| | - Kyosuke Matsumoto
- Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Sou Fujita
- Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Keisuke Miyazawa
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Hirotoshi Furusho
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kazuki Miyata
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Chikashi Nakamura
- AIST-INDIA Diverse Assets and Applications International Laboratory (DAILAB), Cellular and Molecular Biotechnology Research Institute (CMB), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Takeshi Fukuma
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; Division of Nano Life Science, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; Faculty of Frontier Engineering, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
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12
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Irvin EM, Wang H. Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures. DNA Repair (Amst) 2023; 128:103528. [PMID: 37392578 PMCID: PMC10989508 DOI: 10.1016/j.dnarep.2023.103528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
DNA repair pathways are tightly regulated processes that recognize specific hallmarks of DNA damage and coordinate lesion repair through discrete mechanisms, all within the context of a three-dimensional chromatin landscape. Dysregulation or malfunction of any one of the protein constituents in these pathways can contribute to aging and a variety of diseases. While the collective action of these many proteins is what drives DNA repair on the organismal scale, it is the interactions between individual proteins and DNA that facilitate each step of these pathways. In much the same way that ensemble biochemical techniques have characterized the various steps of DNA repair pathways, single-molecule imaging (SMI) approaches zoom in further, characterizing the individual protein-DNA interactions that compose each pathway step. SMI techniques offer the high resolving power needed to characterize the molecular structure and functional dynamics of individual biological interactions on the nanoscale. In this review, we highlight how our lab has used SMI techniques - traditional atomic force microscopy (AFM) imaging in air, high-speed AFM (HS-AFM) in liquids, and the DNA tightrope assay - over the past decade to study protein-nucleic acid interactions involved in DNA repair, mitochondrial DNA replication, and telomere maintenance. We discuss how DNA substrates containing specific DNA sequences or structures that emulate DNA repair intermediates or telomeres were generated and validated. For each highlighted project, we discuss novel findings made possible by the spatial and temporal resolution offered by these SMI techniques and unique DNA substrates.
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Affiliation(s)
| | - Hong Wang
- Toxicology Program, North Carolina State University, Raleigh, NC, USA; Physics Department, North Carolina State University, Raleigh, NC, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
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13
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Miyazawa K, Penedo M, Furusho H, Ichikawa T, Alam MS, Miyata K, Nakamura C, Fukuma T. Nanoendoscopy-AFM for Visualizing Intracellular Nanostructures of Living Cells. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:782. [PMID: 37613502 DOI: 10.1093/micmic/ozad067.387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
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14
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Farokh Payam A, Passian A. Imaging beyond the surface region: Probing hidden materials via atomic force microscopy. SCIENCE ADVANCES 2023; 9:eadg8292. [PMID: 37379392 DOI: 10.1126/sciadv.adg8292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023]
Abstract
Probing material properties at surfaces down to the single-particle scale of atoms and molecules has been achieved, but high-resolution subsurface imaging remains a nanometrology challenge due to electromagnetic and acoustic dispersion and diffraction. The atomically sharp probe used in scanning probe microscopy (SPM) has broken these limits at surfaces. Subsurface imaging is possible under certain physical, chemical, electrical, and thermal gradients present in the material. Of all the SPM techniques, atomic force microscopy has entertained unique opportunities for nondestructive and label-free measurements. Here, we explore the physics of the subsurface imaging problem and the emerging solutions that offer exceptional potential for visualization. We discuss materials science, electronics, biology, polymer and composite sciences, and emerging quantum sensing and quantum bio-imaging applications. The perspectives and prospects of subsurface techniques are presented to stimulate further work toward enabling noninvasive high spatial and spectral resolution investigation of materials including meta- and quantum materials.
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Affiliation(s)
- Amir Farokh Payam
- Nanotechnology and Integrated Bioengineering Centre, School of Engineering, Ulster University, Belfast, UK
| | - Ali Passian
- Quantum Computing and Sensing, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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15
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Liu G, Li J, Wu C. Reciprocal regulation of actin filaments and cellular metabolism. Eur J Cell Biol 2022; 101:151281. [PMID: 36343493 DOI: 10.1016/j.ejcb.2022.151281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/23/2022] [Accepted: 10/25/2022] [Indexed: 12/14/2022] Open
Abstract
For cells to adhere, migrate and proliferate, remodeling of the actin cytoskeleton is required. This process consumes a large amount of ATP while having an intimate connection with cellular metabolism. Signaling pathways that regulate energy homeostasis can also affect actin dynamics, whereas a variety of actin binding proteins directly or indirectly interact with the anabolic and catabolic regulators in cells. Here, we discuss the inter-regulation between actin filaments and cellular metabolism, reviewing recent discoveries on key metabolic enzymes that respond to actin remodeling as well as historical findings on metabolic stress-induced cytoskeletal reorganization. We also address emerging techniques that would benefit the study of cytoskeletal dynamics and cellular metabolism in high spatial-temporal resolution.
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Affiliation(s)
- Geyao Liu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jiayi Li
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Congying Wu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; International Cancer Institute, Peking University, Beijing 100191, China.
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16
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Evolutionary timeline of a modeled cell. J Theor Biol 2022; 551-552:111233. [DOI: 10.1016/j.jtbi.2022.111233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/23/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
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17
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Nanometer-Resolution Imaging of Living Cells Using Soft X-ray Contact Microscopy. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12147030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Soft X-ray microscopy is a powerful technique for imaging cells with nanometer resolution in their native state without chemical fixation, staining, or sectioning. The studies performed in several laboratories have demonstrated the potential of applying this technique for imaging the internal structures of intact cells. However, it is currently used mainly on synchrotrons with restricted access. Moreover, the operation of these instruments and the associated sample-preparation protocols require interdisciplinary and highly specialized personnel, limiting their wide application in practice. This is why soft X-ray microscopy is not commonly used in biological laboratories as an imaging tool. Thus, a laboratory-based and user-friendly soft X-ray contact microscope would facilitate the work of biologists. A compact, desk-top laboratory setup for soft X-ray contact microscopy (SXCM) based on a laser-plasma soft X-ray source, which can be used in any biological laboratory, together with several applications for biological imaging, are described. Moreover, the perspectives of the correlation of SXCM with other super-resolution imaging techniques based on the current literature are discussed.
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18
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Sumikama T, Federici Canova F, Gao DZ, Penedo M, Miyazawa K, Foster AS, Fukuma T. Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality. J Phys Chem Lett 2022; 13:5365-5371. [PMID: 35678499 PMCID: PMC9208010 DOI: 10.1021/acs.jpclett.2c01093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid-liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe.
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Affiliation(s)
- Takashi Sumikama
- PRESTO,
JST, Kawaguchi, Saitama 332-0012, Japan
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
| | - Filippo Federici Canova
- Nanolayers
Research Computing Ltd., 1 Granville Court, Granville Road, London N12 0HL, United Kingdom
- Department
of Applied Physics, Aalto University, Aalto 00076, Finland
| | - David Z. Gao
- Nanolayers
Research Computing Ltd., 1 Granville Court, Granville Road, London N12 0HL, United Kingdom
- Department
of Physics, Norwegian University of Science
and Technology (NTNU), 7491 Trondheim, Norway
| | - Marcos Penedo
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
- Laboratory
for Bio and Nanoinstrumentation, Institute for Bioengineering, École Polytechnique Fédérale
de Lausanne, Lausanne CH-1015, Switzerland
| | - Keisuke Miyazawa
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
- Division
of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
- Faculty of
Frontier Engineering, Kanazawa University, Kanazawa 920-1192, Japan
| | - Adam S. Foster
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
- Department
of Applied Physics, Aalto University, Aalto 00076, Finland
| | - Takeshi Fukuma
- Nano
Life Science Institute (WPI-NanoLSI), Kanazawa
University, Kanazawa 920-1192, Japan
- Division
of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
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