1
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Denisov N, Jannis D, Orekhov A, Müller-Caspary K, Verbeeck J. Characterization of a Timepix detector for use in SEM acceleration voltage range. Ultramicroscopy 2023; 253:113777. [PMID: 37336162 DOI: 10.1016/j.ultramic.2023.113777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Hybrid pixel direct electron detectors are gaining popularity in electron microscopy due to their excellent properties. Some commercial cameras based on this technology are relatively affordable which makes them attractive tools for experimentation especially in combination with an SEM setup. To support this, a detector characterization (Modulation Transfer Function, Detective Quantum Efficiency) of an Advacam Minipix and Advacam Advapix detector in the 15-30 keV range was made. In the current work we present images of Point Spread Function, plots of MTF/DQE curves and values of DQE(0) for these detectors. At low beam currents, the silicon detector layer behaviour should be dominant, which could make these findings transferable to any other available detector based on either Medipix2, Timepix or Timepix3 provided the same detector layer is used.
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Affiliation(s)
- Nikita Denisov
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
| | - Daen Jannis
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium
| | - Andrey Orekhov
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium
| | - Knut Müller-Caspary
- Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Munich, 81377, Germany
| | - Johan Verbeeck
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
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2
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Xue H, Zhang M, Liu J, Wang J, Ren G. Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination. Front Chem 2022; 10:889203. [PMID: 36110139 PMCID: PMC9468540 DOI: 10.3389/fchem.2022.889203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022] Open
Abstract
To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.
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Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianjun Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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3
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An overview of the recent advances in cryo-electron microscopy for life sciences. Emerg Top Life Sci 2021; 5:151-168. [PMID: 33760078 DOI: 10.1042/etls20200295] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Cryo-electron microscopy (CryoEM) has superseded X-ray crystallography and NMR to emerge as a popular and effective tool for structure determination in recent times. It has become indispensable for the characterization of large macromolecular assemblies, membrane proteins, or samples that are limited, conformationally heterogeneous, and recalcitrant to crystallization. Besides, it is the only tool capable of elucidating high-resolution structures of macromolecules and biological assemblies in situ. A state-of-the-art electron microscope operable at cryo-temperature helps preserve high-resolution details of the biological sample. The structures can be determined, either in isolation via single-particle analysis (SPA) or helical reconstruction, electron diffraction (ED) or within the cellular environment via cryo-electron tomography (cryoET). All the three streams of SPA, ED, and cryoET (along with subtomogram averaging) have undergone significant advancements in recent times. This has resulted in breaking the boundaries with respect to both the size of the macromolecules/assemblies whose structures could be determined along with the visualization of atomic details at resolutions unprecedented for cryoEM. In addition, the collection of larger datasets combined with the ability to sort and process multiple conformational states from the same sample are providing the much-needed link between the protein structures and their functions. In overview, these developments are helping scientists decipher the molecular mechanism of critical cellular processes, solve structures of macromolecules that were challenging targets for structure determination until now, propelling forward the fields of biology and biomedicine. Here, we summarize recent advances and key contributions of the three cryo-electron microscopy streams of SPA, ED, and cryoET.
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4
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Ramachandra R, Mackey MR, Hu J, Peltier ST, Xuong NH, Ellisman MH, Adams SR. Elemental mapping of labelled biological specimens at intermediate energy loss in an energy-filtered TEM acquired using a direct detection device. J Microsc 2021; 283:127-144. [PMID: 33844293 PMCID: PMC8316382 DOI: 10.1111/jmi.13014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/11/2021] [Accepted: 04/04/2021] [Indexed: 12/30/2022]
Abstract
The technique of colour EM that was recently developed enabled localisation of specific macromolecules/proteins of interest by the targeted deposition of diaminobenzidine (DAB) conjugated to lanthanide chelates. By acquiring lanthanide elemental maps by energy‐filtered transmission electron microscopy (EFTEM) and overlaying them in pseudo‐colour over the conventional greyscale TEM image, a colour EM image is generated. This provides a powerful tool for visualising subcellular component/s, by the ability to clearly distinguish them from the general staining of the endogenous cellular material. Previously, the lanthanide elemental maps were acquired at the high‐loss M4,5 edge (excitation of 3d electrons), where the characteristic signal is extremely low and required considerably long exposures. In this paper, we explore the possibility of acquiring the elemental maps of lanthanides at their N4,5 edge (excitation of 4d electrons), which occurring at a much lower energy‐loss regime, thereby contains significantly greater total characteristic signal owing to the higher inelastic scattering cross‐sections at the N4,5 edge. Acquiring EFTEM lanthanide elemental maps at the N4,5 edge instead of the M4,5 edge, provides ∼4× increase in signal‐to‐noise and ∼2× increase in resolution. However, the interpretation of the lanthanide maps acquired at the N4,5 edge by the traditional 3‐window method, is complicated due to the broad shape of the edge profile and the lower signal‐above‐background ratio. Most of these problems can be circumvented by the acquisition of elemental maps with the more sophisticated technique of EFTEM Spectrum Imaging (EFTEM SI). Here, we also report the chemical synthesis of novel second‐generation DAB lanthanide metal chelate conjugates that contain 2 lanthanide ions per DAB molecule in comparison with 0.5 lanthanide ion per DAB in the first generation. Thereby, fourfold more Ln3+ per oxidised DAB would be deposited providing significant amplification of signal. This paper applies the colour EM technique at the intermediate‐loss energy‐loss regime to three different cellular targets, namely using mitochondrial matrix‐directed APEX2, histone H2B‐Nucleosome and EdU‐DNA. All the examples shown in the paper are single colour EM images only.
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Affiliation(s)
- Ranjan Ramachandra
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Mason R Mackey
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Junru Hu
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Steven T Peltier
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Nguyen-Huu Xuong
- Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Center for Research in Biological Systems, National Center for Microscopy and, Imaging Research, University of California, San Diego, La Jolla, California, USA
| | - Stephen R Adams
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
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5
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Castano I, Evans AM, Dos Reis R, Dravid VP, Gianneschi NC, Dichtel WR. Mapping Grains, Boundaries, and Defects in 2D Covalent Organic Framework Thin Films. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2021; 33:1341-1352. [PMID: 35296112 PMCID: PMC8922717 DOI: 10.1021/acs.chemmater.0c04382] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
To improve their synthesis and ultimately realize the technical promise of two-dimensional covalent organic frameworks (2D COFs), it is imperative that a robust understanding of their structure be developed. However, high-resolution transmission electron microscopy (HR-TEM) imaging of such beam-sensitive materials is an outstanding characterization challenge. Here, we overcome this challenge by leveraging low electron flux imaging conditions and high-speed direct electron counting detectors to acquire high-resolution images of 2D COF films. We developed a Fourier mapping technique to rapidly extract nanoscale structural information from these TEM images. This postprocessing script analyzes the evolution of 2D Fourier transforms across a TEM image, which yields information about polycrystalline domain orientations and enables quantification of average domain sizes. Moreover, this approach provides information about several types of defects present in a film, such as overlapping grains and various types of grain boundaries. We also find that the pre-eminent origin of defects in COF-5 films, a prototypical boronate ester-linked COF, arises as a consequence of broken B-O bonds formed during polymerization. These results suggest that the nanoscale features observed are a direct consequence of chemical phenomena. Taken together, this mapping approach provides information about the fundamental microstructure and crystallographic underpinnings of 2D COF films, which will guide the development of future 2D polymerization strategies and help realize the goal of using 2D COFs in a host of thin-film device architectures.
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Affiliation(s)
- Ioannina Castano
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Austin M Evans
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Roberto Dos Reis
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University Atomic and Nanoscale Characterization Center, and International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Nathan C Gianneschi
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States; Department of Materials Science and Engineering, International Institute for Nanotechnology, Department of Biomedical Engineering, Department of Pharmacology, Simpson Querrey Institute, and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - William R Dichtel
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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6
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Gong X, Gnanasekaran K, Chen Z, Robison L, Wasson MC, Bentz KC, Cohen SM, Farha OK, Gianneschi NC. Insights into the Structure and Dynamics of Metal–Organic Frameworks via Transmission Electron Microscopy. J Am Chem Soc 2020; 142:17224-17235. [DOI: 10.1021/jacs.0c08773] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xinyi Gong
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Karthikeyan Gnanasekaran
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Zhijie Chen
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lee Robison
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Megan C. Wasson
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Kyle C. Bentz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Omar K. Farha
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Nathan C. Gianneschi
- Department of Chemistry and International Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
- Department of Biomedical Engineering, Materials Science & Engineering, Pharmacology, Simpson-Querrey Institute, Chemistry of Life Processes Institute, Lurie Cancer Center, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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7
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Bulk and local structures of metal-organic frameworks unravelled by high-resolution electron microscopy. Commun Chem 2020; 3:99. [PMID: 36703329 PMCID: PMC9814830 DOI: 10.1038/s42004-020-00361-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/21/2020] [Indexed: 01/29/2023] Open
Abstract
The periodic bulk structures of metal-organic frameworks (MOFs) can be solved by diffraction-based techniques; however, their non-periodic local structures-such as crystal surfaces, grain boundaries, defects, and guest molecules-have long been elusive due to a lack of suitable characterization tools. Recent advances in (scanning) transmission electron microscopy ((S)TEM) has made it possible to probe the local structures of MOFs at atomic resolution. In this article, we discuss why high-resolution (S)TEM of MOFs is challenging and how the new low-dose techniques overcome this challenge, and we review various MOF structural features observed by (S)TEM and important insights gained from these observations. Our discussions focus on real-space imaging, excluding other TEM-related characterization techniques (e.g. electron diffraction and spectroscopy).
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8
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Liu W, Cui Y, Wang C, Li Z, Gong D, Dai X, Bi GQ, Sun R, Zhou ZH. Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus. Nat Microbiol 2020; 5:1285-1298. [PMID: 32719506 DOI: 10.1038/s41564-020-0758-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022]
Abstract
As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies.
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Affiliation(s)
- Wei Liu
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.,Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Caiyan Wang
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.,International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zihang Li
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Therapeutics Discovery, Amgen Research, Amgen Inc., Thousand Oaks, CA, USA
| | - Xinghong Dai
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Guo-Qiang Bi
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ren Sun
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Microbiology Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
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9
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Lau JW, Schliep KB, Katz MB, Gokhale VJ, Gorman JJ, Jing C, Liu A, Zhao Y, Montgomery E, Choe H, Rush W, Kanareykin A, Fu X, Zhu Y. Laser-free GHz stroboscopic transmission electron microscope: Components, system integration, and practical considerations for pump-probe measurements. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:021301. [PMID: 32113442 PMCID: PMC11210549 DOI: 10.1063/1.5131758] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
A 300 keV transmission electron microscope was modified to produce broadband pulsed beams that can be, in principle, between 40 MHz and 12 GHz, corresponding to temporal resolution in the nanosecond to picosecond range without an excitation laser. The key enabling technology is a pair of phase-matched modulating and de-modulating traveling wave metallic comb striplines (pulsers). An initial temporal resolution of 30 ps was achieved with a strobe frequency of 6.0 GHz. The placement of the pulsers, mounted immediately below the gun, allows for preservation of all optical configurations, otherwise available to the unmodified instrument, and therefore makes such a post-modified instrument for dual-use, i.e., both pulsed-beam mode (i.e., stroboscopic time-resolved) and conventional continuous waveform mode. In this article, we describe the elements inserted into the beam path, challenges encountered during integration with an in-service microscope, and early results from an electric-field-driven pump-probe experiment. We conclude with ideas for making this class of instruments broadly applicable for examining cyclical and repeatable phenomena.
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Affiliation(s)
- June W. Lau
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Karl B. Schliep
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Michael B. Katz
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Vikrant J. Gokhale
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Jason J. Gorman
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Chunguang Jing
- Euclid Techlabs, LLC, 365 Remington Blvd., Bolingbrook, Illinois 60440, USA
| | - Ao Liu
- Euclid Techlabs, LLC, 365 Remington Blvd., Bolingbrook, Illinois 60440, USA
| | - Yubin Zhao
- Euclid Techlabs, LLC, 365 Remington Blvd., Bolingbrook, Illinois 60440, USA
| | - Eric Montgomery
- Euclid Techlabs, LLC, 365 Remington Blvd., Bolingbrook, Illinois 60440, USA
| | - Hyeokmin Choe
- Euclid Techlabs, LLC, 365 Remington Blvd., Bolingbrook, Illinois 60440, USA
| | - Wade Rush
- Euclid Techlabs, LLC, 365 Remington Blvd., Bolingbrook, Illinois 60440, USA
| | - Alexei Kanareykin
- Euclid Techlabs, LLC, 365 Remington Blvd., Bolingbrook, Illinois 60440, USA
| | - Xuewen Fu
- Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Yimei Zhu
- Department of Condensed Matter Physics and Materials Science, Brookhaven National Laboratory, Upton, New York 11973, USA
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10
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Abstract
Cryo electron microscopy (cryo-EM) is a powerful technique that can be used to elucidate the structural architecture of a protein molecule in a physiologically relevant environment. In this method, purified protein is frozen in its aqueous buffer in a thin layer of vitreous ice in which the biological macromolecules are embedded in various orientations. Images of this frozen sample are collected with an electron microscope, and the data is processed using different software algorithms resulting in high-resolution structures of the protein. Proteins in the presence of various ligands or other macromolecular complexes can also be studied by this method. Here, we present a protocol for the purification and vitrification of TRP channels for single particle cryo-EM.
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Affiliation(s)
- Amrita Samanta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Taylor E T Hughes
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Zhang C, Feng J, DaCosta LR, Voyles PM. Atomic resolution convergent beam electron diffraction analysis using convolutional neural networks. Ultramicroscopy 2019; 210:112921. [PMID: 31978635 DOI: 10.1016/j.ultramic.2019.112921] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/09/2019] [Accepted: 12/22/2019] [Indexed: 11/17/2022]
Abstract
Two types of convolutional neural network (CNN) models, a discrete classification network and a continuous regression network, were trained to determine local sample thickness from convergent beam diffraction (CBED) patterns of SrTiO3 collected in a scanning transmission electron microscope (STEM) at atomic column resolution. Acquisition of atomic resolution CBED patterns for this purpose requires careful balancing of CBED feature size in pixels, acquisition speed, and detector dynamic range. The training datasets were derived from multislice simulations, which must be convolved with incoherent source broadening. Sample thicknesses were also determined using quantitative high-angle annular dark-field (HAADF) STEM images acquired simultaneously. The regression CNN performed well on sample thinner than 35 nm, with 70% of the CNN results within 1 nm of HAADF thickness, and 1.0 nm overall root mean square error between the two measurements. The classification CNN was trained for a thicknesses up to 100 nm and yielded 66% of CNN results within one classification increment of 2 nm of HAADF thickness. Our approach depends on methods from computer vision including transfer learning and image augmentation.
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Affiliation(s)
- Chenyu Zhang
- Department of Materials Science and Engineering, University of Wisconsin-Madison, United States
| | - Jie Feng
- Department of Materials Science and Engineering, University of Wisconsin-Madison, United States
| | - Luis Rangel DaCosta
- Department of Materials Science and Engineering, University of Wisconsin-Madison, United States
| | - Paul M Voyles
- Department of Materials Science and Engineering, University of Wisconsin-Madison, United States.
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12
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Zhang Y, Liu W, Li Z, Kumar V, Alvarez-Cabrera AL, Leibovitch EC, Cui Y, Mei Y, Bi GQ, Jacobson S, Zhou ZH. Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes. Nat Commun 2019; 10:5346. [PMID: 31767868 PMCID: PMC6877594 DOI: 10.1038/s41467-019-13064-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/09/2019] [Indexed: 12/12/2022] Open
Abstract
Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B capsid and capsid-associated tegument complex (CATC) obtained by cryoEM and sub-particle reconstruction. Compared to other β-herpesviruses, HHV-6B exhibits high similarity in capsid structure but organizational differences in its CATC (pU11 tetramer). 180 "VΛ"-shaped CATCs are observed in HHV-6B, distinguishing from the 255 "Λ"-shaped dimeric CATCs observed in murine cytomegalovirus and the 310 "Δ"-shaped CATCs in human cytomegalovirus. This trend in CATC quantity correlates with the increasing genomes sizes of these β-herpesviruses. Incompatible distances revealed by the atomic structures rationalize the lack of CATC's binding to triplexes Ta, Tc, and Tf in HHV-6B. Our results offer insights into HHV-6B capsid assembly and the roles of its tegument proteins, including not only the β-herpesvirus-specific pU11 and pU14, but also those conserved across all subfamilies of Herpesviridae.
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Affiliation(s)
- Yibo Zhang
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui, 230026, China.,California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095-7151, USA
| | - Wei Liu
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui, 230026, China.,California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095-7151, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095-7364, USA.,State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University (ECNU), Shanghai, 200062, China
| | - Zihang Li
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095-7151, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095-7364, USA
| | - Vinay Kumar
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095-7151, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095-7364, USA
| | - Ana L Alvarez-Cabrera
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095-7151, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095-7364, USA
| | - Emily C Leibovitch
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095-7151, USA
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University (ECNU), Shanghai, 200062, China
| | - Guo-Qiang Bi
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China (USTC), Hefei, Anhui, 230026, China
| | - Steve Jacobson
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, 90095-7151, USA. .,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, 90095-7364, USA.
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13
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Lü Y, Zeng X, Zhao X, Li S, Li H, Gao X, Xu M. Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization. BMC Bioinformatics 2019; 20:443. [PMID: 31455212 PMCID: PMC6712796 DOI: 10.1186/s12859-019-3003-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 07/19/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryo-electron tomography (Cryo-ET) is an imaging technique used to generate three-dimensional structures of cellular macromolecule complexes in their native environment. Due to developing cryo-electron microscopy technology, the image quality of three-dimensional reconstruction of cryo-electron tomography has greatly improved. However, cryo-ET images are characterized by low resolution, partial data loss and low signal-to-noise ratio (SNR). In order to tackle these challenges and improve resolution, a large number of subtomograms containing the same structure needs to be aligned and averaged. Existing methods for refining and aligning subtomograms are still highly time-consuming, requiring many computationally intensive processing steps (i.e. the rotations and translations of subtomograms in three-dimensional space). RESULTS In this article, we propose a Stochastic Average Gradient (SAG) fine-grained alignment method for optimizing the sum of dissimilarity measure in real space. We introduce a Message Passing Interface (MPI) parallel programming model in order to explore further speedup. CONCLUSIONS We compare our stochastic average gradient fine-grained alignment algorithm with two baseline methods, high-precision alignment and fast alignment. Our SAG fine-grained alignment algorithm is much faster than the two baseline methods. Results on simulated data of GroEL from the Protein Data Bank (PDB ID:1KP8) showed that our parallel SAG-based fine-grained alignment method could achieve close-to-optimal rigid transformations with higher precision than both high-precision alignment and fast alignment at a low SNR (SNR=0.003) with tilt angle range ±60∘ or ±40∘. For the experimental subtomograms data structures of GroEL and GroEL/GroES complexes, our parallel SAG-based fine-grained alignment can achieve higher precision and fewer iterations to converge than the two baseline methods.
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Affiliation(s)
- Yongchun Lü
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent Information Processing, CAS, Beijing, China
| | - Xiangrui Zeng
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| | - Xiaofang Zhao
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
| | - Shirui Li
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent Information Processing, CAS, Beijing, China
| | - Hua Li
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent Information Processing, CAS, Beijing, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
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14
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Kabiri Y, Angelin A, Ahmed I, Mutlu H, Bauer J, Niemeyer CM, Zandbergen H, Dekker C. Intercalating Electron Dyes for TEM Visualization of DNA at the Single-Molecule Level. Chembiochem 2019; 20:822-830. [PMID: 30501011 PMCID: PMC6470888 DOI: 10.1002/cbic.201800638] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Indexed: 11/24/2022]
Abstract
Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis-acridine uranyl (BAU). NMR spectroscopy and MS confirmed the validity of the synthetic strategy and gel electrophoresis verified the binding of BAU to DNA. For TEM imaging of DNA, two-dimensional DNA origami nanostructures were used as a robust microscopy test object. By using scanning transmission electron microscopy (STEM) imaging, which is favored over conventional wide-field TEM for improved contrast, and therefore, quantitative image analysis, it is found that the synthesized BAU intercalator can render DNA visible, even at the single-molecule scale. For comparison, other staining compounds with a purported affinity towards DNA, such as dichloroplatinum, cisplatin, osmium tetroxide, and uranyl acetate, have been evaluated. The STEM contrast is discussed in terms of the DNA-dye association constants, number of dye molecules bound per base pair, and the electron-scattering capacity of the metal-containing ligands. These findings pave the way for the future development of electron dyes with specific DNA-binding motifs for high-resolution TEM imaging.
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Affiliation(s)
- Yoones Kabiri
- Kavli Institute of Nanoscience DelftDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
| | - Alessandro Angelin
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG-1)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
| | - Ishtiaq Ahmed
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG-1)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
| | - Hatice Mutlu
- Karlsruhe Institute of Technology (KIT)Soft Matter Synthesis LaboratoryInstitute for Biological Interfaces (IBG-3)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
- Karlsruhe Institute of Technology (KIT)Macromolecular ArchitecturesInstitut für Technische Chemie und PolymerchemieEngesserstrasse 1876128KarlsruheGermany
| | - Jens Bauer
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG-1)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
| | - Christof M. Niemeyer
- Karlsruhe Institute of Technology (KIT)Institute for Biological Interfaces (IBG-1)Hermann-von-Helmholtz-Platz76344Eggenstein-LeopoldshafenGermany
| | - Henny Zandbergen
- Kavli Institute of Nanoscience DelftDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience DelftDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
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15
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Skowron ST, Roberts SL, Khlobystov AN, Besley E. The effects of encapsulation on damage to molecules by electron radiation. Micron 2019; 120:96-103. [PMID: 30818248 DOI: 10.1016/j.micron.2019.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/16/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
Encapsulation of materials imaged by high resolution transmission electron microscopy presents a promising route to the reduction of sample degradation, both independently and in combination with other traditional solutions to controlling radiation damage. In bulk crystals, the main effect of encapsulation (or coating) is the elimination of diffusion routes of beam-induced radical species, enhancing recombination rates and acting to limit overall damage. Moving from bulk to low dimensional materials has significant effects on the nature of damage under the electron beam. We consider the major changes in mechanisms of damage of low dimensional materials by separating the effects of dimensional reduction from the effects of encapsulation. An effect of confinement is discussed using a model example of coronene molecules encapsulated inside single walled carbon nanotubes as determined from molecular dynamics simulations calculating the threshold energy required for hydrogen atom dissociation. The same model system is used to estimate the rate at which the nanotube can dissipate excess thermal energy above room temperature by acting as a thermal sink.
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Affiliation(s)
- Stephen T Skowron
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Sarah L Roberts
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Andrei N Khlobystov
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Elena Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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16
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Xu M, Singla J, Tocheva EI, Chang YW, Stevens RC, Jensen GJ, Alber F. De Novo Structural Pattern Mining in Cellular Electron Cryotomograms. Structure 2019; 27:679-691.e14. [PMID: 30744995 DOI: 10.1016/j.str.2019.01.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/16/2022]
Abstract
Electron cryotomography enables 3D visualization of cells in a near-native state at molecular resolution. The produced cellular tomograms contain detailed information about a plethora of macromolecular complexes, their structures, abundances, and specific spatial locations in the cell. However, extracting this information in a systematic way is very challenging, and current methods usually rely on individual templates of known structures. Here, we propose a framework called "Multi-Pattern Pursuit" for de novo discovery of different complexes from highly heterogeneous sets of particles extracted from entire cellular tomograms without using information of known structures. These initially detected structures can then serve as input for more targeted refinement efforts. Our tests on simulated and experimental tomograms show that our automated method is a promising tool for supporting large-scale template-free visual proteomics analysis.
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Affiliation(s)
- Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Jitin Singla
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymond C Stevens
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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17
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Xu M, Chai X, Muthakana H, Liang X, Yang G, Zeev-Ben-Mordehai T, Xing EP. Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms. Bioinformatics 2018; 33:i13-i22. [PMID: 28881965 PMCID: PMC5946875 DOI: 10.1093/bioinformatics/btx230] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Motivation Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and their spatial organizations inside single cells. However, high degree of structural complexity together with practical imaging limitations makes the systematic de novo discovery of structures within cells challenging. It would likely require averaging and classifying millions of subtomograms potentially containing hundreds of highly heterogeneous structural classes. Although it is no longer difficult to acquire CECT data containing such amount of subtomograms due to advances in data acquisition automation, existing computational approaches have very limited scalability or discrimination ability, making them incapable of processing such amount of data. Results To complement existing approaches, in this article we propose a new approach for subdividing subtomograms into smaller but relatively homogeneous subsets. The structures in these subsets can then be separately recovered using existing computation intensive methods. Our approach is based on supervised structural feature extraction using deep learning, in combination with unsupervised clustering and reference-free classification. Our experiments show that, compared with existing unsupervised rotation invariant feature and pose-normalization based approaches, our new approach achieves significant improvements in both discrimination ability and scalability. More importantly, our new approach is able to discover new structural classes and recover structures that do not exist in training data. Availability and Implementation Source code freely available at http://www.cs.cmu.edu/∼mxu1/software. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaoqi Chai
- Biomedical Engineering Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Hariank Muthakana
- Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaodan Liang
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ge Yang
- Biomedical Engineering Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tzviya Zeev-Ben-Mordehai
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Eric P Xing
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA
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18
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Zhang D, Zhu Y, Liu L, Ying X, Hsiung CE, Sougrat R, Li K, Han Y. Atomic-resolution transmission electron microscopy of electron beam–sensitive crystalline materials. Science 2018; 359:675-679. [DOI: 10.1126/science.aao0865] [Citation(s) in RCA: 256] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/29/2017] [Accepted: 12/27/2017] [Indexed: 12/12/2022]
Abstract
High-resolution imaging of electron beam–sensitive materials is one of the most difficult applications of transmission electron microscopy (TEM). The challenges are manifold, including the acquisition of images with extremely low beam doses, the time-constrained search for crystal zone axes, the precise image alignment, and the accurate determination of the defocus value. We develop a suite of methods to fulfill these requirements and acquire atomic-resolution TEM images of several metal organic frameworks that are generally recognized as highly sensitive to electron beams. The high image resolution allows us to identify individual metal atomic columns, various types of surface termination, and benzene rings in the organic linkers. We also apply our methods to other electron beam–sensitive materials, including the organic-inorganic hybrid perovskite CH3NH3PbBr3.
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Affiliation(s)
- Daliang Zhang
- King Abdullah University of Science and Technology (KAUST), Imaging and Characterization Core Lab, Thuwal 23955-6900, Saudi Arabia
| | - Yihan Zhu
- KAUST, Advanced Membranes and Porous Materials Center, Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Lingmei Liu
- KAUST, Advanced Membranes and Porous Materials Center, Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Xiangrong Ying
- KAUST, Advanced Membranes and Porous Materials Center, Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Chia-En Hsiung
- KAUST, Advanced Membranes and Porous Materials Center, Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Rachid Sougrat
- King Abdullah University of Science and Technology (KAUST), Imaging and Characterization Core Lab, Thuwal 23955-6900, Saudi Arabia
| | - Kun Li
- King Abdullah University of Science and Technology (KAUST), Imaging and Characterization Core Lab, Thuwal 23955-6900, Saudi Arabia
| | - Yu Han
- KAUST, Advanced Membranes and Porous Materials Center, Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
- KAUST, KAUST Catalysis Center, Physical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
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19
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Neumann E, Farias Estrozi L, Effantin G, Breyton C, Schoehn G. Prix Nobel de Chimie 2017 : Jacques Dubochet, Joachim Frank et Richard Henderson. Med Sci (Paris) 2017; 33:1111-1117. [DOI: 10.1051/medsci/20173212019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Direct Detection Electron Energy-Loss Spectroscopy: A Method to Push the Limits of Resolution and Sensitivity. Sci Rep 2017; 7:8243. [PMID: 28811485 PMCID: PMC5557959 DOI: 10.1038/s41598-017-07709-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/03/2017] [Indexed: 12/17/2022] Open
Abstract
In many cases, electron counting with direct detection sensors offers improved resolution, lower noise, and higher pixel density compared to conventional, indirect detection sensors for electron microscopy applications. Direct detection technology has previously been utilized, with great success, for imaging and diffraction, but potential advantages for spectroscopy remain unexplored. Here we compare the performance of a direct detection sensor operated in counting mode and an indirect detection sensor (scintillator/fiber-optic/CCD) for electron energy-loss spectroscopy. Clear improvements in measured detective quantum efficiency and combined energy resolution/energy field-of-view are offered by counting mode direct detection, showing promise for efficient spectrum imaging, low-dose mapping of beam-sensitive specimens, trace element analysis, and time-resolved spectroscopy. Despite the limited counting rate imposed by the readout electronics, we show that both core-loss and low-loss spectral acquisition are practical. These developments will benefit biologists, chemists, physicists, and materials scientists alike.
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21
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Bell JM, Chen M, Baldwin PR, Ludtke SJ. High resolution single particle refinement in EMAN2.1. Methods 2016; 100:25-34. [PMID: 26931650 PMCID: PMC4848122 DOI: 10.1016/j.ymeth.2016.02.018] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 01/01/2023] Open
Abstract
EMAN2.1 is a complete image processing suite for quantitative analysis of grayscale images, with a primary focus on transmission electron microscopy, with complete workflows for performing high resolution single particle reconstruction, 2-D and 3-D heterogeneity analysis, random conical tilt reconstruction and subtomogram averaging, among other tasks. In this manuscript we provide the first detailed description of the high resolution single particle analysis pipeline and the philosophy behind its approach to the reconstruction problem. High resolution refinement is a fully automated process, and involves an advanced set of heuristics to select optimal algorithms for each specific refinement task. A gold standard FSC is produced automatically as part of refinement, providing a robust resolution estimate for the final map, and this is used to optimally filter the final CTF phase and amplitude corrected structure. Additional methods are in-place to reduce model bias during refinement, and to permit cross-validation using other computational methods.
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Affiliation(s)
- James M Bell
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Philip R Baldwin
- Department of Psychiatry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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22
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Galaz-Montoya JG, Hecksel CW, Baldwin PR, Wang E, Weaver SC, Schmid MF, Ludtke SJ, Chiu W. Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography. J Struct Biol 2016; 194:383-94. [PMID: 27016284 DOI: 10.1016/j.jsb.2016.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 10/22/2022]
Abstract
Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions.
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Affiliation(s)
- Jesús G Galaz-Montoya
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Corey W Hecksel
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Philip R Baldwin
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Eryu Wang
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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23
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Tate MW, Purohit P, Chamberlain D, Nguyen KX, Hovden R, Chang CS, Deb P, Turgut E, Heron JT, Schlom DG, Ralph DC, Fuchs GD, Shanks KS, Philipp HT, Muller DA, Gruner SM. High Dynamic Range Pixel Array Detector for Scanning Transmission Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:237-49. [PMID: 26750260 DOI: 10.1017/s1431927615015664] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We describe a hybrid pixel array detector (electron microscope pixel array detector, or EMPAD) adapted for use in electron microscope applications, especially as a universal detector for scanning transmission electron microscopy. The 128×128 pixel detector consists of a 500 µm thick silicon diode array bump-bonded pixel-by-pixel to an application-specific integrated circuit. The in-pixel circuitry provides a 1,000,000:1 dynamic range within a single frame, allowing the direct electron beam to be imaged while still maintaining single electron sensitivity. A 1.1 kHz framing rate enables rapid data collection and minimizes sample drift distortions while scanning. By capturing the entire unsaturated diffraction pattern in scanning mode, one can simultaneously capture bright field, dark field, and phase contrast information, as well as being able to analyze the full scattering distribution, allowing true center of mass imaging. The scattering is recorded on an absolute scale, so that information such as local sample thickness can be directly determined. This paper describes the detector architecture, data acquisition system, and preliminary results from experiments with 80-200 keV electron beams.
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Affiliation(s)
- Mark W Tate
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - Prafull Purohit
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - Darol Chamberlain
- 2Cornell High Energy Synchrotron Source (CHESS),Cornell University,Ithaca,NY 14853,USA
| | - Kayla X Nguyen
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Robert Hovden
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | | | - Pratiti Deb
- 4Physics Department,Cornell University,Ithaca,NY 14853,USA
| | - Emrah Turgut
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - John T Heron
- 4Physics Department,Cornell University,Ithaca,NY 14853,USA
| | - Darrell G Schlom
- 5Department of Materials Science and Engineering,Cornell University,Ithaca,NY 14853,USA
| | - Daniel C Ralph
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - Gregory D Fuchs
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Katherine S Shanks
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - Hugh T Philipp
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - David A Muller
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Sol M Gruner
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
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Wriggers W, He J. Numerical geometry of map and model assessment. J Struct Biol 2015; 192:255-61. [PMID: 26416532 DOI: 10.1016/j.jsb.2015.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/18/2015] [Accepted: 09/24/2015] [Indexed: 10/23/2022]
Abstract
We are describing best practices and assessment strategies for the atomic interpretation of cryo-electron microscopy (cryo-EM) maps. Multiscale numerical geometry strategies in the Situs package and in secondary structure detection software are currently evolving due to the recent increases in cryo-EM resolution. Criteria that aim to predict the accuracy of fitted atomic models at low (worse than 8Å) and medium (4-8 Å) resolutions remain challenging. However, a high level of confidence in atomic models can be achieved by combining such criteria. The observed errors are due to map-model discrepancies and due to the effect of imperfect global docking strategies. Extending the earlier motion capture approach developed for flexible fitting, we use simulated fiducials (pseudoatoms) at varying levels of coarse-graining to track the local drift of structural features. We compare three tracking approaches: naïve vector quantization, a smoothly deformable model, and a tessellation of the structure into rigid Voronoi cells, which are fitted using a multi-fragment refinement approach. The lowest error is an upper bound for the (small) discrepancy between the crystal structure and the EM map due to different conditions in their structure determination. When internal features such as secondary structures are visible in medium-resolution EM maps, it is possible to extend the idea of point-based fiducials to more complex geometric representations such as helical axes, strands, and skeletons. We propose quantitative strategies to assess map-model pairs when such secondary structure patterns are prominent.
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Affiliation(s)
- Willy Wriggers
- Department of Mechanical & Aerospace Engineering, Old Dominion University, Norfolk, VA 23529, United States.
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, United States.
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25
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Developments in cryo-electron tomography for in situ structural analysis. Arch Biochem Biophys 2015; 581:78-85. [DOI: 10.1016/j.abb.2015.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/14/2015] [Accepted: 04/19/2015] [Indexed: 12/31/2022]
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Faruqi A, Henderson R, McMullan G. Progress and Development of Direct Detectors for Electron Cryomicroscopy. ADVANCES IN IMAGING AND ELECTRON PHYSICS 2015. [DOI: 10.1016/bs.aiep.2015.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nat Commun 2014; 5:4808. [PMID: 25185801 PMCID: PMC4155512 DOI: 10.1038/ncomms5808] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/24/2014] [Indexed: 12/11/2022] Open
Abstract
Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure. Recent developments in cryo-electron microscopy have enabled structure determination of large protein complexes at almost atomic resolution. Wang et al. combine some of these technologies into an effective workflow, and demonstrate the protocol by solving the atomic structure of an icosahedral RNA virus.
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Ramachandra R, Bouwer JC, Mackey MR, Bushong E, Peltier ST, Xuong NH, Ellisman MH. Improving signal to noise in labeled biological specimens using energy-filtered TEM of sections with a drift correction strategy and a direct detection device. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:706-14. [PMID: 24641915 PMCID: PMC4178974 DOI: 10.1017/s1431927614000452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Energy filtered transmission electron microscopy techniques are regularly used to build elemental maps of spatially distributed nanoparticles in materials and biological specimens. When working with thick biological sections, electron energy loss spectroscopy techniques involving core-loss electrons often require exposures exceeding several minutes to provide sufficient signal to noise. Image quality with these long exposures is often compromised by specimen drift, which results in blurring and reduced resolution. To mitigate drift artifacts, a series of short exposure images can be acquired, aligned, and merged to form a single image. For samples where the target elements have extremely low signal yields, the use of charge coupled device (CCD)-based detectors for this purpose can be problematic. At short acquisition times, the images produced by CCDs can be noisy and may contain fixed pattern artifacts that impact subsequent correlative alignment. Here we report on the use of direct electron detection devices (DDD's) to increase the signal to noise as compared with CCD's. A 3× improvement in signal is reported with a DDD versus a comparably formatted CCD, with equivalent dose on each detector. With the fast rolling-readout design of the DDD, the duty cycle provides a major benefit, as there is no dead time between successive frames.
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Affiliation(s)
- Ranjan Ramachandra
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - James C. Bouwer
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Mason R. Mackey
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Eric Bushong
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Steven T. Peltier
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Nguyen-Huu Xuong
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Mark H. Ellisman
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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29
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Hoenger A. High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles. PROTOPLASMA 2014; 251:417-427. [PMID: 24390311 PMCID: PMC3927062 DOI: 10.1007/s00709-013-0600-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 12/12/2013] [Indexed: 06/03/2023]
Abstract
Cryo-electron microscopy techniques and computational 3-D reconstruction of macromolecular assemblies are tightly linked tools in modern structural biology. This symbiosis has produced vast amounts of detailed information on the structure and function of biological macromolecules. Typically, one of two fundamentally different strategies is used depending on the specimens and their environment. A: 3-D reconstruction based on repetitive and structurally identical unit cells that allow for averaging, and B: tomographic 3-D reconstructions where tilt-series between approximately ± 60 and ± 70° at small angular increments are collected from highly complex and flexible structures that are beyond averaging procedures, at least during the first round of 3-D reconstruction. Strategies of group A are averaging-based procedures and collect large number of 2-D projections at different angles that are computationally aligned, averaged together, and back-projected in 3-D space to reach a most complete 3-D dataset with high resolution, today often down to atomic detail. Evidently, success relies on structurally repetitive particles and an aligning procedure that unambiguously determines the angular relationship of all 2-D projections with respect to each other. The alignment procedure of small particles may rely on their packing into a regular array such as a 2-D crystal, an icosahedral (viral) particle, or a helical assembly. Critically important for cryo-methods, each particle will only be exposed once to the electron beam, making these procedures optimal for highest-resolution studies where beam-induced damage is a significant concern. In contrast, tomographic 3-D reconstruction procedures (group B) do not rely on averaging, but collect an entire dataset from the very same structure of interest. Data acquisition requires collecting a large series of tilted projections at angular increments of 1-2° or less and a tilt range of ± 60° or more. Accordingly, tomographic data collection exposes its specimens to a large electron dose, which is particularly problematic for frozen-hydrated samples. Currently, cryo-electron tomography is a rapidly emerging technology, on one end driven by the newest developments of hardware such as super-stabile microscopy stages as well as the latest generation of direct electron detectors and cameras. On the other end, success also strongly depends on new software developments on all kinds of fronts such as tilt-series alignment and back-projection procedures that are all adapted to the very low-dose and therefore very noisy primary data. Here, we will review the status quo of cryo-electron microscopy and discuss the future of cellular cryo-electron tomography from data collection to data analysis, CTF-correction of tilt-series, post-tomographic sub-volume averaging, and 3-D particle classification. We will also discuss the pros and cons of plunge freezing of cellular specimens to vitrified sectioning procedures and their suitability for post-tomographic volume averaging despite multiple artifacts that may distort specimens to some degree.
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Affiliation(s)
- Andreas Hoenger
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO, 80309, USA,
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Penczek PA, Fang J, Li X, Cheng Y, Loerke J, Spahn CMT. CTER-rapid estimation of CTF parameters with error assessment. Ultramicroscopy 2014; 140:9-19. [PMID: 24562077 DOI: 10.1016/j.ultramic.2014.01.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/22/2014] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
Abstract
In structural electron microscopy, the accurate estimation of the Contrast Transfer Function (CTF) parameters, particularly defocus and astigmatism, is of utmost importance for both initial evaluation of micrograph quality and for subsequent structure determination. Due to increases in the rate of data collection on modern microscopes equipped with new generation cameras, it is also important that the CTF estimation can be done rapidly and with minimal user intervention. Finally, in order to minimize the necessity for manual screening of the micrographs by a user it is necessary to provide an assessment of the errors of fitted parameters values. In this work we introduce CTER, a CTF parameters estimation method distinguished by its computational efficiency. The efficiency of the method makes it suitable for high-throughput EM data collection, and enables the use of a statistical resampling technique, bootstrap, that yields standard deviations of estimated defocus and astigmatism amplitude and angle, thus facilitating the automation of the process of screening out inferior micrograph data. Furthermore, CTER also outputs the spatial frequency limit imposed by reciprocal space aliasing of the discrete form of the CTF and the finite window size. We demonstrate the efficiency and accuracy of CTER using a data set collected on a 300kV Tecnai Polara (FEI) using the K2 Summit DED camera in super-resolution counting mode. Using CTER we obtained a structure of the 80S ribosome whose large subunit had a resolution of 4.03Å without, and 3.85Å with, inclusion of astigmatism parameters.
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Affiliation(s)
- Pawel A Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, 6431 Fannin MSB 6.220, Houston, TX 77054, USA.
| | - Jia Fang
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, 6431 Fannin MSB 6.220, Houston, TX 77054, USA
| | - Xueming Li
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Yifan Cheng
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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31
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Gontard LC, Moldovan G, Carmona-Galán R, Lin C, Kirkland AI. Detecting single-electron events in TEM using low-cost electronics and a silicon strip sensor. Microscopy (Oxf) 2014; 63:119-30. [PMID: 24401331 DOI: 10.1093/jmicro/dft051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is great interest in developing novel position-sensitive direct detectors for transmission electron microscopy (TEM) that do not rely in the conversion of electrons into photons. Direct imaging improves contrast and efficiency and allows the operation of the microscope at lower energies and at lower doses without loss in resolution, which is especially important for studying soft materials and biological samples. We investigate the feasibility of employing a silicon strip detector as an imaging detector for TEM. This device, routinely used in high-energy particle physics, can detect small variations in electric current associated with the impact of a single charged particle. The main advantages of using this type of sensor for direct imaging in TEM are its intrinsic radiation hardness and large detection area. Here, we detail design, simulation, fabrication and tests in a TEM of the front-end electronics developed using low-cost discrete components and discuss the limitations and applications of this technology for TEM.
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Affiliation(s)
- Lionel C Gontard
- Department of Materials, University of Oxford, 16 Parks Road, Oxford OX1 3PH, UK
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32
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Shigematsu H, Sigworth FJ. Noise models and cryo-EM drift correction with a direct-electron camera. Ultramicroscopy 2013; 131:61-9. [PMID: 23748163 DOI: 10.1016/j.ultramic.2013.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 04/01/2013] [Accepted: 04/05/2013] [Indexed: 10/26/2022]
Abstract
Blurring due to specimen-holder drift is a common occurrence in cryo-EM images. Cameras employing active-pixel sensors are capable of high frame rates such that a single low-dose exposure can be acquired as a series of frames. In this paper we consider the possibility of tracking and compensating for overall drift in typical single-particle specimens through the analysis of frame sequences. A problem that arises in tracking through cross-correlation of frames obtained with the DE-12 camera from Direct Electron LLC is the presence of "hot-pixel noise". This random pattern of bright pixels is highly correlated among frames. We show how a model of this noise can be employed to greatly reduce its effects. A filter function is derived that optimizes the tracking of image shifts by cross-correlation, and we demonstrate the tracking of specimen drift in typical cryo-EM specimens.
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Affiliation(s)
- H Shigematsu
- Department of Cellular and Molecular Physiology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States.
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33
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Tao C, Xia C, Chen X, Zhou ZH, Bi G. Ultrastructural analysis of neuronal synapses using state-of-the-art nano-imaging techniques. Neurosci Bull 2012; 28:321-32. [PMID: 22833032 DOI: 10.1007/s12264-012-1249-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Neuronal synapses are functional nodes in neural circuits. Their organization and activity define an individual's level of intelligence, emotional state and mental health. Changes in the structure and efficacy of synapses are the biological basis of learning and memory. However, investigation of the molecular architecture of synapses has been impeded by the lack of efficient techniques with sufficient resolution. Recent developments in state-of-the-art nano-imaging techniques have opened up a new window for dissecting the molecular organization of neuronal synapses with unprecedented resolution. Here, we review recent technological advances in nano-imaging techniques as well as their applications to the study of synapses, emphasizing super-resolution light microscopy and 3-dimensional electron tomography.
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Affiliation(s)
- Changlu Tao
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
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Bammes BE, Rochat RH, Jakana J, Chen DH, Chiu W. Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency. J Struct Biol 2012; 177:589-601. [PMID: 22285189 PMCID: PMC3314222 DOI: 10.1016/j.jsb.2012.01.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/21/2011] [Accepted: 01/11/2012] [Indexed: 11/28/2022]
Abstract
One limitation in electron cryo-microscopy (cryo-EM) is the inability to recover high-resolution signal from the image-recording media at the full-resolution limit of the transmission electron microscope. Direct electron detection using CMOS-based sensors for digitally recording images has the potential to alleviate this shortcoming. Here, we report a practical performance evaluation of a Direct Detection Device (DDD®) for biological cryo-EM at two different microscope voltages: 200 and 300 kV. Our DDD images of amorphous and graphitized carbon show strong per-pixel contrast with image resolution near the theoretical sampling limit of the data. Single-particle reconstructions of two frozen-hydrated bacteriophages, P22 and ε15, establish that the DDD is capable of recording usable signal for 3D reconstructions at about 4/5 of the Nyquist frequency, which is a vast improvement over the performance of conventional imaging media. We anticipate the unparalleled performance of this digital recording device will dramatically benefit cryo-EM for routine tomographic and single-particle structural determination of biological specimens.
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Affiliation(s)
- Benjamin E. Bammes
- Graduate Program in Structural and Computational Biology and Molecular Biophysics
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan H. Rochat
- Graduate Program in Structural and Computational Biology and Molecular Biophysics
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dong-Hua Chen
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wah Chiu
- Graduate Program in Structural and Computational Biology and Molecular Biophysics
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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35
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Cope J, Heumann J, Hoenger A. Cryo-electron tomography for structural characterization of macromolecular complexes. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 17:Unit17.13. [PMID: 21842467 DOI: 10.1002/0471140864.ps1713s65] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological matter embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions.
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Affiliation(s)
- Julia Cope
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
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36
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Milazzo AC, Cheng A, Moeller A, Lyumkis D, Jacovetty E, Polukas J, Ellisman MH, Xuong NH, Carragher B, Potter CS. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy. J Struct Biol 2011; 176:404-8. [PMID: 21933715 DOI: 10.1016/j.jsb.2011.09.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 09/04/2011] [Accepted: 09/07/2011] [Indexed: 11/18/2022]
Abstract
We report on initial results of using a new direct detection device (DDD) for single particle reconstruction of vitreous ice embedded specimens. Images were acquired on a Tecnai F20 at 200keV and a nominal magnification of 29,000×. This camera has a significantly improved signal to noise ratio and modulation transfer function (MTF) at 200keV compared to a standard CCD camera installed on the same microscope. Control of the DDD has been integrated into Leginon, an automated data collection system. Using GroEL as a test specimen, we obtained images of ∼30K particles with the CCD and the DDD from the same specimen sample using essentially identical imaging conditions. Comparison of the maps reconstructed from the CCD images and the DDD images demonstrates the improved performance of the DDD. We also obtained a 3D reconstruction from ∼70K GroEL particles acquired using the DDD; the quality of the density map demonstrates the potential of this new recording device for cryoEM data acquisition.
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Affiliation(s)
- Anna-Clare Milazzo
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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Abstract
Electron microscopy (EM) is an important tool for high-resolution structure determination in applications ranging from condensed matter to biology. Electronic detectors are now used in most applications in EM as they offer convenience and immediate feedback that is not possible with film or image plates. The earliest forms of electronic detector used routinely in transmission electron microscopy (TEM) were charge coupled devices (CCDs) and for many applications these remain perfectly adequate. There are however applications, such as the study of radiation-sensitive biological samples, where film is still used and improved detectors would be of great value. The emphasis in this review is therefore on detectors for use in such applications. Two of the most promising candidates for improved detection are: monolithic active pixel sensors (MAPS) and hybrid pixel detectors (of which Medipix2 was chosen for this study). From the studies described in this review, a back-thinned MAPS detector appears well suited to replace film in for the study of radiation-sensitive samples at 300 keV, while Medipix2 is suited to use at lower energies and especially in situations with very low count rates. The performance of a detector depends on the energy of electrons to be recorded, which in turn is dependent on the application it is being used for; results are described for a wide range of electron energies ranging from 40 to 300 keV. The basic properties of detectors are discussed in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE) as a function of spatial frequency.
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Pierson J, Vos M, McIntosh JR, Peters PJ. Perspectives on electron cryo-tomography of vitreous cryo-sections. JOURNAL OF ELECTRON MICROSCOPY 2011; 60 Suppl 1:S93-100. [PMID: 21844602 PMCID: PMC3156678 DOI: 10.1093/jmicro/dfr014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A major objective of modern structural biology is to appreciate the cellular organization by elucidating the spatial arrangement of macromolecular complexes within a cell. Cryogenic sample preparation, combined with cryo-ultramicrotomy, enables large cells and pieces of biological tissues to be thinned for electron cryo-tomography, which provides a three-dimensional view of the biological sample. There are, however, limitations associated with the technique that must be realized, addressed and overcome for the procedure to become mainstream. Here, we provide perspectives on the continued advancements in cryogenic sample preparation for vitreous cryo-sectioning, image collection and post-image processing that have expanded the attainable information limit within the three-dimensional reconstructions of cells and pieces of biological tissues.
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Affiliation(s)
- Jason Pierson
- Division of Cell Biology II, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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39
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Glaeser RM, McMullan G, Faruqi AR, Henderson R. Images of paraffin monolayer crystals with perfect contrast: minimization of beam-induced specimen motion. Ultramicroscopy 2010; 111:90-100. [PMID: 21185452 DOI: 10.1016/j.ultramic.2010.10.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 10/15/2010] [Accepted: 10/15/2010] [Indexed: 10/18/2022]
Abstract
Quantitative analysis of electron microscope images of organic and biological two-dimensional crystals has previously shown that the absolute contrast reached only a fraction of that expected theoretically from the electron diffraction amplitudes. The accepted explanation for this is that irradiation of the specimen causes beam-induced charging or movement, which in turn causes blurring of the image due to image or specimen movement. In this paper, we used three different approaches to try to overcome this image-blurring problem in monolayer crystals of paraffin. Our first approach was to use an extreme form of spotscan imaging, in which a single image was assembled on film by the successive illumination of up to 50,000 spots, each of a diameter of around 7 nm. The second approach was to use the Medipix II detector with its zero-noise readout to assemble a time-sliced series of images of the same area in which each frame from a movie with up to 400 frames had an exposure of only 500 electrons. In the third approach, we simply used a much thicker carbon support film to increase the physical strength and conductivity of the support. Surprisingly, the first two methods involving dose fractionation in space or time produced only partial improvements in contrast whereas the third approach produced many virtually perfect images, where the absolute contrast predicted from the electron diffraction amplitudes was observed in the images. We conclude that it is possible to obtain consistently almost perfect images of beam-sensitive specimens if they are attached to an appropriately strong and conductive support; however great care is needed in practice and the problem remains of how to best image ice-embedded biological structures in the absence of a strong, conductive support film.
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Affiliation(s)
- R M Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
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40
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Kolb U, Gorelik TE, Mugnaioli E, Stewart A. Structural Characterization of Organics Using Manual and Automated Electron Diffraction. POLYM REV 2010. [DOI: 10.1080/15583724.2010.494238] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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41
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Milazzo AC, Moldovan G, Lanman J, Jin L, Bouwer JC, Klienfelder S, Peltier ST, Ellisman MH, Kirkland AI, Xuong NH. Characterization of a direct detection device imaging camera for transmission electron microscopy. Ultramicroscopy 2010; 110:744-7. [PMID: 20382479 DOI: 10.1016/j.ultramic.2010.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 09/23/2009] [Accepted: 03/17/2010] [Indexed: 10/19/2022]
Abstract
The complete characterization of a novel direct detection device (DDD) camera for transmission electron microscopy is reported, for the first time at primary electron energies of 120 and 200 keV. Unlike a standard charge coupled device (CCD) camera, this device does not require a scintillator. The DDD transfers signal up to 65 lines/mm providing the basis for a high-performance platform for a new generation of wide field-of-view high-resolution cameras. An image of a thin section of virus particles is presented to illustrate the substantially improved performance of this sensor over current indirectly coupled CCD cameras.
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Affiliation(s)
- Anna-Clare Milazzo
- University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA.
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Pierson J, Sani M, Tomova C, Godsave S, Peters PJ. Toward visualization of nanomachines in their native cellular environment. Histochem Cell Biol 2009; 132:253-62. [PMID: 19649648 PMCID: PMC2729413 DOI: 10.1007/s00418-009-0622-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2009] [Indexed: 11/01/2022]
Abstract
The cellular nanocosm is made up of numerous types of macromolecular complexes or biological nanomachines. These form functional modules that are organized into complex subcellular networks. Information on the ultra-structure of these nanomachines has mainly been obtained by analyzing isolated structures, using imaging techniques such as X-ray crystallography, NMR, or single particle electron microscopy (EM). Yet there is a strong need to image biological complexes in a native state and within a cellular environment, in order to gain a better understanding of their functions. Emerging methods in EM are now making this goal reachable. Cryo-electron tomography bypasses the need for conventional fixatives, dehydration and stains, so that a close-to-native environment is retained. As this technique is approaching macromolecular resolution, it is possible to create maps of individual macromolecular complexes. X-ray and NMR data can be 'docked' or fitted into the lower resolution particle density maps to create a macromolecular atlas of the cell under normal and pathological conditions. The majority of cells, however, are too thick to be imaged in an intact state and therefore methods such as 'high pressure freezing' with 'freeze-substitution followed by room temperature plastic sectioning' or 'cryo-sectioning of unperturbed vitreous fully hydrated samples' have been introduced for electron tomography. Here, we review methodological considerations for visualizing nanomachines in a close-to-physiological, cellular context. EM is in a renaissance, and further innovations and training in this field should be fully supported.
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Affiliation(s)
- Jason Pierson
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
| | - Musa Sani
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
| | - Cveta Tomova
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
| | - Susan Godsave
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
| | - Peter J. Peters
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
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43
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McMullan G, Clark AT, Turchetta R, Faruqi AR. Enhanced imaging in low dose electron microscopy using electron counting. Ultramicroscopy 2009; 109:1411-6. [PMID: 19647366 PMCID: PMC2868354 DOI: 10.1016/j.ultramic.2009.07.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 06/24/2009] [Accepted: 07/07/2009] [Indexed: 10/26/2022]
Abstract
We compare the direct electron imaging performance at 120keV of a monolithic active pixel sensor (MAPS) operated in a conventional integrating mode with the performance obtained when operated in a single event counting mode. For the combination of sensor and incident electron energy used here, we propose a heuristic approach with which to process the single event images in which each event is renormalised to have an integrated weight of unity. Using this approach we find enhancements in the Nyquist frequency modulation transfer function (MTF) and detective quantum efficiency (DQE) over the corresponding integrating mode values by factors of 8 and 3, respectively.
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Affiliation(s)
- G McMullan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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44
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McMullan G, Chen S, Henderson R, Faruqi AR. Detective quantum efficiency of electron area detectors in electron microscopy. Ultramicroscopy 2009; 109:1126-43. [PMID: 19497671 PMCID: PMC2864625 DOI: 10.1016/j.ultramic.2009.04.002] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 04/03/2009] [Accepted: 04/21/2009] [Indexed: 11/17/2022]
Abstract
Recent progress in detector design has created the need for a careful side-by-side comparison of the modulation transfer function (MTF) and resolution-dependent detective quantum efficiency (DQE) of existing electron detectors with those of detectors based on new technology. We present MTF and DQE measurements for four types of detector: Kodak SO-163 film, TVIPS 224 charge coupled device (CCD) detector, the Medipix2 hybrid pixel detector, and an experimental direct electron monolithic active pixel sensor (MAPS) detector. Film and CCD performance was measured at 120 and 300 keV, while results are presented for the Medipix2 at 120 keV and for the MAPS detector at 300 keV. In the case of film, the effects of electron backscattering from both the holder and the plastic support have been investigated. We also show that part of the response of the emulsion in film comes from light generated in the plastic support. Computer simulations of film and the MAPS detector have been carried out and show good agreement with experiment. The agreement enables us to conclude that the DQE of a backthinned direct electron MAPS detector is likely to be equal to, or better than, that of film at 300 keV.
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Affiliation(s)
- G McMullan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB20QH, UK.
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45
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Li Z, Jensen GJ. Electron cryotomography: a new view into microbial ultrastructure. Curr Opin Microbiol 2009; 12:333-40. [PMID: 19427259 PMCID: PMC2747746 DOI: 10.1016/j.mib.2009.03.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 03/20/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
Abstract
Electron cryotomography (ECT) is an emerging technology that allows thin samples such as small bacterial cells to be imaged in 3D in a nearly native state to 'molecular' (approximately 4nm) resolution. As such, ECT is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal filaments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. Here we briefly explain ECT, review its recent contributions to microbiology, and conclude with a discussion of future prospects.
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Affiliation(s)
- Zhuo Li
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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Hoenger A, McIntosh JR. Probing the macromolecular organization of cells by electron tomography. Curr Opin Cell Biol 2009; 21:89-96. [PMID: 19185480 DOI: 10.1016/j.ceb.2008.12.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 11/24/2022]
Abstract
A major goal in cell biology is to understand the functional organization of macromolecular complexes in vivo. Electron microscopy is helping cell biologists to achieve this goal, thanks to its ability to resolve structural details in the nanometer range. While issues related to specimen preparation, imaging, and image interpretation make this approach to cell architecture difficult, recent improvements in methods, equipment, and software have facilitated the study of both important macromolecular complexes and comparatively large volumes from cellular specimens. Here, we describe recent progress in electron microscopy of cells and the ways in which the relevant methodologies are helping to elucidate cell architecture.
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Affiliation(s)
- Andreas Hoenger
- Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells and Molecules, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
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