Chemical mapping of mammalian cells by atom probe tomography

Narayan, Kedar; Prosa, Ty J.; Fu, Jianzhong; Kelly, Tom; Subramaniam, Sriram

doi:10.1016/j.jsb.2011.12.016

Cited by 42 publications

(56 citation statements)

References 36 publications

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“…Moreover, a peak at 58 Da was detected in the cell envelope of the polymyxin-susceptible strain. The 58 Da species was not present in the intracellular specimens of the both bacterial strains in the current work, nor in the mammalian cell study by Narayan et al 15 . In addition, 58 Da was also below the detection limit in the polymyxin-resistant strain.…”

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confidence: 57%

“…Using both FIB lift-out and laser-assisted APT, it has been demonstrated that 3D atomic imaging is feasible from a single mammalian cell (e.g. HeLa cell) 15 . However, there exists a well-known challenge of optimizing the laser parameters, namely laser duration, wavelength and energy, which collectively can contribute to spatial and compositional errors 16, 17 .…”

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confidence: 99%

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Near-Atomic Three-Dimensional Mapping for Site-Specific Chemistry of ‘Superbugs’

et al. 2016

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Emergence of multi-drug resistant Gram-negative bacteria has caused a global health crisis and last-line class of antibiotics such as polymyxins are increasingly used. The chemical composition at the cell surface plays a key role in antibiotic resistance. Unlike imaging the cellular ultrastructure with well-developed electron microscopy, acquisition of a high-resolution chemical map of the bacterial surface still remains a technological challenge. In this study, we developed an atom probe tomography (APT) analysis approach to acquire mass spectra in the pulsed-voltage mode and reconstructed the 3D chemical distribution of atoms and molecules in the subcellular domain at the near-atomic scale. Using focused ion beam (FIB) milling together with micromanipulation, site-specific samples were retrieved from a single cell of Acinetobacter baumannii prepared as needle-shaped tips with end radii less than 60 nm, followed by a nano-scale coating of silver in the order of 10 nm. The significantly elevated conductivity provided by the metallic coating enabled successful and routine field evaporation of the biological material, with all the benefits of pulsed-voltage APT. In parallel with conventional cryo-TEM imaging, our novel approach was applied to investigate polymyxin-susceptible and -resistant strains of A. baumannii after treatment of polymyxin B. Acquired atom probe mass spectra from the cell envelope revealed characteristic fragments of phosphocholine from the polymyxin-susceptible strain, but limited signals from this molecule were detected in the polymyxin-resistant strain. This study promises unprecedented capacity for 3D nanoscale imaging and chemical mapping of bacterial cells at the ultimate 3D spatial resolution using APT.

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confidence: 99%

Near-Atomic Three-Dimensional Mapping for Site-Specific Chemistry of ‘Superbugs’

et al. 2016

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“…The development of strategies to combine clonable tags for electron microscopy (49, 73) and correlative light-electron microscopy (19,63) with immunoelectron microscopy (146,147) would be a major achievement. Methods to extend ultrastructural imaging to include chemical mapping of cells, to discern gradients in ions and metabolites at specialized structures such as virological synapses, are still in their infancy (148,149). Finally, soft X-ray cryo-microscopy/tomography is a promising technique that offers new possibilities to study viruses in whole cells (150,151).…”

Section: Resultsmentioning

confidence: 99%

Three-Dimensional Imaging of Viral Infections

et al. 2014

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Three-dimensional (3D) imaging technologies are beginning to have significant impact in the field of virology, as they are helping us understand how viruses take control of cells. In this article we review several methodologies for 3D imaging of cells and show how these technologies are contributing to the study of viral infections and the characterization of specialized structures formed in virus-infected cells. We include 3D reconstruction by transmission electron microscopy (TEM) using serial sections, electron tomography, and focused ion beam scanning electron microscopy (FIB-SEM). We summarize from these methods selected contributions to our understanding of viral entry, replication, morphogenesis, egress and propagation, and changes in the spatial architecture of virus-infected cells. In combination with live-cell imaging, correlative microscopy, and new techniques for molecular mapping in situ, the availability of these methods for 3D imaging is expected to provide deeper insights into understanding the structural and dynamic aspects of viral infection.

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“…Although a large number of reports on APT focus on inorganic materials, only a few studies report on organic materials because of the associated challenges * This paper was presented at the 10th International Symposium on Atomic Level Characterizations for New Materials and Devices '15, Shimane Prefectural Convention Center (Kunibiki Messe), Matsue, Japan, October 25-30, 2015. † Corresponding author: y-hirai@iis.u-tokyo.ac.jp such as difficulties in sample preparation, measurements, and three dimensional reconstruction of organic materials [10][11][12][13][14].…”

Section: Introductionmentioning

confidence: 99%

Study on a Novel Sample Preparation Method for Organic Materials in Atom Probe Tomography

Hirai

Kim

Yukawa

et al. 2016

e-J. Surf. Sci. Nanotech.

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It is important to study the distribution of host and guest molecules in organic electroluminescence materials because their distribution dramatically affects the functionalities of these materials. In order to understand this distribution, a new analysis method should be developed to obtain sub-nanometer scale information. In this regard, we used Atom Probe Tomography (APT). APT is a three-dimensional analysis technique with sub-nanometer scale resolution and is frequently used in material science and engineering. There are many reports on the analysis of inorganic materials using APT analysis, however only a few studies report the analysis of organic materials because of difficulties in the sample preparation, measurements, and the three-dimensional reconstruction of organic materials. In this study, we focused on developing a new sample preparation method and suggested the new sample preparation method for the analysis of organic materials. This new preparation method needs only a small amount of organic materials for analysis. Moreover, it is very simple and combines electrolytic polishing with the dipping method.

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Chemical mapping of mammalian cells by atom probe tomography

Cited by 42 publications

References 36 publications

Near-Atomic Three-Dimensional Mapping for Site-Specific Chemistry of ‘Superbugs’

Near-Atomic Three-Dimensional Mapping for Site-Specific Chemistry of ‘Superbugs’

Three-Dimensional Imaging of Viral Infections

Study on a Novel Sample Preparation Method for Organic Materials in Atom Probe Tomography

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