scholarly journals DNA mapping in the capsid of giant bacteriophage phiEL (Caudovirales: Myoviridae: Elvirus) by analytical electron microscopy

2022 ◽  
Vol 66 (6) ◽  
pp. 434-441
Author(s):  
T. S. Trifonova ◽  
A. V. Moiseenko ◽  
M. V. Bourkaltseva ◽  
O. V. Shaburova ◽  
A. K. Shaytan ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Analytical Approach ◽  
Theoretical Calculations ◽  
Analytical Electron Microscopy ◽  
Dark Field ◽  
High Dose ◽  
Distribution Maps ◽  
Cryo Electron Microscopy ◽  
Low Concentrations ◽  
Microscopy Techniques

Introduction. Giant phiKZ-like bacteriophages have a unique protein formation inside the capsid, an inner body (IB) with supercoiled DNA molecule wrapped around it. Standard cryo-electron microscopy (cryo-EM) approaches do not allow to distinguish this structure from the surrounding nucleic acid of the phage. We previously developed an analytical approach to visualize protein-DNA complexes on Escherichia coli bacterial cell slices using the chemical element phosphorus as a marker. In the study presented, we adapted this technique for much smaller objects, namely the capsids of phiKZ-like bacteriophages.Material and methods. Following electron microscopy techniques were used in the study: analytical (AEM) (electron energy loss spectroscopy, EELS), and cryo-EM (images of samples subjected to low and high dose of electron irradiation were compared).Results. We studied DNA packaging inside the capsids of giant bacteriophages phiEL from the Myoviridae family that infect Pseudomonas aeruginosa. Phosphorus distribution maps were obtained, showing an asymmetrical arrangement of DNA inside the capsid.Discussion. We developed and applied an IB imaging technique using a high angle dark-field detector (HAADF) and the STEM-EELS analytical approach. Phosphorus mapping by EELS and cryo-electron microscopy revealed a protein formation as IB within the phage phiEL capsid. The size of IB was estimated using theoretical calculations.Conclusion. The developed technique can be applied to study the distribution of phosphorus in other DNA- or RNA-containing viruses at relatively low concentrations of the element sought.

Electron Beam Damage of Biomolecules Assessed by Energy Loss Spectroscopy

1978 ◽  
Vol 36 (3) ◽  
pp. 61-69
Author(s):  
M. Isaacson ◽  
M.L. Collins ◽  
M. Listvan
Keyword(s):  
Electron Microscopy ◽  
Radiation Damage ◽  
Structural Integrity ◽  
Analytical Electron Microscopy ◽  
High Dose ◽  
Dose Rates ◽  
Special Cases ◽  
Analytical Electron ◽  
Atom Migration ◽  
Beam Damage

Over the past five years it has become evident that radiation damage provides the fundamental limit to the study of blomolecular structure by electron microscopy. In some special cases structural determinations at very low doses can be achieved through superposition techniques to study periodic (Unwin & Henderson, 1975) and nonperiodic (Saxton & Frank, 1977) specimens. In addition, protection methods such as glucose embedding (Unwin & Henderson, 1975) and maintenance of specimen hydration at low temperatures (Taylor & Glaeser, 1976) have also shown promise. Despite these successes, the basic nature of radiation damage in the electron microscope is far from clear. In general we cannot predict exactly how different structures will behave during electron Irradiation at high dose rates. Moreover, with the rapid rise of analytical electron microscopy over the last few years, nvicroscopists are becoming concerned with questions of compositional as well as structural integrity. It is important to measure changes in elemental composition arising from atom migration in or loss from the specimen as a result of electron bombardment.

scholarly journals Analytical High-resolution Electron Microscopy Reveals Organ-specific Nanoceria Bioprocessing

2017 ◽  
Vol 46 (1) ◽  
pp. 47-61 ◽  
Author(s):  
Uschi M. Graham ◽  
Robert A. Yokel ◽  
Alan K. Dozier ◽  
Lawrence Drummy ◽  
Krishnamurthy Mahalingam ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
High Resolution ◽  
Analytical Electron Microscopy ◽  
High Resolution Electron Microscopy ◽  
Dark Field ◽  
Transmission Electron ◽  
Analytical Electron ◽  
Organ Specific

This is the first utilization of advanced analytical electron microscopy methods, including high-resolution transmission electron microscopy, high-angle annular dark field scanning transmission electron microscopy, electron energy loss spectroscopy, and energy-dispersive X-ray spectroscopy mapping to characterize the organ-specific bioprocessing of a relatively inert nanomaterial (nanoceria). Liver and spleen samples from rats given a single intravenous infusion of nanoceria were obtained after prolonged (90 days) in vivo exposure. These advanced analytical electron microscopy methods were applied to elucidate the organ-specific cellular and subcellular fate of nanoceria after its uptake. Nanoceria is bioprocessed differently in the spleen than in the liver.

Investigation of Copper Segregation to the Σ5(310)/[001] Symmetric Tilt Grain Boundary in Aluminum

1999 ◽  
Vol 589 ◽  
Author(s):  
Jürgen M. Plitzko ◽  
Geoffrey H. Campbell ◽  
Wayne E. King ◽  
Stephen M. Foiles
Keyword(s):  
Electron Microscopy ◽  
Grain Boundary ◽  
Low Voltage ◽  
Theoretical Calculations ◽  
High Vacuum ◽  
Analytical Electron Microscopy ◽  
Ultra High Vacuum ◽  
Face Centered Cubic ◽  
Symmetric Tilt ◽  
Tilt Grain Boundary

AbstractThe Σ5 (31O)/[001] symmetric tilt grain boundary (STGB) in the face centered cubic (FCC) metal aluminum with 1at% copper has been studied. The model grain boundary has been fabricated by ultra-high vacuum diffusion bonding of alloy single crystals. The segregation of the copper has been encouraged by annealing the sample after bonding at 200 °C. TEM samples of this FCCmaterial were prepared with a new low voltage ion mill under very low angles.The atomic structure of the Σ5(310)/[001] STGB for this system was modeled with electronic structure calculations. These theoretical calculations of the interface structure indicate that the Cu atoms segregate to distinct sites at the interface. High resolution electron microscopy (HRTEM) and analytical electron microscopy including electron energy spectroscopic imaging and X-ray energy dispersive spectrometry have been used to explore the segregation to the grain boundary. The HRTEM images and the analytical measurements were performed using different kinds of microscopes, including a Philips CM300 FEG equipped with an imaging energy filter. The amount of the segregated species at the interface was quantified in a preliminary way. To determine the atomic positions of the segregated atoms at the interface, HRTEM coupled with image simulation and a first attempt of a holographic reconstruction from a through-focal series have been used.

Inroads through the bacterial cell envelope: seeing is believing

2018 ◽  
Vol 64 (9) ◽  
pp. 601-617 ◽  
Author(s):  
Cezar M. Khursigara ◽  
Susan F. Koval ◽  
Dianne M. Moyles ◽  
Robert J. Harris
Keyword(s):  
Electron Microscopy ◽  
Bacterial Cell ◽  
Caulobacter Crescentus ◽  
Cell Envelope ◽  
Cell Fractionation ◽  
Doctoral Studies ◽  
Cryo Electron Microscopy ◽  
A Cell ◽  
Cell Envelopes ◽  
Microscopy Techniques

A singular feature of all prokaryotic cells is the presence of a cell envelope composed of a cytoplasmic membrane and a cell wall. The introduction of bacterial cell fractionation techniques in the 1950s and 1960s along with developments in procedures for electron microscopy opened the window towards an understanding of the chemical composition and architecture of the cell envelope. This review traces the contribution of Terry Beveridge in these endeavours, beginning with his doctoral studies in the 1970s on the structure of paracrystalline surface arrays (S-layers), followed by an exploration of cryogenic methods for preserving bacteria for ultrastructural analyses. His insights are reflected in a current example of the contribution of cryo-electron microscopy to S-layer studies — the structure and assembly of the surface array of Caulobacter crescentus. The review then focuses on Terry’s contributions to imaging the ultrastructure of bacterial cell envelopes and to the development of cryo-electron microscopy techniques, including the use of CEMOVIS (Cryo-electron Microscopy of Vitreous Sections) to “see” the ultrastructure of the Gram-positive cell envelope — his last scientific endeavour.

The Raft-Like Structure of Supported PtRu5

1997 ◽  
Vol 497 ◽  
Author(s):  
J. C. Yang ◽  
S. Bradley ◽  
M. N. Nashner ◽  
R. Nuzzo ◽  
J. M. Gibson
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Carbon Black ◽  
Analytical Electron Microscopy ◽  
Average Diameter ◽  
Atomic Concentration ◽  
Analytical Electron ◽  
Microscopy Techniques

ABSTRACTWe have examined supported PtRus specimens by a variety of electron microscopy techniques, including high resolution, analytical and a novel mass-spectroscopic electron microscopy techniques. Analytical electron microscopy results showed that the relative atomic concentration of Pt to Ru for each PtRu5 cluster is 1 to 5. The average diameter of the clusters was a 15.6Å, and the average number of atoms was measured to be 24 atoms per cluster. The combination of these techniques demonstrate that the PtRu5 clusters are raft-like on the carbon black support.

scholarly journals Characterization of Ni-base Superalloys on the Atomic Scale by Atom Probe Tomography and Spherical-Aberration Corrected Analytical Electron Microscopy Techniques

2006 ◽  
Vol 12 (S02) ◽  
pp. 534-535 ◽  
Author(s):  
M Watanabe ◽  
D Saxey ◽  
R Zheng ◽  
D Williams ◽  
S Ringer
Keyword(s):  
Electron Microscopy ◽  
Atom Probe Tomography ◽  
Spherical Aberration ◽  
Analytical Electron Microscopy ◽  
Atom Probe ◽  
Atomic Scale ◽  
Analytical Electron ◽  
Microscopy Techniques ◽  
Aberration Corrected

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2006

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