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Title: High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM

Abstract

High-lateral-resolution secondary ion mass spectrometry (SIMS) has the potential to provide functional and depth resolved information from small biological structures, such as viral particles (virions) and phage, but sputter rate and sensitivity are not characterized at shallow depths relevant to these structures. Here we combine stable isotope labeling of the DNA of vaccinia virions with correlated SIMS imaging depth profiling and atomic force microscopy (AFM) to develop a nonlinear, nonequilibrium sputter rate model for the virions and validate the model on the basis of reconstructing the location of the DNA within individual virions. Our experiments with a Cs+ beam show an unexpectedly high initial sputter rate (~100 um 2·nm·pA –1·s –1) with a rapid decline to an asymptotic rate of 0.7 um 2·nm·pA –1·s –1 at an approximate depth of 70 nm. Correlated experiments were also conducted with glutaraldehyde-fixed virions, as well as O and Ga + beams, yielding similar results. Based on our Cs + sputter rate model, the labeled DNA in the virion was between 50 and 90 nm depth in the virion core, consistent with expectations, supporting our conclusions. Virion densification was found to be a secondary effect. In conclusion, accurate isotopic ratios were obtained frommore » the initiation of sputtering, suggesting that isotopic tracers could be successfully used for smaller virions and phage.« less

Authors:
ORCiD logo [1];  [2];  [2];  [1];  [1]; ORCiD logo [1]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  2. Univ. of Florida, Gainesville, FL (United States)
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1476870
Report Number(s):
LLNL-JRNL-729380
Journal ID: ISSN 0003-2700; 879600
Grant/Contract Number:  
AC52-07NA27344
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Analytical Chemistry
Additional Journal Information:
Journal Volume: 90; Journal Issue: 3; Journal ID: ISSN 0003-2700
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Gates, Sean D., Condit, Richard C., Moussatche, Nissin, Stewart, Benjamin J., Malkin, Alexander J., and Weber, Peter K. High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM. United States: N. p., 2018. Web. doi:10.1021/acs.analchem.7b02786.
Gates, Sean D., Condit, Richard C., Moussatche, Nissin, Stewart, Benjamin J., Malkin, Alexander J., & Weber, Peter K. High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM. United States. doi:10.1021/acs.analchem.7b02786.
Gates, Sean D., Condit, Richard C., Moussatche, Nissin, Stewart, Benjamin J., Malkin, Alexander J., and Weber, Peter K. Wed . "High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM". United States. doi:10.1021/acs.analchem.7b02786. https://www.osti.gov/servlets/purl/1476870.
@article{osti_1476870,
title = {High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM},
author = {Gates, Sean D. and Condit, Richard C. and Moussatche, Nissin and Stewart, Benjamin J. and Malkin, Alexander J. and Weber, Peter K.},
abstractNote = {High-lateral-resolution secondary ion mass spectrometry (SIMS) has the potential to provide functional and depth resolved information from small biological structures, such as viral particles (virions) and phage, but sputter rate and sensitivity are not characterized at shallow depths relevant to these structures. Here we combine stable isotope labeling of the DNA of vaccinia virions with correlated SIMS imaging depth profiling and atomic force microscopy (AFM) to develop a nonlinear, nonequilibrium sputter rate model for the virions and validate the model on the basis of reconstructing the location of the DNA within individual virions. Our experiments with a Cs+ beam show an unexpectedly high initial sputter rate (~100 um2·nm·pA–1·s–1) with a rapid decline to an asymptotic rate of 0.7 um2·nm·pA–1·s–1 at an approximate depth of 70 nm. Correlated experiments were also conducted with glutaraldehyde-fixed virions, as well as O– and Ga+ beams, yielding similar results. Based on our Cs+ sputter rate model, the labeled DNA in the virion was between 50 and 90 nm depth in the virion core, consistent with expectations, supporting our conclusions. Virion densification was found to be a secondary effect. In conclusion, accurate isotopic ratios were obtained from the initiation of sputtering, suggesting that isotopic tracers could be successfully used for smaller virions and phage.},
doi = {10.1021/acs.analchem.7b02786},
journal = {Analytical Chemistry},
issn = {0003-2700},
number = 3,
volume = 90,
place = {United States},
year = {2018},
month = {1}
}

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Cited by: 2 works
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Figures / Tables:

Figure 1: Figure 1:: Correlated AFM and SIMS images of vaccinia virions demonstrating colocalization in the two instruments and general nature of virion surface erosion during sputtering. However, data from clusters of virions such as these were not used for the height measurements and sputtering experiments. The AFM image (A) is amore » contrast-enhanced height image that corresponds to the region in the SIMS images (B - E). The sequence of SIMS images detail the distribution of the 12C14N species counts during each scan. SIMS image (B), (C), (D) and (E) correspond to scan number 1, 15 25 and 39, respectively. The decrease in species counts as a function of scan number is a result of lateral erosion caused by sputtering. Scale bar: 500 nm.« less

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Works referencing / citing this record:

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
journal, January 2019