View source for Electron microscopy of cells

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! Viral infection prevalence (TEM)
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| '''Approach:''' transmission electron microscopy (TEM); scoring intracellular virions
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| '''Context:''' ''in situ'', lab
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| '''Spatial scale:''' point sample
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| '''Temporal scale:''' hours to days
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| '''Units:''' % of cells with intracellular virions (virus-like particles)
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| '''Community captured:''' bulk
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| '''Co-measurements:''' total cell abundance
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== Method Overview ==

Seawater samples are fixed with glutaraldehyde and concentrated by ultracentrifugation or ultrafiltration onto electron microscopy grids. Sections or whole-mount preparations are stained with uranyl acetate and examined by transmission electron microscopy (TEM). Cells containing intracellular virus-like particles (VLPs) assembled within their cytoplasm or nucleus are scored as virally infected. The percentage of infected cells and the burst size (number of assembled VLPs per infected cell) are calculated from the images. Early-stage infections may be detected before visible VLP assembly through cytopathic effects in the cell ultrastructure<ref name="Proctor1990">Proctor, L. M., & Fuhrman, J. A. (1990). Viral mortality of marine bacteria and cyanobacteria. ''Nature'', 343, 60–62. https://doi.org/10.1038/343060a0</ref>.

=== Scale of measurement ===

TEM preparation and imaging are labor-intensive, limiting throughput to tens to hundreds of cells per sample.

=== Data generated ===

Proportion of cells with intracellular VLPs (% infected cells); mean burst size (VLPs per infected cell). Multiplied by cell lysis rate, these yield viral-mediated mortality rates.

=== Units & currency ===

Units are % (proportion of infected cells). The currency is cells.

=== Sample size ===

Typical samples are < 1 L in volume.

=== Repositories & databases ===

== Limitations ==

The key assumption is that intracellular VLP presence always leads to cell lysis. In practice, latent or chronic infections may exist where VLPs are produced without lysis, leading to overestimation of viral mortality. Conversely, early-stage infections without visible VLP assembly are not detected, leading to underestimation. TEM throughput is inherently low, limiting statistical power.

== Example Applications & Protocols ==

=== Classic examples ===
* Proctor & Fuhrman (1990) ''Viral mortality of marine bacteria and cyanobacteria'' <ref name="Proctor1990" />

=== Recent applications ===
* Parada et al. (2006) ''Viral burst size of heterotrophic prokaryotes in aquatic systems'' <ref name="Parada2006">Parada, V., Herndl, G. J., & Weinbauer, M. G. (2006). Viral burst size of heterotrophic prokaryotes in aquatic systems. ''Journal of the Marine Biological Association of the United Kingdom'', 86(3), 613–621. https://doi.org/10.1017/S002531540601352X</ref>

=== Common calculations/conversions ===
* Viral-mediated bacterial mortality (cells L<sup>-1</sup> d<sup>-1</sup>) = % infected cells × bacterial abundance × lysis rate.
* Burst size (VLPs cell<sup>-1</sup>) estimated by counting VLPs in TEM images of infected cells.

== References ==

[[Category:Main Pages|Model types]]