Cryo-EM and super-resolution microscopy on the same cell - when will we see this in biofilm?

Two of the most powerful imaging techniques have been combined in spectacular fashion in a study published today in Science.
Cryo-EM and super-resolution microscopy on the same cell - when will we see this in biofilm?

Cryo-EM and super-resolution microscopy have been responsible for some of the most spectacular images in microbiology over the last few years. Now, a new study describes a way to combine them for unprecedented resolution of the inside of mammalian cells.  

The technique termed '"Correlative three-dimensional super-resolution and block-face electron microscopy" allows for nano-scale imaging of whole mammalian cells. The research team from the USA where able to generate detailed, 3-dimensional maps of proteins throughout extremely well preserved cells of differing type. 

Unsurprisingly with this level of detail, the researchers explained that: 

"Nearly every system we studied revealed unexpected results."

The mind blowing thing from this study is that the unexpected results came from every part of the cell, from transcriptional activity in the nucleus to peroxisome morphology. This level of detail on such a wide scale has never been seen before. 

As a microbiologist I'm now desperate to see this technique applied to biofilm imaging, I hope someone is already working on it!


Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells

Science (2020)

David P. Hoffman, Gleb Shtengel, C. Shan Xu, Kirby R. Campbell, Melanie Freeman, Lei Wang, Daniel E. Milkie, H. Amalia Pasolli, Nirmala Iyer, John A. Bogovic, Daniel R. Stabley, Abbas Shirinifard, Song Pang, David Peale, Kathy Schaefer, Wim Pomp, Chi-Lun Chang, Jennifer Lippincott-Schwartz, Tom Kirchhausen, David J. Solecki, Eric Betzig, Harald F. Hess

Structured Abstract

Our textbook understanding of the nanoscale organization of the cell and its relationship to the thousands of proteins that drive cellular metabolism comes largely from a synthesis of biochemistry, molecular biology, and electron microscopy, and is therefore speculative in its details. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) promises to elucidate these details by directly visualizing the nanoscale relationship of specific proteins in the context of the global cellular ultrastructure. However, to date such correlative imaging has involved compromises with respect to ultrastructure preservation and imaging sensitivity, resolution, and/or field of view.

We developed a pipeline to (i) preserve fluorescently labeled, cultured mammalian cells in vitreous ice; (ii) image selected cells in their entirety below 10 K by multicolor three-dimensional structured illumination (3D SIM) and single-molecule localization microscopy (SMLM); (iii) image the same cells by 3D focused ion beam scanning EM (FIB-SEM) at 4- or 8-nm isotropic resolution; and (iv) register all image volumes to nanoscale precision. The pipeline ensures accurate ultrastructure preservation, permits independent optimization of SR and EM imaging modalities, and provides a comprehensive view of how specific subcellular components vary across the cellular volume.

Nearly every system we studied revealed unexpected results: intranuclear vesicles positive for a marker of the endoplasmic reticulum; peroxisomes of increasingly irregular morphology with increasing size; endolysosomal compartments of exceptionally diverse and convoluted morphology; a web-like adhesion network between cerebellar granule neurons; and classically EM-defined domains of heterochromatin and euchromatin each sub-characterized by the presence or absence of markers of transcriptional activity. Two-color cryo-SMLM enabled whole-cell image registration quantifiable down to ~40 nm accuracy. Cryo-SIM, even with its lower resolution, enabled unique discrimination between vesicles of like morphology and aided in segmenting complex 3D structures at FIB-SEM resolution within the crowded intracellular milieu.

Our pipeline serves as a powerful hypothesis generator to better understand the findings of biochemistry in the context of the spatially compartmentalized cell. Our approach also carefully preserves the native ultrastructure upon which such hypotheses are based, thus enabling cell-wide or cell-to-cell investigation of the natural variability in protein-ultrastructure relationships.

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