Mar 07, 2022
Preparation of Cultured Cells for Serial Block Face Scanning Electron Microscopy (SBEM)
- Daniela Boassa1,2,
- Thomas J. Deerinck1,2,
- Eric A. Bushong1,2,
- Andrea Thor1,2,
- Mark Ellisman1,2
- 1National Center for Microscopy and Imaging Research University of California San DiegoLa Jolla USA;
- 2Center for Research on Biological SystemsUniversity of California San DiegoLa Jolla USA
- NCMIR@UCSD
Protocol Citation: Daniela Boassa, Thomas J. Deerinck, Eric A. Bushong, Andrea Thor, Mark Ellisman 2022. Preparation of Cultured Cells for Serial Block Face Scanning Electron Microscopy (SBEM). protocols.io https://dx.doi.org/10.17504/protocols.io.b5naq5ae
Manuscript citation:
Replication-dependent size reduction precedes differentiation in Chlamydia trachomatis. Lee JK, Enciso GA, Boassa D, Chander CN, Lou TH, Pairawan SS, Guo MC, Wan FYM, Ellisman MH, Sütterlin C, Tan M. Nat Commun. 2018 Jan 3;9(1):45. doi: 10.1038/s41467-017-02432-0. PMID: 29298975. Click-EM for imaging metabolically tagged nonprotein biomolecules. Ngo JT, Adams SR, Deerinck TJ, Boassa D, Rodriguez-Rivera F, Palida SF, Bertozzi CR, Ellisman MH, Tsien RY. Nat Chem Biol. 2016 Jun;12(6):459-65. doi: 10.1038/nchembio.2076. Epub 2016 Apr 25. PMID: 27110681
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it’s working
Created: February 25, 2022
Last Modified: March 07, 2022
Protocol Integer ID: 58786
Keywords: SBEM, Cultured Cells, UCSD, NCMIR, serial block face scanning electron microscopy, sbem, cultured cell, preparation of cultured cell, electron microscopy, scanning electron microscopy, volume reconstruction of biological sample, processing of cell, biological sample, cell, volume reconstruction, 3d em method, serial block
Funders Acknowledgements:
NIH/National Institute of General Medical Sciences
Grant ID: R24GM137200
NIH/National Institute of Neurological Disorders and Stroke
Grant ID: U24NS120055
NIH, NIAID
Grant ID: R01 AI151212
NIH, NIGMS
Grant ID: R01GM086197
Abstract
Serial block-face scanning electron microscopy (SBEM) is a 3D EM method that allows volume reconstruction of biological samples. This protocol has been adapted for processing of cells in culture grown on glass-bottom dishes.
Safety warnings
Fixatives and electro-microscopy stains are extremely hazardous and should be prepared and handled in a fume hood. Gloves and protective eyewear should be used at all times.
Cells are fixed in glutaraldehyde (2.5% in 0.1M sodium cacodylate) for 60 minutes (room temperature to ice).
Cells are washed 5 x 2 minutes in cold cacodylate buffer containing 3mM calcium chloride.
Right before use, a solution containing 3% potassium ferrocyanide in 0.2M cacodylate buffer with 6mM calcium chloride is combined with an equal volume of 4% aqueous osmium tetroxide (EMS). The cells are incubated in this solution for 30 minutes on ice.
While the initial osmium incubation (step 3 above) is occurring, prepare the following thiocarbohydrazide (TCH) solution. This reagent needs to be fresh and available right at the end of step 3. Add 0.1 gm thiocarbohydrazide (Ted Pella) to 10 ml ddH2O and place in a 60° C oven for 30 minutes, (agitate by swirling gently every 10 minutes to facilitate dissolving). Filter this solution through a 0.22 um Millipore syringe filter right before use.
At the end of the first heavy metal incubation described in Step 3 (before adding the TCH), the cells are washed with ddH2O at room temperature 5 x 2 minutes.
Cells are then placed in the 0.22 micron Millipore filtered TCH solution for 10 minutes at room temperature.
Cells are then rinsed again 5 x 2 minutes in ddH2O at room temperature, and thereafter placed in 2% osmium tetroxide (NOT osmium ferrocyanide) in ddH2O for 10 minutes at room temperature.
Following this second exposure to osmium the tissues are washed 5 x 2 minutes at room temperature in ddH2O then placed in 2% uranyl acetate (aqueous) and left in a refrigerator (~4°) overnight.
The next day, en bloc Walton’s lead aspartate staining is performed. First, prepare an aspartic acid stock solution by dissolving 0.998 gm of L-aspartic acid (Sigma-Aldrich) in 250 ml of ddH2O. Note: the aspartic acid will dissolve more quickly if the pH raised to 3.8. This stock solution is stable for 1-2 months if refrigerated. To make the stain dissolve 0.066 gm of lead nitrate in 10 ml of aspartic acid stock and pH adjusted to 5.5 with 1N KOH. The lead aspartate solution is placed in a 60°C oven for 30 minutes (no precipitate should form). The cells are washed 5 x 2 minutes in ddH2O at room temperature and then placed in the lead aspartate solution and then returned to the oven for 10 minutes.
The cells are washed 5 x 2 minutes in room temperature ddH2O and dehydrated using ice-cold solutions of freshly prepared 20%, 50%, 70%, 90%, 100%, 100% ethanol (anhydrous), 3 minutes each, then placed in anhydrous 100% ethanol at room temp, 3min.
Durcupan ACM resin (EMS) is formulated by weight as follows: 11.4 g part A, 10 g part B, 0.3 g part C and 0.05-0.1 g part D, yielding a hard resin when polymerized. The resin is mixed thoroughly samples are placed into 50% Durcupan:ethanol for 30 minutes, then into 100% Durcupan overnight. The following day: 3 changes of 100% Durcupan for 1-2 hours.
A small amount of resin is placed over the cells and a square piece of aclar (large enough to cover the hole) is placed over the top opening to create a flat surface and placed in a 60° oven for 48 hours.