Abstract
Synaptic function depends upon interactions among sets of proteins that assemble into complex machines. Molecular biology, electrophysiology, and live-cell imaging studies have provided glimpses into the inner workings of the synapse, but the functional organization of these supramolecular nano-assemblies remains obscure. Electron tomography reveals the internal structure of synapses in three dimensions with exceptional spatial resolution. We here describe an approach to the study of ultrastructure that relies on plastic-embedded aldehyde-fixed material stabilized with tannic acid instead of osmium tetroxide. This approach offers a new window into the structural basis of synaptic processing in the mammalian brain.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Leung BO, Chou KC (2011) Review of super-resolution fluorescence microscopy for biology. Appl Spectrosc 65(9):967–980. doi:10.1366/11-06398
Huang B, Babcock H, Zhuang X (2010) Breaking the diffraction barrier: super-resolution imaging of cells. Cell 143(7):1047–1058. doi:S0092-8674(10)01420-0 [pii] 10.1016/j.cell.2010.12.002
Giepmans BN, Adams SR, Ellisman MH, Tsien RY (2006) The fluorescent toolbox for assessing protein location and function. Science 312(5771):217–224. doi:312/5771/217 [pii] 10.1126/science.1124618
Amsterdam A, Schramm M (1966) Rapid release of the zymogen granule protein by osmium tetroxide and its retention during fixation by glutaraldehyde. J Cell Biol 29(2):199–207
McMillan PN, Luftig RB (1973) Preservation of erythrocyte ghost ultrastructure achieved by various fixatives. Proc Natl Acad Sci U S A 70(11):3060–3064
Chen X, Winters CA, Reese TS (2008) Life inside a thin section: tomography. J Neurosci 28(38):9321–9327. doi:28/38/9321 [pii] 10.1523/JNEUROSCI.2992-08.2008
Frey TG, Perkins GA, Ellisman MH (2006) Electron tomography of membrane-bound cellular organelles. Annu Rev Biophys Biomol Struct 35:199–224. doi:10.1146/annurev.biophys.35.040405.102039
Leis A, Rockel B, Andrees L, Baumeister W (2009) Visualizing cells at the nanoscale. Trends Biochem Sci 34(2):60–70. doi:S0968-0004(08)00256-9 [pii] 10.1016/j.tibs.2008.10.011
Sato T (1968) A modified method for lead staining of thin sections. J Electron Microsc (Tokyo) 17(2):158–159
Good NE, Winget GD, Winter W, Connolly TN, Izawa S, Singh RM (1966) Hydrogen ion buffers for biological research. Biochemistry 5(2):467–477
Penczek P, Marko M, Buttle K, Frank J (1995) Double-tilt electron tomography. Ultramicroscopy 60(3):393–410
Hata S, Miyazaki H, Miyazaki S, Mitsuhara M, Tanaka M, Kaneko K, Higashida K, Ikeda K, Nakashima H, Matsumura S, Barnard JS, Sharp JH, Midgley PA (2011) High-angle triple-axis specimen holder for three-dimensional diffraction contrast imaging in transmission electron microscopy. Ultramicroscopy 111(8):1168–1175. doi:S0304-3991(11)00137-9 [pii] 10.1016/j.ultramic.2011.03.021
Amira software package. http://www.amira.com/
Volkmann N, Hanein D (1999) Quantitative fitting of atomic models into observed densities derived by electron microscopy. J Struct Biol 125(2–3):176–184. doi:S1047-8477(98)94074-6 [pii] 10.1006/jsbi.1998.4074
CoAn software package. http://coan.burnham.org
Cytoseg software package. https://confluence.crbs.ucsd.edu/display/ncmir/NCMIR+Software
EM3D software package. http://em3d.stanford.edu/
Ress D, Harlow ML, Schwarz M, Marshall RM, McMahan UJ (1999) Automatic acquisition of fiducial markers and alignment of images in tilt series for electron tomography. J Electron Microsc (Tokyo) 48(3):277–287
Ress DB, Harlow ML, Marshall RM, McMahan UJ (2004) Methods for generating high-resolution structural models from electron microscope tomography data. Structure 12(10):1763–1774. doi:10.1016/j.str.2004.07.022 S0969212604003090 [pii]
Fiji software package. http://fiji.sc/wiki/index.php/Fiji
JUST software package. http://dcssi.istm.cnr.it/Lanzavecchia/Just/
Salvi E, Cantele F, Zampighi L, Fain N, Pigino G, Zampighi G, Lanzavecchia S (2008) JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps. J Struct Biol 161(3):287–297. doi:S1047-8477(07)00146-3 [pii] 10.1016/j.jsb.2007.06.011
ImageJ software package. http://rsbweb.nih.gov/ij/
Mastronarde DN (2005) Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol 152(1):36–51. doi:S1047-8477(05)00152-8 [pii] 10.1016/j.jsb.2005.07.007
IMOD software package. http://bio3d.colorado.edu/imod/
Amat F, Moussavi F, Comolli LR, Elidan G, Downing KH, Horowitz M (2008) Markov random field based automatic image alignment for electron tomography. J Struct Biol 161(3):260–275. doi:S1047-8477(07)00155-4 [pii] 10.1016/j.jsb.2007.07.007
RAPTOR software package. http://www-vlsi.stanford.edu/TEM/software.htm
Reconstruct software package. http://synapses.clm.utexas.edu/tools/reconstruct/reconstruct.stm
Fiala JC (2005) Reconstruct: a free editor for serial section microscopy. J Microsc 218(Pt 1):52–61. doi:JMI1466 [pii] 10.1111/j.1365-2818.2005.01466.x
Nickell S, Forster F, Linaroudis A, Net WD, Beck F, Hegerl R, Baumeister W, Plitzko JM (2005) TOM software toolbox: acquisition and analysis for electron tomography. J Struct Biol 149(3):227–234. doi:S1047-8477(04)00187-X [pii] 10.1016/j.jsb.2004.10.006
TOM Toolbox. http://www.biochem.mpg.de/en/rd/baumeister/tom_e/
Fernandez JJ (2009) TOMOBFLOW: feature-preserving noise filtering for electron tomography. BMC Bioinformatics 10:178. doi:1471-2105-10-178 [pii] 10.1186/1471-2105-10-178
TOMOBFLOW software package. https://sites.google.com/site/3demimageprocessing/tomobflow
Messaoudii C, Boudier T, Sanchez Sorzano CO, Marco S (2007) TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy. BMC Bioinformatics 8:288. doi:1471-2105-8-288 [pii] 10.1186/1471-2105-8-288
Lawrence A, Bouwer JC, Perkins G, Ellisman MH (2006) Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. J Struct Biol 154(2):144–167. doi:S1047-8477(06)00015-3 [pii] 10.1016/j.jsb.2005.12.012
TxBR software package. https://confluence.crbs.ucsd.edu/display/ncmir/TxBR
SerialEM software package. http://bio3d.colorado.edu/SerialEM/
UCSF Tomography software package. http://www.msg.ucsf.edu/Tomography/tomography_main.html
Burette AC, Lesperance T, Crum J, Martone M, Volkmann N, Ellisman MH, Weinberg RJ (2012) Electron tomographic analysis of synaptic ultrastructure. J Comp Neurol 520(12):2697–2711
Parekh R, Ascoli GA (2013) Neuronal morphology goes digital: a research hub for cellular and system neuroscience. Neuron 77(6):1017–1038. doi:10.1016/j.neuron.2013.03.008
Rasband WS (1997–2011) ImageJ. U. S. National Institutes of Health, Bethesda, Maryland, USA. http://rsb.info.nih.gov/ij/
Fujii T, Iwane AH, Yanagida T, Namba K (2010) Direct visualization of secondary structures of F-actin by electron cryomicroscopy. Nature 467(7316):724–728. doi:nature09372 [pii] 10.1038/nature09372
Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson S, Lamont SP, Gupta A, Ellisman MH (2008) The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. J Struct Biol 161(3):220–231. doi:S1047-8477(07)00254-7 [pii] 10.1016/j.jsb.2007.10.003
The Cell Centered Database. http://ccdb.ucsd.edu/index.shtm
Acknowledgements
Grant support: R01 NS039444 (RJW).
We thank Kristen Phend for histological assistance; Michael Franke for his help with the segmentation presented in Fig. 2.8; Niels Volkmann for his assistance with image denoising, filament extraction, and atomic docking; Maryann Martone and Mark H Ellisman for assistance with preparation of electron tomograms; and the CCDB.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this protocol
Cite this protocol
Burette, A.C., Weinberg, R.J. (2014). Electron Tomography for the Study of Synaptic Ultrastructure in Fixed Brain Sections. In: Nägerl, U., Triller, A. (eds) Nanoscale Imaging of Synapses. Neuromethods, vol 84. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4614-9179-8_2
Download citation
DOI: https://doi.org/10.1007/978-1-4614-9179-8_2
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4614-9178-1
Online ISBN: 978-1-4614-9179-8
eBook Packages: Springer Protocols