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Three-Dimensional Reconstruction of Chromosomes Using Electron Tomography

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Electron Microscopy

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 369))

Abstract

The evolvement of preparative methods in structural studies has always been as important as the development of sophisticated equipment. Software development is also a significant part for three-dimensional (3D) structural studies using electron tomography methods (ETMs). Advanced computing makes amenable procedures that relatively recently were only visionary, such as the 3D reconstruction of chromosomes with ETM. Morphological guidelines and beauty are occasionally the only standard for a method to be acceptable in the realms of preparative as well as software development. Bulk isolation of metaphase chromosomes using acetic acid is such an apparent accomplishment in preparative methods. Our ETM with maximum entropy and, more so, the ongoing development toward fully automatic alignments, are contributions in the software line. Furthermore, whole mounting of chromosomes on holey-carbon grids makes it possible to use even yesterday’s 80-kV transmission electron microscope with a standard goniometer to collect tilt series. These advances in preparing whole-mount metaphase chromosomes enable laboratories that do not have access to a medium- or high-voltage transmission electron microscope to study complex structures like chromosomes in 3D using today’s desktop computers.

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References

  1. Frank, J. (ed.) (1992) Electron Tomography: Three-Dimensional Imaging With the Transmission Electron Microscopy. Plenum Press, New York.

    Google Scholar 

  2. Zheng, S. Q., Braunfeld, B. M., Sedat, W. J., and Agard, A. D. (2004) An improved strategy for automated electron microscopic tomography. J. Struct. Biol. 147, 10–22.

    Article  Google Scholar 

  3. Engelhardt, P. (2000) Electron tomography of chromosome structure, in Encyclopedia of Analytical Chemistry vol. 6 (Meyers, R. A., ed.), John Wiley & Sons Ltd, Chichester, pp. 4948–4984. Available at: http://www.lce.hut.fi/~engelhar/. Accessed May 29, 2006.

    Google Scholar 

  4. IMOD (2005). Available at: URL: http://bio3d.colorado.edu/imod/. Accessed May 29, 2006.

  5. Engelhardt, P., Meriläinen, J., Zhao, F., Uchiyama, S., Fukui, K., and Lehto, V.-P. (2006) Whole-mount immunoelectron tomography of chromosomes and cells, in Electron Microscopy Methods and Protocols, 2nd ed (Kuo, J., ed.), Humana, Totowa, NJ, pp. 387–405.

    Google Scholar 

  6. Brandt, S., Heikkonen, J., and Engelhardt, P. (2001) Multiphase method for automatic alignment of transmission electron microscope images using markers. J. Struct. Biol. 133, 10–22.

    Article  CAS  PubMed  Google Scholar 

  7. Brandt, S., Heikkonen, J., and Engelhardt, P. (2001) Automatic alignment of transmission electron microscope tilt-series without fiducial markers. J. Struct. Biol. 136, 201–213.

    Article  CAS  PubMed  Google Scholar 

  8. Brandt, S. S. and Ziese, U. (2006) Automatic TEM image alignment by trifocal geometry. J. Microsc. (Oxford) 222, 1–4.

    Article  CAS  Google Scholar 

  9. Brandt, S. S. and Kolehmainen, V. (2004) Motion without correspondence from tomographic projections by Bayesian Inversion Theory, in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2004) Vol. 1, Washington DC, pp. 582–587.

    Article  Google Scholar 

  10. Brandt, S. S. (2006) Markerless alignment in electron tomography in Electron Tomography, 2nd ed. (Frank, J., ed.), Springer, New York, pp. 187–215.

    Chapter  Google Scholar 

  11. BOB (2005) Available at: http://www.ahpcrc.org/software/bob/. Accessed May 30, 2006.

  12. AnimaBob (2005) Available at: http://www.borg.umn.edu/~grant/AnimaBob/. Accessed May 30, 2006.

  13. Chimera (2005) Available at: http://www.cgl.ucsf.edu/chimera/. Accessed May 30, 2006.

  14. VMD (2005) Available at: http://www.ks.uiuc.edu/Research/vmd/. Accessed May 30, 2006.

  15. SITUS (2005) Available at: http://situs.biomachina.org/. Accessed May 30, 2006.

  16. Vis5D (2005) Available at: http://www.ssec.wisc.edu/~billh/vis5d.html. Accessed May 30, 2006.

  17. Sullivan, A. (2005) 3-Deep. IEEE Spectrum, INT. April 22–27.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Haartman Institute, Department of Pathology and Virology, University of Helsinki, Helsinki, Finland

    Peter Engelhardt

  2. Laboratory of Computational Engineering, Helsinki University of Technology, Helsinki, Finland

    Peter Engelhardt

Authors
  1. Peter Engelhardt
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Editor information

Editors and Affiliations

  1. Centre for Microscopy and Microanalysis, The University of Western Australia, Crawley, Western Australia, Australia

    John Kuo

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© 2007 Humana Press Inc.

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Engelhardt, P. (2007). Three-Dimensional Reconstruction of Chromosomes Using Electron Tomography. In: Kuo, J. (eds) Electron Microscopy. Methods in Molecular Biology™, vol 369. Humana Press. https://doi.org/10.1007/978-1-59745-294-6_18

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  • DOI: https://doi.org/10.1007/978-1-59745-294-6_18

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-573-6

  • Online ISBN: 978-1-59745-294-6

  • eBook Packages: Springer Protocols

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