Computer Analysis of Ordered Microbiological Objects

  • Murray Stewart


Electron microscopy has yielded a wealth of information on the structure of microorganisms and their constituents and in many instances simple inspection of micrographs has given considerable insight into the structures being investigated. However, to obtain high-resolution information from electron micrographs of microbiological material, the simple, subjective methods generally used to interpret images are often inadequate. Objective methods of image analysis are needed to extract as much reliable information as possible, for example, about the position of individual protein subunits within an assembly or to give an indication of subunit size and shape.


Spatial Frequency Optical Diffraction Purple Membrane Bacillus Brevis Computer Image Processing 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Admiral, G., Mellema, J. E., 1976, The structure of the contractile sheath of bacteriophage Mu, J. Ultrastruct. Res. 56: 48–64.CrossRefGoogle Scholar
  2. Aebi, U., Smith, P. R., Dubochet, J., Henry, C., Kellenberger, E., 1973, A study of the structure of the T-layer of Bacillus brevis, J. Supramol. Struct. 1: 498–522.PubMedCrossRefGoogle Scholar
  3. Amos, L. A., 1974, Image analysis of macromolecular structures, J. Microsc. (Oxford) 100: 143–152.CrossRefGoogle Scholar
  4. Amos, L. A., Klug, A., 1974, The arrangement of subunits in flagellar microtubules, J. Cell Sci. 14: 523–549.PubMedGoogle Scholar
  5. Amos, L. A., Klug, A., 1975, Three-dimensional image reconstruction of the contractile tail of T-4 bacteriophage, J. Mol. Biol. 99: 51–73.PubMedCrossRefGoogle Scholar
  6. Amos, L. A., Henderson, R., Unwin, P. N. T., 1982, Three-dimensional structure determination by electron microscopy of two-dimensional crystals, Prog. Biophys. Mol. Biol. 39: 183–231.PubMedCrossRefGoogle Scholar
  7. Baker, T. S., Casper, D. L. D., Murakami, W. T., 1983, Polyoma virus ‘hexamer’ tubes consist of paired pentamers, Nature (London) 303: 446–448.CrossRefGoogle Scholar
  8. Baumeister, W., Kiibler, O., Zingsheim, H. P., 1981, The structure of the cell envelope of Micrococcus radiodurans revealed by metal shadowing and decoration, J. Ultrastruct. Res. 75: 60–71.PubMedCrossRefGoogle Scholar
  9. Beveridge, T. J., 1981, Ultrastructure, chemistry and function of the bacterial cell wall, Int. Rev. Cytol. 72: 229–317.PubMedCrossRefGoogle Scholar
  10. Burley, S. K., Murray, R. G. E., 1983, Structure of the regular surface layer of Bacillus polymyxa, Can. J. Microbiol. 29: 775–780.CrossRefGoogle Scholar
  11. Carrascosa, J. L., Vinuela, E., Garcia, N., and Santisteban, A., 1982, Structure of the head-tail connector of bacteriophage ϕ 29, J. Mol. Biol. 154: 311–324.PubMedCrossRefGoogle Scholar
  12. Chang, J.-J., Leonard, K., Talmon, A., Pitt, T., Zhang, Y.-X., Lihua, Z., 1982, Structural studies of the outer envelope of Chlamydia trachomatis by electron microscopy, J. Mol. Biol. 161: 579–590.PubMedCrossRefGoogle Scholar
  13. Cremers, A. F. M., Sam, A. P., Bosch, L., Mellema, J. E., 1981, Characterisation of regular polymeric products of elongation factor EF-Tu from Escherichia coli, J. Mol. Biol. 153: 477–486.PubMedCrossRefGoogle Scholar
  14. Crowther, R. A., Amos, L. A., 1971, Harmonic analysis of electron microscope images with rotational symmetry, J. Mol. Biol. 60: 123–130.PubMedCrossRefGoogle Scholar
  15. Crowther, R. A., Klug, A., 1975, Structural analysis of macromolecular assemblies by image reconstruction from electron micrographs, Annu. Rev. Biochem. 44: 161–182.PubMedCrossRefGoogle Scholar
  16. Crowther, R. A., Sleytr, U. B., 1977, An analysis of the fine structure of the surface layers from two strains of Clostridia, including correction for distorted images, J. Ultrastruct. Res. 58: 41–49.PubMedCrossRefGoogle Scholar
  17. Crowther, R. A., Lenk, E. V., Kikuchi, Y., King, J., 1977, Molecular reorganisation in the hexagon to star transition of the baseplate of bacteriophage T4, J. Mol. Biol. 116: 489–523.PubMedCrossRefGoogle Scholar
  18. Deatherage, J. F., Taylor, K. A., Amos, L. A., 1983, Three-dimensional arrangement of the cell wall protein of Sulfolobus acidocaldarius, J. Mol. Biol. 167: 823–852.PubMedCrossRefGoogle Scholar
  19. DeRosier, D. J., Klug, A., 1968, Reconstruction of three-dimensional structures from electron micrographs, Nature (London) 217: 130–134.CrossRefGoogle Scholar
  20. DeRosier, D. J., Klug, A., 1972, Structure of tubular variants of the head of bacteriophage T4 (polyheads). I. Arrangement of the subunits in some classes of polyhead, J. Mol. Biol. 65: 469–488.PubMedCrossRefGoogle Scholar
  21. DeRosier, D. J., Moore, P. B., 1970, Reconstruction of three-dimensional images from electron micrographs of structures having helical symmetry, J. Mol. Biol. 52: 355–369.PubMedCrossRefGoogle Scholar
  22. Driedonks, R. A., Engel, A., ten Heggeler, B., van Driel, R., 1981, Gene 20 product of bacteriophage T4: Its purification and structure, J. Mol. Biol. 152: 641–662.PubMedCrossRefGoogle Scholar
  23. Dubochet, J., Lepault, J., Freeman, R., Berriman, J. A., and Homo, J.-C., 1982, Electron microscopy of frozen water and acqueous solutions, J. Microscopy 128: 219 - 237.CrossRefGoogle Scholar
  24. Dumont, M. E., Wiggins, W. E., Hayward, S. C., 1981, Location of platinum binding sites on bacteriorhodopsin by electron diffraction, Proc. Natl. Acad. Sci. USA 78: 2947–2952.PubMedCrossRefGoogle Scholar
  25. Erickson, H. A., Klug, A., 1971, Measurement and compensation of defocusing and aberrations by Fourier processing of electron micrographs, Philos. Trans. R. Soc. London Ser. B 261: 105–118.CrossRefGoogle Scholar
  26. Fraser, R. D. B., MacRae, T. P., 1973, Conformation in Fibrous Proteins and Related Synthetic Polypeptides, Academic Press, New York.Google Scholar
  27. Fraser, R. D. B., Millward, G. R., 1970, Image averaging by optical filtering, J. Ultrastruct. Res. 31: 203–211.PubMedCrossRefGoogle Scholar
  28. Henderson, R., Unwin, P. N. T., 1975, Three-dimensional model of purple membrane obtained by electron microscopy, Nature (London) 257: 28–32.CrossRefGoogle Scholar
  29. Henry, N. F. M., and Lonsdale, K. (eds.), 1969, International Tables for X-ray Crystallography, Vol. I, Kynoch Press, Birmingham, England.Google Scholar
  30. Kistler, J., Aebi, U., Onorato, L., ten Heggeler, B., Showe, M. K., 1978, Structural changes during the transformation of bacteriophage T4 polyheads—Characterisation of the initial and final stages by freeze-drying and shadowing of Fab-labelled preparations, J. Mol. Biol. 126: 571–589.PubMedCrossRefGoogle Scholar
  31. Klug, A., DeRosier, D. J., 1966, Optical filtering of electron micrographs: Reconstruction of one-sided images, Nature (London) 212: 29–32.CrossRefGoogle Scholar
  32. Klug, A., Crick, F. H. C., Wykoff, H. W., 1958, Diffraction by helical structures, Acta Crystallogr. 11: 199–213.CrossRefGoogle Scholar
  33. Laemmli, U., Amos, L. A., Klug, A., 1976, Correlation between structural transformation and cleavage of the major head protein of T4 bacteriophage, Cell 7: 191–203.PubMedCrossRefGoogle Scholar
  34. Lepault, J., Pitt, T., 1984, Projected structure of unstained, frozen-hydrated T-layer from Bacillus brevis, EMBO J. 3: 101–105.PubMedGoogle Scholar
  35. Lepault, J., Booy, F. P., Dubochet, J., 1983, Electron microscopy of frozen biological specimens, J. Microsc. (Oxford) 129: 89–102.CrossRefGoogle Scholar
  36. Markahm, R., Frey, S., Hills, G., 1963, Methods for the enhancement of detail and accentuation of structure in electron micrographs, Virology 20: 88–102.CrossRefGoogle Scholar
  37. Misell, D. L., 1978, Image analysis, enhancement and interpretation, in: Practical Methods in Electron Microscopy, Vol. 7 (A. M. Glauert, ed.), North-Holland, Amsterdam.Google Scholar
  38. Moody, M. F., 1967, Structure of the sheath of bacteriophage T4. I. Structure of the contracted sheath and polysheath, J. Mol. Biol. 25: 167–200.PubMedCrossRefGoogle Scholar
  39. O’Brien, E. J., and Bennett, P. M., 1972, Structure of a straight flagella from a mutant Salmonella, J. Mol. Biol. 70: 133–152.PubMedCrossRefGoogle Scholar
  40. Saxton, O. W., Baumeister, W., 1982, The correlation averaging of a regularly arranged bacterial cell envelope, J. Microsc. (Oxford) 127: 127–138.CrossRefGoogle Scholar
  41. Sleytr, U. B., Messner, P., 1983, Crystalline surface layers on bacteria, Annu. Rev. Microbiol. 37: 311–339.PubMedCrossRefGoogle Scholar
  42. Steven, A. C., Couture, E., Aebi, U., Showe, M. K., 1976, Structure of T4 polyheads. II. A pathway of polyhead transformations as a model for T4 capsid maturation, J. Mol. Biol. 106: 187–221.PubMedCrossRefGoogle Scholar
  43. Steven, A. C., ten Heggeler, B., Muller, R., Kistler, J., Rosenbruch, J. P., 1977, The ultra- structure of a periodic protein layer on the outer membrane of Escherichia coli, J. Cell Biol. 72: 292–301.PubMedCrossRefGoogle Scholar
  44. Stewart, M., 1975, Location of the troponin binding site on tropomyosin, Proc. R. Soc. London Ser. B 190: 257–266.CrossRefGoogle Scholar
  45. Stewart, M., Beveridge, T. J., 1980, Structure of the regular surface layer of Sporosarcina ureae, J. Bacteriol. 142: 302–309.PubMedGoogle Scholar
  46. Stewart, M., Murray, R. G. E., 1982, Structure of the regular surface layer of Aquaspirillum serpens MW5, J. Bacteriol. 150: 348–357.PubMedGoogle Scholar
  47. Stewart, M., Vigers, G., 1986, Electron microscopy of frozen hydrated biological material, Nature (London) 319: 631–636.CrossRefGoogle Scholar
  48. Stewart, M., Beveridge, T. J., Murray, R. G. E., 1980, Structure of the regular surface layer of Spirillum putridiconchylium, J. Mol. Biol. 137: 1–8.PubMedCrossRefGoogle Scholar
  49. Stewart, M., Beveridge, T. J., Sprott, G. D., 1985, Crystalline order to high resolution in the sheath of Methanospirillum hungatei, J. Mol. Biol. 183: 509–515.PubMedCrossRefGoogle Scholar
  50. Taylor, K., Deatherage, J. F., Amos, L. A., 1982, Structure of the S-layer of Sulfolobus acidocaldarius, Nature (London) 299: 840–842.CrossRefGoogle Scholar
  51. Unwin, P. N. T., 1974, Electron microscopy of the stacked disc aggregate of tobacco mosaic virus. II. The influence of electron irradiation on stain distribution, J. Mol. Biol. 87: 657–670.PubMedCrossRefGoogle Scholar
  52. Unwin, P. N. T., Henderson, R., 1975, Molecular structure determination by electron microscopy of unstained crystalline specimens, J. Mol. Biol. 94: 425–440.PubMedCrossRefGoogle Scholar
  53. Unwin, P. N. T., Klug, A., 1974, Electron microscopy of the stacked disc aggregate of tobacco mosaic virus protein. I. Three-dimensional reconstruction, J. Mol. Biol. 87: 641–656.PubMedCrossRefGoogle Scholar
  54. Wagenknecht, T., DeRosier, D., Shapiro, L., and Weissborn, A., 1981, Three-dimensional reconstruction of the flagellar hook from Caulobacter crescentus, J. Mol. Biol. 151: 439–465.PubMedCrossRefGoogle Scholar
  55. Yanagida, M., DeRosier, D. J., Klug, A., 1972, The structure of the tubular variants of the head of bacteriophage T4 (polyheads). II. Structural transition from a hexamer to a 6+1 morphological unit, J. Mol. Biol. 65: 489–499.PubMedCrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1986

Authors and Affiliations

  • Murray Stewart
    • 1
  1. 1.Laboratory of Molecular BiologyMedical Research CouncilCambridgeEngland

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