Reprint of "Three-dimensional elemental mapping of phosphorus by quantitative electron spectroscopic tomography (QuEST)" [J. Struct. Biol. 160 (2007) 35-48]

Journal of Structural Biology

Volumn 161, Issue 3, 2008, Pages 322-335

  Aronova, M A ^a   Kim, Y C ^b   Harmon, R ^c   Sousa, A A ^a   Zhang, G ^a   Leapman, R D ^a  

^a NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING   (United States)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^c GATAN INC   (United States)

Author keywords

3 D reconstruction; Chromatin; Electron energy loss spectroscopy; Electron tomography; Energy filtered transmission electron microscopy (EFTEM); Nucleus; Phosphorus; Quantitative elemental imaging; Ribosome

Indexed keywords

ELEMENT; NUCLEIC ACID; PHOSPHORUS;

ACCURACY; ALGORITHM; ARTICLE; CELL DENSITY; CELL NUCLEUS; CHROMATIN; ENERGY FILTERED TRANSMISSION ELECTRON MICROSCOPY; EUKARYOTIC CELL; IMAGE QUALITY; IMAGE RECONSTRUCTION; NANOANALYSIS; PRIORITY JOURNAL; QUANTITATIVE ELECTRON SPECTROSCOPIC TOMOGRAPHY; RIBOSOME; SENSITIVITY ANALYSIS; SIMULTANEOUS ITERATIVE RECONSTRUCTION TECHNIQUE; SPECTROSCOPY; THREE DIMENSIONAL IMAGING;

ANIMALS; DROSOPHILA; ELECTRONS; PHOSPHORUS; TOMOGRAPHY;

EUKARYOTA;

EID: 40649093068     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/S1047-8477(08)00062-2     Document Type: Article

References (49)

1. Abolhassani-Dadrasa S., Mayerb J., and Fakana S. Estimation of phosphorus and sulphur contents in nuclear constituents by means of image-EELS analysis using ribosomes as internal standards. Micron 29 (1998) 461-468
2. Andersen A.H., and Kak A.C. Simultaneous algebraic reconstruction technique (SART): a superior implementation of the ART algorithm. Ultrasonic Imaging 6 (1984) 81-94
3. Aronova M.A., Kim Y.C., Zhang G., and Leapman R.D. Quantification and thickness correction of EFTEM phosphorus maps. Ultramicroscopy 107 (2007) 232-244
4. Bazett-Jones D.P., Locklear L., and Rattner J.B. Electron spectroscopic imaging of DNA. J. Ultrastruc. Mol. Struc. Res. 99 (1988) 48-58
5. Bazett-Jones D.P., Mendez E., Czarnota G.J., Ottensmeyer F.P., and Allfrey V.G. Visualization and analysis of unfolded nucleosomes associated with transcribing chromatin. Nucleic Acids Res. 24 (1996) 321-329
6. Bazett-Jones D.P., and Hendzel M.J. Electron spectroscopic imaging of chromatin. Methods Enzymol 17 (1999) 188-200
7. Bazett-Jones D.P., Hendzel M.J., and Kruhlak M.J. Stoichiometric analysis of protein- and nucleic acid-based structures in the cell nucleus. Micron 30 (1999) 151-157
8. Braunfeld M.B., Koster A.J., Sedat J.W., and Agard D.A. Cryo automated electron tomography: towards high-resolution reconstructions of plastic-embedded structures. J. Micros. 174 (1993) 75-84
9. De Rosier D.J., and Klug A. Reconstruction of three dimensional structures from electron micrographs. Nature 217 (1968) 130-134
10. Deans S.R. The Radon Transform and Some of its Applications (1983), John Wiley & Sons, New York pp. 96-100
11. Draper N.R., and Smith H. Applied Regression Analysis. second ed. (1981), Wiley, New York
12. Egerton R.F. K-shell ionization cross-sections for use in microanalysis. Ultramicroscopy 4 (1979) 169-179
13. Egerton R.F. Electron Energy Loss Spectroscopy. second ed. (1996), Plenum, New York
14. Egerton R.F. New techniques in electron energy-loss spectroscopy and energy-filtered imaging. Micron 34 (2003) 127-139
15. Egerton R.F., Wang F., and Crozier P.A. Beam-induced damage to this specimens in an intense electron probe. Microsc. Microanal. 12 (2006) 65-71
16. Frank J. Electron Tomography: Three-Dimensional Imaging with the Transmission Electron Microscope (1992), Plenum, New York
17. Frank J. Electron Tomography: Methods for Three-Dimensional Visualization of Structures in the Cell. second ed. (2006), Springer, New York
18. Friedrich H., McCartney M.R., and Buseck P.R. Comparison of intensity distributions in tomograms from BF, TEM, ADF STEM, HAADF STEM, and calculated tilt series. Ultramicroscopy 106 (2005) 18-27
19. Gilbert P. Iterative methods for the three-dimensional reconstructin of an object from projections. J. Theor. Biol. 36 (1972) 105-117
20. Gilbert P. The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. II. Direct methods. Proc. R. Soc. Lond. B. 182 (1972) 89-102
21. Goitein M. Three-dimensional density reconstruction from a series of two-dimensional projections. Nucl. Instrum. Methods 101 (1972) 509-518
22. Goping G., Pollard H.B., Srivastava M., and Leapman R. Mapping protein expression in mouse pancreatic islets by immunolabeling and electron energy loss spectrum-imaging. Microsc. Res. Tech. 61 (2003) 448-456
23. Gordon R., Bender R., and Herman G.T. Algebraic reconstruction techniques (ART) for three-dimensional electron microscopy and X-ray photography. J. Theor. Biol. 29 (1970) 471-481
24. Haking A., Troester H., Richter K., Crucifix C., Spring H., and Trenderlenburg F. An approach to an objective background subtraction for elemental mapping with core-edges down to 50 eV: description, evaluation and application. Ultramicrosocopy 80 (1999) 163-182
25. Harmon R.T., Meyer S., and Hunt J.A. Software for EFTEM Tomography Incorporated into Digital Micrograph/GMS (2005), Gatan, Inc., Pleasanton, CA
26. Herman, G.T., 1980. Image Reconstruction from Projections, the Fundamentals of Computerized Tomography. Academic Press, New York (Chapters 6 and 11).
27. Hofer F., and Warbichler P. Elemental mapping using energy filtered imaging. In: Ahn C. (Ed). Transmission Electron Energy Loss Spectrometry in Materials Science and the EELS Atlas. second ed. (2004), Wiley-VCH, Berlin Chapter 6
28. Kak A.C., and Slaney M. Principles of Computerized Tomographic Imaging (1988), IEEE Press, New York Chapter 7
29. König, P., Braunfeld, M.B., Sedat, J.W., Agard, D.A., 2007. The three-dimensional structure of in vitro reconstituted Xenopus laevis chromosomes by EM tomography. Chromosoma, online reference (doi:10.1007/s00412-007-0101-0).
30. Korn A., Spitnik-Elson P., Elson D., and Ottensmeyer F.P. Specific visualization of ribosomal RNA in the intact ribosome by electron spectroscopic imaging. Eur. J. Cell Biol. 31 (1983) 334-340
31. Koster A.J., Grimm R., Typke D., Hegerl R., Stoschek A., Walz J., and Baumeister W. Perspectives of molecular and cellular electron tomography. J. Struct. Biol. 120 (1997) 276-308
32. Kremer J.S., Mastronarde D.N., and McIntosh J.R. Computer visualization of three dimensional image data using IMOD. J. Struct. Biol. 116 (1996) 71-76
33. Krivanek O., Friedman S., Gubbens A., and Kraus B. An imaging filter for biological applications. Ultramicroscopy 59 (1995) 267-282
34. Leapman R.D. STEM elemental mapping by electron energy-loss spectroscopy. Ann. N.Y. Acad. Sci. 483 (1986) 326-338
35. Leapman R.D., Jarnik M., and Steven A.C. Spatial distributions of sulfur-rich proteins in cornifying epithelia. J. Struct Biol. 120 (1997) 168-179
36. Leapman R.D., and Rizzo N.W. Towards single atom analysis of biological structures. Ultramicroscopy 78 (1999) 251-268
37. Leapman R.D., Kocsis E., Zhang G., Talbot T.L., and Laquerriere P. Three-dimensional distributions of elements in biological samples by energy-filtered electron tomography. Ultramicroscopy 100 (2004) 115
38. Mastronarde D.N. Dual axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120 (1997) 343-352
39. McIntosh R., Nicastro D., and Mastronarde D. New views of cells in 3D: and introduction to electron tomography. Trends Cell Biol. 15 1 (2005) 1-9
40. Mercury Computer Systems. 2006. Amira, Version 4.1.
41. Midgley P.A., and Weyland M. 3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography. Ultramicroscopy 96 (2003) 413
42. Muller S.A., Coldie K.N., Bürki R., Häring R., and Engel A. Factors influencing the precision of quantitative scanning transmission electron microscopy. Ultramircoscopy 46 (1992) 317-334
43. Ottensmeyer F.P., and Andrew J.W. High-resolution microanalysis of biological specimens by electron energy loss spectroscopy and by electron spectroscopic imaging. J. Ultrastruct. Res. 72 (1980) 336-348
44. Ottensmeyer F.P. Electron spectroscopic imaging: parallel energy filtering and microanalysis in the fixed-beam electron microscope. J. Ultrastruct. Res. 88 (1984) 121-134
45. Penczek P., Marko M., Buttle K., and Frank J. Double-tilt electron tomography. Ultramicroscopy 60 (1995) 393-410
46. Schalch T., Duda S., Sargent D.F., and Richmond T.J. X-ray structure of a tetranucleosome and its applications for the chromatin fibre. Nature 436 (2005) 138-141
47. Semmler K., Wunderlich J., Richter W., and Meyer H.W. High-pressure freezing causes structural alterations in phospholipid model membranes. J. Microsc. 190 (1998) 317-327
48. Shepp L.A. Computerized tomography and nuclear magnetic resonance. J. Comp. Assist. Tomo. 4 1 (1980) 94-107
49. Tong J., Arslan I., and Midgley P. A novel dual axis iterative algorithm for electron tomography. J. Struct. Biol. 153 (2006) 55-63