Lessons from tomographic studies of the mammalian Golgi

Biochimica et Biophysica Acta - Molecular Cell Research

Volumn 1744, Issue 3 SPEC. ISS., 2005, Pages 273-292

  Marsh, Brad J ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

EM; Golgi; Mammalian; Membrane traffic; Tomography

Indexed keywords

LIPID; PROTEIN;

ACCURACY; AUTOMATION; BIOSYNTHESIS; CELL ORGANELLE; CELL SECRETION; CELL STRUCTURE; CORRELATION ANALYSIS; ELECTRON MICROSCOPY; GENETICS; GOLGI COMPLEX; MAMMAL; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; REVIEW; STRUCTURE ACTIVITY RELATION; TOMOGRAPHY; ULTRASTRUCTURE;

MAMMALIA;

EID: 20544476675     PISSN: 01674889     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamcr.2005.04.002     Document Type: Review

References (174)

1. G.F. Bahr, B.E. Schell, and W.F. Engler Instrumentation for the three-dimensional reconstruction of cellular organelles by electron microscopy Ultramicroscopy 6 1981 251 258
2. D.E. Olins, A.L. Olins, H.A. Levy, R.C. Durfee, S.M. Margle, E.P. Tinnel, and S.D. Dover Electron microscope tomography: transcription in three dimensions Science 220 1983 498 500
3. M.H. Ellisman, J.D. Lindsey, B.O. Carragher, S.H. Kiyonaga, L.R. McEwen, and B.F. McEwen Three dimensional tomographic reconstructions of components of the Golgi apparatus imaged by selective staining and high voltage electron microscopy J. Cell Biol. III 1990 199a
4. M.S. Ladinsky, J.R. Kremer, P.S. Furcinitti, J.R. McIntosh, and K.E. Howell HVEM tomography of the trans-Golgi network: structural insights and identification of a lace-like vesicle coat J. Cell Biol. 127 1994 29 38
5. J. Frank Approaches to large-scale structures Curr. Opin. Struct. Biol. 5 1995 194 201
6. G.E. Soto, S.J. Young, M.E. Martone, T.J. Deerinck, S. Lamont, B.O. Carragher, K. Hama, and M.H. Ellisman Serial section electron tomography: a method for three-dimensional reconstruction of large structures NeuroImage 1 1994 230 243
7. J.D. Lindsey, and M.H. Ellisman The neuronal endomembrane system: I. Direct links between rough endoplasmic reticulum and the cis element of the Golgi apparatus J. Neurosci. 5 1985 3111 3123
8. A. Rambourg, and Y. Clermont E.G. Berger J. Roth The Golgi Apparatus 1997 Birkhauser Verlag Basel 37 61
9. A. Rambourg, and Y. Clermont Three-dimensional electron microscopy: structure of the Golgi apparatus Eur. J. Cell Biol. 51 1990 189 200
10. Y. Clermont, A. Rambourg, and L. Hermo Trans-Golgi network (TGN) of different cell types: three-dimensional structural characteristics and variability Anat. Rec. 242 1995 289 301
11. J. Frank, T. Wagenknecht, B.F. McEwen, M. Marko, C.E. Hsieh, and C.A. Mannella Three-dimensional imaging of biological complexity J. Struct. Biol. 138 2002 85 91
12. J.R. McIntosh Electron microscopy of cells. A new beginning for a new century J. Cell Biol. 153 2001 F25 F32
13. C.A. Larabell, and M.A. Le Gros X-ray tomography generates 3-D reconstructions of the yeast, Saccharomyces cerevisiae, at 60-nm resolution Mol. Biol. Cell 15 2004 957 962
14. R.D. Leapman Novel techniques in electron microscopy Curr. Opin. Neurobiol. 14 2004 591 598
15. G. Schneider X-ray microscopy: methods and perspectives Anal. Bioanal. Chem. 376 2003 558 561
16. J. Kirz, C. Jacobsen, and M. Howells Soft X-ray microscopes and their biological applications Q. Rev. Biophys. 28 1995 33 130
17. M. Howells, C. Jacobsen, J. Kirz, R. Feder, K. McQuaid, and S. Rothman X-ray holograms at improved resolution: a study of zymogen granules Science 238 1987 514 517
18. D. Weiss, G. Schneider, B. Niemann, P. Guttmann, D. Rudolph, and G. Schmahl Computed tomography of cryogenic biological specimens based on X-ray microscopic images Ultramicroscopy 84 2000 185 197
19. M.S. Ladinsky, D.N. Mastronarde, J.R. McIntosh, K.E. Howell, and L.A. Staehelin Golgi structure in three dimensions: functional insights from the normal rat kidney cell J. Cell Biol. 144 1999 1135 1149
20. B.J. Marsh, D.N. Mastronarde, K.F. Buttle, K.E. Howell, and J.R. McIntosh Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography Proc. Natl. Acad. Sci. U. S. A. 98 2001 2399 2406
21. A.B. Novikoff GERL, its form and function in neurons of rat spinal ganglia Biol. Bull. 127 1964 358
22. J.E. Rothman The golgi apparatus: two organelles in tandem Science 213 1981 1212 1219
23. B.J. Marsh, D.N. Mastronarde, J.R. McIntosh, and K.E. Howell Structural evidence for multiple transport mechanisms through the Golgi in the pancreatic beta-cell line, HIT-T15 Biochem. Soc. Trans. 29 2001 461 467
24. J.R. Quatacker Different aspects of membrane differentiation at the inner side (GERL) of the Golgi apparatus in rabbit luteal cells Histochem. J. 11 1979 399 416
25. A.B. Novikoff The endoplasmic reticulum: a cytochemist's view (a review) Proc. Natl. Acad. Sci. U. S. A. 73 1976 2781 2787
26. L. Hermo, H. Green, and Y. Clermont Golgi apparatus of epithelial principal cells of the epididymal initial segment of the rat: structure, relationship with endoplasmic reticulum, and role in the formation of secretory vesicles Anat. Rec. 229 1991 159 176
27. G. Thorne-Tjomsland, Y. Clermont, and X.M. Tang Glucose-6-phosphatase activity of endoplasmic reticulum and Golgi apparatus in spermatocytes and spermatids of the rat: an electron microscopic cytochemical study Biol. Cell 71 1991 33 41
28. S. Mogelsvang, B.J. Marsh, M.S. Ladinsky, and K.E. Howell Predicting function from structure: 3D structure studies of the mammalian Golgi complex Traffic 5 2004 338 345
29. B.J. Marsh, and K.E. Howell The mammalian Golgi-complex debates Nat. Rev., Mol. Cell Biol. 3 2002 789 795
30. A.A. Mironov, P. Weidman, and A. Luini Variations on the intracellular transport theme: maturing cisternae and trafficking tubules J. Cell Biol. 138 1997 481 484
31. H.S. Kweon, G.V. Beznoussenko, M. Micaroni, R.S. Polishchuk, A. Trucco, O. Martella, D. Di Giandomenico, P. Marra, A. Fusella, A. Di Pentima, E.G. Berger, W.J. Geerts, A.J. Koster, K.N. Burger, A. Luini, and A.A. Mironov Golgi enzymes are enriched in perforated zones of golgi cisternae but are depleted in COPI vesicles Mol. Biol. Cell 15 2004 4710 4724
32. A. Trucco, R.S. Polishchuk, O. Martella, A. Di Pentima, A. Fusella, D. Di Giandomenico, E. San Pietro, G.V. Beznoussenko, E.V. Polishchuk, M. Baldassarre, R. Buccione, W.J. Geerts, A.J. Koster, K.N. Burger, A.A. Mironov, and A. Luini Secretory traffic triggers the formation of tubular continuities across Golgi sub-compartments Nat. Cell Biol. 6 2004 1071 1081
33. A.A. Mironov, A.A. Mironov Jr., G.V. Beznoussenko, A. Trucco, P. Lupetti, J.D. Smith, W.J. Geerts, A.J. Koster, K.N. Burger, M.E. Martone, T.J. Deerinck, M.H. Ellisman, and A. Luini ER-to-Golgi carriers arise through direct en bloc protrusion and multistage maturation of specialized ER exit domains Dev. Cell 5 2003 583 594
34. B.J. Marsh, N. Volkmann, J.R. McIntosh, and K.E. Howell Direct continuities between cisternae at different levels of the Golgi complex in glucose-stimulated mouse islet beta cells Proc. Natl. Acad. Sci. U. S. A. 101 2004 5565 5570
35. S. Mogelsvang, N. Gomez-Ospina, J. Soderholm, B.S. Glick, and L.A. Staehelin Tomographic evidence for continuous turnover of Golgi cisternae in Pichia pastoris Mol. Biol. Cell 14 2003 2277 2291
36. P.J. Weidman Anterograde transport through the Golgi complex: do Golgi tubules hold the key? Trends Cell Biol. 5 1995 302 307
37. R. Sannerud, J. Saraste, and B. Goud Retrograde traffic in the biosynthetic-secretory route: pathways and machinery Curr. Opin. Cell Biol. 15 2003 438 445
38. L. Orci, M. Ravazzola, A. Volchuk, T. Engel, M. Gmachl, M. Amherdt, A. Perrelet, T.H. Sollner, and J.E. Rothman Anterograde flow of cargo across the golgi stack potentially mediated via bidirectional "percolating" COPI vesicles Proc. Natl. Acad. Sci. U. S. A. 97 2000 10400 10405
39. L. Orci, M. Amherdt, M. Ravazzola, A. Perrelet, and J.E. Rothman Exclusion of golgi residents from transport vesicles budding from Golgi cisternae in intact cells J. Cell Biol. 150 2000 1263 1270
40. L. Orci, M. Stamnes, M. Ravazzola, M. Amherdt, A. Perrelet, T.H. Sollner, and J.E. Rothman Bidirectional transport by distinct populations of COPI-coated vesicles Cell 90 1997 335 349
41. A. Volchuk, M. Amherdt, M. Ravazzola, B. Brugger, V.M. Rivera, T. Clackson, A. Perrelet, T.H. Sollner, J.E. Rothman, and L. Orci Megavesicles implicated in the rapid transport of intracisternal aggregates across the Golgi stack Cell 102 2000 335 348
42. L.A. Staehelin, and O. Kiermayer Membrane differentiation in the Golgi complex of Micrasterias denticulata Breb. visualized by freeze-etching J. Cell Sci. 7 1970 787 792
43. P. Weidman, R. Roth, and J. Heuser Golgi membrane dynamics imaged by freeze-etch electron microscopy: views of different membrane coatings involved in tubulation versus vesiculation Cell 75 1993 123 133
44. H.C. Ho, C.Y. Tang, and S.S. Suarez Three-dimensional structure of the Golgi apparatus in mouse spermatids: a scanning electron microscopic study Anat. Rec. 256 1999 189 194
45. S. Craig, and L.A. Staehelin High pressure freezing of intact plant tissues. Evaluation and characterization of novel features of the endoplasmic reticulum and associated membrane systems Eur. J. Cell Biol. 46 1988 81 93
46. C.W. Kendall, A.V. Rao, S.A. Janezic, R.J. Temkin, M.J. Hollenberg, and P.J. Lea Tridimensional ultrastructure of perfusion fixed gastrointestinal epithelial cells by high resolution scanning electron microscopy J. Electron Microsc. Tech. 18 1991 223 230
47. G. Thorne-Tjomsland, M. Dumontier, and J.C. Jamieson 3D topography of noncompact zone Golgi tubules in rat spermatids: a computer-assisted serial section reconstruction study Anat. Rec. 250 1998 381 396
48. D.Y. So, R.J. Temkin, and P.J. Lea Effects of brefeldin-A on Golgi morphology in human cultured fibroblasts observed in three-dimensional stereo scanning electron microscopy Scanning 17 1995 161 170
49. W. Denk, and H. Horstmann Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure PLoS Biol. 2 2004 e329
50. A.J. Koster, and J. Klumperman Electron microscopy in cell biology: integrating structure and function Nat. Rev., Mol. Cell Biol. 2003 SS6 SS10 Suppl.
51. P.F. Gilbert The reconstruction of a three-dimensional structure from projections and its application to electron microscopy: II. Direct methods Proc. R. Soc. Lond., B Biol. Sci. 182 1972 89 102
52. D.N. Mastronarde Dual-axis tomography: an approach with alignment methods that preserve resolution J. Struct. Biol. 120 1997 343 352
53. K. Sandberg, D.N. Mastronarde, and G. Beylkin A fast reconstruction algorithm for electron microscope tomography J. Struct. Biol. 144 2003 61 72
54. J.A. Subirana, S. Munoz-Guerra, M. Radermacher, and J. Frank Three-dimensional reconstruction of chromatin fibers J. Biomol. Struct. Dyn. 1 1983 705 714
55. D.P. Barnard, J.N. Turner, J. Frank, and B.F. McEwen A 360 degrees single-axis tilt stage for the high-voltage electron microscope J. Microsc. 167 1992 39 48
56. R. McIntosh, D. Nicastro, and D. Mastronarde New views of cells in 3D: an introduction to electron tomography Trends Cell Biol. 15 2005 43 51
57. A.J. Koster, R. Grimm, D. Typke, R. Hegerl, A. Stoschek, J. Walz, and W. Baumeister Perspectives of molecular and cellular electron tomography J. Struct. Biol. 120 1997 276 308
58. M. Radermacher J. Frank Electron Tomography 1992 Plenum Press New York 91 115
59. P. Penczek, M. Marko, K. Buttle, and J. Frank Double-tilt electron tomography Ultramicroscopy 60 1995 393 410
60. K.A. Taylor, M.C. Reedy, L. Cordova, and M.K. Reedy Three-dimensional reconstruction of rigor insect flight muscle from tilted thin sections Nature 310 1984 285 291
61. E.T. O'Toole, M. Winey, and J.R. McIntosh High-voltage electron tomography of spindle pole bodies and early mitotic spindles in the yeast Saccharomyces cerevisiae Mol. Biol. Cell 10 1999 2017 2031
62. J.L. Murk, G. Posthuma, A.J. Koster, H.J. Geuze, A.J. Verkleij, M.J. Kleijmeer, and B.M. Humbel Influence of aldehyde fixation on the morphology of endosomes and lysosomes: quantitative analysis and electron tomography J. Microsc. 212 2003 81 90
63. J.L. Murk, B.M. Humbel, U. Ziese, J.M. Griffith, G. Posthuma, J.W. Slot, A.J. Koster, A.J. Verkleij, H.J. Geuze, and M.J. Kleijmeer Endosomal compartmentalization in three dimensions: implications for membrane fusion Proc. Natl. Acad. Sci. U. S. A. 100 2003 13332 13337
64. J.L. Murk, M.N. Lebbink, B.M. Humbel, W.J. Geerts, J.M. Griffith, D.M. Langenberg, F.A. Verreck, A.J. Verkleij, A.J. Koster, H.J. Geuze, and M.J. Kleijmeer 3D structure of multilaminar lysosomes in antigen presenting cells reveals trapping of MHC II on the internal membranes Traffic 5 2004 936 945
65. C.E. Hsieh, M. Marko, J. Frank, and C.A. Mannella Electron tomographic analysis of frozen-hydrated tissue sections J. Struct. Biol. 138 2002 63 73
66. B.F. McEwen, M. Marko, C.E. Hsieh, and C. Mannella Use of frozen-hydrated axonemes to assess imaging parameters and resolution limits in cryoelectron tomography J. Struct. Biol. 138 2002 47 57
67. W. Baumeister Electron tomography: towards visualizing the molecular organization of the cytoplasm Curr. Opin. Struct. Biol. 12 2002 679 684
68. J.C. Gilkey, and L.A. Staehelin Advances in ultrarapid freezing for the preservation of cellular ultrastructure J. Electron Microsc. Tech. 3 1986 177 210
69. R. Dahl, and L.A. Staehelin High-pressure freezing for the preservation of biological structure: theory and practice J. Electron. Microsc. Tech. 13 1989 165 174
70. B.F. McEwen, and M. Marko The emergence of electron tomography as an important tool for investigating cellular ultrastructure J. Histochem. Cytochem. 49 2001 553 564
71. C.J. Wilson, D.N. Mastronarde, B. McEwen, and J. Frank Measurement of neuronal surface area using high-voltage electron microscope tomography NeuroImage 1 1992 11 22
72. J.C. Bouwer, M.R. Mackey, A. Lawrence, T.J. Deerinck, Y.Z. Jones, M. Terada, M.E. Martone, S. Peltier, and M.H. Ellisman Automated most-probable loss tomography of thick selectively stained biological specimens with quantitative measurement of resolution improvement J. Struct. Biol. 148 2004 297 306
73. J. Frank Electron Tomography 1992 Plenum New York
74. B.F. McEwen, M. Radermacher, C.L. Rieder, and J. Frank Tomographic three-dimensional reconstruction of cilia ultrastructure from thick sections Proc. Natl. Acad. Sci. U. S. A. 83 1986 9040 9044
75. M.S. Ladinsky, C.C. Wu, S. McIntosh, J.R. McIntosh, and K.E. Howell Structure of the Golgi and distribution of reporter molecules at 20°C reveals the complexity of the exit compartments Mol. Biol. Cell 13 2002 2810 2825
76. P.K. Luther, M.C. Lawrence, and R.A. Crowther A method for monitoring the collapse of plastic sections as a function of electron dose Ultramicroscopy 24 1988 7 18
77. J.R. Kremer, E.T. O'Toole, G.P. Wray, D.N. Mastronarde, S.J. Mitchell, and J.R. McIntosh Proc. XII Int. Congr. Electr. Microsc. vol. 3 1990 752 753
78. G.Y. Fan, S. Peltier, S. Lamont, D.G. Dunkelberger, B.E. Burke, and M.H. Ellisman Multiport-readout frame-transfer 5 megapixel CCD imaging system for TEM applications Ultramicroscopy 84 2000 75 84
79. G.Y. Fan, and M.H. Ellisman Optimization of thin-foil based phosphor screens for CCD imaging in TEM in the voltage range of 80-400 kV Ultramicroscopy 66 1996 11 19
80. P. Zhang, A. Beatty, J.L. Milne, and S. Subramaniam Automated data collection with a Tecnai 12 electron microscope: applications for molecular imaging by cryomicroscopy J. Struct. Biol. 135 2001 251 261
81. A.J. Koster, H. Chen, J.W. Sedat, and D.A. Agard Automated microscopy for electron tomography Ultramicroscopy 46 1992 207 227
82. M.B. Braunfeld, A.J. Koster, J.W. Sedat, and D.A. Agard Cryo automated electron tomography: towards high-resolution reconstructions of plastic-embedded structures J. Microsc. 174 1994 75 84
83. D.N. Mastronarde SerialEM: a program for automated tilt series acquisition on Tecnai microscopes using prediction of specimen position Microsc. Microanal. 9 2003 1182 1183
84. D.N. Mastronarde, B.J. Marsh, and M. Otegui Automated montaging HVEM tomography of large cellular volumes Microsc. Microanal. 7 2001 90 91
85. B.K. Rath, M. Marko, M. Radermacher, and J. Frank Low-dose automated electron tomography: a recent implementation J. Struct. Biol. 120 1997 210 218
86. M. Winey, G.P. Morgan, P.D. Straight, T.H. Giddings Jr., and D.N. Mastronarde Three-dimensional ultrastructure of Saccharomyces cerevisiae meiotic spindles Mol. Biol. Cell 16 3 2005 1178 1188
87. E.T. O'Toole, T.H. Giddings, J.R. McIntosh, and S.K. Dutcher Three-dimensional organization of basal bodies from wild-type and delta-tubulin deletion strains of Chlamydomonas reinhardtii Mol. Biol. Cell 14 2003 2999 3012
88. J. Walz, D. Typke, M. Nitsch, A.J. Koster, R. Hegerl, and W. Baumeister Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification J. Struct. Biol. 120 1997 387 395
89. J.C. Fung, W. Liu, W.J. de Ruijter, H. Chen, C.K. Abbey, J.W. Sedat, and D.A. Agard Toward fully automated high-resolution electron tomography J. Struct. Biol. 116 1996 181 189
90. Q.S. Zheng, M.B. Braunfeld, J.W. Sedat, and D.A. Agard An improved strategy for automated electron microscopic tomography J. Struct. Biol. 147 2004 91 101
91. G.Y. Fan, S.J. Young, P. Miller, and M.H. Ellisman Conditions for electron tomographic data acquisition J. Electron Microsc. (Tokyo) 44 1995 15 21
92. M.S. Otegui, D.N. Mastronarde, B.H. Kang, S.Y. Bednarek, and L.A. Staehelin Three-dimensional analysis of syncytial-type cell plates during endosperm cellularization visualized by high resolution electron tomography Plant Cell 13 2001 2033 2051
93. P. Zhang, M.J. Borgnia, P. Mooney, D. Shi, M. Pan, P. O'Herron, A. Mao, D. Brogan, J.L. Milne, and S. Subramaniam Automated image acquisition and processing using a new generation of 4K × 4K CCD cameras for cryo electron microscopic studies of macromolecular assemblies J. Struct. Biol. 143 2003 135 144
94. J.M. Segui-Simarro, J.R. Austin II, E.A. White, and L.A. Staehelin Electron tomographic analysis of somatic cell plate formation in meristematic cells of Arabidopsis preserved by high-pressure freezing Plant Cell 16 2004 836 856
95. M.S. Otegui, and L.A. Staehelin Electron tomographic analysis of post-meiotic cytokinesis during pollen development in Arabidopsis thaliana Planta 218 2004 501 515
96. G. Perkins, C. Renken, M.E. Martone, S.J. Young, M. Ellisman, and T. Frey Electron tomography of neuronal mitochondria: three-dimensional structure and organization of cristae and membrane contacts J. Struct. Biol. 119 1997 260 272
97. U. Ziese, A.H. Janssen, J.L. Murk, W.J. Geerts, T. Van der Krift, A.J. Verkleij, and A.J. Koster Automated high-throughput electron tomography by pre-calibration of image shifts J. Microsc. 205 2002 187 200
98. R. Grimm, H. Singh, R. Rachel, D. Typke, W. Zillig, and W. Baumeister Electron tomography of ice-embedded prokaryotic cells Biophys. J. 74 1998 1031 1042
99. J. Kurner, O. Medalia, A.A. Linaroudis, and W. Baumeister New insights into the structural organization of eukaryotic and prokaryotic cytoskeletons using cryo-electron tomography Exp. Cell Res. 301 2004 38 42
100. S. Nickell, R. Hegerl, W. Baumeister, and R. Rachel Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography J. Struct. Biol. 141 2003 34 42
101. W. Baumeister Mapping molecular landscapes inside cells Biol. Chem. 385 2004 865 872
102. M. Beck, F. Forster, M. Ecke, J.M. Plitzko, F. Melchior, G. Gerisch, W. Baumeister, and O. Medalia Nuclear pore complex structure and dynamics revealed by cryoelectron tomography Science 306 2004 1387 1390
103. J. Kurner, A.S. Frangakis, and W. Baumeister Cryo-electron tomography reveals the cytoskeletal structure of Spiroplasma melliferum Science 307 2005 436 438
104. J. Bohm, A.S. Frangakis, R. Hegerl, S. Nickell, D. Typke, and W. Baumeister Toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms Proc. Natl. Acad. Sci. U. S. A. 97 2000 14245 14250
105. W. Baumeister, and A.C. Steven Macromolecular electron microscopy in the era of structural genomics Trends Biochem. Sci. 25 2000 624 631
106. D. Nicastro, A.S. Frangakis, D. Typke, and W. Baumeister Cryo-electron tomography of neurospora mitochondria J. Struct. Biol. 129 2000 48 56
107. J. Bohm, O. Lambert, A.S. Frangakis, L. Letellier, W. Baumeister, and J.L. Rigaud FhuA-mediated phage genome transfer into liposomes: a cryo-electron tomography study Curr. Biol. 11 2001 1168 1175
108. A.S. Frangakis, J. Bohm, F. Forster, S. Nickell, D. Nicastro, D. Typke, R. Hegerl, and W. Baumeister Identification of macromolecular complexes in cryoelectron tomograms of phantom cells Proc. Natl. Acad. Sci. U. S. A. 99 2002 14153 14158
109. O. Medalia, I. Weber, A.S. Frangakis, D. Nicastro, G. Gerisch, and W. Baumeister Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography Science 298 2002 1209 1213
110. T. Bretschneider, J. Jonkman, J. Kohler, O. Medalia, K. Barisic, I. Weber, E.H. Stelzer, W. Baumeister, and G. Gerisch Dynamic organization of the actin system in the motile cells of Dictyostelium J. Muscle Res. Cell Motil. 23 2002 639 649
111. K. Grunewald, O. Medalia, A. Gross, A.C. Steven, and W. Baumeister Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding Biophys. Chem. 100 2003 577 591
112. A. Sali, R. Glaeser, T. Earnest, and W. Baumeister From words to literature in structural proteomics Nature 422 2003 216 225
113. K. Grunewald, P. Desai, D.C. Winkler, J.B. Heymann, D.M. Belnap, W. Baumeister, and A.C. Steven Three-dimensional structure of herpes simplex virus from cryo-electron tomography Science 302 2003 1396 1398
114. W. Baumeister, R. Grimm, and J. Walz Electron tomography of molecules and cells Trends Cell Biol. 9 1999 81 85
115. W. Baumeister From proteomic inventory to architecture FEBS Lett. 579 2005 933 937
116. R. Grimm, M. Barmann, W. Hackl, D. Typke, E. Sackmann, and W. Baumeister Energy filtered electron tomography of ice-embedded actin and vesicles Biophys. J. 72 1997 482 489
117. K.R. Porter, A. Claude, and E.F. Fullam A study of tissue culture cells by electron microscopy: methods and preliminary observations J. Exp. Med. 81 1945 233 246
118. P. Zhang, E. Bos, J. Heymann, H. Gnaegi, M. Kessel, P.J. Peters, and S. Subramaniam Direct visualization of receptor arrays in frozen-hydrated sections and plunge-frozen specimens of E. coli engineered to overproduce the chemotaxis receptor Tsr J. Microsc. 216 2004 76 83
119. B.L. Trus, A.C. Steven, A.W. McDowall, M. Unser, J. Dubochet, and R.J. Podolsky Interactions between actin and myosin filaments in skeletal muscle visualized in frozen-hydrated thin sections Biophys. J. 55 1989 713 724
120. A. Al-Amoudi, J.J. Chang, A. Leforestier, A. McDowall, L.M. Salamin, L.P. Norlen, K. Richter, N.S. Blanc, D. Studer, and J. Dubochet Cryo-electron microscopy of vitreous sections EMBO J. 23 2004 3583 3588
121. A. Al-Amoudi, L.P. Norlen, and J. Dubochet Cryo-electron microscopy of vitreous sections of native biological cells and tissues J. Struct. Biol. 148 2004 131 135
122. A. McDowall, J. Gruenberg, K. Romisch, and G. Griffiths The structure of organelles of the endocytic pathway in hydrated cryosections of cultured cells Eur. J. Cell Biol. 49 1989 281 294
123. G.A. Perkins, C.W. Renken, J.Y. Song, T.G. Frey, S.J. Young, S. Lamont, M.E. Martone, S. Lindsey, and M.H. Ellisman Electron tomography of large, multicomponent biological structures J. Struct. Biol. 120 1997 219 227
124. J.R. Kremer, D.N. Mastronarde, and J.R. McIntosh Computer visualization of three-dimensional image data using IMOD J. Struct. Biol. 116 1996 71 76
125. N. Volkmann A novel three-dimensional variant of the watershed transform for segmentation of electron density maps J. Struct. Biol. 138 2002 123 129
126. R.T. Whitaker, and V. Elangovan A direct approach to estimating surfaces in tomographic data Med. Image Anal. 6 2002 235 249
127. C. Bajaj, Z. Yu, and M. Auer Volumetric feature extraction and visualization of tomographic molecular imaging J. Struct. Biol. 144 2003 132 143
128. D.B. Ress, M.L. Harlow, R.M. Marshall, and U.J. McMahan Methods for generating high-resolution structural models from electron microscope tomography data Structure (Camb.) 12 2004 1763 1774
129. A.S. Frangakis, and R. Hegerl Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion J. Struct. Biol. 135 2001 239 250
130. A.S. Frangakis, and R. Hegerl Segmentation of two- and three-dimensional data from electron microscopy using Eigenvector analysis J. Struct. Biol. 138 2002 105 113
131. A.S. Frangakis, and F. Forster Computational exploration of structural information from cryo-electron tomograms Curr. Opin. Struct. Biol. 14 2004 325 331
132. A.S. Frangakis, A. Stoschek, and R. Hegerl Wavelet transform filtering and nonlinear anisotropic diffusion assessed for signal reconstruction performance on multidimensional biomedical data IEEE Trans. Biomed. Eng. 48 2001 213 222
133. K. Mitra, I. Ubarretxena-Belandia, T. Taguchi, G. Warren, and D.M. Engelman Modulation of the bilayer thickness of exocytic pathway membranes by membrane proteins rather than cholesterol Proc. Natl. Acad. Sci. U. S. A. 101 2004 4083 4088
134. P. de Figueiredo, and W.J. Brown A role for calmodulin in organelle membrane tubulation Mol. Biol. Cell 6 1995 871 887
135. W. Stoorvogel, V. Oorschot, and H.J. Geuze A novel class of clathrin-coated vesicles budding from endosomes J. Cell Biol. 132 1996 21 33
136. M. Sachse, G. Ramm, G. Strous, and J. Klumperman Endosomes: multipurpose designs for integrating housekeeping and specialized tasks Histochem. Cell Biol. 117 2002 91 104
137. W. Mobius, E. van Donselaar, Y. Ohno-Iwashita, Y. Shimada, H.F. Heijnen, J.W. Slot, and H.J. Geuze Recycling compartments and the internal vesicles of multivesicular bodies harbor most of the cholesterol found in the endocytic pathway Traffic 4 2003 222 231
138. T. Nilsson, M. Pypaert, M.H. Hoe, P. Slusarewicz, E.G. Berger, and G. Warren Overlapping distribution of two glycosyltransferases in the Golgi apparatus of HeLa cells J. Cell Biol. 120 1993 5 13
139. M.E. Martone, A. Gupta, M. Wong, X. Qian, G. Sosinsky, B. Ludascher, and M.H. Ellisman A cell-centered database for electron tomographic data J. Struct. Biol. 138 2002 145 155
140. C.S. Potter, J. Pulokas, P. Smith, C. Suloway, and B. Carragher Robotic grid loading system for a transmission electron microscope J. Struct. Biol. 146 2004 431 440
141. B. Carragher, N. Kisseberth, D. Kriegman, R.A. Milligan, C.S. Potter, J. Pulokas, and A. Reilein Leginon: an automated system for acquisition of images from vitreous ice specimens J. Struct. Biol. 132 2000 33 45
142. D. Fellmann, J. Pulokas, R.A. Milligan, B. Carragher, and C.S. Potter A relational database for cryoEM: experience at one year and 50,000 images J. Struct. Biol. 137 2002 273 282
143. Y. Zhu, B. Carragher, F. Mouche, and C.S. Potter Automatic particle detection through efficient Hough transforms IEEE Trans. Med. Imaging 22 2003 1053 1062
144. K.R. Diller, and S.J. Aggarwal Computer automated cell size and shape analysis in cryomicroscopy J. Microsc. 146 1987 209 219
145. Y. Zhu, B. Carragher, and C.S. Potter Proceedings of the 2004 IEEE International Symposium on Biomedical Imaging: From Macro to Nano 2004 IEEE Arlington, VA
146. R.S. Polishchuk, E.V. Polishchuk, P. Marra, S. Alberti, R. Buccione, A. Luini, and A.A. Mironov Correlative light-electron microscopy reveals the tubular-saccular ultrastructure of carriers operating between golgi apparatus and plasma membrane J. Cell Biol. 148 2000 45 58
147. S.S. Biel, K. Kawaschinski, K.P. Wittern, U. Hintze, and R. Wepf From tissue to cellular ultrastructure: closing the gap between micro- and nanostructural imaging J. Microsc. 212 2003 91 99
148. A. Egner, S. Verrier, A. Goroshkov, H.D. Soling, and S.W. Hell 4Pi-microscopy of the Golgi apparatus in live mammalian cells J. Struct. Biol. 147 2004 70 76
149. A.A. Mironov, G.V. Beznoussenko, P. Nicoziani, O. Martella, A. Trucco, H.S. Kweon, D. Di Giandomenico, R.S. Polishchuk, A. Fusella, P. Lupetti, E.G. Berger, W.J. Geerts, A.J. Koster, K.N. Burger, and A. Luini Small cargo proteins and large aggregates can traverse the Golgi by a common mechanism without leaving the lumen of cisternae J. Cell Biol. 155 2001 1225 1238
150. F. Capani, M.E. Martone, T.J. Deerinck, and M.H. Ellisman Selective localization of high concentrations of F-actin in subpopulations of dendritic spines in rat central nervous system: a three-dimensional electron microscopic study J. Comp. Neurol. 435 2001 156 170
151. D.K. Sharma, J.C. Brown, A. Choudhury, T.E. Peterson, E. Holicky, D.L. Marks, R. Simari, R.G. Parton, and R.E. Pagano Selective stimulation of caveolar endocytosis by glycosphingolipids and cholesterol Mol. Biol. Cell 15 2004 3114 3122
152. R.E. Pagano, M.A. Sepanski, and O.C. Martin Molecular trapping of a fluorescent ceramide analogue at the Golgi apparatus of fixed cells: interaction with endogenous lipids provides a trans-Golgi marker for both light and electron microscopy J. Cell Biol. 109 1989 2067 2079
153. S.R. Adams, R.E. Campbell, L.A. Gross, B.R. Martin, G.K. Walkup, Y. Yao, J. Llopis, and R.Y. Tsien New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications J. Am. Chem. Soc. 124 2002 6063 6076
154. G. Gaietta, T.J. Deerinck, S.R. Adams, J. Bouwer, O. Tour, D.W. Laird, G.E. Sosinsky, R.Y. Tsien, and M.H. Ellisman Multicolor and electron microscopic imaging of connexin trafficking Science 296 2002 503 507
155. W. Ju, W. Morishita, J. Tsui, G. Gaietta, T.J. Deerinck, S.R. Adams, C.C. Garner, R.Y. Tsien, M.H. Ellisman, and R.C. Malenka Activity-dependent regulation of dendritic synthesis and trafficking of AMPA receptors Nat. Neurosci. 7 2004 244 253
156. G.E. Sosinsky, G.M. Gaietta, G. Hand, T.J. Deerinck, A. Han, M. Mackey, S.R. Adams, J. Bouwer, R.Y. Tsien, and M.H. Ellisman Tetracysteine genetic tags complexed with biarsenical ligands as a tool for investigating gap junction structure and dynamics Cell Commun. Adhes. 10 2003 181 186
157. R.D. Leapman, and R.L. Ornberg Quantitative electron energy loss spectroscopy in biology Ultramicroscopy 24 1988 251 268
158. R.D. Leapman, E. Kocsis, G. Zhang, T.L. Talbot, and P. Laquerriere Three-dimensional distributions of elements in biological samples by energy-filtered electron tomography Ultramicroscopy 100 2004 115 125
159. R.W. Dudek, A.F. Boyne, An excursion through the ultrastructural world of quick-frozen pancreatic islets. Am. J. Anat. 175 (1986) 217-243, 354.
160. R.W. Dudek, A.F. Boyne, and N. Freinkel Quick-freeze fixation and freeze-drying of isolated rat pancreatic islets: application to the ultrastructural localization of inorganic phosphate in the pancreatic beta cell J. Histochem. Cytochem. 29 1981 321 325
161. R.L. Ornberg, and T.S. Reese A freeze-substitution method for localizing divalent cations: examples from secretory systems Fed. Proc. 39 1980 2802 2808
162. R.L. Ornberg, G.A. Kuijpers, and R.D. Leapman Electron probe microanalysis of the subcellular compartments of bovine adrenal chromaffin cells. Comparison of chromaffin granules in situ and in vitro J. Biol. Chem. 263 1988 1488 1493
163. J.C. Linder, and L.A. Staehelin A novel model for fluid secretion by the trypanosomatid contractile vacuole apparatus J. Cell Biol. 83 1979 371 382
164. N. Hirokawa, and T. Kirino An ultrastructural study of nerve and glial cells by freeze-substitution J. Neurocytol. 9 1980 243 254
165. L.D. Pozzo Miller, and D.M. Landis Cytoplasmic structure in organotypic cultures of rat hippocampus prepared by rapid freezing and freeze-substitution fixation Synapse 13 1993 195 205
166. J. Dubochet High-pressure freezing for cryoelectron microscopy Trends Cell Biol. 5 1995 366 368
167. A.L. Olins, D.E. Olins, H.A. Levy, S.M. Margle, E.P. Tinnel, and R.C. Durfee Tomographic reconstruction from energy-filtered images of thick biological sections J. Microsc. 154 Pt. 3 1989 257 265
168. K.F. Han, A.J. Gubbens, J.W. Sedat, and D.A. Agard Optimal strategies for imaging thick biological specimens: exit wavefront reconstruction and energy-filtered imaging J. Microsc. 183 Pt. 2 1996 124 132
169. K.F. Han, J.W. Sedat, and D.A. Agard Mechanism of image formation for thick biological specimens: exit wavefront reconstruction and electron energy-loss spectroscopic imaging J. Microsc. 178 Pt. 2 1995 107 119
170. P. Zhang, W. Land, S. Lee, J. Juliani, J. Lefman, S.R. Smith, D. Germain, M. Kessel, R.D. Leapman, T.A. Rouault, and S. Subramaniam Electron tomography of degenerating neurons in mice with abnormal regulation of iron metabolism J. Struct. Biol. 150 2 2005 144 153
171. U. Ziese, C. Kubel, A. Verkleij, and A.J. Koster Three-dimensional localization of ultrasmall immuno-gold labels by HAADF-STEM tomography J. Struct. Biol. 138 2002 58 62
172. P.A. Midgley, and M. Weyland 3D electron microscopy in the physical sciences: the development of Z-contrast and EFTEM tomography Ultramicroscopy 96 2003 413 431
173. G.J. Yang, and T.S. Huang The effect of median filtering on the edge location estimation Comput. Graph. Image Process. 15 1981 224 245
174. C.S. Potter, H. Chu, B. Frey, C. Green, N. Kisseberth, T.J. Madden, K.L. Miller, K. Nahrstedt, J. Pulokas, A. Reilein, D. Tcheng, D. Weber, and B. Carragher Leginon: a system for fully automated acquisition of 1000 electron micrographs a day Ultramicroscopy 77 1999 153 161