Histochem Cell Biol (2009) 132:253–262 Open Access This article is distributed under the terms of the Crea- tive Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. References Al-Amoudi A, Studer D, Dubochet J (2005) Cutting artifacts and cutting process in vitreous sections for cryo-electron microscopy. J Struct Biol 150:109–121 Al-Amoudi A, Castano-Diez D, Betts MJ, Frangakis AS (2007) The molecular architecture of cadherins in native epidermal desmo- somes. Nature 450:832–837 Alberts B (1998) The cell as a collection of protein machines: prepar- ing the next generation of molecular biologists. Cell 92:291–294 Amos LA, Henderson R, Unwin PN (1982) Three-dimensional struc- ture determination by electron microscopy of two-dimensional crystals. Prog Biophys Mol Biol 39:183–231 Bohm J, Frangakis AS, Hegerl R, Nickell S, Typke D, Baumeister W (2000) Toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomo- grams. Proc Natl Acad Sci USA 97:14245–14250 Böttcher B, Wynne SA, Crowther RA (1997) Determination of the fold of the core protein of hepatitis B virus by electron cryomicrosco- py. Nature 386:88–91 Bouchet-Marquis C, Zuber B, Glynn AM, Eltsov M, Gradenbauer M, Goldie KN, Thomas D, Frangakis AS, Dubochet J, Chretien D (2007) Visualization of cell microtubules in their native state. Biol Cell 99:45–53 Brenner S, Horne RW (1959) A negative staining method for high-res- olution electron microscopy of viruses. Biochim Biophys Acta 34:103–110 Dubochet J, Adrian M, Chang JJ, Homo JC, Lepault J, McDowall AW, Schultz P (1988) Cryo-electron microscopy of vitriWed speci- mens. Q Rev Biophys 21:129–228 Dubochet J, Zuber B, Eltsov M, Bouchet-Marquis C, Al-Amoudi A, Livolant F (2007) How to “read” a vitreous section. In: McIntosh JR (ed) Cellular electron microscopy. Academic, New York, pp 385–406 Edelman L (1991) Freeze-substitution and the preservation of diVus- ible ions. J Microsc 161:217–228 Eltsov M, Maclellan KM, Maeshima K, Frangakis AS, Dubochet J (2008) Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin Wbers in mitotic chro- mosomes in situ. Proc Natl Acad Sci USA 105:19732–19737 Engel A (2003) Robert Feulgen Lecture. Microscopic assessment of membrane protein structure and function. Histochem Cell Biol 120:93–102 Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A (1996) SPIDER and WEB: processing and visualization of imag- es in 3D electron microscopy and related Welds. J Struct Biol 116:190–199 Glaeser RM, Taylor KA (1978) Radiation damage relative to transmis- sion electron microscopy of biological specimens at low temper- ature. J Microsc 112:127–138 Hegerl R, Hoppe W (1976) InXuence of electron noise on three-dimen- sional image reconstruction. Z Naturforsch 31:1717–1721 Henderson R (1995) The potential and limitations of neutrons, elec- trons and X-rays for atomic resolution microscopy of unstained biological molecules. Q Rev Biophys 28:171–193 Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, Down- ing KH (1990) Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol 213:899–929 261 Hobot JA, Villiger W, Escaig J, Maeder M, Ryter A, Kellenberger E (1985) The shape and Wne structure of the nucleoid observed on sections of ultrarapid frozen and cryosubstituted bacteria. J Bac- teriol 162:960–971 Humbel B, Müller M (1986) Freeze substitution and low temperature embedding. In: Müller M, Becker RP, Boyde A, Wolosewick JJ (eds) The science of biological specimen preparation 1985. AMF O’Hare, SEM Inc., pp 175–183 Jin L, Milazzo AC, Kleinfelder S, Li S, Leblanc P, Duttweiler F, Bouwer JC, Peltier ST, Ellisman MH, Xuong NH (2008) Appli- cations of direct detection device in transmission electron micros- copy. J Struct Biol 161:352–358 Kellenberger E (1991) The potential of cryoWxation and freeze substi- tution: observations and theoretical considerations. J Microsc 163:183–203 Kelly DF, Dukovshi D, Walz T (2008) Monolayer puriWcation: a rapid method for isolating protein complexes for single-particle elec- tron microscopy. Proc Natl Acad Sci USA 105:4703–4708 Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visuali- zation of three-dimensional image data using IMOD. J Struct Biol 116:71–76 Lucic V, Leis A, Baumeister W (2008) Cryo-electron tomography of cells: connecting structure and function. Histochem Cell Biol 130:185–196 Marko M, Hsieh C, Schalek R, Frank J, Mannella C (2007) Focused- ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy. Nat Methods 4:215–217 Marsh BJ, Mastronarde DN, Buttle KF, Howell KE, McIntosh JR (2001) Organellar relationships in the Golgi region of the pancre- atic beta cell line, HIT-T15, visualized by high resolution electron tomography. Proc Natl Acad Sci USA 98:2399–2406 McIntosh JR (2001) Electron microscopy of cells: a new beginning for a new century. J Cell Biol 153:25–32 McIntosh JR (2007) Cellular electron microscopy. Academic, San Diego McIntosh JR, Grishchuk EL, Morphew MK, Efremov AK, Zhudenkov K, Volkov VA, Cheeseman IM, Desai A, Mastronarde DN, Atau- llakhanov FI (2008) Fibrils connect microtubule tips with kineto- chores: a mechanism to couple tubulin dynamics to chromosome motion. Cell 135:322–333 Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W (2002) Macromolecular architecture in eukaryotic cells visual- ized by cryoelectron tomography. Science 298:1155–1157 Mercogliano CP, DeRosier DJ (2007) Concatenated metallothionein as a clonable gold label for electron microscopy. J Struct Biol 160:70–82 Millen JI, Pierson J, Kvam E, Olsen LJ, Goldfarb DS (2008) The lumi- nal N-terminus of yeast Nvj1 is an inner nuclear membrane anchor. TraYc 9:1653–1664 Miyazawa A, Fujiyoshi Y, Unwin N (2003) Structure and gating mech- anism of the acetylcholine receptor pore. Nature 423:949–955 Müller M (1992) The integrating power of cryoWxation-based electron microscopy in biology. Acta Microsc 1:37–44 Müller M, Marti T, Kriz S (1980) Improved structural preservation by freeze substitution. In: Brederoo P, de Priester W (eds) Proceed- ings of the 7th European congress on electron microscopy. Leiden University Press, Leiden, pp 720–721 Murata K, Mitsuoka K, Hirai T, Walz T, Agre P, Heymann JB, Engel A, Fujiyoshi Y (2000) Structural determinants of water perme- ation through aquaporin-1. Nature 407:599–605 Murk JL, Posthuma G, Koster AJ, Geuze HJ, Verkleij AJ, Kleijmeer MJ, Humbel BM (2003) InXuence of aldehyde Wxation on the morphology of endosomes and lysosomes: quantitative analysis and electron tomography. J Microsc 212:81–90 Nicastro D, Schwartz C, Pierson J, Gaudette R, Porter ME, McIntosh JR (2006) The molecular architecture of axonemes revealed by cryoelectron tomography. Science 313:944–948 123