Abstract
Soft X-ray microscopy is ideally suited to visualizing and quantifying biological cells. Specimens, including eukaryotic cells, are imaged intact, unstained and fully hydrated, and therefore visualized in a near-native state. The contrast in soft X-ray microscopy is generated by the differential attenuation of X-rays by the molecules in the specimen—water is relatively transmissive to this type of illumination compared to carbon and nitrogen. The attenuation of X-rays by the specimen follows the Beer–Lambert law, and therefore both linear and a quantitative measure of thickness and chemical species present at each point in the cell. In this chapter, we will describe the procedures and computational methods that lead to 50 nm (or better) tomographic reconstructions of cells using soft X-ray microscope data, and the subsequent segmentation and analysis of these volumetric reconstructions. In addition to being a high-fidelity imaging modality, soft X-ray tomography is relatively high-throughput; a complete tomographic data set can be collected in a matter of minutes. This new modality is being applied to imaging cells that range from small prokaryotes to stem cells obtained from mammalian tissues.
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References
Larabell CA, Nugent KA (2010) Imaging cellular architecture with X-rays. Curr Opin Struct Biol 20:623–631
Leis A, Rockel B, Andrees L, Baumeister W (2009) Visualizing cells at the nanoscale. Trends Biochem Sci 34:60–70
Fagarasanu A, Fagarasanu M, Rachubinski RA (2007) Maintaining peroxisome populations: a story of division and inheritance. Annu Rev Cell Dev Biol 23:321–344
Warren G, Wickner W (1996) Organelle inheritance. Cell 84:395–400
Uchida M, Sun Y, McDermott G et al (2011) Quantitative analysis of yeast internal architecture using soft X-ray tomography. Yeast 28:227–236
Baumeister W (2002) Electron tomography: towards visualizing the molecular organization of the cytoplasm. Curr Opin Struct Biol 12:679–684
Natterer F (1986) The mathematics of computerized tomography. Wiley, New York
Larabell CA, McDermott G, Le Gros MA (2005) X-ray tomography of whole cells. Curr Opin Struct Biol 15:593–600
McDermott G, Le Gros MA, Knoechel CG, Uchida M, Larabell CA (2009) Soft X-ray tomography and cryogenic light microscopy: the cool combination in cellular imaging. Trends Cell Biol 19:587–595
Uchida M, McDermott G, Wetzler M et al (2009) Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans. Proc Natl Acad Sci USA 106:19375–19380
Attwood DT (1999) Soft X-rays and extreme ultraviolet radioation: principles and applications. Cambridge University Press, New York
Weiss D (2000) Computed tomography based on cryo X-ray microscopic images of unsectioned biological specimens. Georg-August University of Göttingen, Göttingen
Le Gros MA, McDermott G, Larabell CA (2005) X-ray tomography of whole cells. Curr Opin Struct Biol 15:593–600
Parkinson DY, McDermott G, Etkin LD, Le Gros MA, Larabell CA (2008) Quantitative 3-D imaging of eukaryotic cells using soft X-ray tomography. J Struc Biol 162:380–386
Larabell C, McDermott G, Uchida M, Knoechel C, Le Gros MA (2009) Imaging whole cells at better than 50 nm isotropic resolution with X-rays. Abst, Papers Am Chem Soc, 238
Larabell CA, Le Gros MA (2004) X-ray tomography generates 3-D reconstructions of the yeast, saccharomyces cerevisiae, at 60-nm resolution. Mol Biol Cell 15:957–962
Bertilson M, Von Hofsten O, Lindblom M, Wilhein T, Hertz H, Vogt U (2008) Compact high-resolution differential interference contrast soft X-ray microscopy. App Phys Lett 92:064104
Bertilson MC, Takman PAC, Holmberg A, Vogt U, Hertz HM (2007) Laboratory arrangement for soft X-ray zone plate efficiency measurements. Rev Sci Instrum 78:026103–026101
Takman PAC, Stollberg H, Johansson GA, Holmberg A, Lindblom M, Hertz HM (2007) High-resolution compact X-ray microscopy. J Microsc 226:175–181
Bell PB, SafiejkoMroczka B (1997) Preparing whole mounts of biological specimens for imaging macromolecular structures by light and electron microscopy. Int J Imaging Syst Tech 8:225–239
Quintana C (1994) Cryofixation, Cryosubstitution, Cryoembedding for Ultrastructural, Immunocytochemical and Microanalytical Studies. Micron 25:63–99
Ryan KP (1992) Cryofixation of tissues for electron-microscopy—a review of plunge cooling methods. Scanning Microsc 6:715–743
Studer D, Humbel BM, Chiquet M (2008) Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution. Histochem Cell Biol 130:877–889
Le Gros MA, McDermott G, Uchida M, Knoechel CG, Larabell CA (2009) High-aperture cryogenic light microscopy. J Microsc 235:1–8
Acknowledgments
XM-2 and associated research is funded by the Department of Energy Office of Biological and Environmental Research Grant DE-AC02-05CH11231, and the NIH National Center for Research Resources Grant RR019664.
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Parkinson, D.Y., Epperly, L.R., McDermott, G., Le Gros, M.A., Boudreau, R.M., Larabell, C.A. (2013). Nanoimaging Cells Using Soft X-Ray Tomography. In: Sousa, A., Kruhlak, M. (eds) Nanoimaging. Methods in Molecular Biology, vol 950. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-137-0_25
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DOI: https://doi.org/10.1007/978-1-62703-137-0_25
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