Correlative microscopy methods that maximize specimen fidelity and data completeness, and improve molecular localization capabilities

Journal of Structural Biology

Volumn 184, Issue 1, 2013, Pages 12-20

  Smith, Elizabeth A ^a   Cinquin, Bertrand P ^a   McDermott, Gerry ^a   Le Gros, Mark A ^a,b   Parkinson, Dilworth Y ^b   Kim, Hong Tae ^c   Larabell, Carolyn A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c Catholic University of Daegu   (South Korea)

Author keywords

Cellular imaging; Cryo Flourescence microscopy; Hybrid methods; Localization; Tomography

Indexed keywords

ARTICLE; CELLULAR DISTRIBUTION; CHEMICAL STRUCTURE; COMPUTED TOMOGRAPHY SCANNER; CRYOELECTRON MICROSCOPY; ELECTRON TOMOGRAPHY; FLUORESCENCE MICROSCOPY; HUMAN; IN VIVO STUDY; INFORMATION PROCESSING; LYMPHOCYTE; NONHUMAN; POSITION; PRIORITY JOURNAL;

CELLULAR IMAGING; CFM; CRYO-FLOURESCENCE MICROSCOPY; CRYOGENIC FLUORESCENCE MICROSCOPY; FLUORESCENCE MICROSCOPY; FM; HYBRID METHODS; LAC; LINEAR ABSORPTION COEFFICIENT; LOCALIZATION; POINT SPREAD FUNCTION; PSF; SOFT X-RAY TOMOGRAPHY; SXT; TOMOGRAPHY; YELLOW FLUORESCENT PROTEIN; YFP;

CRYOPRESERVATION; MICROSCOPY, FLUORESCENCE; TOMOGRAPHY, X-RAY;

EID: 84884819857     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2013.03.006     Document Type: Article

References (58)

1. Al-Amoudi A., Chang J.J., Leforestier A., McDowall A., Salamin L.M., et al. Cryo-electron microscopy of vitreous sections. Embo J. 2004, 23:3583-3588.
2. Attwood D.T. Soft X-rays and Extreme Ultraviolet Radiation: Principles and Applications 1999, Cambridge University Press, Cambridge, New York.
3. Baumeister W. Electron tomography: towards visualizing the molecular organization of the cytoplasm. Curr. Opin. Struct. Biol. 2002, 12:679-684.
4. Baumeister W., Gruska M., Medalia O., Leis A. Electron tomography of vitreous sections from cultured mammalian cells. J. Struct. Biol. 2008, 161:384-392.
5. Baumeister W., Vanhecke D., Asano S., Kochovski Z., Fernandez-Busnadiego R., et al. Cryo-electron tomography: methodology, developments and biological applications. J. Microsc. 2011, 242:221-227.
6. Bell P.B., SafiejkoMroczka B. Preparing whole mounts of biological specimens for imaging macromolecular structures by light and electron microscopy. Int. J. Imaging Syst. Technol. 1997, 8:225-239.
7. Chao W., Kim J., Rekawa S., Fischer P., Anderson E.H. Demonstration of 12nm resolution Fresnel zone plate lens based soft X-ray microscopy. Opt. Express 2009, 17:17669-17677.
8. Cyrklaff M., Kudryashev M., Leis A., Leonard K., Baumeister W., et al. Cryoelectron tomography reveals periodic material at the inner side of subpellicular microtubules in apicomplexan parasites. J. Exp. Med. 2007, 204:1281-1287.
9. Dubochet J., Knapek E., Dietrich I. Reduction of beam damage by cryoprotection at 4k. Ultramicroscopy 1981, 6:77-80.
10. Dubochet J., Adrian M., Chang J.J., Homo J.C., Lepault J., et al. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 1988, 21:129-228.
11. Falcone R., Jacobsen C., Kirz J., Marchesini S., Shapiro D., et al. New directions in X-ray microscopy. Contemp. Phys. 2011, 52:293-318.
12. Fischer P., Kim D.H., Chao W.L., Liddle J.A., Anderson E.H., et al. Soft X-ray microscopy of nanomagnetism. Mater. Today 2006, 9:26-33.
13. Giepmans B.N., Adams S.R., Ellisman M.H., Tsien R.Y. The fluorescent toolbox for assessing protein location and function. Science 2006, 312:217-224.
14. Giepmans B.N., Deerinck T.J., Smarr B.L., Jones Y.Z., Ellisman M.H. Correlated light and electron microscopic imaging of multiple endogenous proteins using Quantum dots. Nat. Methods 2005, 2:743-749.
15. Gilman M.D., Fischman A.J., Krishnasetty V., Halpern E.F., Aquino S.L. Hybrid PET/CT of the thorax: when is computer registration necessary?. J. Comput. Assist. Tomogr. 2007, 31:395-401.
16. Hagen C., Guttmann P., Klupp B., Werner S., Rehbein S., et al. Correlative VIS-fluorescence and soft X-ray cryo-microscopy/tomography of adherent cells. J. Struct. Biol. 2012, 177:193-201.
17. Heintzmann R., Cremer C. Axial tomographic confocal fluorescence microscopy. J. Microsc. 2002, 206:7-23.
18. Kirz J., Jacobsen C., Howells M. Soft X-ray microscopes and their biological applications. Q. Rev. Biophys. 1995, 28:33-130.
19. Kremer J.R., Mastronarde D.N., McIntosh J.R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 1996, 116:71-76.
20. Krishnasetty V., Fischman A.J., Halpern E.L., Aquino S.L. Comparison of alignment of computer-registered data sets: combined PET/CT versus independent PET and CT of the thorax. Radiology 2005, 237:635-639.
21. Larabell C., Le Gros M. Whole cell cryo X-ray tomography and protein localization at 50micron resolution. Biophys. J. 2004, 86:185A. 185A.
22. Larabell C.A., Le Gros M.A. X-ray tomography generates 3-D reconstructions of the yeast, saccharomyces cerevisiae, at 60-nm resolution. Mol. Biol. Cell 2004, 15:957-962.
23. Larabell C.A., Nugent K.A. Imaging cellular architecture with X-rays. Curr. Opin. Struct. Biol. 2010, 20:623-631.
24. Le Gros M.A., McDermott G., Larabell C.A. X-ray tomography of whole cells. Curr. Opin. Struct. Biol. 2005, 15:593-600.
25. Le Gros M.A., McDermott G., Uchida M., Knoechel C.G., Larabell C.A. High-aperture cryogenic light microscopy. J. Microsc. 2009, 235:1-8.
26. Leforestier A., Richter K., Livolant F., Dubochet J. Comparison of slam-freezing and high-pressure freezing effects on the DNA cholesteric liquid crystalline structure. J. Microsc. 1996, 184:4-13.
27. Leis A., Rockel B., Andrees L., Baumeister W. Visualizing cells at the nanoscale. Trends Biochem. Sci. 2009, 34:60-70.
28. Leis A.P., Beck M., Gruska M., Best C., Hegerl R., et al. Cryo-electron tomography of biological specimens. IEEE Signal Process. Mag. 2006, 23:95-103.
29. Lucic V., Kossel A.H., Yang T., Bonhoeffer T., Baumeister W., et al. Multiscale imaging of neurons grown in culture: from light microscopy to cryo-electron tomography. J. Struct. Biol. 2007, 160:146-156.
30. Martone M.E., Deerinck T.J., Yamada N., Bushong E., Ellisman M.H. Correlated 3D light and electron microscopy: use of high voltage electron microscopy and electron tomography for imaging large biological structures. J. Histotechnol. 2000, 23:261-270.
31. Mastronarde D.N. Fiducial marker and hybrid alignment methods for single-and double-axis tomography. Electron Tomography: Methods for Three-Dimensional Visualization of Structures in the Cell 2005, 163-185. Springer, New York, NY. J. Frank (Ed.).
32. McDermott G., Le Gros M.A., Larabell C.A. Visualizing cell architecture and molecular location using soft X-ray tomography and correlated cryo-light microscopy. Annu. Rev. Phys. Chem. 2012, 63(63):225-239.
33. McDermott G., Le Gros M.A., Knoechel C.G., Uchida M., Larabell C.A. Soft X-ray tomography and cryogenic light microscopy: the cool combination in cellular imaging. Trends Cell Biol. 2009, 19:587-595.
34. McDermott G., Fox D.M., Epperly L., Wetzler M., Barron A.E., et al. Visualizing and quantifying cell phenotype using soft X-ray tomography. BioEssays 2012, 34:320-327.
35. Moerner W.E., Orrit M. Illuminating single molecules in condensed matter. Science 1999, 283:1670-1676.
36. Natterer F. The Mathematics of Computerized Tomography 1986, Wiley, New York, NY.
37. Natterer F., Wübbeling F. Mathematical Methods in Image Reconstruction 2001, Cambridge University Press, Cambridge, New York.
38. Nicastro D., Frangakis A.S., Typke D., Baumeister W. Cryo-electron tomography of Neurospora mitochondria. J. Struct. Biol. 2000, 129:48-56.
39. Parkinson D.Y., Knoechel C., Yang C., Larabell C.A., Le Gros M.A. Automatic alignment and reconstruction of images for soft X-ray tomography. J. Struct. Biol. 2012, 177:259-266.
40. Quintana C. Cryofixation, cryosubstitution, cryoembedding for ultrastructural, immunocytochemical and microanalytical studies. Micron 1994, 25:63-99.
41. Ryan K.P. Cryofixation of tissues for electron-microscopy - a review of plunge cooling methods. Scanning Microsc. 1992, 6:715-743.
42. Sartori A., Gatz R., Beck F., Rigort A., Baumeister W., et al. Correlative microscopy: bridging the gap between fluorescence light microscopy and cryo-electron tomography. J. Struct. Biol. 2007, 160:135-145.
43. Sartori A., Gatz R., Beck F., Kossel A., Leis A., et al. Correlation microscopy: bridging the gap between light- and cryo-electron microscopy. Microsc. Microanal. 2005, 11:16-17.
44. Satzler K., Eils R. Resolution improvement by 3-D reconstructions from tilted views in axial tomography and confocal theta microscopy. Bioimaging 1997, 5:171-182182.
45. Schneider G. High-resolution X-ray microscopy of radiation sensitive material 1999, Cuvillier Verlag, Gottingen, Germany.
46. Schneider G. X-ray microscopy: methods and perspectives. Anal. Bioanal. Chem. 2003, 376:558-561.
47. Schneider G., Denbeaux G., Anderson E., Pearson A., Bates W., et al. High resolution X-ray tomography with applications in biology and materials science. J. Phys. IV 2003, 104:607-613.
48. Shaner N.C., Steinbach P.A., Tsien R.Y. A guide to choosing fluorescent proteins. Nat. Methods 2005, 2:905-909.
49. Shaw P.J., Agard D.A., Hiraoka Y., Sedat J.W. Tilted view reconstruction in optical microscopy - 3-dimensional reconstruction of Drosophila melanogaster embryo nuclei. Biophys. J. 1989, 55:101-110.
50. Spector D.L. Nuclear organization and gene expression. Exp. Cell Res. 1996, 229:189-197.
51. Spector D.L. Nuclear domains. J. Cell Sci. 2001, 114:2891-2893.
52. Stayman J.W., Fessler J.A. Compensation for nonuniform resolution using penalized-likelihood reconstruction in space-variant imaging systems. IEEE Trans. Med. Imaging 2004, 23:269-284.
53. Swoger J., Huisken J., Stelzer E.H.K. Multiple imaging axis microscopy improves resolution for thick-sample applications. Opt. Lett. 2003, 28:1654-1656.
54. Swoger J., Verveer P., Greger K., Huisken J., Stelzer E.H.K. Multi-view image fusion improves resolution in three-dimensional microscopy. Opt. Express 2007, 15:8029-8042.
55. Thompson R.E., Larson D.R., Webb W.W. Precise nanometer localization analysis for individual fluorescent probes. Biophys. J. 2002, 82:2775-2783.
56. Tsien R.Y. Building and breeding molecules to spy on cells and tumors. FEBS Lett. 2005, 579:927-932.
57. Viola P., Wells W.M. Alignment by maximization of mutual information. Int. J. Comput. Vision 1997, 24:137-154.
58. Weiss D., Schneider G., Niemann B., Guttmann P., Rudolph D., et al. Computed tomography of cryogenic biological specimens based on X-ray microscopic images. Ultramicroscopy 2000, 84:185-197.