The gain in brain: Novel imaging techniques and multiplexed proteomic imaging of brain tissue ultrastructure

Current Opinion in Neurobiology

Volumn 22, Issue 1, 2012, Pages 94-100

  Micheva, Kristina D ^a   Bruchez, Marcel P ^b  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANTIBODY LABELING; AUTOMATED TRANSMISSION ELECTRON MICROSCOPY; BRAIN TISSUE; BRAIN TOMOGRAPHY; CELL ULTRASTRUCTURE; HUMAN; IMAGE QUALITY; IMMUNOELECTRON MICROSCOPY; MICROSCOPY; MOLECULAR IMAGING; NERVE CELL PLASTICITY; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN TARGETING; REVIEW; SENSITIVITY AND SPECIFICITY; STIMULATED EMISSION DEPLETION MICROSCOPY; STOCHASTIC OPTICAL RECONSTRUCTION MICROSCOPY; STRUCTURAL PROTEOMICS; SYNAPTIC MEMBRANE; TISSUE STRUCTURE;

ANIMALS; BRAIN; DIAGNOSTIC IMAGING; HUMANS; NEUROSCIENCES; PROTEOMICS;

EID: 84857687672     PISSN: 09594388     EISSN: 18736882     Source Type: Journal    
DOI: 10.1016/j.conb.2011.08.004     Document Type: Review

References (51)

1. Masland R.H. Neuronal diversity in the retina. Curr Opin Neurobiol 2001, 11:431-436.
2. Klausberger T., Somogyi P. Neuronal diversity and temporal dynamics: the unity of hippocampal circuit operations. Science 2008, 321:53-57.
3. Takamori S., Holt M., Stenius K., Lemke E.A., Grønborg M., Riedel D., Urlaub H., Schenck S., Brügger B., Ringler P., et al. Molecular anatomy of a trafficking organelle. Cell 2006, 127:831-846.
4. Cheng D., Hoogenraad C.C., Rush J., Ramm E., Schlager M.A., Duong D.M., Xu P., Wijayawardana S.R., Hanfelt J., Nakagawa T., et al. Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol Cell Proteomics 2006, 5:1158-1170.
5. Collins M.O., Husi H., Yu L., Brandon J.M., Anderson C.N., Blackstock W.P., Choudhary J.S., Grant S.G. Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome. J Neurochem 2006, 97(Suppl. 1):16-23.
6. Dosemeci A., Makusky A.J., Jankowska-Stephens E., Yang X., Slotta D.J., Markey S.P. Composition of the synaptic PSD-95 complex. Mol Cell Proteomics 2007, 6:1749-1760.
7. Trinidad J.C., Thalhammer A., Specht C.G., Lynn A.J., Baker P.R., Schoepfer R., Burlingame A.L. Quantitative analysis of synaptic phosphorylation and protein expression. Mol Cell Proteomics 2008, 7:684-696.
8. Coons A.H., Creech H.J., Jones R.N. Immunological properties of an antibody containing a fluorescent group. Proc Soc Exp Biol Med 1941, 47:200-202.
9. Chung J.-Y., Braunschweig T., Baibakov G., Galperin M., Ramesh A., Skacel M., Gannot G., Knezevic V., Hewitt S.M. Transfer and multiplex immunoblotting of a paraffin embedded tissue. Proteomics 2006, 6:767-774.
10. Gannot G., Tangrea M.A., Erickson H.S., Pinto P.A., Hewitt S.M., Chuaqui R.F., Gillespie J.W., Emmert-Buck M.R. Layered peptide array for multiplex immunohistochemistry. J Mol Diagn 2007, 9:297-304.
11. Chung J.-Y., Hong S.M., Choi B.Y., Cho H., Yu E., Hewitt S.M. The expression of phospho-AKT, phospho-mTOR, and PTEN in extrahepatic cholangiocarcinoma. Clin Cancer Res 2009, 15:660-667.
12. Peng H., Chung P., Long F., Qu L., Jenett A., Seeds A.M., Myers E.W., Simpson J.H. BrainAligner: 3D registration atlases of Drosophila brains. Nat Methods 2011, 8:493-498.
13. Schubert W., Bonnekoh B., Pommer A.J., Philipsen L., Bockelmann R., Malykh Y., Gollnick H., Friedenberger M., Bode M., Dress A.W.M. Analyzing proteome topology and function by automated multidimensional fluorescence microscopy. Nat Biotechnol 2006, 24:1270-1278.
14. Bode M., Irmler M., Friedenberger M., May C., Jung K., Stephan C., Meyer H.E., Lach C., Hillert R., Krusche A., et al. Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in murine hippocampus. Proteomics 2008, 8:1170-1178.
15. Micheva K.D., Smith S.J. Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron 2007, 55:25-36.
16. Micheva K.D., Busse B., Weiler N.C., O'Rourke N., Smith S.J. Single-synapse analysis of a diverse synapse population: proteomic imaging methods and markers. Neuron 2010, 68:639-653.
17. Betzig E., Patterson G.H., Sougrat R., Lindwasser O.W., Olenych S., Bonifacino J.S., Davidson M.W., et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 2006, 313:1642-1645.
18. Hess S.T., Girirajan T.P.K., Mason M.D. Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophys J 2006, 91:4258-4272.
19. Rust M.J., Bates M., Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 2006, 3:793-795.
20. Hell S.W., Wichmann J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Opt Lett 1994, 19:780-782.
21. Schmidt R., Wurm C.A., Jakobs S., Engelhardt J., Egner A., Hell S.W. Spherical nanosized focal spot unravels the interior of cells. Nature Methods 2008, 5:539-544.
22. Punge A., Rizzoli S.O., Jahn R., Wildanger J.D., Meyer L., Schönle A., Kastrup L., Hell S.W. 3D reconstruction of high-resolution STED microscope images. Microsc Res Tech 2008, 71:644-650.
23. Bückers J., Wildanger D., Vicidomini G., Kastrup L., Hell S.W. Simultaneous multi-lifetime multi-color STED imaging for colocalization analyses. Opt Express 2011, 19:3130-3143.
24. Dani A., Huang B., Bergan J., Dulac C., Zhuang X. Superresolution imaging of chemical synapses in the brain. Neuron 2010, 68:843-856.
25. Bates M., Huang B., Dempsey G.T., Zhuang X. Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science 2007, 317:1749-1753.
26. Folling J., Belov V., Kunetsky R., Medda R., Schönle A., Egner A., Eggeling C., Bossi M., Hell S.W. Photochromic rhodamines provide nanoscopy with optical sectioning. Angew Chem Int Ed 2007, 46:6266-6270.
27. York A.G., Ghitani A., Vaziri A., Davidson M.W., Shroff H. Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes. Nat Methods 2011, 8:327-333.
28. Baddeley D., Crossman D., Rossberger S., Cheyne J.E., Montgomery J.M., Jayasinghe I.D., Cremer C., Cannell M.B., Soeller C. 4D Super-Resolution Microscopy with Conventional Fluorophores and Single Wavelength Excitation in Optically Thick Cells and Tissues. PLoS One 2011, 6(5):e20645.
29. Anderson J.R., Jones B.W., Yang J.-H., Shaw M.V., Watt C.B., Koshevoy P., Spaltenstein J., Jurrus E., UV K., Whitaker R.T., et al. A computational framework for ultrastructural mapping of neural circuitry. PLoS Biol 2009, 7:e1000074.
30. Anderson J.R., Jones B.W., Watt C.B., Shaw M.V., Yang J.H., Demill D., Lauritzen J.S., Lin Y., Rapp K.D., Mastronarde D., et al. Exploring the retinal connectome. Mol Vis 2011, 17:355-379.
31. Jones B.W., Kondo M., Terasaki H., Watt C.B., Rapp K., Anderson J., Lin Y., Shaw M.V., Yang J.H., Marc R.E. Retinal remodeling in the TgP347L rabbit, a large-eye model of retinal degeneration. J Comp Neurol 2011 Jun 16, [Epub ahead of print]. 10.1002/cne.22703.
32. Jones S.A., Shim S.H., He J., Zhuang X. Fast, three-dimensional super-resolution imaging of live cells. Nat Methods 2011, 8:499-505.
33. Pellett P.A., Sun X., Gould T.J., Rothman J.E., Xu M.-Q., Corrêa I.R., Bewersdorf J. Two-color STED microscopy in living cells. Biomed Optics Express 2011, 2:2364-2371.
34. Bürli T., Baer K., Ewers H., Sidler C., Fuhrer C., Fritschy J.M. Single particle tracking of alpha7 nicotinic AChR in hippocampal neurons reveals regulated confinement at glutamatergic and GABAergic perisynaptic sites. PLoS One. 2010, 5:e11507.
35. Giannone G., Hosy E., Levet F., Constals A., Schulze K., Sobolevsky A.I., Rosconi M.P., Gouaux E., Tampé, Choquet D., et al. Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density. Biophys J 2010, 99:1303-1310.
36. Rubio M.D., Johnson R., Miller C.A., Huganir R.L., Rumbaugh G. Regulation of synapse structure and function by distinct myosin II motors. J Neurosci 2011, 31:1448-1460.
37. Bergersen L.H., Storm-Mathisen J., Gundersen V. Immunogold quantification of amino acids and proteins in complex subcellular compartments. Nat Protoc 2008, 3:144-152.
38. Nizak C., Monier S., del Nery E., Moutel S., Goud B., Perez F. Recombinant antibodies to the small GTPase Rab6 as conformation sensors. Science 2003, 300:984-987.
39. Schmidthals K., Helma J., Zolghadr K., Rothbauer U., Leonhardt H. Novel antibody derivatives for proteome and high-content analysis. Anal Bioanal Chem 2010, 397:3203-3208.
40. Olichon A., Surrey T. Selection of genetically encoded fluorescent single domain antibodies engineered for efficient expression in Escherichia coli. J Biol Chem 2007, 282:36314-36320.
41. Gebauer M., Skerra A. Engineered protein scaffolds as next-generation antibody therapeurics. Curr Opin Chem Biol 2009, 13:245-255.
42. Diehnelt C.W., Shah M., Gupta N., Belcher P.E., Greving M.P., Stafford P., Johnston S.A. Discovery of high-affinity protein binding ligands - backwards. PLoS One 2010, 5(5):e10728.
43. Kasthuri N., Lichtman J.W. Neurocartography. Neuropsychopharm 2010, 35:342-343.
44. Uhlen M., Oksvold P., Fagerberg L., Lundberg E., Jonasson K., Forsberg M., Zwahlen M., Kampf C., Wester K., Hober S., et al. Towards a knowledge-based Human Protein Atlas. Nat Biotechnol 2010, 28:1248-1250.
45. Feng G., Mellor R.H., Bernstein M., Keller-Peck C., Nguyen Q.T., Wallace M., Nerbonne J.M., Lichtman J.W., Sanes J.R. Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP. Neuron 2000, 28:41-51.
46. Kuhlman S.J., Huang Z.J. High-resolution labeling and functional manipulation of specific neuron types in mouse brain by Cre-activated viral gene expression. PLoS One 2008, 3:e2005.
47. Benavides-Piccione R., Arellano J.I., De Felipe J. Catecholaminergic innervation of pyramidal neurons in the human temporal cortex. Cereb Cortex 2005, 15:1584-1591.
48. Oberti D., Kirschmann M.A., Hahnloser R.H. Projection neuron circuits resolved using correlative array tomography. Front Neurosci 2011, 5:50.
49. Appel N.M. Classical and contemporary histochemical approaches for evaluating central nervous system microanatomy. Ann NY Acad Sci 1997, 820:14-28.
50. Lauterbach M.A., Keller J., Schönle A., Kamin D., Westphal V., Rizzoli S.O., Hell S.W. Comparing video-rate STED nanoscopy and confocal microscopy of living neurons. J Biophotonics 2010, 3:417-424.
51. Muyldermans S. Single domain camel antibodies: current status. J Biotechnol 2001, 74:277-302.