SeeDB: A simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction

Nature Neuroscience

Volumn 16, Issue 8, 2013, Pages 1154-1161

  Ke, Meng Tsen ^a,b   Fujimoto, Satoshi ^a   Imai, Takeshi ^a,b,c  

^a RIKEN Center for Biosystems Dynamics Research   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

NEURONAL TRACT TRACER; SEEDB; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; BRAIN NERVE CELL; CELL STRUCTURE; DENDRITE; FLUORESCENCE IMAGING; GLOMERULUS; MITRAL CELL; MOUSE; MULTIPHOTON MICROSCOPY; NONHUMAN; OLFACTORY BULB; PRIORITY JOURNAL; PROCEDURES CONCERNING CELLS;

ANIMALS; BENZOATES; BENZYL ALCOHOL; BRAIN; DENDRITES; ELECTROPORATION; FEMALE; FIXATIVES; FLUORESCENT DYES; FORMALDEHYDE; FRUCTOSE; GENE KNOCK-IN TECHNIQUES; GLYCEROL; HISTOCYTOLOGICAL PREPARATION TECHNIQUES; LIGHT; MICE; MICE, INBRED C57BL; MICE, INBRED ICR; MICE, TRANSGENIC; MICROSCOPY; NERVE NET; NEURONS; ODORS; OLFACTORY BULB; OLFACTORY PERCEPTION; PHENYL ETHERS; POLYMERS; PREGNANCY; SCATTERING, RADIATION; SOLUTIONS; SUCROSE; TISSUE FIXATION; UREA;

EID: 84880920117     PISSN: 10976256     EISSN: 15461726     Source Type: Journal    
DOI: 10.1038/nn.3447     Document Type: Article

References (50)

1. Tsai, P.S. et al. Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels. J. Neurosci. 29, 14553-14570 (2009).
2. Helmchen, F. & Denk, W. Deep tissue two-photon microscopy. Nat. Methods 2, 932-940 (2005). (Pubitemid 43108729)
3. Tuchin, V. Tissue Optics: Light Scattering Methods and Instruments for Medical Diagnosis, 2nd edn. (SPIE Press, 2007).
4. Dent, J.A., Polson, A.G. & Klymkowsky, M.W. A whole-mount immunocytochemical analysis of the expression of the intermediate filament protein vimentin in Xenopus. Development 105, 61-74 (1989). (Pubitemid 19046650)
5. Dodt, H.U. et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat. Methods 4, 331-336 (2007).
6. Staudt, T., Lang, M.C., Medda, R., Engelhardt, J. & Hell, S.W. 2,2′-thiodiethanol: a new water soluble mounting medium for high resolution optical microscopy. Microsc. Res. Tech. 70, 1-9 (2007). (Pubitemid 46059161)
7. Gonzalez-Bellido, P.T. & Wardill, T.J. Labeling and confocal imaging of neurons in thick invertebrate tissue samples. Cold Spring Harb. Protoc. published online, http://dx.doi.org/doi:10.1101/pdb.prot069625 (1 September 2012).
8. Becker, K., Jahrling, N., Saghafi, S., Weiler, R. & Dodt, H.U. Chemical clearing and dehydration of GFP expressing mouse brains. PLoS ONE 7, e33916 (2012).
9. Ertürk, A. et al. Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. Nat. Med. 18, 166-171 (2012).
10. Taylor, W.R. An enzyme method of clearing and staining small vertebrates. Proc. USA Natl. Museum 122, 1-17 (1967).
11. Dingerkus, G. & Uhler, L.D. Enzyme clearing of alcian blue stained whole small vertebrates for demonstration of cartilage. Stain Technol. 52, 229-232 (1977). (Pubitemid 8198057)
12. Hama, H. et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat. Neurosci. 14, 1481-1488 (2011).
13. Klymkowsky, M.W. & Hanken, J. Whole-mount staining of Xenopus and other vertebrates. Methods Cell Biol. 36, 419-441 (1991).
14. Bancroft, J.D. & Gamble, M. Theory and Practice of Histological Techniques (Churchill Livingstone, 2007).
15. Dills, W.L. Jr. Protein fructosylation: fructose and the Maillard reaction. Am. J. Clin. Nutr. 58, 779S-787S (1993). (Pubitemid 23319976)
16. Feng, G. et al. Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP. Neuron 28, 41-51 (2000).
17. Hofer, S. & Frahm, J. Topography of the human corpus callosum revisited-comprehensive fiber tractography using diffusion tensor magnetic resonance imaging. Neuroimage 32, 989-994 (2006). (Pubitemid 44278703)
18. Imai, T. et al. Pre-target axon sorting establishes the neural map topography. Science 325, 585-590 (2009).
19. Nishikimi, M., Oishi, K., Tabata, H., Torii, K. & Nakajima, K. Segregation and pathfinding of callosal axons through EphA3 signaling. J. Neurosci. 31, 16251-16260 (2011).
20. Schoppa, N.E. & Westbrook, G.L. Glomerulus-specific synchronization of mitral cells in the olfactory bulb. Neuron 31, 639-651 (2001). (Pubitemid 32835118)
21. Murthy, V.N. Olfactory maps in the brain. Annu. Rev. Neurosci. 34, 233-258 (2011).
22. Nagayama, S. et al. In vivo simultaneous tracing and Ca2+ imaging of local neuronal circuits. Neuron 53, 789-803 (2007). (Pubitemid 46367554)
23. Potter, S.M. et al. Structure and emergence of specific olfactory glomeruli in the mouse. J. Neurosci. 21, 9713-9723 (2001). (Pubitemid 34184057)
24. Orona, E., Rainer, E.C. & Scott, J.W. Dendritic and axonal organization of mitral and tufted cells in the rat olfactory bulb. J. Comp. Neurol. 226, 346-356 (1984). (Pubitemid 14094313)
25. Ghosh, S. et al. Sensory maps in the olfactory cortex defined by long-range viral tracing of single neurons. Nature 472, 217-220 (2011).
26. Igarashi, K.M. et al. Parallel mitral and tufted cell pathways route distinct odor information to different targets in the olfactory cortex. J. Neurosci. 32, 7970-7985 (2012).
27. Mori, K., Kishi, K. & Ojima, H. Distribution of dendrites of mitral, displaced mitral, tufted, and granule cells in the rabbit olfactory bulb. J. Comp. Neurol. 219, 339-355 (1983). (Pubitemid 13015656)
28. Nagayama, S. et al. Differential axonal projection of mitral and tufted cells in the mouse main olfactory system. Front. Neural Circuits 4, 120 (2010).
29. Sosulski, D.L., Bloom, M.L., Cutforth, T., Axel, R. & Datta, S.R. Distinct representations of olfactory information in different cortical centres. Nature 472, 213-216 (2011).
30. Kim, D.H. et al. Lateral connectivity in the olfactory bulb is sparse and segregated. Front. Neural Circuits 5, 5 (2011).
31. Orona, E., Scott, J.W. & Rainer, E.C. Different granule cell populations innervate superficial and deep regions of the external plexiform layer in rat olfactory bulb. J. Comp. Neurol. 217, 227-237 (1983). (Pubitemid 13058393)
32. Fantana, A.L., Soucy, E.R. & Meister, M. Rat olfactory bulb mitral cells receive sparse glomerular inputs. Neuron 59, 802-814 (2008).
33. Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature 497, 332-337 (2013).
34. Kazama, H. & Wilson, R.I. Origins of correlated activity in an olfactory circuit. Nat. Neurosci. 12, 1136-1144 (2009).
35. Chen, T.W., Lin, B.J. & Schild, D. Odor coding by modules of coherent mitral/tufted cells in the vertebrate olfactory bulb. Proc. Natl. Acad. Sci. USA 106, 2401-2406 (2009).
36. Kaplan, M.S., McNelly, N.A. & Hinds, J.W. Population dynamics of adult-formed granule neurons of the rat olfactory bulb. J. Comp. Neurol. 239, 117-125 (1985). (Pubitemid 16246600)
37. Hinds, J.W. & McNelly, N.A. Aging of the rat olfactory bulb: growth and atrophy of constituent layers and changes in size and number of mitral cells. J. Comp. Neurol. 72, 345-367 (1977). (Pubitemid 8034991)
38. Dhawale, A.K., Hagiwara, A., Bhalla, U.S., Murthy, V.N. & Albeanu, D.F. Non-redundant odor coding by sister mitral cells revealed by light addressable glomeruli in the mouse. Nat. Neurosci. 13, 1404-1412 (2010).
39. Kikuta, S., Fletcher, M.L., Homma, R., Yamasoba, T. & Nagayama, S. Odorant response properties of individual neurons in an olfactory glomerular module. Neuron 77, 1122-1135 (2013).
40. Miyasaka, N. et al. From the olfactory bulb to higher brain centers: genetic visualization of secondary olfactory pathways in zebrafish. J. Neurosci. 29, 4756-4767 (2009).
41. Miyamichi, K. et al. Cortical representations of olfactory input by trans-synaptic tracing. Nature 472, 191-196 (2011).
42. Yu, Y.C. et al. Preferential electrical coupling regulates neocortical lineage-dependent microcircuit assembly. Nature 486, 113-117 (2012).
43. Li, Y. et al. Clonally related visual cortical neurons show similar stimulus feature selectivity. Nature 486, 118-121 (2012).
44. Ohtsuki, G. et al. Similarity of visual selectivity among clonally related neurons in visual cortex. Neuron 75, 65-72 (2012).
45. Livet, J. et al. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450, 56-62 (2007). (Pubitemid 350070576)
46. Marshel, J.H., Mori, T., Nielsen, K.J. & Callaway, E.M. Targeting single neuronal networks for gene expression and cell labeling in vivo. Neuron 67, 562-574 (2010).
47. Lo, L. & Anderson, D.J.A. Cre-dependent, anterograde transsynaptic viral tracer for mapping output pathways of genetically marked neurons. Neuron 72, 938-950 (2011).
48. Kim, J. et al. mGRASP enables mapping mammalian synaptic connectivity with light microscopy. Nat. Methods 9, 96-102 (2012).
49. Lin, D.M. et al. Formation of precise connections in the olfactory bulb occurs in the absence of odorant-evoked neuronal activity. Neuron 26, 69-80 (2000).
50. Saito, T. In vivo electroporation in the embryonic mouse central nervous system. Nat. Protoc. 1, 1552-1558 (2006).