Tracing activity across the whole brain neural network with optogenetic functional magnetic resonance imaging

Frontiers in Neuroinformatics

Volumn 5, Issue , 2011, Pages

  Lee, Jin Hyung ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

BOLD; Connectomics; OfMRI; Opto fMRI; Optogenetics

Indexed keywords

AXON; CELL BODY; CONNECTOME; FUNCTIONAL MAGNETIC RESONANCE IMAGING; IDENTITY; OPTOGENETICS; SYNAPSE;

EID: 84994060945     PISSN: None     EISSN: 16625196     Source Type: Journal    
DOI: 10.3389/fninf.2011.00021     Document Type: Article

References (39)

1. Aravanis, A. M., Wang, L. P., Zhang, F., Meltzer, L. A., Mogri, M. Z., Schneider, M. B., and Deisseroth, K. (2007). An optical neural interface: in vivo control of rodent motor cortex with integrated fiberoptic and optogenetic technology. J. Neural Eng. 4, S143-S156.
2. Bandettini, P. A., and Wong, E. C. (1997). Magnetic resonance imaging of human brain function. Principles, practicalities, and possibilities. Neurosurg. Clin. N. Am. 8, 345-371.
3. Berndt, A., Yizhar, O., Gunaydin, L. A., Hegemann, P., and Deisseroth, K. (2009). Bi-stable neural state switches. Nat. Neurosci. 12, 229-234.
4. Bock, D. D., Lee, W. C., Kerlin, A. M., Andermann, M. L., Hood, G., Wetzel, A. W., Yurgenson, S., Soucy, E. R., Kim, H. S., and Reid, R. C. (2011). Network anatomy and in vivo physiology of visual cortical neurons. Nature 471, 177-182.
5. Bohland, J. W., Wu, C., Barbas, H., Bokil, H., Bota, M., Breiter, H. C., Cline, H. T., Doyle, J. C., Freed, P. J., Greenspan, R. J., Haber, S. N., Hawrylycz, M., Herrera, D. G., Hilgetag, C. C., Huang, Z. J., Jones, A., Jones, E. G., Karten, H. J., Kleinfeld, D., Kotter, R., Lester, H. A., Lin, J. M., Mensh, B. D., Mikula, S., Panksepp, J., Price, J. L., Safdieh, J., Saper, C. B., Schiff, N. D., Schmahmann, J. D., Stillman, B. W., Svoboda, K., Swanson, L. W., Toga, A. W., Van Essen, D. C., Watson, J. D., and Mitra, P. P. (2009). A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Comput. Biol. 5, e1000334. doi: 10.1371/journal.pcbi.1000334
6. Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G., and Deisseroth, K. (2005). Millisecond-timescale, genetically targeted optical control of neural activity. Nat. Neurosci. 8, 1263-1268.
7. Briggman, K. L., and Denk, W. (2006). Towards neural circuit reconstruction with volume electron microscopy techniques. Curr. Opin. Neurobiol. 16, 562-570.
8. Briggman, K. L., Helmstaedter, M., and Denk, W. (2011). Wiring specificity in the direction-selectivity circuit of the retina. Nature 471, 183-188.
9. Cardin, J. A., Carlen, M., Meletis, K., Knoblich, U., Zhang, F., Deisseroth, K., Tsai, L. H., and Moore, C. I. (2009). Driving fast-spiking cells induces gamma rhythm and controls sensory responses. Nature 459, 663-667.
10. Choe, Y., Abbott, L. C., Han, D., Huang, P.-S., Keyser, J., Kwon, J., Mayerich, D., Melek, Z., and McCormick, B. H. (2008). “Knife-edge scanning microscopy: high-throughput imaging and analysis of massive volumes of biological microstructures,” in High-Throughput Image Reconstruction and Analysis: Intelligent Microscopy Applications, eds R. Rao and G. Cecchi (Boston, MA: Artech House), 11-37.
11. Chow, B. Y., Han, X., Dobry, A. S., Qian, X., Chuong, A. S., Li, M., Henninger, M. A., Belfort, G. M., Lin, Y., Monahan, P. E., and Boyden, E. S. (2010). High-performance genetically targetable optical neural silencing by light-driven proton pumps. Nature 463, 98-102.
12. Fox, M. D., and Raichle, M. E. (2007). Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nat. Rev. Neurosci. 8, 700-711.
13. Goebel, R., Roebroeck, A., Kim, D. S., and Formisano, E. (2003). Investigating directed cortical interactions in time-resolved fMRI data using vector autoregressive modeling and Granger causality mapping. Magn. Reson. Imaging 21, 1251-1261.
14. Gradinaru, V., Mogri, M., Thompson, K. R., Henderson, J. M., and Deisseroth, K. (2009). Optical deconstruction of parkinsonian neural circuitry. Science 324, 354-359.
15. Gradinaru, V., Thompson, K. R., and Deisseroth, K. (2008). eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications. Brain Cell Biol. 36, 129-139.
16. Gunaydin, L. A., Yizhar, O., Berndt, A., Sohal, V. S., Deisseroth, K., and Hegemann, P. (2010). Ultrafast optogenetic control. Nat. Neurosci. 13, 387-392.
17. Hilgetag, C. C., Burns, G. A., O’Neill, M. A., Scannell, J. W., and Young, M. P. (2000). Anatomical connectivity defines the organization of clusters of cortical areas in the macaque monkey and the cat. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355, 91-110.
18. Histed, M. H., Bonin, V., and Reid, R. C. (2009). Direct activation of sparse, distributed populations of cortical neurons by electrical microstimulation. Neuron 63, 508-522.
19. Honey, C. J., Kotter, R., Breakspear, M., and Sporns, O. (2007). Network structure of cerebral cortex shapes functional connectivity on multiple time scales. Proc. Natl. Acad. Sci. U.S.A. 104, 10240-10245.
20. Kravitz, A. V., Freeze, B. S., Parker, P. R., Kay, K., Thwin, M. T., Deisseroth, K., and Kreitzer, A. C. (2010). Regulation of parkinsonian motor behaviours by optogenetic control of basal ganglia circuitry. Nature 466, 622-626.
21. Lee, J. H., Dumoulin, S. O., Saritas, E. U., Glover, G. H., Wandell, B. A., Nishimura, D. G., and Pauly, J. M. (2008). Full-brain coverage and high-resolution imaging capabilities of passband b-SSFP fMRI at 3T. Magn. Reson. Med. 59, 1099-1110.
22. Lee, J. H., Durand, R., Gradinaru, V., Zhang, F., Goshen, I., Kim, D. S., Fenno, L. E., Ramakrishnan, C., and Deisseroth, K. (2010). Global and local fMRI signals driven by neurons defined optogenetically by type and wiring. Nature 465, 788-792.
23. Livet, J., Weissman, T. A., Kang, H., Draft, R. W., Lu, J., Bennis, R. A., Sanes, J. R., and Lichtman, J. W. (2007). Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature 450, 56-62.
24. Micheva, K. D., and Smith, S. J. (2007). Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron 55, 25-36.
25. Miyamichi, K., Amat, F., Moussavi, F., Wang, C., Wickersham, I., Wall, N. R., Taniguchi, H., Tasic, B., Huang, Z. J., He, Z., Callaway, E. M., Horowitz, M. A., and Luo, L. (2011). Cortical representations of olfactory input by trans-synaptic tracing. Nature 472, 191-196.
26. Mori, S., and Zhang, J. (2006). Principles of diffusion tensor imaging and its applications to basic neuroscience research. Neuron 51, 527-539.
27. Ogawa, S., Tank, D. W., Menon, R., Ellermann, J. M., Kim, S.-G., Merkle, H., and Ugurbil, K. (1992). Intrinsic signal changes accompanying sensory stimulation: functional brain mapping with magnetic resonance imaging. Proc. Natl. Acad. Sci. U.S.A. 89, 5951-5955.
28. Pautler, R. G., Silva, A. C., and Koretsky, A. P. (1998). In vivo neuronal tract tracing using manganese-enhanced magnetic resonance imaging. Magn. Reson. Med. 40, 740-748.
29. Pearl, J. (2002). Reasoning with Cause and Effect. AI Mag. 23, 95-111.
30. Raju, D. V., and Smith, Y. (2006). Anterograde axonal tract tracing. Curr. Protoc. Neurosci. Chap. 1, Unit 1.14.
31. Song, A. W., Popp, C. A., Mao, J., and Dixon, W. T. (2000). fMRI: methodology-acquisition and processing. Adv. Neurol. 83, 177-185.
32. Sporns, O., Tononi, G., and Kotter, R. (2005). The human connectome: a structural description of the human brain. PLoS Comput. Biol. 1, e42. doi: 10.1371/journal.pcbi.0010042
33. Stephan, K. E., and Friston, K. J. (2011). Analyzing effective connectivity with fMRI. Wiley Interdiscip. Rev. Cogn. Sci. 1, 446-459.
34. Stephan, K. E., Hilgetag, C. C., Burns, G. A., O’Neill, M. A., Young, M. P., and Kotter, R. (2000). Computational analysis of functional connectivity between areas of primate cerebral cortex. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355, 111-126.
35. Tolias, A. S., Sultan, F., Augath, M., Oeltermann, A., Tehovnik, E. J., Schiller, P. H., and Logothetis, N. K. (2005). Mapping cortical activity elicited with electrical microstimulation using FMRI in the macaque. Neuron 48, 901-911.
36. Wall, N. R., Wickersham, I. R., Cetin, A., De La Parra, M., and Callaway, E. M. (2010). Monosynaptic circuit tracing in vivo through Cre-dependent targeting and complementation of modified rabies virus. Proc. Natl. Acad. Sci. U.S.A. 107, 21848-21853.
37. Zhang, F., Aravanis, A. M., Adamantidis, A., de Lecea, L., and Deisseroth, K. (2007a). Circuit-breakers: optical technologies for probing neural signals and systems. Nat. Rev. Neurosci. 8, 577-581.
38. Zhang, F., Wang, L. P., Brauner, M., Liewald, J. F., Kay, K., Watzke, N., Wood, P. G., Bamberg, E., Nagel, G., Gottschalk, A., and Deisseroth, K. (2007b). Multimodal fast optical interrogation of neural circuitry. Nature 446, 633-639.
39. Zhang, F., Wang, L. P., Boyden, E. S., and Deisseroth, K. (2006). Channelrhodopsin-2 and optical control of excitable cells. Nat. Methods 3, 785-792.