Mapping functional connectivity between neuronal ensembles with larval zebrafsh transgenic for a ratiometric calcium indicator

Frontiers in Neural Circuits

Volumn 5, Issue FEB, 2011, Pages

  Tao, Louis ^a   Lauderdale, James D ^b   Sornborger, Andrew T ^b  

^a PEKING UNIVERSITY   (China)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Bursting activity; Calcium imaging; Calcium wave; Chemoconvulsant; Epilepsy; Ratiometry; Seizure; Zebrafish

Indexed keywords

CALCIUM;

ACTION POTENTIAL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BRAIN MAPPING; CALCIUM CURRENT; CALCIUM TRANSPORT; CENTRAL NERVOUS SYSTEM; LARVA; NERVE CELL NETWORK; NONHUMAN; SEIZURE; SIGNAL NOISE RATIO; TRANSGENIC ANIMAL; ZEBRA FISH;

EID: 84875821506     PISSN: 16625110     EISSN: None     Source Type: Journal    
DOI: 10.3389/fncir.2011.00002     Document Type: Article

References (48)

1. Ali, D. W., Buss, R. R., and Drapeau, P. (2000). Properties of miniature glutamatergic EPSCs in neurons of the locomotor regions of the developing zebrafsh. J. Neurophysiol. 83, 181-191.
2. Babajani-Feremi, A., and Soltanian-Zadeh, H. (2010). Multi-area neural mass modeling of EEG and MEG signals. Neuroimage 52, 793-811.
3. Badea, T., Goldberg, J., Mao, B., and Yuste, R. (2001). Calcium imaging of epilep-tiform events with single-cell resolution. J. Neurobiol. 48, 215-227.
4. Baraban, S. C. (2005). "Modeling epilepsy and seizures in developing zebrafsh larvae," in Models of Seizures and Epilepsy, eds A. Pitkänen, P. A. Schwartzkroin, and S. L. Moshé, (New York: Elsevier, Academic Press), 189-198.
5. Baraban, S. C. (2007). Emerging epilepsy models: insights from mice, flies, worms and fsh. Curr. Opin. Neurol. 20, 164-168.
6. Baraban, S. C., Dinday, M. T., Castro, P. A., Chege, S., Guyenet, S., and Taylor, M. R. (2007). A large-scale mutagenesis screen to identify seizure-resistant zebrafish. Epilepsia 48, 1151-1157.
7. Baraban, S. C., Taylor, M. R., Castro, P. A., and Baier, H. (2005). Pentylenetetrazole induced changes in zebrafsh behavior, neural activity and c-fos expression. Neuroscience 131, 759-768.
8. Broder, J., Majumder, A., Porter, E., Srinivasamoorthy, G., Keith, C., Lauderdale, J., and Sornborger, A. (2007). Estimating weak ratiomet-ric signals in imaging data. I. Dual-channel data. J. Opt. Soc. Am. A Opt. Image Sci. Vis. 24, 2921-2931.
9. Brunet, J. P., Tamayo, P., Golub, T. R., and Mesirov, J. P. (2004). Metagenes and molecular pattern discovery using matrix factorization. Proc. Natl. Acad. Sci. U.S.A. 101, 4164-4169.
10. Cacciatore, T. W., Brodfuehrer, P. D., Gonzalez, J. E., Jiang, T., Adams, S. R., Tsien, R. Y., Kristan, W. B. Jr., and Kleinfeld, D. (1999). Identifcation of neural circuits by imaging coherent electrical activity with FRET-based dyes. Neuron 23, 449-459.
11. Cantero, J. L., Atienza, M., Gomez-Herrero, G., Cruz-Vadell, A., Gil-Neciga, E., Rodriguez-Romero, R., and Garcia-Solis, D. (2009). Functional integrity of thalamocortical circuits differentiates normal aging from mild cognitive impairment. Hum. Brain Mapp. 30, 3944-3957.
12. Carbonell, F., Worsley, K. J., Trujillo-Barreto, N. J., and Sotero, R. C. (2009). Random felds - union intersection tests for detecting functional connectivity in EEG/MEG imaging. Hum. Brain Mapp. 30, 2477-2486.
13. Chiu, C., and Weliky, M. (2002). Relationship of correlated spontaneous activity to functional ocular dominance columns in the developing visual cortex. Neuron 35, 1123-1134.
14. de Haan, W., Pijnenburg, Y. A., Strijers, R. L., van der Made, Y., van der Flier, W. M., Scheltens, P., and Stam, C. J. (2009). Functional neural network analysis in frontotemporal dementia and Alzheimer's disease using EEG and graph theory. BMC Neurosci. 10, 101. doi: 10.1186/1471-2202-10-101
15. Devarajan, K. (2008). Nonnegative matrix factorization: an analytical and interpretive tool in computational biology. PLoS Comput. Biol. 4, e1000029. doi: 10.1371/journal.pcbi.1000029
16. Donoho, D., and Stodden, V. (2004). "When does non-negative matrix factorization give a correct decomposition into parts?" in Advances in Neural Information Processing Systems Vol. 16 (Cambridge, MA: MIT Press), 1141-1148.
17. Fan, X., Majumder, A., Reagin, S. S., Porter, E. L., Sornborger, A. T., Keith, C. H., and Lauderdale, J. D. (2007). New statistical methods enhance imaging of cameleon fuorescence resonance energy transfer in cultured zebrafsh spinal neurons. J. Biomed. Opt. 12, 034017.
18. Field, G. D., Gauthier, J. L., Sher, A., Greschner, M., Machado, T. A., Jepson, L. H., Shlens, J., Gunning, D. E., Mathieson, K., Dabrowski, W., Paninski, L., Litke, A. M., and Chichilnisky, E. J. (2010). Functional connectivity in the retina at the resolution of photoreceptors. Nature 467, 673-677.
19. Garaschuk, O., Griesbeck, O., and Konnerth, A. (2007). Troponin C-based biosensors: a new family of genetically encoded indicators for in vivo calcium imaging in the nervous system. Cell Calcium 42, 351-361.
20. Higashijima, S., Masino, M. A., Mandel, G., and Fetcho, J. R. (2003). Imaging neuronal activity during zebrafish behavior with a genetically encoded calcium indicator. J. Neurophysiol. 90, 3986-3997.
21. Hires, S. A., Tian, L., and Looger, L. L. (2008). Reporting neural activity with genetically encoded calcium indicators. Brain Cell Biol. 36, 69-86.
22. Kimmel, C. B., Ballard, W. W., Kimmel, S. R., Ullmann, B., and Schilling, T. F. (1995). Stages of embryonic development of the zebrafsh. De v. Dyn. 203, 253-310.
23. Kimmel, C. B., Powell, S. L., and Metcalfe, W. K. (1982). Brain neurons which project to the spinal cord in young larvae of the zebrafsh. J. Comp. Neurol. 205, 112-127.
24. Lee, D. D., and Seung, H. S. (1999). Learning the parts of objects by non-negative matrix factorization. Nature 401, 788-791.
25. Lee, D. D., and Seung, H. S. (2001). "Algorithms for non-negative matrix factorization," in Advances in Neural Information Processing Systems Vol. 13 (Cambridge, MA: MIT Press), 556-562.
26. Logothetis, N. K. (2003). MR imaging in the non-human primate: studies of function and of dynamic connectivity. Curr. Opin. Neurobiol. 13, 630-642.
27. Makeig, S., Jung, T. P., Bell, A. J., Ghahremani, D., and Sejnowski, T. J. (1997). Blind separation of auditory event-related brain responses into independent components. Proc. Natl. Acad. Sci. U.S.A. 94, 10979-10984.
28. Mank, M., Santos, A. F., Direnberger, S., Mrsic-Flogel, T. D., Hofer, S. B., Stein, V., Hendel, T., Reiff, D. F., Levelt, C., Borst, A., Bonhoeffer, T., Hubener, M., and Griesbeck, O. (2008). A genetically encoded calcium indicator for chronic in vivo two-photon imaging. Nat. Methods 5, 805-811.
29. Mendelson, B. (1986). Development of reticulospinal neurons of the zebrafsh. II. Early axonal outgrowth and cell body position. J. Comp. Neurol. 251, 172-184.
30. Metcalfe, W. K., Mendelson, B., and Kimmel, C. B. (1986). Segmental homologies among reticulospinal neurons in the hindbrain of the zebrafsh larva. J. Comp. Neurol. 251, 147-159.
31. Miyawaki, A., Griesbeck, O., Heim, R., and Tsien, R. Y. (1999). Dynamic and quantitative Ca2+ measurements using improved cameleons. Proc. Natl. Acad. Sci. U.S.A. 96, 2135-2140.
32. Owen, J. P., Wipf, D. P., Attias, H. T., Sekihara, K., and Nagarajan, S. S. (2009). Accurate reconstruction of brain activity and functional connectivity from noisy MEG data. Conf. Proc. IEEE Eng. Med. Biol. Soc. 1, 65-68.
33. Perez-Perez, M. P., Luque, M. A., Herrero, L., Nunez-Abades, P. A., and Torres, B. (2003a). Afferent connectivity to different functional zones of the optic tectum in goldfsh. Vis. Neurosci. 20, 397-410.
34. Perez-Perez, M. P., Luque, M. A., Herrero, L., Nunez-Abades, P. A., and Torres, B. (2003b). Connectivity of the goldfsh optic tectum with the mesencephalic and rhombencephalic reticular formation. Exp. Brain Res. 151, 123-135.
35. Pillow, J. W., Shlens, J., Paninski, L., Sher, A., Litke, A. M., Chichilnisky, E. J., and Simoncelli, E. P. (2008). Spatio-temporal correlations and visual signalling in a complete neuronal population. Nature 454, 995-999.
36. Sirovich, L., and Uglesich, R. (2004). The organization of orientation and spatial frequency in primary visual cortex. Proc. Natl. Acad. Sci. U.S.A. 101, 16941-16946.
37. Sornborger, A., Broder, J., Majumder, A., Srinivasamoorthy, G., Porter, E., Reagin, S. S., Keith, C., and Lauderdale, J. D. (2008). Estimating weak ratiomet-ric signals in imaging data. II. Meta-analysis with multiple, dual-channel datasets. J. Opt. Soc. Am. A. Opt. Image Sci. Vis. 25, 2185-2194.
38. Stam, C. J. (2009). Use of magnetoen-cephalography (MEG) to study functional brain networks in neuro-degenerative disorders. J. Neurol. Sci. 289, 128-134.
39. Tao, L., and Sornborger, A. T. (2010). Dimensionally-reduced visual cortical network model predicts network response and connects system- and cellular-level descriptions. J. Comput. Neurosci. 28, 91-106.
40. Taylor, A. L., Cottrell, G. W., Kleinfeld, D., Kristan, W. B. Jr. (2003). Imaging reveals synaptic targets of a swim-terminating neuron in the leech CNS. J. Neurosci. 23, 11402-11410.
41. Vogelstein, J. T., Packer, A. M., Machado, T. A., Sippy, T., Babadi, B., Yuste, R., and Paninski, L. (2010). Fast non-negative deconvolution for spike train inference from population calcium imaging. J. Neurophysiol. 104, 3691-3704.
42. Vogelstein, J. T., Watson, B. O., Packer, A. M., Yuste, R., Jedynak, B., and Paninski, L. (2009). Spike inference from calcium imaging using sequential Monte Carlo methods. Biophys. J. 97, 636-655.
43. Westerfeld, M. (ed.) (2000). The Zebrafsh Book: A Guide for the Laboratory use of Zebrafsh (Danio rerio), 4th Edn. Eugene, OR: University of Oregon Press.
44. Wulliman, M. F., Rupp, B., and Reichert, H. (1996). Neuroanatomy of the Zebrafsh Brain: A Topological Atlas, 1st Edn. Basel: Birkhauser.
45. Xu, J., Sornborger, A. T., Lee, J. K., and Shen, P. (2008). Drosophila TRPA channel modulates sugar-stimulated neural excitation, avoidance and social response. Nat. Neurosci. 11, 676-682.
46. Yaksi, E., and Friedrich, R. W. (2006). Reconstruction of fring rate changes across neuronal populations by temporally deconvolved Ca2+ imaging. Nat. Methods 3, 377-383.
47. Ye, J. H., Ryu, S. B., Kim, K. H., and Goo, Y. S. (2008). Functional connectivity map of retinal ganglion cells for retinal prosthesis. Korean J. Physiol. Pharmacol. 12, 307-314.
48. Zhou, Z., Ding, M., Chen, Y., Wright, P., Lu, Z., and Liu, Y. (2009). Detecting directional influence in fMRI connectivity analysis using PCA based Granger causality. Brain Res. 1289, 22-29.