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This study addresses current methods of in vivo two-photon imaging of the activity of neurons involved in episodes of cognitive activity in animals. The principles of fluorescent twophoton microscopy are described and methods for in vivo imaging of neuron activity using calcium indicators of two types – calcium stains and genetically encoded calcium indictors (GECI) – are discussed. A new approach is also considered, using in vivo imaging of genomic activation of cerebral neurons in transgenic animals with fluorescent probes for the expression of the immediate early genes c-fos, Arc, and Egr-1. Moreover, in current study we describe the new approach to investigate the calcium activity of engram neurons, that are involved into the memory coding. We present new Fos-Cre-GCaMP transgenic mice to investigate long-term changes of calcium dynamic in memory engram neurons captured with TRAP technique during training. After genetic recombination and expression of GCaMP, we performed two-photon imaging of calcium fluorescence in the body and dendritic spines of such neurons in cortex during memory recall. Finally, in present study we describe a novel learning task in the Mobile Home Cage setup directly during two-photon imaging. Supported by RSCF 14-15-00685 and RFBR 17-04-02054