Monitoring activity in neural circuits with genetically encoded indicators

Abstract

Recent developments in genetically encoded indicators of neural activity (GINAs) have greatly advanced the field of systems neuroscience. As they are encoded by DNA, GINAs can be targeted to genetically defined cellular populations. Combined with fluorescence microscopy, most notably multi-photon imaging, GINAs allow chronic simultaneous optical recordings from large populations of neurons or glial cells in awake, behaving mammals, particularly rodents. This large-scale recording of neural activity at multiple temporal and spatial scales has greatly advanced our understanding of the dynamics of neural circuitry underlying behavior—a critical first step toward understanding the complexities of brain function, such as sensorimotor integration and learning. Here, we summarize the recent development and applications of the major classes of GINAs. In particular, we take an in-depth look at the design of available GINA families with a particular focus on genetically encoded calcium indicators (GCaMPs), sensors probing synaptic activity, and genetically encoded voltage indicators. Using the family of the GCaMP as an example, we review established sensor optimization pipelines. We also discuss practical considerations for end users of GINAs about experimental methods including approaches for gene delivery, imaging system requirements, and data analysis techniques. With the growing toolbox of GINAs and with new microscopy techniques pushing beyond their current limits, the age of light can finally achieve the goal of broad and dense sampling of neuronal activity across time and brain structures to obtain a dynamic picture of brain function.

Image Informatics Strategies for Deciphering Neuronal Network Connectivity

“…extracted from mouse embryos), bust, synchronized network activity 14,18 . Neuronal electrical activity can be visualized by means of voltage or calcium sensors, both of which are available as synthetic dyes or genetically encoded fluorescent proteins [30][31][32][33] . Such a functional approach not only allows assessing the effect of chronic treatments on neuronal connectivity, but can also provide information about acute responses to pharmacological perturbations.…”

“…Non-ratiometric calcium probes, such as Fluo4-AM, display an increase in fluorescence intensity upon calcium binding, while ratiometric probes like Fura-2 exhibit a shift in excitation or emission spectra, allowing precise measurements of intracellular calcium concentration, not biased by uneven dye loading. In addition to synthetic calcium probes, genetically encoded sensors like chameleons or GCaMPs have emerged over the last years 30 . These sensors allow long-term follow-up of neuronal activity and their expression can be limited to neurons, e.g.…”

Targeted manipulation of neuronal activity in behaving adult flies

“…The activity of neurons can be assessed through the use of different genetically encoded indicators of neural activity (Grienberger and Konnerth 2012;Masuyama et al 2012;Broussard et al 2014;Fosque et al 2015;Gao et al 2015;Dana et al 2016). For example, genetically encoded calcium indicators (GECIs) increase their fluorescence as calcium levels rise in active neurons.…”

“…Finally, additional tools have been developed to examine the functional relationships among different neurons that each contribute to a given behavior. This includes assessment of the functional connectivity between neurons using genetically encoded indicators of neural activity (Broussard et al 2014). This suite of innovations now empower researchers to make substantial progress in probing the functions of neural circuits across a range of different species (White 2016).…”

Scalable electrophysiology in intact small animals with nanoscale suspended electrode arrays

“…Recently developed optical recording methods based on calcium- and voltage-sensitive fluorescence can record a proxy for electrical activity of individual cells in intact C. elegans 7–18 ; however, compared to electrical recordings, optical measurements typically have a lower signal-to-noise ratio and reduced temporal resolution 19 . As a result, optical methods have yet to resolve individual action potentials (APs) or synaptic potentials in C. elegans 7–18 .…”