Recording neuronal activity in 3D using calcium and voltage genetically encoded indicators

Genetically encoded voltage indicators (GEVIs) can measure millisecond-scale subthreshold neural responses with cell type specificity. Here, we successfully expressed, for the first time, a GEVI in excitatory V1 neurons in macaque monkeys. We then used widefield fluorescent imaging to measure V1 dynamics in response to visual stimuli with diverse temporal waveforms and contrasts, and compared these responses to signals measured using a genetically encoded calcium indicator (GECI) and a synthetic voltage-sensitive dye (VSD). When compared to GECI, GEVI captures faster response dynamics, tracks higher temporal frequencies, and responds to lower contrasts. To quantitatively characterize these three signals, we developed a simple nonlinear model that predicts the response dynamics to stimuli with arbitrary temporal waveforms and contrasts. Our results are consistent with the hypothesis that GEVI signals reflect the dynamics of locally summed membrane potentials, thus opening the door for a new class of experiments in behaving primates.

This review addresses the challenges of obtaining high-quality quantitative data in the optical imaging of membrane voltage and calcium dynamics. The paper provides a comprehensive overview and systematization of recent studies that analyze factors limiting signal fidelity and propose strategies to enhance data quality. The primary sources of signal degradation in biological optical imaging, with an emphasis on membrane voltage and calcium imaging, are systematically explored across four major indicator classes: voltage-sensitive dyes (VSDs), genetically encoded voltage indicators (GEVIs), calcium-sensitive dyes (CSDs), and genetically encoded calcium indicators (GECIs). Common mechanisms that compromise data quality are classified into three main categories: fundamental photon shot noise, device-related errors, and sample-related measurement errors. For each class of limitation, its physical or biological origin and characteristic manifestations are described, which are followed by an analysis of available mitigation strategies, including hardware optimization, choice of sensors, sample preparation and experimental design, post-processing and computational correction methods.

A trafficking motif alters GEVI activity implicating persistent protein interactions at the membrane

Genetically encoded calcium indicators (GECIs), based on recombinant fluorescent proteins, have been engineered to observe calcium transients in living cells and organisms. Through observation of calcium, these indicators also report neural activity. We review progress in GECI construction and application, particularly toward in vivo monitoring of sparse action potentials (APs). We summarize the extrinsic and intrinsic factors that influence GECI performance. A simple model of GECI response to AP firing demonstrates the relative significance of these factors. We recommend a standardized protocol for evaluating GECIs in a physiologically relevant context. A potential method of simultaneous optical control and recording of neuronal circuits is presented.

Astrocytes display spontaneous intracellular Ca(2+) concentration fluctuations ([Ca(2+)]i) and in several settings respond to neuronal excitation with enhanced [Ca(2+)]i signals. It has been proposed that astrocytes in turn regulate neurons and blood vessels through calcium-dependent mechanisms, such as the release of signaling molecules. However, [Ca(2+)]i imaging in entire astrocytes has only recently become feasible with genetically encoded calcium indicators (GECIs) such as the GCaMP series. The use of GECIs in astrocytes now provides opportunities to study astrocyte [Ca(2+)]i signals in detail within model microcircuits such as the striatum, which is the largest nucleus of the basal ganglia. In the present report, detailed surgical methods to express GECIs in astrocytes in vivo, and confocal imaging approaches to record [Ca(2+)]i signals in striatal astrocytes in situ, are described. We highlight precautions, necessary controls and tests to determine if GECI expression is selective for astrocytes and to evaluate signs of overt astrocyte reactivity. We also describe brain slice and imaging conditions in detail that permit reliable [Ca(2+)]i imaging in striatal astrocytes in situ. The use of these approaches revealed the entire territories of single striatal astrocytes and spontaneous [Ca(2+)]i signals within their somata, branches and branchlets. The further use and expansion of these approaches in the striatum will allow for the detailed study of astrocyte [Ca(2+)]i signals in the striatal microcircuitry.

Voltage-sensing phosphatases (VSPs) provide a conserved framework for dissecting the mechanics of voltage sensing and for engineering genetically encoded voltage indicators (GEVIs). To evaluate how natural sequence diversity shapes function, we compared VSP voltage-sensing domains (VSDs) from multiple species by replacing the phosphatase domain with a fluorescent protein to enable optical detection of VSD responses. Every construct that reached the plasma membrane produced a voltage-dependent optical signal, underscoring the deep conservation of voltage sensing across VSP orthologs. Yet lineage-specific substitutions generated strikingly different phenotypes. A plankton VSP ortholog from Eurytemora carolleeae and the Sea Hare (Aplysia californica) VSP exhibited left-shifted activation ranges, producing robust fluorescence transitions during modest depolarizations of the plasma membrane. The human VSD of hVSP2 yielded weak, sluggish responses with poor recovery, but reintroduction of a conserved arginine in S1 (G95R) partially restored reversibility, implicating lipid-facing residues in conformational stability. The Chinese hamster (Cricetulus griseus) VSD, with atypical S4 sensing charges (RWIR), generated a slow fluorescence increase during depolarization, while reverting to the consensus arginine (RRIR) inverted the polarity to a decrease. These contrasting behaviors show that single residue changes can reshape how VSD movements influence the fluorescent reporter, highlighting the molecular precision revealed by GEVI measurements. Together, these results show that voltage-dependent signaling is deeply conserved across VSPs but shaped by lineage-specific sequence variation, establishing VSPs as powerful models for probing voltage sensing and guiding GEVI design.

Genetically encoded voltage indicators (GEVIs) have found wide applications as molecular tools for visualization of changes in cell membrane potential. Among others, several classes of archaerhodopsin-3-based GEVIs have been developed and have proved themselves promising in various molecular imaging studies. To expand the application range for this type of GEVIs, new variants with absorption band maxima shifted toward the first biological window and enhanced fluorescence signal are required. Here, we integrate computational and experimental strategies to reveal structural factors that distinguish far-red bright archaerhodopsin-3-based GEVIs, Archers, obtained by directed evolution in a previous study (McIsaac et al., PNAS, 2014) and the wild-type archaerhodopsin-3 with an extremely dim fluorescence signal, aiming to use the obtained information in subsequent rational design. We found that the fluorescence can be enhanced by stabilization of a certain conformation of the protein, which, in turn, can be achieved by tuning the pK a value of two titratable residues. These findings were supported further by introducing mutations into wild-type archeorhodopsin-3 and detecting the enhancement of the fluorescence signal. Finally, we came up with a rational design and proposed previously unknown Archers variants with red-shifted absorption bands (λmax up to 640 nm) and potential-dependent bright fluorescence (quantum yield up to 0.97%).

We present a frequency-multiplexed multi-site two-photon imaging method utilizing amplitude modulation of femtosecond laser pulses in the MHz range to tag each excitation beam and the corresponding fluorescence signals with specific frequencies. The frequency tags are generated with an interferometric setup employing acousto-optic deflectors (AODs) to achieve precise spatial overlap of femtosecond pulses with acoustically-shifted frequencies. Creating matching excitation beam patterns in each interferometer arm using multiple AOD driving frequencies and subsequently overlapping these matching patterns results in multiple excitation beams with unique beat frequencies available for scanning. As a proof-of-concept, we demonstrate multiplexed two-photon image acquisition using test samples, and compare the performance of this approach to conventional two-photon laser scanning microscopy.

Neuronal activity occurs simultaneously and in a highly coordinated fashion in many different areas across the brain. Real-time visualization of large-scale neural dynamics in whole mammalian brains is hindered with the existing neuroimaging methods that are limited in their ability to image large tissue volumes at high speeds. Genetically encoded calcium indicators (GECIs) that modulate their fluorescence intensity as a function of intracellular calcium concentrations are powerful tools for the observation of large neuronal networks. Optoacoustic imaging has been shown capable of real-time three-dimensional imaging of multiple cerebral hemodynamic parameters in rodents. However, optoacoustic imaging of calcium activity deep in mammalian brain is hampered by strong blood absorption in the visible light spectrum as well as lack of activity labels excitable in the near-infrared window. We developed and validated an isolated whole mouse brain preparation labelled with genetically encoded calcium indicator GCaMP6f, which can closely resemble in vivo conditions and exhibit functional activity for several hours to several days. An optoacoustic imaging system coupled to a superfusion system was further devised and used for rapid volumetric monitoring of calcium dynamics in the brain evoked using an epilepsy-inducing drug. The new technique captures calcium fluxes as true 3D information across the entire brain with temporal resolution of 10ms and spatial resolution of 150µm, thus enabling large-scale neural recording at penetration depths and spatio-temporal resolution scales not covered with the existing neuroimaging techniques. The system could be readily adapted to work with future generations of far-red- and near-infrared GECIs.

Genetically encoded calcium indicators (GECIs) are mainly represented by two- or one-fluorophore-based sensors. One type of two-fluorophore-based sensor, carrying Opsanus troponin C (TnC) as the Ca2+-binding moiety, has two binding sites for calcium ions, providing a linear response to calcium ions. One-fluorophore-based sensors have four Ca2+-binding sites but are better suited for in vivo experiments. Herein, we describe a novel design for a one-fluorophore-based GECI with two Ca2+-binding sites. The engineered sensor, called NTnC, uses TnC as the Ca2+-binding moiety, inserted in the mNeonGreen fluorescent protein. Monomeric NTnC has higher brightness and pH-stability in vitro compared with the standard GECI GCaMP6s. In addition, NTnC shows an inverted fluorescence response to Ca2+. Using NTnC, we have visualized Ca2+ dynamics during spontaneous activity of neuronal cultures as confirmed by control NTnC and its mutant, in which the affinity to Ca2+ is eliminated. Using whole-cell patch clamp, we have demonstrated that NTnC dynamics in neurons are similar to those of GCaMP6s and allow robust detection of single action potentials. Finally, we have used NTnC to visualize Ca2+ neuronal activity in vivo in the V1 cortical area in awake and freely moving mice using two-photon microscopy or an nVista miniaturized microscope.

Establishment of a NanoBiT-Based Cytosolic Ca2+ Sensor by Optimizing Calmodulin-Binding Motif and Protein Expression Levels

Cholinergic interneurons (CINs) are believed to form synchronous cell assemblies that modulate the striatal microcircuitry and possibly orchestrate local dopamine release. We expressed GCaMP6s, a genetically encoded calcium indicator (GECIs), selectively in CINs, and used microendoscopes to visualize the putative CIN assemblies in the dorsal striatum of freely moving mice. The GECI fluorescence signal from the dorsal striatum was composed of signals from individual CIN somata that were engulfed by a widespread fluorescent neuropil. Bouts of synchronous activation of the cholinergic neuropil revealed patterns of activity that preceded the signal from individual somata. To investigate the nature of the neuropil signal and why it precedes the somatic signal, we target-patched GECI-expressing CINs in acute striatal slices in conjunction with multiphoton imaging or wide-field imaging that emulates the microendoscopes' specifications. The ability to detect fluorescent transients associated with individual action potential was constrained by the long decay constant of GECIs (relative to common inorganic dyes) to slowly firing (<2 spikes/s) CINs. The microendoscopes' resolving power and sampling rate further diminished this ability. Additionally, we found that only back-propagating action potentials but not synchronous optogenetic activation of thalamic inputs elicited observable calcium transients in CIN dendrites. Our data suggest that only bursts of CIN activity (but not their tonic firing) are visible using endoscopic imaging, and that the neuropil patterns are a physiological measure of the collective recurrent CIN network spiking activity.

Despite many association studies linking gene polymorphisms and mutations of L-type voltage-gated Ca2+ channels (VGCCs) in neurodevelopmental disorders such as autism and schizophrenia, the roles of specific L-type VGCC during brain development remain unclear. Calcium signaling has been shown to be essential for neurodevelopmental processes such as sculpting of neurites, functional wiring, and fine tuning of growing networks. To investigate this relationship, we performed submembraneous calcium imaging using a membrane-tethered genetically encoded calcium indicator (GECI) Lck-G-CaMP7. We successfully recorded spontaneous regenerative calcium transients (SRCaTs) in developing mouse excitatory cortical neurons prepared from both sexes before synapse formation. SRCaTs originated locally in immature neurites independently of somatic calcium rises and were significantly more elevated in the axons than in dendrites. SRCaTs were not blocked by tetrodoxin, a Na+ channel blocker, but were strongly inhibited by hyperpolarization, suggesting a voltage-dependent source. Pharmacological and genetic manipulations revealed the critical importance of the Cav1.2 (CACNA1C) pore-forming subunit of L-type VGCCs, which were indeed expressed in immature mouse brains. Consistently, knocking out Cav1.2 resulted in significant alterations of neurite outgrowth. Furthermore, expression of a gain-of-function Cav1.2 mutant found in Timothy syndrome, an autosomal dominant multisystem disorder exhibiting syndromic autism, resulted in impaired radial migration of layer 2/3 excitatory neurons, whereas postnatal abrogation of Cav1.2 enhancement could rescue cortical malformation. Together, these lines of evidence suggest a critical role for spontaneous opening of L-type VGCCs in neural development and corticogenesis and indicate that L-type VGCCs might constitute a perinatal therapeutic target for neuropsychiatric calciochannelopathies.SIGNIFICANCE STATEMENT Despite many association studies linking gene polymorphisms and mutations of L-type voltage-gated Ca2+ channels (VGCCs) in neurodevelopmental disorders such as autism and schizophrenia, the roles of specific L-type VGCCs during brain development remain unclear. We here combined the latest Ca2+ indicator technology, quantitative pharmacology, and in utero electroporation and found a hitherto unsuspected role for L-type VGCCs in determining the Ca2+ signaling landscape of mouse immature neurons. We found that malfunctional L-type VGCCs in immature neurons before birth might cause errors in neuritic growth and cortical migration. Interestingly, the retarded corticogenesis phenotype was rescued by postnatal correction of L-type VGCC signal aberration. These findings suggest that L-type VGCCs might constitute a perinatal therapeutic target for neurodevelopment-associated psychiatric disorders.

Voltage-sensing phosphatases (VSPs) provide a conserved framework for dissecting the mechanics of voltage sensing and for engineering genetically encoded voltage indicators (GEVIs). To evaluate how natural sequence diversity shapes function, we compared VSP voltage-sensing domains (VSDs) from multiple species. Every construct that reached the plasma membrane produced a voltage-dependent optical signal, underscoring the deep conservation of voltage sensing across the family. Yet lineage-specific substitutions generated strikingly different phenotypes. A plankton ortholog exhibited a strongly left-shifted activation range, producing robust signals at modest depolarizations. The human VSD yielded weak, sluggish responses with poor recovery, but reintroduction of a conserved arginine in S1 (G95R) partially restored reversibility, implicating lipid-facing residues in conformational stability. The hamster VSD, with atypical S4 sensing charges (RWIR), generated a slow fluorescence increase during depolarization, while reverting to the consensus arginine (RRIR) inverted the polarity to a decrease. These contrasting behaviors demonstrate that even single residue changes can reorient the coupling between VSD motion and the fused fluorescent protein, revealing the fine mechanistic resolution accessible through GEVI readouts. Together, these results show that voltage-dependent signaling is deeply conserved across VSPs but shaped by lineage-specific sequence variation, establishing VSPs as powerful models for probing voltage sensing and guiding GEVI design.

A Fluorescent Protein Voltage Sensor in the Endoplasmic Reticulum