Imaging and Optically Manipulating Neuronal Ensembles

Recurrent activity propagates through labile ensembles in macaque dorsolateral prefrontal microcircuits

Human and non-human primate studies clearly implicate the dorsolateral prefrontal cortex (dlPFC) as critical for advanced cognitive functions.1,2 It is thought that intracortical synaptic architectures within the dlPFC are the integral neurobiological substrate that gives rise to these processes.3,4,5,6,7 In the prevailing model, each cortical column makes up one fundamental processing unit composed of dense intrinsic connectivity, conceptualized as the "canonical" cortical microcircuit.3,8 Each cortical microcircuit receives sensory and cognitive information from upstream sources, which are represented by sustained activity within the microcircuit, referred to as persistent or recurrent activity.4,9 Via recurrent connections within the microcircuit, activity propagates for a variable length of time, thereby allowing temporary storage and computations to occur locally before ultimately passing a transformed representation to a downstream output.4,5,10 Competing theories regarding how microcircuit activity is coordinated have proven difficult to reconcile in vivo, where intercortical and intracortical computations cannot be fully dissociated.5,9,11,12 Here, using high-density calcium imaging of macaque dlPFC, we isolated intracortical computations by interrogating microcircuit networks ex vivo. Using peri-sulcal stimulation to evoke recurrent activity in deep layers, we found that activity propagates through stochastically assembled intracortical networks wherein orderly, predictable, low-dimensional collective dynamics arise from ensembles with highly labile cellular memberships. Microcircuit excitability covaried with individual cognitive performance, thus anchoring heuristic models of abstract cortical functions within quantifiable constraints imposed by the underlying synaptic architecture. Our findings argue against engram or localist architectures, together demonstrating that generation of high-fidelity population-level signals from distributed, labile networks is an intrinsic feature of dlPFC microcircuitry.

Neural ensembles: role of intrinsic excitability and its plasticity

Synaptic connectivity defines groups of neurons that engage in correlated activity during specific functional tasks. These co-active groups of neurons form ensembles, the operational units involved in, for example, sensory perception, motor coordination and memory (then called an engram). Traditionally, ensemble formation has been thought to occur via strengthening of synaptic connections via long-term potentiation (LTP) as a plasticity mechanism. This synaptic theory of memory arises from the learning rules formulated by Hebb and is consistent with many experimental observations. Here, we propose, as an alternative, that the intrinsic excitability of neurons and its plasticity constitute a second, non-synaptic mechanism that could be important for the initial formation of ensembles. Indeed, enhanced neural excitability is widely observed in multiple brain areas subsequent to behavioral learning. In cortical structures and the amygdala, excitability changes are often reported as transient, even though they can last tens of minutes to a few days. Perhaps it is for this reason that they have been traditionally considered as modulatory, merely supporting ensemble formation by facilitating LTP induction, without further involvement in memory function (memory allocation hypothesis). We here suggest-based on two lines of evidence-that beyond modulating LTP allocation, enhanced excitability plays a more fundamental role in learning. First, enhanced excitability constitutes a signature of active ensembles and, due to it, subthreshold synaptic connections become suprathreshold in the absence of synaptic plasticity (iceberg model). Second, enhanced excitability promotes the propagation of dendritic potentials toward the soma and allows for enhanced coupling of EPSP amplitude (LTP) to the spike output (and thus ensemble participation). This permissive gate model describes a need for permanently increased excitability, which seems at odds with its traditional consideration as a short-lived mechanism. We propose that longer modifications in excitability are made possible by a low threshold for intrinsic plasticity induction, suggesting that excitability might be on/off-modulated at short intervals. Consistent with this, in cerebellar Purkinje cells, excitability lasts days to weeks, which shows that in some circuits the duration of the phenomenon is not a limiting factor in the first place. In our model, synaptic plasticity defines the information content received by neurons through the connectivity network that they are embedded in. However, the plasticity of cell-autonomous excitability could dynamically regulate the ensemble participation of individual neurons as well as the overall activity state of an ensemble.

Simultaneous, cortex-wide dynamics of up to 1 million neurons reveal unbounded scaling of dimensionality with neuron number

The brain's remarkable properties arise from the collective activity of millions of neurons. Widespread application of dimensionality reduction to multi-neuron recordings implies that neural dynamics can be approximated by low-dimensional "latent" signals reflecting neural computations. However, can such low-dimensional representations truly explain the vast range of brain activity, and if not, what is the appropriate resolution and scale of recording to capture them? Imaging neural activity at cellular resolution and near-simultaneously across the mouse cortex, we demonstrate an unbounded scaling of dimensionality with neuron number in populations up to 1 million neurons. Although half of the neural variance is contained within sixteen dimensions correlated with behavior, our discovered scaling of dimensionality corresponds to an ever-increasing number of neuronal ensembles without immediate behavioral or sensory correlates. The activity patterns underlying these higher dimensions are fine grained and cortex wide, highlighting that large-scale, cellular-resolution recording is required to uncover the full substrates of neuronal computations.

Large-scale coupling of prefrontal activity patterns as a mechanism for cognitive control in health and disease: evidence from rodent models

Cognitive control of behavior is crucial for well-being, as allows subject to adapt to changing environments in a goal-directed way. Changes in cognitive control of behavior is observed during cognitive decline in elderly and in pathological mental conditions. Therefore, the recovery of cognitive control may provide a reliable preventive and therapeutic strategy. However, its neural basis is not completely understood. Cognitive control is supported by the prefrontal cortex, structure that integrates relevant information for the appropriate organization of behavior. At neurophysiological level, it is suggested that cognitive control is supported by local and large-scale synchronization of oscillatory activity patterns and neural spiking activity between the prefrontal cortex and distributed neural networks. In this review, we focus mainly on rodent models approaching the neuronal origin of these prefrontal patterns, and the cognitive and behavioral relevance of its coordination with distributed brain systems. We also examine the relationship between cognitive control and neural activity patterns in the prefrontal cortex, and its role in normal cognitive decline and pathological mental conditions. Finally, based on these body of evidence, we propose a common mechanism that may underlie the impaired cognitive control of behavior.

All-optical interrogation of millimeter-scale networks and application to developing ferret cortex

BACKGROUND

Perception and behavior require coordinated activity of thousands of neurons operating in networks that span millimeters of brain area. In vivo calcium imaging approaches have proven exceptionally powerful for examining the structure of these networks at large scales, and optogenetics can allow for causal manipulations of large populations of neurons. However, realizing the full potential of these techniques requires the ability to simultaneously measure and manipulate distinct circuit elements on the scale of millimeters.

NEW METHOD

We describe an opto-macroscope, an artifact-free, all-optical system capable of delivering patterned optogenetic stimulation with high spatial and temporal resolution across millimeters of brain while simultaneously imaging functional neural activity.

RESULTS

We find that this approach provides direct manipulation of cortical regions ranging from hundreds of microns to several millimeters in area, allowing for the perturbation of individual brain areas or networks of functional domains. Using this system we find that spatially complex endogenous networks in the developing ferret visual cortex can be readily reactivated by precisely designed patterned optogenetic stimuli.

COMPARISON WITH EXISTING METHODS

Our opto-macroscope extends current all-optical optogenetic approaches which operate on a cellular scale with multiphoton stimulation, and are poorly suited to investigate the millimeter-scale of many functional networks. It also builds upon other mesoscopic optogenetic techniques that lack simultaneous optical readouts of neural activity.

CONCLUSIONS

The large-scale all-optical capabilities of our system make it a powerful new tool for investigating the contribution of cortical domains and brain areas to the functional neural networks that underlie perception and behavior.

Driving valence-specific behavior through single-cell resolution control in the amygdala

In this issue of Neuron, Piantadosi et al.1 demonstrate that by precisely controlling the activity of individual negative-valence neurons and positive-valence neurons in the basolateral amygdala, one can alter animals' appetitive or aversive responses, respectively, establishing a causal role of these neurons in valence-specific behavior.

Holographic stimulation of opposing amygdala ensembles bidirectionally modulates valence-specific behavior via mutual inhibition

The basolateral amygdala (BLA) is an evolutionarily conserved brain region, well known for valence processing. Despite this central role, the relationship between activity of BLA neuronal ensembles in response to appetitive and aversive stimuli and the subsequent expression of valence-specific behavior has remained elusive. Here, we leverage two-photon calcium imaging combined with single-cell holographic photostimulation through an endoscopic lens to demonstrate a direct causal role for opposing ensembles of BLA neurons in the control of oppositely valenced behavior in mice. We report that targeted photostimulation of either appetitive or aversive BLA ensembles results in mutual inhibition and shifts behavioral responses to promote consumption of an aversive tastant or reduce consumption of an appetitive tastant, respectively. Here, we identify that neuronal encoding of valence in the BLA is graded and relies on the relative proportion of individual BLA neurons recruited in a stable appetitive or quinine ensemble.

Simultaneous, cortex-wide and cellular-resolution neuronal population dynamics reveal an unbounded scaling of dimensionality with neuron number

The brain's remarkable properties arise from collective activity of millions of neurons. Widespread application of dimensionality reduction to multi-neuron recordings implies that neural dynamics can be approximated by low-dimensional "latent" signals reflecting neural computations. However, what would be the biological utility of such a redundant and metabolically costly encoding scheme and what is the appropriate resolution and scale of neural recording to understand brain function? Imaging the activity of one million neurons at cellular resolution and near-simultaneously across mouse cortex, we demonstrate an unbounded scaling of dimensionality with neuron number. While half of the neural variance lies within sixteen behavior-related dimensions, we find this unbounded scaling of dimensionality to correspond to an ever-increasing number of internal variables without immediate behavioral correlates. The activity patterns underlying these higher dimensions are fine-grained and cortex-wide, highlighting that large-scale recording is required to uncover the full neural substrates of internal and potentially cognitive processes.

Photoactivated Protein Degrader for Optical Control of Synaptic Function

Hundreds of proteins determine the function of synapses, and synapses define the neuronal circuits that subserve myriad brain, cognitive, and behavioral functions. It is thus necessary to precisely manipulate specific proteins at specific sub-cellular locations and times to elucidate the roles of particular proteins and synapses in brain function. We developed PHOtochemically TArgeting Chimeras (PHOTACs) as a strategy to optically degrade specific proteins with high spatial and temporal precision. PHOTACs are small molecules that, upon wavelength-selective illumination, catalyze ubiquitylation and degradation of target proteins through endogenous proteasomes. Here, we describe the design and chemical properties of a PHOTAC that targets Ca2+/calmodulin-dependent protein kinase II alpha (CaMKIIα), which is abundant and crucial for the baseline synaptic function of excitatory neurons. We validate the PHOTAC strategy, showing that the CaMKIIα-PHOTAC is effective in mouse brain tissue. Light activation of CaMKIIα-PHOTAC removed CaMKIIα from regions of the mouse hippocampus only within 25 μm of the illuminated brain surface. The optically controlled degradation decreases synaptic function within minutes of light activation, measured by the light-initiated attenuation of evoked field excitatory postsynaptic potential (fEPSP) responses to physiological stimulation. The PHOTACs methodology should be broadly applicable to other key proteins implicated in synaptic function, especially for evaluating their precise roles in the maintenance of long-term potentiation and memory within subcellular dendritic domains.

Aberration-free holographic microscope for simultaneous imaging and stimulation of neuronal populations

A technical challenge in neuroscience is to record and specifically manipulate the activity of neurons in living animals. This can be achieved in some preparations with two-photon calcium imaging and photostimulation. These methods can be extended to three dimensions by holographic light sculpting with spatial light modulators (SLMs). At the same time, performing simultaneous holographic imaging and photostimulation is still cumbersome, requiring two light paths with separate SLMs. Here we present an integrated optical design using a single SLM for simultaneous imaging and photostimulation. Furthermore, we applied axially dependent adaptive optics to make the system aberration-free, and developed software for calibrations and closed-loop neuroscience experiments. Finally, we demonstrate the performance of the system with simultaneous calcium imaging and optogenetics in mouse primary auditory cortex in vivo. Our integrated holographic system could facilitate the systematic investigation of neural circuit function in awake behaving animals.

Prominent in vivo influence of single interneurons in the developing barrel cortex

Spontaneous synchronous activity is a hallmark of developing brain circuits and promotes their formation. Ex vivo, synchronous activity was shown to be orchestrated by a sparse population of highly connected GABAergic 'hub' neurons. The recent development of all-optical methods to record and manipulate neuronal activity in vivo now offers the unprecedented opportunity to probe the existence and function of hub cells in vivo. Using calcium imaging, connectivity analysis and holographic optical stimulation, we show that single GABAergic, but not glutamatergic, neurons influence population dynamics in the barrel cortex of non-anaesthetized mouse pups. Single GABAergic cells mainly exert an inhibitory influence on both spontaneous and sensory-evoked population bursts. Their network influence scales with their functional connectivity, with highly connected hub neurons displaying the strongest impact. We propose that hub neurons function in tailoring intrinsic cortical dynamics to external sensory inputs.

Physiological Needs: Sensations and Predictions in the Insular Cortex

Physiological needs create powerful motivations (e.g., thirst and hunger). Studies in humans and animal models have implicated the insular cortex in the neural regulation of physiological needs and need-driven behavior. We review prominent mechanistic models of how the insular cortex might achieve this regulation and present a conceptual and analytical framework for testing these models in healthy and pathological conditions.

A Photoactivated Protein Degrader for Optical Control of Synaptic Function

Hundreds of proteins determine the function of synapses, and synapses define the neuronal circuits that subserve myriad brain, cognitive, and behavioral functions. It is thus necessary to precisely manipulate specific proteins at specific sub-cellular locations and times to elucidate the roles of particular proteins and synapses in brain function. We developed PHOtochemically TArgeting Chimeras (PHOTACs) as a strategy to optically degrade specific proteins with high spatial and temporal precision. PHOTACs are small molecules that, upon wavelength-selective illumination, catalyze ubiquitylation and degradation of target proteins through endogenous proteasomes. Here we describe the design and chemical properties of a PHOTAC that targets Ca 2+ /calmodulin-dependent protein kinase II alpha (CaMKIIα), which is abundant and crucial for baseline synaptic function of excitatory neurons. We validate the PHOTAC strategy, showing that the CaMKIIα-PHOTAC is effective in mouse brain tissue. Light activation of CaMKIIα-PHOTAC removed CaMKIIα from regions of the mouse hippocampus only within 25 μm of the illuminated brain surface. The optically-controlled degradation decreases synaptic function within minutes of light activation, measured by the light-initiated attenuation of evoked field excitatory postsynaptic potential (fEPSP) responses to physiological stimulation. The PHOTACs methodology should be broadly applicable to other key proteins implicated in synaptic function, especially for evaluating their precise roles in the maintenance of long-term potentiation and memory within subcellular dendritic domains.

Wide-Field Calcium Imaging of Neuronal Network Dynamics In Vivo

A central tenet of neuroscience is that sensory, motor, and cognitive behaviors are generated by the communications and interactions among neurons, distributed within and across anatomically and functionally distinct brain regions. Therefore, to decipher how the brain plans, learns, and executes behaviors requires characterizing neuronal activity at multiple spatial and temporal scales. This includes simultaneously recording neuronal dynamics at the mesoscale level to understand the interactions among brain regions during different behavioral and brain states. Wide-field Ca2+ imaging, which uses single photon excitation and improved genetically encoded Ca2+ indicators, allows for simultaneous recordings of large brain areas and is proving to be a powerful tool to study neuronal activity at the mesoscopic scale in behaving animals. This review details the techniques used for wide-field Ca2+ imaging and the various approaches employed for the analyses of the rich neuronal-behavioral data sets obtained. Also discussed is how wide-field Ca2+ imaging is providing novel insights into both normal and altered neural processing in disease. Finally, we examine the limitations of the approach and new developments in wide-field Ca2+ imaging that are bringing new capabilities to this important technique for investigating large-scale neuronal dynamics.

Conceptual framework for neuronal ensemble identification and manipulation related to behavior using calcium imaging

Significance: The identification and manipulation of spatially identified neuronal ensembles with optical methods have been recently used to prove the causal link between neuronal ensemble activity and learned behaviors. However, the standardization of a conceptual framework to identify and manipulate neuronal ensembles from calcium imaging recordings is still lacking. Aim: We propose a conceptual framework for the identification and manipulation of neuronal ensembles using simultaneous calcium imaging and two-photon optogenetics in behaving mice. Approach: We review the computational approaches that have been used to identify and manipulate neuronal ensembles with single cell resolution during behavior in different brain regions using all-optical methods. Results: We proposed three steps as a conceptual framework that could be applied to calcium imaging recordings to identify and manipulate neuronal ensembles in behaving mice: (1) transformation of calcium transients into binary arrays; (2) identification of neuronal ensembles as similar population vectors; and (3) targeting of neuronal ensemble members that significantly impact behavioral performance. Conclusions: The use of simultaneous two-photon calcium imaging and two-photon optogenetics allowed for the experimental demonstration of the causal relation of population activity and learned behaviors. The standardization of analytical tools to identify and manipulate neuronal ensembles could accelerate interventional experiments aiming to reprogram the brain in normal and pathological conditions.

Transformation of primary sensory cortical representations from layer 4 to layer 2

Sensory input arrives from thalamus in cortical layer (L) 4, which outputs predominantly to superficial layers. L4 to L2 thus constitutes one of the earliest cortical feedforward networks. Despite extensive study, the transformation performed by this network remains poorly understood. We use two-photon calcium imaging to record neural activity in L2-4 of primary vibrissal somatosensory cortex (vS1) as mice perform an object localization task with two whiskers. Touch responses sparsen and become more reliable from L4 to L2, with nearly half of the superficial touch response confined to ~1 % of excitatory neurons. These highly responsive neurons have broad receptive fields and can more accurately decode stimulus features. They participate disproportionately in ensembles, small subnetworks with elevated pairwise correlations. Thus, from L4 to L2, cortex transitions from distributed probabilistic coding to sparse and robust ensemble-based coding, resulting in more efficient and accurate representations.

Formation and computational implications of assemblies in neural circuits

In the brain, patterns of neural activity represent sensory information and store it in non-random synaptic connectivity. A prominent theoretical hypothesis states that assemblies, groups of neurons that are strongly connected to each other, are the key computational units underlying perception and memory formation. Compatible with these hypothesised assemblies, experiments have revealed groups of neurons that display synchronous activity, either spontaneously or upon stimulus presentation, and exhibit behavioural relevance. While it remains unclear how assemblies form in the brain, theoretical work has vastly contributed to the understanding of various interacting mechanisms in this process. Here, we review the recent theoretical literature on assembly formation by categorising the involved mechanisms into four components: synaptic plasticity, symmetry breaking, competition and stability. We highlight different approaches and assumptions behind assembly formation and discuss recent ideas of assemblies as the key computational unit in the brain. Abstract figure legend Assembly Formation. Assemblies are groups of strongly connected neurons formed by the interaction of multiple mechanisms and with vast computational implications. Four interacting components are thought to drive assembly formation: synaptic plasticity, symmetry breaking, competition and stability. This article is protected by copyright. All rights reserved.

A one-photon endoscope for simultaneous patterned optogenetic stimulation and calcium imaging in freely behaving mice

Optogenetics and calcium imaging can be combined to simultaneously stimulate and record neural activity in vivo. However, this usually requires two-photon microscopes, which are not portable nor affordable. Here we report the design and implementation of a miniaturized one-photon endoscope for performing simultaneous optogenetic stimulation and calcium imaging. By integrating digital micromirrors, the endoscope makes it possible to activate any neuron of choice within the field of view, and to apply arbitrary spatiotemporal patterns of photostimulation while imaging calcium activity. We used the endoscope to image striatal neurons from either the direct pathway or the indirect pathway in freely moving mice while activating any chosen neuron in the field of view. The endoscope also allows for the selection of neurons based on their relationship with specific animal behaviour, and to recreate the behaviour by mimicking the natural neural activity with photostimulation. The miniaturized endoscope may facilitate the study of how neural activity gives rise to behaviour in freely moving animals.

Advancements in the Quest to Map, Monitor, and Manipulate Neural Circuitry

Neural circuits and the cells that comprise them represent the functional units of the brain. Circuits relay and process sensory information, maintain homeostasis, drive behaviors, and facilitate cognitive functions such as learning and memory. Creating a functionally-precise map of the mammalian brain requires anatomically tracing neural circuits, monitoring their activity patterns, and manipulating their activity to infer function. Advancements in cell-type-specific genetic tools allow interrogation of neural circuits with increased precision. This review provides a broad overview of recombination-based and activity-driven genetic targeting approaches, contemporary viral tracing strategies, electrophysiological recording methods, newly developed calcium, and voltage indicators, and neurotransmitter/neuropeptide biosensors currently being used to investigate circuit architecture and function. Finally, it discusses methods for acute or chronic manipulation of neural activity, including genetically-targeted cellular ablation, optogenetics, chemogenetics, and over-expression of ion channels. With this ever-evolving genetic toolbox, scientists are continuing to probe neural circuits with increasing resolution, elucidating the structure and function of the incredibly complex mammalian brain.

Chemical Targeting of Rhodol Voltage-Sensitive Dyes to Dopaminergic Neurons

Optical imaging of changes in the membrane potential of living cells can be achieved by means of fluorescent voltage-sensitive dyes (VSDs). A particularly challenging task is to efficiently deliver these highly lipophilic probes to specific neuronal subpopulations in brain tissue. We have tackled this task by designing a solubilizing, hydrophilic polymer platform that carries a high-affinity ligand for a membrane protein marker of interest and a fluorescent VSD. Here, we disclose an improved design of polymer-supported probes for chemical, nongenetic targeting of voltage sensors to axons natively expressing the dopamine transporter in ex vivo mouse brain tissue. We first show that for negatively charged rhodol VSDs functioning on the photoinduced electron transfer principle, poly(ethylene glycol) as a carrier enables targeting with higher selectivity than the polysaccharide dextran in HEK cell culture. In the same experimental setting, we also demonstrate that incorporation of an azetidine ring into the rhodol chromophore substantially increases the brightness and voltage sensitivity of the respective VSD. We show that the superior properties of the optimized sensor are transferable to recording of electrically evoked activity from dopaminergic axons in mouse striatal slices after averaging of multiple trials. Finally, we suggest the next milestones for the field to achieve single-scan recordings with nongenetically targeted VSDs in native brain tissue.

Autocrine Neuromodulation and Network Activity Patterns in the Locus Coeruleus of Newborn Rat Slices

Already in newborns, the locus coeruleus (LC) controls multiple brain functions and may have a complex organization as in adults. Our findings in newborn rat brain slices indicate that LC neurons (i) generate at ~1 Hz a ~0.3 s-lasting local field potential (LFP) comprising summated phase-locked single spike discharge, (ii) express intrinsic ‘pacemaker’ or ‘burster’ properties and (iii) receive solely excitatory or initially excitatory−secondary inhibitory inputs. μ-opioid or ɑ2 noradrenaline receptor agonists block LFP rhythm at 100−250 nM whereas slightly lower doses transform its bell-shaped pattern into slower crescendo-shaped multipeak bursts. GABAA and glycine receptors hyperpolarize LC neurons to abolish rhythm which remains though unaffected by blocking them. Rhythm persists also during ionotropic glutamate receptor (iGluR) inhibition whereas <10 mV depolarization during iGluR agonists accelerates spiking to cause subtype-specific fast (spindle-shaped) LFP oscillations. Similar modest neuronal depolarization causing a cytosolic Ca2+ rise occurs (without effect on neighboring astrocytes) during LFP acceleration by CNQX activating a TARP-AMPA-type iGluR complex. In contrast, noradrenaline lowers neuronal Ca2+ baseline via ɑ2 receptors, but evokes an ɑ1 receptor-mediated ‘concentric’ astrocytic Ca2+ wave. In summary, the neonatal LC has a complex (possibly modular) organization to enable discharge pattern transformations that might facilitate discrete actions on target circuits.

A deep-learning approach for online cell identification and trace extraction in functional two-photon calcium imaging

In vivo two-photon calcium imaging is a powerful approach in neuroscience. However, processing two-photon calcium imaging data is computationally intensive and time-consuming, making online frame-by-frame analysis challenging. This is especially true for large field-of-view (FOV) imaging. Here, we present CITE-On (Cell Identification and Trace Extraction Online), a convolutional neural network-based algorithm for fast automatic cell identification, segmentation, identity tracking, and trace extraction in two-photon calcium imaging data. CITE-On processes thousands of cells online, including during mesoscopic two-photon imaging, and extracts functional measurements from most neurons in the FOV. Applied to publicly available datasets, the offline version of CITE-On achieves performance similar to that of state-of-the-art methods for offline analysis. Moreover, CITE-On generalizes across calcium indicators, brain regions, and acquisition parameters in anesthetized and awake head-fixed mice. CITE-On represents a powerful tool to speed up image analysis and facilitate closed-loop approaches, for example in combined all-optical imaging and manipulation experiments.

Inhibition of Neuronal Necroptosis Mediated by RIPK1 Provides Neuroprotective Effects on Hypoxia and Ischemia In Vitro and In Vivo

Ischemic brain injury is a widespread pathological condition, the main components of which are a deficiency of oxygen and energy substrates. In recent years, a number of new forms of cell death, including necroptosis, have been described. In necroptosis, a cascade of interactions between the kinases RIPK1 and RIPK3 and the MLKL protein leads to the formation of a specialized death complex called the necrosome, which triggers MLKL-mediated destruction of the cell membrane and necroptotic cell death. Necroptosis probably plays an important role in the development of ischemia/reperfusion injury and can be considered as a potential target for finding methods to correct the disruption of neural networks in ischemic damage. In the present study, we demonstrated that blockade of RIPK1 kinase by Necrostatin-1 preserved the viability of cells in primary hippocampal cultures in an in vitro model of glucose deprivation. The effect of RIPK1 blockade on the bioelectrical and metabolic calcium activity of neuron-glial networks in vitro using calcium imaging and multi-electrode arrays was assessed for the first time. RIPK1 blockade was shown to partially preserve both calcium and bioelectric activity of neuron-glial networks under ischemic factors. However, it should be noted that RIPK1 blockade does not preserve the network parameters of the collective calcium dynamics of neuron-glial networks, despite the maintenance of network bioelectrical activity (the number of bursts and the number of spikes in the bursts). To confirm the data obtained in vitro, we studied the effect of RIPK1 blockade on the resistance of small laboratory animals to in vivo modeling of hypoxia and cerebral ischemia. The use of Necrostatin-1 increases the survival rate of C57BL mice in modeling both acute hypobaric hypoxia and ischemic brain damage.

Identification of Pattern Completion Neurons in Neuronal Ensembles Using Probabilistic Graphical Models

Neuronal ensembles are groups of neurons with coordinated activity that could represent sensory, motor, or cognitive states. The study of how neuronal ensembles are built, recalled, and involved in the guiding of complex behaviors has been limited by the lack of experimental and analytical tools to reliably identify and manipulate neurons that have the ability to activate entire ensembles. Such pattern completion neurons have also been proposed as key elements of artificial and biological neural networks. Indeed, the relevance of pattern completion neurons is highlighted by growing evidence that targeting them can activate neuronal ensembles and trigger behavior. As a method to reliably detect pattern completion neurons, we use conditional random fields (CRFs), a type of probabilistic graphical model. We apply CRFs to identify pattern completion neurons in ensembles in experiments using in vivo two-photon calcium imaging from primary visual cortex of male mice and confirm the CRFs predictions with two-photon optogenetics. To test the broader applicability of CRFs we also analyze publicly available calcium imaging data (Allen Institute Brain Observatory dataset) and demonstrate that CRFs can reliably identify neurons that predict specific features of visual stimuli. Finally, to explore the scalability of CRFs we apply them to in silico network simulations and show that CRFs-identified pattern completion neurons have increased functional connectivity. These results demonstrate the potential of CRFs to characterize and selectively manipulate neural circuits.SIGNIFICANCE STATEMENT We describe a graph theory method to identify and optically manipulate neurons with pattern completion capability in mouse cortical circuits. Using calcium imaging and two-photon optogenetics in vivo we confirm that key neurons identified by this method can recall entire neuronal ensembles. This method could be broadly applied to manipulate neuronal ensemble activity to trigger behavior or for therapeutic applications in brain prostheses.

Probing neural codes with two-photon holographic optogenetics

Optogenetics ushered in a revolution in how neuroscientists interrogate brain function. Because of technical limitations, the majority of optogenetic studies have used low spatial resolution activation schemes that limit the types of perturbations that can be made. However, neural activity manipulations at finer spatial scales are likely to be important to more fully understand neural computation. Spatially precise multiphoton holographic optogenetics promises to address this challenge and opens up many new classes of experiments that were not previously possible. More specifically, by offering the ability to recreate extremely specific neural activity patterns in both space and time in functionally defined ensembles of neurons, multiphoton holographic optogenetics could allow neuroscientists to reveal fundamental aspects of the neural codes for sensation, cognition and behavior that have been beyond reach. This Review summarizes recent advances in multiphoton holographic optogenetics that substantially expand its capabilities, highlights outstanding technical challenges and provides an overview of the classes of experiments it can execute to test and validate key theoretical models of brain function. Multiphoton holographic optogenetics could substantially accelerate the pace of neuroscience discovery by helping to close the loop between experimental and theoretical neuroscience, leading to fundamental new insights into nervous system function and disorder.

Manipulating neuronal circuits, in concert

Two-photon holographic optogenetics enables precise modulation of brain activity

Scalable and accurate method for neuronal ensemble detection in spiking neural networks

We propose a novel, scalable, and accurate method for detecting neuronal ensembles from a population of spiking neurons. Our approach offers a simple yet powerful tool to study ensemble activity. It relies on clustering synchronous population activity (population vectors), allows the participation of neurons in different ensembles, has few parameters to tune and is computationally efficient. To validate the performance and generality of our method, we generated synthetic data, where we found that our method accurately detects neuronal ensembles for a wide range of simulation parameters. We found that our method outperforms current alternative methodologies. We used spike trains of retinal ganglion cells obtained from multi-electrode array recordings under a simple ON-OFF light stimulus to test our method. We found a consistent stimuli-evoked ensemble activity intermingled with spontaneously active ensembles and irregular activity. Our results suggest that the early visual system activity could be organized in distinguishable functional ensembles. We provide a Graphic User Interface, which facilitates the use of our method by the scientific community.

Visual stimulation with blue wavelength light drives V1 effectively eliminating stray light contamination during two-photon calcium imaging

BACKGROUND

Brain visual circuits are often studied in vivo by imaging Ca²⁺ indicators with green-shifted emission spectra. Polychromatic white visual stimuli have a spectrum that partially overlaps indicators´ emission spectra, resulting in significant contamination of calcium signals.

NEW METHOD

To overcome light contamination problems we choose blue visual stimuli, having a spectral composition not overlapping with Ca²⁺ indicator´s emission spectrum. To compare visual responsiveness to blue and white stimuli we used electrophysiology (visual evoked potentials -VEPs) and 3D acousto-optic two-photon (2P) population Ca²⁺ imaging in mouse primary visual cortex (V1).

RESULTS

VEPs in response to blue and white stimuli had comparable peak amplitudes and latencies. Ca²⁺ imaging in a Thy1 GP4.3 line revealed that the populations of neurons responding to blue and white stimuli were largely overlapping, that their responses had similar amplitudes, and that functional response properties such as orientation and direction selectivities were also comparable.

COMPARISON WITH EXISTING METHODS

Masking or shielding the microscope are often used to minimize the contamination of Ca²⁺ signal by white light, but they are time consuming, bulky and thus can limit experimental design, particularly in the more and more frequently used awake set-up. Blue stimuli not interfering with imaging allow to omit shielding.

CONCLUSIONS

Together, our results show that the selected blue light stimuli evoke responses comparable to those evoked by white stimuli in mouse V1. This will make complex designs of imaging experiments in behavioral set-ups easier, and facilitate the combination of Ca²⁺ imaging with electrophysiology and optogenetics.

Inverted Ion Current Rectification-Based Chemical Delivery Probes for Stimulation of Neurons

Ion current rectification (ICR), diodelike behavior in surface-charged nanopores, shows promise in the design of delivery probes for manipulation of neural networks as it can solve diffusive leakages that might be critical in clinical and research applications. However, it has not been achieved because ICR has restrictions in nanosized dimension and low electrolyte concentration, and rectification direction is inappropriate for delivery. Herein, we present a polyelectrolyte gel-filled (PGF) micropipette harnessing inverted ICR as a delivery probe, which quantitatively transports glutamate to stimulate primary cultured neurons with high efficiency while minimizing leakages. Since the gel works as an ensemble of numerous surface-charged nanopores, the current is rectified in the micro-opening and physiological environment. By extending the charge-selective region using the gel, inverted ICR is generated, which drives outward deliveries of major charge carriers. This study will help in exploring new aspects of ICR and broaden its applications for advanced chemical delivery.

Long-term plasticity in the hippocampus: maintaining within and 'tagging' between synapses

Synapses between neurons are malleable biochemical structures, strengthening and diminishing over time dependent on the type of information they receive. This phenomenon known as synaptic plasticity underlies learning and memory, and its different forms, long-term potentiation (LTP) and long-term depression (LTD), perform varied cognitive roles in reinforcement, relearning and associating memories. Moreover, both LTP and LTD can exist in an early transient form (early-LTP/LTD) or a late persistent form (late-LTP/LTD), which are triggered by different induction protocols, and also differ in their dependence on protein synthesis and the involvement of key molecular players. Beyond homosynaptic modifications, synapses can also interact with one another. This is encapsulated in the synaptic tagging and capture hypothesis (STC), where synapses expressing early-LTP/LTD present a 'tag' that can capture the protein synthesis products generated during a temporally proximal late-LTP/LTD induction. This 'tagging' phenomenon forms the framework of synaptic interactions in various conditions and accounts for the cellular basis of the time-dependent associativity of short-lasting and long-lasting memories. All these synaptic modifications take place under controlled neuronal conditions, regulated by subcellular elements such as epigenetic regulation, proteasomal degradation and neuromodulatory signals. Here, we review current understanding of the different forms of synaptic plasticity and its regulatory mechanisms in the hippocampus, a brain region critical for memory formation. We also discuss expression of plasticity in hippocampal CA2 area, a long-overlooked narrow hippocampal subfield and the behavioural correlate of STC. Lastly, we put forth perspectives for an integrated view of memory representation in synapses.

Optogenetic strategies for high-efficiency all-optical interrogation using blue-light-sensitive opsins

All-optical methods for imaging and manipulating brain networks with high spatial resolution are fundamental to study how neuronal ensembles drive behavior. Stimulation of neuronal ensembles using two-photon holographic techniques requires high-sensitivity actuators to avoid photodamage and heating. Moreover, two-photon-excitable opsins should be insensitive to light at wavelengths used for imaging. To achieve this goal, we developed a novel soma-targeted variant of the large-conductance blue-light-sensitive opsin CoChR (stCoChR). In the mouse cortex in vivo, we combined holographic two-photon stimulation of stCoChR with an amplified laser tuned at the opsin absorption peak and two-photon imaging of the red-shifted indicator jRCaMP1a. Compared to previously characterized blue-light-sensitive soma-targeted opsins in vivo, stCoChR allowed neuronal stimulation with more than 10-fold lower average power and no spectral crosstalk. The combination of stCoChR, tuned amplified laser stimulation, and red-shifted functional indicators promises to be a powerful tool for large-scale interrogation of neural networks in the intact brain.

Neuronal ensembles in memory processes

A neuronal ensemble represents the concomitant activity of a specific group of neurons that could encompass a broad repertoire of brain functions such as motor, perceptual, memory or cognitive states. On the other hand, a memory engram portrays the physical manifestation of memory or the changes that enable learning and retrieval. Engram studies focused for many years on finding where memories are stored as in, which cells or brain regions represent a memory trace, and disregarded the investigation of how neuronal activity patterns give rise to such memories. Recent experiments suggest that the association and reactivation of specific neuronal groups could be the main mechanism underlying the brain's ability to remember past experiences and envision future actions. Thus, the growing consensus is that the interaction between neuronal ensembles could allow sequential activity patterns to become memories and recurrent memories to compose complex behaviors. The goal of this review is to propose how the neuronal ensemble framework could be translated and useful to understand memory processes.

Neuroprotective Effect of Kinase Inhibition in Ischemic Factor Modeling In Vitro

The contribution of many neuronal kinases to the adaptation of nerve cells to ischemic damage and their effect on functional neural network activity has not yet been studied. The aim of this work is to study the role of the four kinases belonging to different metabolic cascades (SRC, Ikkb, eEF2K, and FLT4) in the adaptive potential of the neuron-glial network for modeling the key factors of ischemic damage. We carried out a comprehensive study on the effects of kinases blockade on the viability and network functional calcium activity of nerve cells under ischemic factor modeling in vitro. Ischemic factor modelling was performed on day 14 of culturing primary hippocampal cells obtained from mouse embryos (E18). The most significant neuroprotective effect was shown in the blockade of FLT4 kinase in the simulation of hypoxia. The studies performed revealed the role of FLT4 in the development of functional dysfunction in cerebrovascular accidents and created new opportunities for the study of this enzyme and its blockers in the formation of new therapeutic strategies.

Configuration and dynamics of dominant inspiratory multineuronal activity patterns during eupnea and gasping generation in vitro

The pre-Bötzinger complex (preBötC), located within the ventral respiratory column, produces inspiratory bursts in varying degrees of synchronization/amplitude. This wide range of population burst patterns reflects the flexibility of the preBötC neurons, which is expressed in variations in the onset/offset times of their activations and their activity during the population bursts, with respiratory neurons exhibiting a large cycle-to-cycle timing jitter both at the population activity onset and at the population activity peak, suggesting that respiratory neurons are stochastically activated before and during the inspiratory bursts. However, it is still unknown whether this stochasticity is maintained while evaluating the coactivity of respiratory neuronal ensembles. Moreover, the preBötC topology also remains unknown. In this study, by simultaneously recording tens of preBötC neurons and using coactivation analysis during the inspiratory periods, we found that the preBötC has a scale-free configuration (mixture of not many highly connected nodes, hubs, with abundant poorly connected elements) exhibiting the rich-club phenomenon (hubs more likely interconnected with each other). PreBötC neurons also produce multineuronal activity patterns (MAPs) that are highly stable and change during the hypoxia-induced reconfiguration. Moreover, preBötC contains a coactivating core network shared by all its MAPs. Finally, we found a distinctive pattern of sequential coactivation of core network neurons at the beginning of the inspiratory periods, indicating that, when evaluated at the multicellular level, the coactivation of respiratory neurons seems not to be stochastic.NEW & NOTEWORTHY By means of multielectrode recordings of preBötC neurons, we evaluated their configuration in normoxia and hypoxia, finding that the preBötC exhibits a scale-free configuration with a rich-club phenomenon. preBötC neurons produce multineuronal activity patterns that are highly stable but change during hypoxia. The preBötC contains a coactivating core network that exhibit a distinctive pattern of coactivation at the beginning of inspirations. These results reveal some network basis of inspiratory rhythm generation and its reconfiguration during hypoxia.

Identification and quantification of neuronal ensembles in optical imaging experiments

Recent technical advances in molecular biology and optical imaging have made it possible to record from up to thousands of densely packed neurons in superficial and deep brain regions in vivo, with cellular subtype specificity and high spatiotemporal fidelity. Such optical neurotechnologies are enabling increasingly fine-scaled studies of neuronal circuits and reliably co-active groups of neurons, so-called ensembles. Neuronal ensembles are thought to constitute the basic functional building blocks of brain systems, potentially exhibiting collective computational properties. While the technical framework of in vivo optical imaging and quantification of neuronal activity follows certain widely held standards, analytical methods for study of neuronal co-activity and ensembles lack consensus and are highly varied across the field. Here we provide a comprehensive step-by-step overview of theoretical, experimental, and analytical considerations for the identification and quantification of neuronal ensemble dynamics in high-resolution in vivo optical imaging studies.

Mild metabolic stress is sufficient to disturb the formation of pyramidal cell ensembles during gamma oscillations

Disturbances of cognitive functions occur rapidly during acute metabolic stress. However, the underlying mechanisms are not fully understood. Cortical gamma oscillations (30-100 Hz) emerging from precise synaptic transmission between excitatory principal neurons and inhibitory interneurons, such as fast-spiking GABAergic basket cells, are associated with higher brain functions, like sensory perception, selective attention and memory formation. We investigated the alterations of cholinergic gamma oscillations at the level of neuronal ensembles in the CA3 region of rat hippocampal slice cultures. We combined electrophysiology, calcium imaging (CamKII.GCaMP6f) and mild metabolic stress that was induced by rotenone, a lipophilic and highly selective inhibitor of complex I in the respiratory chain of mitochondria. The detected pyramidal cell ensembles showing repetitive patterns of activity were highly sensitive to mild metabolic stress. Whereas such synchronised multicellular activity diminished, the overall activity of individual pyramidal cells was unaffected. Additionally, mild metabolic stress had no effect on the rate of action potential generation in fast-spiking neural units. However, the partial disinhibition of slow-spiking neural units suggests that disturbances of ensemble formation likely result from alterations in synaptic inhibition. Our study bridges disturbances on the (multi-)cellular and network level to putative cognitive impairment on the system level.

Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits

Experimental studies in neuroscience are producing data at a rapidly increasing rate, providing exciting opportunities and formidable challenges to existing theoretical and modeling approaches. To turn massive datasets into predictive quantitative frameworks, the field needs software solutions for systematic integration of data into realistic, multiscale models. Here we describe the Brain Modeling ToolKit (BMTK), a software suite for building models and performing simulations at multiple levels of resolution, from biophysically detailed multi-compartmental, to point-neuron, to population-statistical approaches. Leveraging the SONATA file format and existing software such as NEURON, NEST, and others, BMTK offers a consistent user experience across multiple levels of resolution. It permits highly sophisticated simulations to be set up with little coding required, thus lowering entry barriers to new users. We illustrate successful applications of BMTK to large-scale simulations of a cortical area. BMTK is an open-source package provided as a resource supporting modeling-based discovery in the community.

Dissecting Neuronal Activation on a Brain-Wide Scale With Immediate Early Genes

Visualizing neuronal activation on a brain-wide scale yet with cellular resolution is a fundamental technical challenge for neuroscience. This would enable analyzing how different neuronal circuits are disrupted in pathology and how they could be rescued by pharmacological treatments. Although this goal would have appeared visionary a decade ago, recent technological advances make it eventually feasible. Here, we review the latest developments in the fields of genetics, sample preparation, imaging, and image analysis that could be combined to afford whole-brain cell-resolution activation mapping. We show how the different biochemical and optical methods have been coupled to study neuronal circuits at different spatial and temporal scales, and with cell-type specificity. The inventory of techniques presented here could be useful to find the tools best suited for a specific experiment. We envision that in the next years, mapping of neuronal activation could become routine in many laboratories, allowing dissecting the neuronal counterpart of behavior.

Concussion increases CA1 activity during prolonged inactivity in a familiar environment

Although hippocampal damage plays a key role in impairments after concussion, differences in hippocampal information processing during recovery are unknown. Micro-endoscopic calcium imaging was performed before and after primary blast injury in freely behaving mice in two environments: their familiar home cage and a novel open field. Results show that after concussion CA1 activity increased in the familiar environment in which animals were awake and mostly immobile but was unaltered in a novel environment which the animals actively and constantly explored. As awake immobility parallels cognitive rest, a common treatment for patients, the results imply that prolonged cognitive rest may unwittingly impede concussion recovery.

Neuroprotective Effect of HIF Prolyl Hydroxylase Inhibition in an In Vitro Hypoxia Model

A novel potent analog of the branched tail oxyquinoline group of hypoxia-inducible factor (HIF) prolyl hydroxylase inhibitors, neuradapt, has been studied in two treatment regimes in an in vitro hypoxia model on murine primary hippocampal cultures. Neuradapt activates the expression of HIF1 and HIF2 target genes and shows no toxicity up to 20 μM, which is more than an order of magnitude higher than its biologically active concentration. Cell viability, functional activity, and network connectivity between the elements of neuronal networks have been studied using a pairwise correlation analysis of the intracellular calcium fluctuations in the individual cells. An immediate treatment with 1 μМ and 15 μМ neuradapt right at the onset of hypoxia not only protects from the death, but also maintains the spontaneous calcium activity in nervous cells at the level of the intact cultures. A similar neuroprotective effect in the post-treatment scenario is observed for 15 μМ, but not for 1 μМ neuradapt. Network connectivity is better preserved with immediate treatment using 1 μМ neuradapt than with 15 μМ, which is still beneficial. Post-treatment with neuradapt did not restore the network connectivity despite the observation that neuradapt significantly increased cell viability at 1 μМ and functional activity at 15 μМ. The preservation of cell viability and functional activity makes neuradapt promising for further studies in a post-treatment scenario, since it can be combined with other drugs and treatments restoring the network connectivity of functionally competent cells.

Dopamine D1 Receptors Regulate Spines in Striatal Direct-Pathway and Indirect-Pathway Neurons

BACKGROUND

Dopamine transmission is involved in the maintenance of the structural plasticity of direct-pathway and indirect-pathway striatal projection neurons (d-SPNs and i-SPNs, respectively). The lack of dopamine in Parkinson's disease produces synaptic remodeling in both types of SPNs, reducing the length of the dendritic arbor and spine density and increasing the intrinsic excitability. Meanwhile, the elevation of dopamine levels by levodopa recovers these alterations selectively in i-SPNs. However, little is known about the specific role of the D1 receptor (D1R) in these alterations.

METHODS

To explore the specific role of D1R in the synaptic remodeling of SPNs, we used knockout D1R mice (D1R^-/- ) and wild-type mice crossed with drd2-enhanced green fluorescent protein (eGFP) to identify d-SPNs and i-SPNs. Corticostriatal slices were used for reconstruction of the dendritic arbors after Lucifer yellow intracellular injection and for whole-cell recordings in naïve and parkinsonian mice treated with saline or levodopa.

RESULTS

The genetic inactivation of D1R reduces the length of the dendritic tree and the spine density in all SPNs, although more so in d-SPNs, which also increases their spiking. In parkinsonian D1R^-/- mice, the spine density decreases in i-SPNs, and this spine loss recovers after chronic levodopa.

CONCLUSIONS

D1R is essential for the maintenance of spine plasticity in d-SPNs but also affects i-SPNs, indicating an important crosstalk between these 2 types of neurons. © 2020 International Parkinson and Movement Disorder Society.

Playing the piano with the cortex: role of neuronal ensembles and pattern completion in perception and behavior

Neuronal ensembles, i.e. coactive groups of neurons, have been long postulated to be functional building blocks of cortical circuits and units of the neural code. Calcium imaging of neuronal populations has demonstrated the widespread existence of spontaneous and sensory-evoked ensembles in cortical circuits in vivo. The development of two-photon optical techniques to simultaneously record and activate neurons with single cell resolution ("piano" experiments) has revealed the existence of pattern completion neurons, which can trigger an entire ensemble, and demonstrated a causal relation between ensembles and behavior. We review recent results controlling visual perception with targeted holographic manipulation of cortical ensembles by stimulating pattern completion neurons. Analyzing population activity as neuronal ensembles and exploiting pattern completion could enable control of brain states in health and disease.

Stability of spontaneous, correlated activity in mouse auditory cortex

Neural systems can be modeled as complex networks in which neural elements are represented as nodes linked to one another through structural or functional connections. The resulting network can be analyzed using mathematical tools from network science and graph theory to quantify the system’s topological organization and to better understand its function. Here, we used two-photon calcium imaging to record spontaneous activity from the same set of cells in mouse auditory cortex over the course of several weeks. We reconstruct functional networks in which cells are linked to one another by edges weighted according to the correlation of their fluorescence traces. We show that the networks exhibit modular structure across multiple topological scales and that these multi-scale modules unfold as part of a hierarchy. We also show that, on average, network architecture becomes increasingly dissimilar over time, with similarity decaying monotonically with the distance (in time) between sessions. Finally, we show that a small fraction of cells maintain strongly-correlated activity over multiple days, forming a stable temporal core surrounded by a fluctuating and variable periphery. Our work indicates a framework for studying spontaneous activity measured by two-photon calcium imaging using computational methods and graphical models from network science. The methods are flexible and easily extended to additional datasets, opening the possibility of studying cellular level network organization of neural systems and how that organization is modulated by stimuli or altered in models of disease.

Neurons coordinate their activity with one another, forming networks that help support adaptive, flexible behavior. Still, little is known about the organization of these networks at the cellular scale and their stability over time. Here, we reconstruct networks from calcium imaging data recorded in mouse primary auditory cortex. We show that these networks exhibit spatially constrained, hierarchical modular structure, which may facilitate specialized information processing. However, we show that connection weights and modular structure are also variable over time, changing on a timescale of days and adopting novel network configurations. Despite this, a small subset of neurons maintain their connections to one another and preserve their modular organization across time, forming a stable temporal core surrounded by a flexible periphery. These findings represent a conceptual bridge linking network analyses of macroscale and cellular-level neuroimaging data. They also represent a complementary approach to existing circuits- and systems-based interrogation of nervous system function, opening the door for deeper and more targeted analysis in the future.

Contemporary strategies for dissecting the neuronal basis of neurodevelopmental disorders

Great efforts in clinical and basic research have shown progress in understanding the neurobiological mechanisms of neurodevelopmental disorders, such as autism, schizophrenia, and attention-deficit hyperactive disorders. Literature on this field have suggested that these disorders are affected by the complex interaction of genetic, biological, psychosocial and environmental risk factors. However, this complexity of interplaying risk factors during neurodevelopment has prevented a complete understanding of the causes of those neuropsychiatric symptoms. Recently, with advances in modern high-resolution neuroscience methods, the neural circuitry analysis approach has provided new solutions for understanding the causal relationship between dysfunction of a neural circuit and behavioral alteration in neurodevelopmental disorders. In this review we will discuss recent progress in developing novel optogenetic and chemogenetic strategies to investigate neurodevelopmental disorders.

Bayesian inference of neuronal assemblies

In many areas of the brain, both spontaneous and stimulus-evoked activity can manifest as synchronous activation of neuronal assemblies. The characterization of assembly structure and dynamics provides important insights into how brain computations are distributed across neural networks. The proliferation of experimental techniques for recording the activity of neuronal assemblies calls for a comprehensive statistical method to describe, analyze and characterize these high dimensional datasets. The performance of existing methods for defining assemblies is sensitive to noise and stochasticity in neuronal firing patterns and assembly heterogeneity. To address these problems, we introduce a generative hierarchical model of synchronous activity to describe the organization of neurons into assemblies. Unlike existing methods, our analysis provides a simultaneous estimation of assembly composition, dynamics and within-assembly statistical features, such as the levels of activity, noise and assembly synchrony. We have used our method to characterize population activity throughout the tectum of larval zebrafish, allowing us to make statistical inference on the spatiotemporal organization of tectal assemblies, their composition and the logic of their interactions. We have also applied our method to functional imaging and neuropixels recordings from the mouse, allowing us to relate the activity of identified assemblies to specific behaviours such as running or changes in pupil diameter.

Principles of Optogenetic Methods and Their Application to Cardiac Experimental Systems

Optogenetic techniques permit studies of excitable tissue through genetically expressed light-gated microbial channels or pumps permitting transmembrane ion movement. Light activation of these proteins modulates cellular excitability with millisecond precision. This review summarizes optogenetic approaches, using examples from neurobiological applications, and then explores their application in cardiac electrophysiology. We review the available opsins, including depolarizing and hyperpolarizing variants, as well as modulators of G-protein coupled intracellular signaling. We discuss the biophysical properties that determine the ability of microbial opsins to evoke reliable, precise stimulation or silencing of electrophysiological activity. We also review spectrally shifted variants offering possibilities for enhanced depth of tissue penetration, combinatorial stimulation for targeting different cell subpopulations, or all-optical read-in and read-out studies. Expression of the chosen optogenetic tool in the cardiac cell of interest then requires, at the single-cell level, introduction of opsin-encoding genes by viral transduction, or coupling "spark cells" to primary cardiomyocytes or a stem-cell derived counterpart. At the system-level, this requires construction of transgenic mice expressing ChR2 in their cardiomyocytes, or in vivo injection (myocardial or systemic) of adenoviral expression systems. Light delivery, by laser or LED, with widespread or multipoint illumination, although relatively straightforward in vitro may be technically challenged by cardiac motion and light-scattering in biological tissue. Physiological read outs from cardiac optogenetic stimulation include single cell patch clamp recordings, multi-unit microarray recordings from cell monolayers or slices, and electrical recordings from isolated Langendorff perfused hearts. Optical readouts of specific cellular events, including ion transients, voltage changes or activity in biochemical signaling cascades, using small detecting molecules or genetically encoded sensors now offer powerful opportunities for all-optical control and monitoring of cellular activity. Use of optogenetics has expanded in cardiac physiology, mainly using optically controlled depolarizing ion channels to control heart rate and for optogenetic defibrillation. ChR2-expressing cardiomyocytes show normal baseline and active excitable membrane and Ca2+ signaling properties and are sensitive even to ~1 ms light pulses. They have been employed in studies of the intrinsic cardiac adrenergic system and of cardiac arrhythmic properties.