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We develop a phenomenological coarse--graining procedure for activity in a large network of neurons, and apply this to recordings from a population of 1000+ cells in the hippocampus. Distributions of coarse--grained variables seem to approach a fixed non--Gaussian form, and we see evidence of scaling in both static and dynamic quantities. These results suggest that the collective behavior of the network is described by a non--trivial fixed point.

The hippocampus plays a critical role in goal-directed navigation. Across different environments, however, hippocampal maps are randomized, making it unclear how goal locations could be encoded consistently. To address this question, we developed a virtual reality task with shifting reward contingencies to distinguish place versus reward encoding. In mice performing the task, large-scale recordings in CA1 and subiculum revealed a small, specialized cell population that was only active near reward yet whose activity could not be explained by sensory cues or stereotyped reward anticipation behavior. Across different virtual environments, most cells remapped randomly, but reward encoding consistently arose from a single pool of cells, suggesting that they formed a dedicated channel for reward. These observations represent a significant departure from the current understanding of CA1 as a relatively homogeneous ensemble without fixed coding properties and provide a new candidate for the cellular basis of goal memory in the hippocampus.

The gradual accumulation of sensory evidence is a crucial component of perceptual decision making, but its neural mechanisms are still poorly understood. Given the wide availability of genetic and optical tools for mice, they can be useful model organisms for the study of these phenomena; however, behavioral tools are largely lacking. Here, we describe a new evidence-accumulation task for head-fixed mice navigating in a virtual reality environment. As they navigate down the stem of a virtual T-maze, they see brief pulses of visual evidence on either side, and retrieve a reward on the arm with the highest number of pulses. The pulses occur randomly with Poisson statistics, yielding a diverse yet well-controlled stimulus set, making the data conducive to a variety of computational approaches. A large number of mice of different genotypes were able to learn and consistently perform the task, at levels similar to rats in analogous tasks. They are sensitive to side differences of a single pulse, and their memory of the cues is stable over time. Moreover, using non-parametric as well as modeling approaches, we show that the mice indeed accumulate evidence: they use multiple pulses of evidence from throughout the cue region of the maze to make their decision, albeit with a small overweighting of earlier cues, and their performance is affected by the magnitude but not the duration of evidence. Additionally, analysis of the mice's running patterns revealed that trajectories are fairly stereotyped yet modulated by the amount of sensory evidence, suggesting that the navigational component of this task may provide a continuous readout correlated to the underlying cognitive variables. Our task, which can be readily integrated with state-of-the-art techniques, is thus a valuable tool to study the circuit mechanisms and dynamics underlying perceptual decision making, particularly under more complex behavioral contexts.

The hippocampus plays a critical role in goal-directed navigation. Across different environments, however, the hippocampal map seems to be randomized, making it unclear how goal locations might be encoded. To address this question, we trained mice to seek reward at several locations on virtual linear tracks, and optical recordings of calcium activity were made at cellular resolution from two major hippocampal output structures, CA1 and the subiculum. These experiments revealed a population of neurons that were consistently active near reward locations. Their pattern of activity sharply contrasted with simultaneously-recorded place cells and even persisted across environments, when other cells remapped randomly. Their timing was closely correlated with reward anticipation behaviors, yet could not be explained by the behaviors themselves, raising the possibility that reward-associated cell signals were used by mice to identify the reward location. These results demonstrate that the hippocampus employs a context-invariant marker of goal locations, and reveal a novel target for studying how the hippocampus contributes to navigation.

To explore theories of predictive coding, we presented mice with repeated sequences of images with novel images sparsely substituted. Under these conditions, mice could be rapidly trained to lick in response to a novel image, demonstrating a high level of performance on the first day of testing. Using 2-photon calcium imaging to record from layer 2/3 neurons in the primary visual cortex, we found that novel images evoked excess activity in the majority of neurons. When a new stimulus sequence was repeatedly presented, a majority of neurons had similarly elevated activity for the first few presentations, which then decayed to almost zero activity. The decay time of these transient responses was not fixed, but instead scaled with the length of the stimulus sequence. However, at the same time, we also found a small fraction of the neurons within the population (∼2%) that continued to respond strongly and periodically to the repeated stimulus. Decoding analysis demonstrated that both the transient and sustained responses encoded information about stimulus identity. We conclude that the layer 2/3 population uses a two-channel predictive code: a dense transient code for novel stimuli and a sparse sustained code for familiar stimuli. These results extend and unify existing theories about the nature of predictive neural codes.

Two-photon (TP) calcium imaging is an important imaging modality in neuroscience, allowing for large-scale recording of neural activity in awake, behaving animals at behavior-relevant timescales. Interpretation of TP data requires the accurate extraction of temporal neural activity traces, which can be accomplished via manual or automated methods. In this work we seek to improve the accuracy of both manual and automated TP microscopy demixing methods by introducing a denoising algorithm based on a statistical model of TP data which includes spatial contiguity, sparse activity and Poisson observations. Our method leverages recent developments in stochastic filtering of structured signals based on Laplacian-scale mixture models (LSMs) to model the neural activity in TP data as a set of spatially correlated sparse variables. We apply our method on TP images taken from the visual cortex of an awake, behaving mouse, and demonstrate improved neural activity demixing over current pre-processing techniques.

Linking neural microcircuit function to emergent properties of the mammalian brain requires fine-scale manipulation and measurement of neural activity during behavior, where each neuron’s coding and dynamics can be characterized. We developed an optical method for simultaneous cellular-resolution stimulation and large-scale recording of neuronal activity in behaving mice. Dual-wavelength two-photon excitation allowed largely independent functional imaging with a green fluorescent calcium sensor (GCaMP3, λ = 920 ± 6 nm) and single-neuron photostimulation with a red-shifted optogenetic probe (C1V1, λ = 1,064 ± 6 nm) in neurons coexpressing the two proteins. We manipulated task-modulated activity in individual hippocampal CA1 place cells during spatial navigation in a virtual reality environment, mimicking natural place-field activity, or ‘biasing’, to reveal subthreshold dynamics. Notably, manipulating single place-cell activity also affected activity in small groups of other place cells that were active around the same time in the task, suggesting a functional role for local place cell interactions in shaping firing fields.

Summary Virtual reality (VR) enables precise control of an animal's environment and otherwise impossible experimental manipulations. Neural activity in rodents has been studied on virtual 1D tracks. However, 2D navigation imposes additional requirements, such as the processing of head direction and environment boundaries, and it is unknown whether the neural circuits underlying 2D representations can be sufficiently engaged in VR. We implemented a VR setup for rats, including software and large-scale electrophysiology, that supports 2D navigation by allowing rotation and walking in any direction. The entorhinal-hippocampal circuit, including place, head direction, and grid cells, showed 2D activity patterns similar to those in the real world. Furthermore, border cells were observed, and hippocampal remapping was driven by environment shape, suggesting functional processing of virtual boundaries. These results illustrate that 2D spatial representations can be engaged by visual and rotational vestibular stimuli alone and suggest a novel VR tool for studying rat navigation.

During navigation, grid cells increase their spike rates in firing fields arranged on a markedly regular triangular lattice, whereas their spike timing is often modulated by theta oscillations. Oscillatory interference models of grid cells predict theta amplitude modulations of membrane potential during firing field traversals, whereas competing attractor network models predict slow depolarizing ramps. Here, using in vivo whole-cell recordings, we tested these models by directly measuring grid cell intracellular potentials in mice running along linear tracks in virtual reality. Grid cells had large and reproducible ramps of membrane potential depolarization that were the characteristic signature tightly correlated with firing fields. Grid cells also demonstrated intracellular theta oscillations that influenced their spike timing. However, the properties of theta amplitude modulations were not consistent with the view that they determine firing field locations. Our results support cellular and network mechanisms in which grid fields are produced by slow ramps, as in attractor models, whereas theta oscillations control spike timing.

Discussions of the hippocampus often focus on place cells, but many neurons are not place cells in any given environment. Here we describe the collective activity in such mixed populations, treating place and non-place cells on the same footing. We start with optical imaging experiments on CA1 in mice as they run along a virtual linear track, and use maximum entropy methods to approximate the distribution of patterns of activity in the population, matching the correlations between pairs of cells but otherwise assuming as little structure as possible. We find that these simple models accurately predict the activity of each neuron from the state of all the other neurons in the network, regardless of how well that neuron codes for position. Our results suggest that understanding the neural activity may require not only knowledge of the external variables modulating it, but also of the internal network state.

Two-photon laser scanning microscopy of calcium dynamics using fluorescent indicators is a widely used imaging method for large scale recording of neural activity in vivo. Here we introduce volumetric Two-photon Imaging of Neurons using Stereoscopy (vTwINS), a volumetric calcium imaging method that employs an elongated, V-shaped point spread function to image a 3D brain volume. Single neurons project to spatially displaced image pairs in the resulting 2D image, and the separation distance between images is proportional to depth in the volume. To demix the fluorescence time series of individual neurons, we introduce a novel orthogonal matching pursuit algorithm that also infers source locations within the 3D volume. We illustrate vTwINS by imaging neural population activity in mouse primary visual cortex and hippocampus. Our results demonstrate that vTwINS provides an effective method for volumetric two-photon calcium imaging that increases the number of neurons recorded while maintaining a high frame-rate.

The posterior parietal cortex (PPC) has an important role in many cognitive behaviours; however, the neural circuit dynamics underlying PPC function are not well understood. Here we optically imaged the spatial and temporal activity patterns of neuronal populations in mice performing a PPC-dependent task that combined a perceptual decision and memory-guided navigation in a virtual environment. Individual neurons had transient activation staggered relative to one another in time, forming a sequence of neuronal activation spanning the entire length of a task trial. Distinct sequences of neurons were triggered on trials with opposite behavioural choices and defined divergent, choice-specific trajectories through a state space of neuronal population activity. Cells participating in the different sequences and at distinct time points in the task were anatomically intermixed over microcircuit length scales (

The authors measure the time constant of decay of persistent firing (persistence time) across a population of larval zebrafish oculomotor velocity-to-position neural integrator neurons. They find that persistence times are heterogeneous and topographically organized. This could arise from a circuit architecture in which nearby neurons are more strongly interconnected than distant ones. In a neural integrator, the variability and topographical organization of neuronal firing-rate persistence can provide information about the circuit's functional architecture. We used optical recording to measure the time constant of decay of persistent firing (persistence time) across a population of neurons comprising the larval zebrafish oculomotor velocity-to-position neural integrator. We found extensive persistence time variation (tenfold; coefficients of variation = 0.58–1.20) across cells in individual larvae. We also found that the similarity in firing between two neurons decreased as the distance between them increased and that a gradient in persistence time was mapped along the rostrocaudal and dorsoventral axes. This topography is consistent with the emergence of persistence time heterogeneity from a circuit architecture in which nearby neurons are more strongly interconnected than distant ones. Integrator circuit models characterized by multiple dimensions of slow firing-rate dynamics can account for our results.

Summary Widefield imaging of calcium dynamics is an emerging method for mapping regional neural activity but is currently limited to restrained animals. Here we describe cScope, a head-mounted widefield macroscope developed to image large-scale cortical dynamics in rats during natural behavior. cScope provides a 7.8 × 4 mm field of view and dual illumination paths for both fluorescence and hemodynamic correction and can be fabricated at low cost using readily attainable components. We also report the development of Thy-1 transgenic rat strains with widespread neuronal expression of the calcium indicator GCaMP6f. We combined these two technologies to image large-scale calcium dynamics in the dorsal neocortex during a visual evidence accumulation task. Quantitative analysis of task-related dynamics revealed multiple regions having neural signals that encode behavioral choice and sensory evidence. Our results provide a new transgenic resource for calcium imaging in rats and extend the domain of head-mounted microscopes to larger-scale cortical dynamics. Video Abstract Download : Download video (63MB)

Spatial navigation is often used as a behavioral task in studies of the neuronal circuits that underlie cognition, learning and memory in rodents. The combination of in vivo microscopy with genetically encoded indicators has provided an important new tool for studying neuronal circuits, but has been technically difficult to apply during navigation. Here we describe methods for imaging the activity of neurons in the CA1 region of the hippocampus with subcellular resolution in behaving mice. Neurons that expressed the genetically encoded calcium indicator GCaMP3 were imaged through a chronic hippocampal window. Head-restrained mice performed spatial behaviors in a setup combining a virtual reality system and a custom-built two-photon microscope. We optically identified populations of place cells and determined the correlation between the location of their place fields in the virtual environment and their anatomical location in the local circuit. The combination of virtual reality and high-resolution functional imaging should allow a new generation of studies to investigate neuronal circuit dynamics during behavior.

Macroscopic (millimeter scale) functional clustering is a hallmark characteristic of motor cortex spatial organization in awake behaving mammals; however, almost no information is known about the functional micro-organization (approximately 100 microm scale). Here, we optically recorded intracellular calcium transients of layer 2/3 neurons with cellular resolution over approximately 200-microm-diameter fields in the forelimb motor cortex of mobile, head-restrained mice during two distinct movements (running and grooming). We showed that the temporal correlation between neurons was statistically larger the closer the neurons were to each other. We further explored this correlation by using two separate methods to spatially segment the neurons within each imaging field: K-means clustering and correlations between single neuron activity and mouse movements. The two methods segmented the neurons similarly and led to the conclusion that the origin of the inverse relationship between correlation and distance seen statistically was twofold: clusters of highly temporally correlated neurons were often spatially distinct from one another, and (even when the clusters were spatially intermingled) within the clusters, the more correlated the neurons were to each other, the shorter the distance between them. Our results represent a direct observation of functional clustering within the microcircuitry of the awake mouse motor cortex.

Hippocampal place cells encode spatial information in rate and temporal codes. To examine the mechanisms underlying hippocampal coding, we measured the intracellular dynamics of place cells by combining in vivo whole cell recordings with a virtual reality system. Head-restrained mice, running on a spherical treadmill, interacted with a computer-generated visual environment to perform spatial behaviors. Robust place cell activity was present during movement along a virtual linear track. From whole cell recordings, we identified three subthreshold signatures of place fields: (1) an asymmetric ramp-like depolarization of the baseline membrane potential; (2) an increase in the amplitude of intracellular theta oscillations; and, (3) a phase precession of the intracellular theta oscillation relative to the extracellularly-recorded theta rhythm. These intracellular dynamics underlie the primary features of place cell rate and temporal codes. The virtual reality system developed here will enable new experimental approaches to study the neural circuits underlying navigation.

Although gamma frequency oscillations are common in the brain, their functional contributions to neural computation are not understood. Here we report in vitro electrophysiological recordings to evaluate how noisy gamma frequency oscillatory input interacts with the overall activation level of a neuron to determine the precise timing of its action potentials. The experiments were designed to evaluate spike synchrony in a neural circuit architecture in which a population of neurons receives a common noisy gamma oscillatory synaptic drive while the firing rate of each individual neuron is determined by a slowly varying independent input. We demonstrate that similarity of firing rate is a major determinant of synchrony under common noisy oscillatory input: Near coincidence of spikes at similar rates gives way to substantial desynchronization at larger firing rate differences. Analysis of this rate-specific synchrony phenomenon reveals distinct spike timing “fingerprints” at different firing rates that emerge through a combination of phase shifting and abrupt changes in spike patterns. We further demonstrate that rate-specific synchrony permits robust detection of rate similarity in a population of neurons through synchronous activation of a postsynaptic neuron, supporting the biological plausibility of a Many Are Equal computation. Our results reveal that spatially coherent noisy oscillations, which are common throughout the brain, can generate previously unknown relationships among neural rate codes, noisy interspike intervals, and precise spike synchrony codes. All of these can coexist in a self-consistent manner because of rate-specific synchrony.

Glutamatergic inputs clustered over approximately 20-40 microm can elicit local N-methyl-D-aspartate (NMDA) spike/plateau potentials in terminal dendrites of cortical pyramidal neurons, inspiring the notion that a single terminal dendrite can function as a decision-making computational subunit. A typical terminal basal dendrite is approximately 100-200 microm long: could it function as multiple decision-making subunits? We test this by sequential focal stimulation of multiple sites along terminal basal dendrites of layer 5 pyramidal neurons in rat somatosensory cortical brain slices, using iontophoresis or uncaging of brief glutamate pulses. There was an approximately sevenfold spatial gradient in average spike/plateau amplitude measured at the soma, from approximately 3 mV for distal inputs to approximately 23 mV for proximal inputs. Spike/plateaus were NMDA receptor (NMDAR) conductance-dominated at all locations. Large Ca(2+) transients accompanied spike/plateaus over a approximately 10- to 40-microm zone around the input site; smaller Ca(2+) transients extended approximately uniformly to the dendritic tip. Spike/plateau duration grew with increasing glutamate and depolarization; high Ca(2+) zone size grew with spike/plateau duration. The minimum high Ca(2+) zone half-width (just above NMDA spike threshold) increased from distal (approximately 10 microm) to proximal locations (approximately 25 microm), as did the NMDA spike glutamate threshold. Depolarization reduced glutamate thresholds. Simulations exploring multi-site interactions based on this demonstrate that if appropriately timed and localized inputs occur in vivo, a single basal dendrite could correspond to a cascade of multiple co-operating dynamic decision-making subunits able to retain information for hundreds of milliseconds, with increasing influence on neural output from distal to proximal. Dendritic NMDA spike/plateaus are thus well-suited to support graded persistent firing.

We report a technique for two-photon fluorescence imaging with cellular resolution in awake, behaving mice with minimal motion artifact. The apparatus combines an upright, table-mounted two-photon microscope with a spherical treadmill consisting of a large, air-supported Styrofoam ball. Mice, with implanted cranial windows, are head restrained under the objective while their limbs rest on the ball's upper surface. Following adaptation to head restraint, mice maneuver on the spherical treadmill as their heads remain motionless. Image sequences demonstrate that running-associated brain motion is limited to approximately 2-5 microm. In addition, motion is predominantly in the focal plane, with little out-of-plane motion, making the application of a custom-designed Hidden-Markov-Model-based motion correction algorithm useful for postprocessing. Behaviorally correlated calcium transients from large neuronal and astrocytic populations were routinely measured, with an estimated motion-induced false positive error rate of

Summary The reproducibility and precision of biological patterning is limited by the accuracy with which concentration profiles of morphogen molecules can be established and read out by their targets. We consider four measures of precision for the Bicoid morphogen in the Drosophila embryo: the concentration differences that distinguish neighboring cells, the limits set by the random arrival of Bicoid molecules at their targets (which depends on absolute concentration), the noise in readout of Bicoid by the activation of Hunchback, and the reproducibility of Bicoid concentration at corresponding positions in multiple embryos. We show, through a combination of different experiments, that all of these quantities are ∼10%. This agreement among different measures of accuracy indicates that the embryo is not faced with noisy input signals and readout mechanisms; rather, the system exerts precise control over absolute concentrations and responds reliably to small concentration differences, approaching the limits set by basic physical principles.

Decision-making behavior is often characterized by substantial variability, but its source remains unclear. We developed a visual accumulation of evidence task designed to quantify sources of noise and to be performed during voluntary head restraint, enabling cellular resolution imaging in future studies. Rats accumulated discrete numbers of flashes presented to the left and right visual hemifields and indicated the side that had the greater number of flashes. Using a signal-detection theory-based model, we found that the standard deviation in their internal estimate of flash number scaled linearly with the number of flashes. This indicates a major source of noise that, surprisingly, is not consistent with the widely used 'drift-diffusion modeling' (DDM) approach but is instead closely related to proposed models of numerical cognition and counting. We speculate that this form of noise could be important in accumulation of evidence tasks generally. DOI: http://dx.doi.org/10.7554/eLife.11308.001, eLife digest Perceptual decision-making, i.e. making choices based on observed evidence, is rarely perfect. Humans and other animals tend to respond correctly on some trials and incorrectly on others. For over a century, this variability has been used to study the basis of decision-making. Most behavioral models assume that random fluctuations or 'noise' in the decision-making process is the primary source of variability and errors. However, the nature of this noise is unclear and the subject of intense scrutiny. To investigate the sources of the behavioral variability during decision-making, Scott, Constantinople et al. trained rats to perform a visual 'accumulation of evidence' task. The animals counted flashes of light that appeared on either their left or their right. Up to 15 flashes occurred on each side, in a random order, and the rats then received a reward if they selected the side that the greatest number of flashes had occurred on. The rats chose correctly on many occasions but not on every single one. Using a computer-controlled rat training facility or 'rat academy', Scott, Constantinople et al. collected hundreds of thousands of behavioral trials from over a dozen rats. This large dataset provided the statistical power necessary to test the assumptions of leading models of behavioral variability during decision-making, and revealed that noise grew more rapidly with the number of flashes than previously predicted. This finding explained patterns of behavior that previous models struggled with, most notably the fact that individuals make errors even on the easiest trials. The analysis also revealed that animals maintain two separate running totals – one of stimuli on the left and another of stimuli on the right – rather than a single tally of the difference between the two. Scott, Constantinople et al. further demonstrated that rats could be trained to perform this task using a new system that enables functional brain imaging. The next step is to repeat these experiments while simultaneously recording brain activity to study the neural circuits that underlie decision-making and its variability. DOI: http://dx.doi.org/10.7554/eLife.11308.002

The evolution of the field of neuroscience has been propelled by the advent of novel technological capabilities, and the pace at which these capabilities are being developed has accelerated dramatically in the past decade. Capitalizing on this momentum, the United States launched the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative to develop and apply new tools and technologies for revolutionizing our understanding of the brain. In this article, we review the scientific vision for this initiative set forth by the National Institutes of Health and discuss its implications for the future of neuroscience research. Particular emphasis is given to its potential impact on the mapping and study of neural circuits, and how this knowledge will transform our understanding of the complexity of the human brain and its diverse array of behaviours, perceptions, thoughts and emotions., National Institutes of Health (U.S.), Howard Hughes Medical Institute

We show here that upconversion phosphors can be imaged both by infrared excitation and in a scanning electron microscope. We have synthesized and characterized for this work up-converting phosphor nanoparticles nonaggregated nanocrystals of size range 50-200 nm. We have investigated the optical properties of 50-200 nm nanoparticles and found a square dependence of the emitted visible fluorescence on the infrared excitation and verified that under electron excitation similar narrow band emission spectra can be obtained as is seen with IR upconversion. The viability of the nanoparticles for biological imaging was confirmed by imaging the digestive system of the nematode worm Caenorhabditis elegans, and we have confirmed using energy-dispersive X-ray analysis that the up-conversion nanoparticles can be identified in a scanning electron microscope at high spatial resolution.

Persistent neural activity refers to a sustained change in action potential discharge that long outlasts a stimulus. It is found in a diverse set of brain regions and organisms and several in vitro systems, suggesting that it can be considered a universal form of circuit dynamics that can be used as a mechanism for short-term storage and accumulation of sensory or motor information. Both single cell and network mechanisms are likely to co-operate in generating persistent activity in many brain areas.

We quantitatively studied the ontogeny of oculomotor behavior in larval fish as a foundation for studies linking oculomotor structure and function with genetics. Horizontal optokinetic and vestibuloocular reflexes (OKR and VOR, respectively) were measured in three different species (goldfish, zebrafish, and medaka) during the first month after hatching. For all sizes of medaka, and most zebrafish, Bode plots of OKR (0.065–3.0 Hz, ±10°/s) revealed that eye velocity closely followed stimulus velocity (gain > 0.8) at low frequency but dropped sharply above 1 Hz (gain < 0.3 at 3 Hz). Goldfish showed increased gain proportional to size across frequencies. Linearity testing with steps and sinusoids showed excellent visual performance (gain > 0.8) in medaka almost from hatching; but zebrafish and goldfish exhibited progressive improvement, with only the largest equaling medaka performance. Monocular visual stimulation in zebrafish and goldfish produced gains of 0.5 versus 200°/s at 0.5 Hz), first in medaka followed by larger (8.11 mm) zebrafish; but it was virtually nonexistent in goldfish. Velocity storage was not observed except for an eye velocity build-up in the largest medaka. In summary, a robust OKR was achieved shortly after hatching in all three species. In contrast, larval fish seem to be unique among vertebrates tested in their lack of significant angular VOR at stages where active movement is required for feeding and survival.

In a companion paper, we reported that the goldfish oculomotor neural integrator could be trained to instability or leak by rotating the visual surround with a velocity proportional to +/- horizontal eye position, respectively. Here we analyze changes in the firing rate behavior of neurons in area I in the caudal brainstem, a central component of the oculomotor neural integrator. Persistent firing could be detuned to instability and leak, respectively, along with fixation behavior. Prolonged training could reduce the time constant of persistent firing of some cells by more than an order of magnitude, to

Short-term memory is often correlated with persistent changes in neuronal firing rates in response to transient inputs. We model the persistent maintenance of an analog eye position signal by an oculomotor neural integrator receiving transient eye movement commands. Previous models of this network rely on precisely tuned positive feedback with

Persistent firing in response to a brief stimulus is a neural correlate of short-term memory in a variety of systems. In the oculomotor neural integrator, persistent firing that encodes eye position is maintained in response to transient saccadic eye-velocity commands. To a first approximation, firing rates in the integrator vary linearly with eye position. Thus, viewed across many cells, the pattern of persistent firing in the integrator may be constrained to a unique line of stable states. Here this idea was tested by examining the relationship between firing rates of simultaneously recorded neurons. Paired recordings were obtained in awake goldfish from neurons in hindbrain area I, an essential part of the horizontal eye-position integrator. During spontaneous eye movements consisting of sequential fixations at different horizontal positions, the pair relationship between the majority of cells on the same side of the integrator was not unique: for a given rate of one cell, the rate of the paired cell assumed different values that depended systematically on the preceding saccade history. This finding suggests that the set of persistent firing states that encode eye position is not constrained to a unique line, and that models with stable states restricted to a such a line need to be modified accordingly.

This introduction describes a single-compartment model of calcium dynamics that has been applied to fluorescence measurements of intracellular free calcium concentration ([Ca2+]i) changes in neurons. The model describes intracellular calcium handling under simplified conditions, for which analytical expressions for the amplitude and the time constants of [Ca2+]i changes can be explicitly derived. In particular, it reveals the dependence of the measured [Ca2+]i changes on the calcium indicator concentration. Applied to experimental data from small cells or subcellular compartments, the model equations have been extremely useful for obtaining quantitative information about essential parameters of Ca2+ influx, buffering, and clearance. We illustrate also several changes that occur when the basic assumptions do not hold (e.g., when calcium diffusion, dye saturation, or kinetic effects become significant). Finally, we discuss how the changes in calcium dynamics, which are explained by the model, have been exploited for measuring properties of calcium-driven reactions, such as those regulating short-term synaptic enhancement, vesicle recycling, and adaptation.

The oculomotor system produces eye-position signals during fixations and head movements by integrating velocity-coded saccadic and vestibular inputs. A previous analysis of nucleus prepositus hypoglossi (nph) lesions in monkeys found that the integration time constant for maintaining fixations decreased, while that for the vestibulo-ocular reflex (VOR) did not. On this basis, it was concluded that saccadic inputs are integrated by the nph, but that the vestibular inputs are integrated elsewhere. We re-analyze the data from which this conclusion was drawn by performing a linear regression of eye velocity on eye position and head velocity to derive the time constant and velocity bias of an imperfect oculomotor neural integrator. The velocity-position regression procedure reveals that the integration time constants for both VOR and saccades decrease in tandem with consecutive nph lesions, consistent with the hypothesis of a single common integrator. The previous evaluation of the integrator time constant relied upon fitting methods that are prone to error in the presence of velocity bias and saccades. The algorithm used to evaluate imperfect fixations in the dark did not account for the nonzero null position of the eyes associated with velocity bias. The phase-shift analysis used in evaluating the response to sinusoidal vestibular input neglects the effect of saccadic resets of eye position on intersaccadic eye velocity, resulting in gross underestimates of the imperfections in integration during VOR. The linear regression method presented here is valid for both fixation and low head velocity VOR data and is easy to implement.

In vivo two-photon microscopy provides the foundation for an array of powerful techniques for optically measuring and perturbing neural circuits. However, challenging tissue properties and geometry have prevented high-resolution optical access to regions situated within deep fissures. These regions include the medial prefrontal and medial entorhinal cortex (mPFC and MEC), which are of broad scientific and clinical interest. Here, we present a method for in vivo, subcellular resolution optical access to the mPFC and MEC using microprisms inserted into the fissures. We chronically imaged the mPFC and MEC in mice running on a spherical treadmill, using two-photon laser-scanning microscopy and genetically encoded calcium indicators to measure network activity. In the MEC, we imaged grid cells, a widely studied cell type essential to memory and spatial information processing. These cells exhibited spatially modulated activity during navigation in a virtual reality environment. This method should be extendable to other brain regions situated within deep fissures, and opens up these regions for study at cellular resolution in behaving animals using a rapidly expanding palette of optical tools for perturbing and measuring network structure and function.

Larval zebrafish offer the potential for large-scale optical imaging of neural activity throughout the central nervous system; however, several barriers challenge their utility. First, ~panneuronal probe expression has to date only been demonstrated at early larval stages up to 7 days post-fertilization (dpf), precluding imaging at later time points when circuits are more mature. Second, nuclear exclusion of genetically-encoded calcium indicators (GECIs) limits the resolution of functional fluorescence signals collected during imaging. Here, we report the creation of transgenic zebrafish strains exhibiting robust, nuclearly targeted expression of GCaMP3 across the brain up to at least 14 dpf utilizing a previously described optimized Gal4-UAS system. We confirmed both nuclear targeting and functionality of the modified probe in vitro and measured its kinetics in response to action potentials (APs). We then demonstrated in vivo functionality of nuclear-localized GCaMP3 in transgenic zebrafish strains by identifying eye position-sensitive fluorescence fluctuations in caudal hindbrain neurons during spontaneous eye movements. Our methodological approach will facilitate studies of larval zebrafish circuitry by both improving resolution of functional Ca(2+) signals and by allowing brain-wide expression of improved GECIs, or potentially any probe, further into development.

Two-photon microscopy has enabled anatomical and functional fluorescence imaging in the intact brain of rats. Here, we extend two-photon imaging from anesthetized, head-stabilized to awake, freely moving animals by using a miniaturized head-mounted microscope. Excitation light is conducted to the microscope in a single-mode optical fiber, and images are scanned using vibrations of the fiber tip. Microscope performance was first characterized in the neocortex of anesthetized rats. We readily obtained images of vasculature filled with fluorescently labeled blood and of layer 2/3 pyramidal neurons filled with a calcium indicator. Capillary blood flow and dendritic calcium transients were measured with high time resolution using line scans. In awake, freely moving rats, stable imaging was possible except during sudden head movements.

Studies of the neural correlates of short-term memory in a wide variety of brain areas have found that transient inputs can cause persistent changes in rates of action potential firing, through a mechanism that remains unknown. In a premotor area that is responsible for holding the eyes still during fixation, persistent neural firing encodes the angular position of the eyes in a characteristic manner: below a threshold position the neuron is silent, and above it the firing rate is linearly related to position. Both the threshold and linear slope vary from neuron to neuron. We have reproduced this behavior in a biophysically plausible network model. Persistence depends on precise tuning of the strength of synaptic feedback, and a relatively long synaptic time constant improves the robustness to mistuning.

According to a popular hypothesis, short-term memories are stored as persistent neural activity maintained by synaptic feedback loops. This hypothesis has been formulated mathematically in a number of recurrent network models. Here we study an abstraction of these models, a single neuron with a synapse onto itself, or autapse. This abstraction cannot simulate the way in which persistent activity patterns are distributed over neural populations in the brain. However, with proper tuning of parameters, it does reproduce the continuously graded, or analog, nature of many examples of persistent activity. The conditions for tuning are derived for the dynamics of a conductance-based model neuron with a slow excitatory autapse. The derivation uses the method of averaging to approximate the spiking model with a nonspiking, reduced model. Short-term analog memory storage is possible if the reduced model is approximately linear and if its feedforward bias and autapse strength are precisely tuned.

The functional magnetic resonance (fMRI) technique can be robustly used to map functional activation of the visual pathway including the primary visual cortex (V1), the lateral geniculate nucleus (LGN), and other nuclei of humans during visual perception stimulation. One of the major controversies in visual neuroscience is whether lower-order visual areas involve the visual imagery process. This issue was examined using fMRI at high magnetic field. It was demonstrated for the first time that the LGN was activated during visual imagery process in the human brain together with V1 and other activation. There was a tight coupling of the activation between V1 and the LGN during visual imagery.

The dendrites of mammalian pyramidal neurons contain a rich collection of active conductances that can support Na+ and Ca2+ action potentials (for a review see ref. 1). The presence, site of initiation, and direction of propagation of Na+ and Ca2+ action potentials are, however, controversial, and seem to be sensitive to resting membrane potential, ionic composition, and degree of channel inactivation, and depend on the intensity and pattern of synaptic stimulation. This makes it difficult to extrapolate from in vitro experiments to the situation in the intact brain. Here we show that two-photon excitation laser scanning microscopy can penetrate the highly scattering tissue of the intact brain. We used this property to measure sensory stimulus-induced dendritic [Ca2+] dynamics of layer 2/3 pyramidal neurons of the rat primary vibrissa (Sm1) cortex in vivo. Simultaneous recordings of intracellular voltage and dendritic [Ca2+] dynamics during whisker stimulation or current injection showed increases in [Ca2+] only in coincidence with Na+ action potentials. The amplitude of these [Ca2+] transients at a given location was approximately proportional to the number of Na+ action potentials in a short burst. The amplitude for a given number of action potentials was greatest in the proximal apical dendrite and declined steeply with increasing distance from the soma, with little Ca2+ accumulation in the most distal branches, in layer 1. This suggests that widespread Ca2+ action potentials were not generated, and any significant [Ca2+] increase depends on somatically triggered Na+ action potentials.

1. We characterized the kinetics of presynaptic Ca2+ ion concentration in optic nerve fibers and terminals of the optic tectum in Rana pipiens with the use of microfluorimetry. Isolated frog brains were incubated with the membrane-permeant tetraacetoxymethyl ester (AM) of the Ca2+ indicator fura-2. An optic nerve shock caused a transient decrease in the 380-nm excited fluorescence in the optic tectum with a rise time of

Recent advances in optical imaging technology have enabled the measurement of Ca2+ dynamics in individual synaptic spines with high time resolution. Results from work using this new technology have confirmed the view that individual synaptic spines can act as functional chemical compartments with independent dynamics of second-messenger concentration. In particular, the ability of Ca2+ to directly mediate Hebbian coincidence detection has been confirmed.

We thank A. Borst, B. W. Connors, T. Freund, S. J. Redman, W. N. Ross, T. J. Sejnowski, and R. D. Traub for sharing their results before publication, A. Borst, S. Cash, B. W. Connors, W. Denk, S. R. Golob, R. Llinas, W. Regehr, P. A. Rhodes, I. Segev, and K. Svoboda for helpful comments, and A. Gelperin, J. Lichtman, Z. Mainem, V. Murthy, G. M. Shepherd, L. Trussell, and R. O. L. Wong for their help. R. Y. was supported by the Office of Naval Research.

Augmentation and posttetanic potentiation--two forms of short-term synaptic enhancement produced by repetitive presynaptic action potentials--are dependent on the buildup and decay of nerve terminal residual calcium that occurs on the seconds to minutes time scale. With the goal of providing a quantitative understanding of these kinetics, we measured the buildup and decay of calcium ions in nerve terminals at the crayfish neuromuscular junction under a variety of intracellular buffer conditions and stimulation paradigms. The calcium extrusion process in the terminals was characterized by analysis of calcium levels reached during long stimulus trains as a function of action potential frequency. The extrusion was linearly dependent on the free calcium ion concentration. Using this result, we developed a mathematical model and computer simulation of the residual calcium kinetics. The model demonstrates the experimentally observed dependence of decay rate on exogenous calcium buffer concentration, and can be explicitly solved to provide an expression for the limiting exponential time course of calcium decay following trains in terms of calcium buffer and extrusion characteristics. Methods to determine the calcium influx per action potential, characteristics of endogenous buffer, and the rate of calcium extrusion are suggested by our analysis and demonstrated experimentally.

Precise formation of morphogen gradients is essential to the establishment of reproducible pattern in development. Mechanisms proposed for obtaining the requisite precision range from simple models with few parameters to more complex models involving many regulated quantities. The synthesis–diffusion–degradation (SDD) model is a relatively simple model explaining the formation of the Bicoid gradient in Drosophila melanogaster, in which the steady-state characteristic length of the gradient is determined solely by the rates of diffusion and degradation of the morphogen. In this work, we test the SDD model in unfertilized D. melanogaster eggs, which contain a single female pronucleus and lack the nuclear division cycles and other zygotic regulatory processes seen in fertilized eggs. Using two-photon live imaging as well as a novel method for quantitative imaging based on decorrelation of photoswitching waveforms, we find that the Bicoid gradient is longer and shallower in unfertilized eggs as compared to the gradient at the same time points in fertilized eggs. Using a means of measuring the Bicoid lifetime by conjugation to a photoconvertible fluorophore, we find that the lifetime is correspondingly longer in unfertilized eggs, providing qualitative and quantitative agreement with the predictions of the SDD model.

Excitatory drive enters the cerebellum via mossy fibers, which activate granule cells, and climbing fibers, which activate Purkinje cell dendrites. Until now, the coordinated regulation of these pathways has gone unmonitored in spatially resolved neuronal ensembles, especially in awake animals. We imaged cerebellar activity using functional two-photon microscopy and extracellular recording in awake mice locomoting on an air-cushioned spherical treadmill. We recorded from putative granule cells, molecular layer interneurons, and Purkinje cell dendrites in zone A of lobule IV/V, representing sensation and movement from trunk and limbs. Locomotion was associated with widespread increased activity in granule cells and interneurons, consistent with an increase in mossy fiber drive. At the same time, dendrites of different Purkinje cells showed increased co-activation, reflecting increased synchrony of climbing fiber activity. In resting animals, aversive stimuli triggered increased activity in granule cells and interneurons, as well as increased Purkinje cell co-activation that was strongest for neighboring dendrites and decreased smoothly as a function of mediolateral distance. In contrast with anesthetized recordings, no 1-10 Hz oscillations in climbing fiber activity were evident. Once locomotion began, responses to external stimuli in all three cell types were strongly suppressed. Thus climbing and mossy fiber representations can shift together within a fraction of a second, reflecting in turn either movement-associated activity or external stimuli.

1. The procerebral (PC) lobe of the terrestrial mollusk Limax maximus contains a highly interconnected network of local olfactory interneurons that receives ipsilateral axonal projections from superior and inferior noses. This network exhibits an approximately 0.7-Hz intrinsic oscillation in its local field potential (LFP). 2. Intracellular recordings show that the lobe contains at least two classes of neurons with activity phase locked to the oscillation. Neurons in one class produce periodic bursts of spikes, followed by a period of hyperpolarization and subsequently a depolarizing afterpotential. There is a small but significant chance for a second burst to occur during the depolarizing afterpotential; this leads to a double event in the LFP. Bursting neurons constitute approximately 10% of the neurons in the lobe. 3. Neurons in the other class fire infrequently and do not produce periodic bursts of action potentials. However, they receive strong, periodic inhibitory input during every event in the LFP. These nonbursting cells constitute the major fraction of neurons in the lobe. There is a clear correlation between the periodic burst of action potentials in the bursting neurons and the hyperpolarization seen in nonbursting neurons. 4. Optical techniques are used to image the spatially averaged transmembrane potentials in preparations stained with voltage-sensitive dyes. The results of simultaneous optical and electrical measurements show that the major part of the optical signal can be interpreted as a superposition of the intracellular signals arising from the bursting and nonbursting neurons. 5. Successive images of the entire PC lobe show waves of electrical activity that span the width of the lobe and travel its full length along a longitudinal axis. The direction of propagation in the unperturbed lobe is always from the distal to the proximal end. The wavelength varies between preparations but is on the order of the length of the preparation. 6. One-dimensional images along the longitudinal axis of the lobe are used to construct a space-time map of the optical activity, from which we calculate the absolute contribution of bursting and nonbursting neurons to the optical signal. The contribution of the intracellular signals from the two cell types appears to vary systematically across the lobe; bursting cells dominate at middle and proximal locations, and nonbursting cells dominate at distal locations. 7. The direction and form of the waves can be perturbed either by microsurgical manipulation of the preparation or by chemical modulation of its synaptic and neuronal properties.(ABSTRACT TRUNCATED AT 400 WORDS)

Apical dendrites constitute a prominent feature of the microcircuitry in the neocortex, yet their function is poorly understood. Using fura-2 imaging of layer 5 pyramidal neurons from slices of rat somatosensory cortex, we have investigated the Ca2+ influx into dendrites under intracellular, antidromic, synaptic, and receptor-agonist stimulation. We find three spatial patterns of Ca2+ accumulations: an apical band in the apical dendrite approximately 500 microns from the soma, an accumulation restricted to the basal dendrites, soma, and proximal apical dendrite, and a combination of both of these. We show that the apical band can be activated antidromically and synaptically and that, under blocked Na+ and K+ conductances, it generates Ca2+ spikes. Thus, the apical band may serve as a dendritic trigger zone for regenerative Ca2+ spikes or as a current amplifier for distal synaptic events. Our results suggest that the distal apical dendrite should be considered a separate functional compartment from the rest of the cell.

Further characterization of the biochemical components that contribute to calcium handling, together with advances in optical imaging of ion concentration, are providing quantitative information on the dynamics of calcium in the dendrites of neurons in tissue culture, brain slices and in vivo. It has recently been demonstrated that strong spatial gradients and transient calcium elevations result from the geometry and membrane properties of dendrites. These studies are adding to our understanding of calcium's role in synaptic plasticity and in shaping the electrophysiological properties of neurons.

Multi-echo measurements of photic stimulation-induced signal changes in human visual cortex were made at 4 Tesla in order to quantify the nature of the signal change and its vascular origin, and to determine the optimum echo time for detection of the changes. Utilizing high resolution images, two distinct regions (ascribed to be microvasculature and visible venous vessels) were identified as giving rise to the signal increase. The fractional signal changes in gray matter areas depended linearly on echo time (TE) in the range of 10 to 60 ms and extrapolated to virtually zero for TE = 0, indicating that in-flow effects secondary to stimulation-induced blood flow increases were negligible in our functional imaging studies; instead, signal change due to photic stimulation originated from the increase in the apparent transverse relaxation rate, 1/T2*. This decrease in (1/T2*, brought about by the alterations in hemodynamic parameters, was 1.3 ± 0.4 s−1 for gray matter and 3.0 ± 0.7 s−1 (averaged over 10 individuals) for venous vessels visible in the images. The optimum choice of echo time was found to be TE ≥ T2*.

1. The effect of the timing between nasal airflow and ongoing tracheal respiration on single-unit activity in the olfactory bulb (OB) of the rat was examined. Nasal and tracheal breathing were dissociated with the use of a double tracheal cannulation technique that allowed independent control of nasal airflow and control of the synchronization of nasal airflow and tracheal breathing. 2. When amyl acetate-saturated air was presented to the nose, OB units showed a distinct reorganization of activity known as respiratory patterning. Of 43 cells examined, 29 fired maximally after inspiration, and 14 fired maximally after expiration. In all 43 cells the patterning of OB activity was synchronized with the time course of the nasal stimulation. This synchronization was independent of the point in the ongoing respiratory cycle (tracheal breathing) at which the odor stimulation was applied. 3. Patterning of OB single-unit activity was also observed when odor was applied as a series of "inspirations" without intervening expirations. Patterning was observed to follow the time course of the odor stimulation even when this was considerably longer and slower than normal breathing. No patterning of activity was observed during continuous odor stimulation or in the absence of odor stimulation. 4. It is concluded that respiratory patterning of OB single-unit activity in the rat is not directly dependent on centrifugal inputs synchronized to respiration. Rather, the observed pattern of neural activity reflects the phasic stimulation of the olfactory receptors with each inspiration and the dynamics of the circuitry intrinsic to the bulb itself.