Biology subjects

Smirnakis, S. M.

Publications and source records attributed to Smirnakis, S. M..

13 recordsLinked to original sources

bioRxiv2025

On Temporal Robustness & Brain-State Stability of Functional Connectivity in Mouse Primary Visual Area V1 compared to Higher Visual Area AL

Understanding how the structure of functional connectivity in the visual cortex changes over time and across brain states is crucial for elucidating the mechanisms by which neurons coordinate to process information and support behavior. Higher-order visual areas in mice are known to exhibit more distinct, segregated functional roles compared to the primary visual cortex (V1) [1], and they maintain stimulus representations over extended time scales [2]. However, the stability of the architecture of their functional connectivity across time and brain states remains less understood. In vivo mesoscopic two-photon calcium imaging was used to simultaneously record activity from thousands of neurons across V1 and the extra-striate anterolateral area (AL) in mice, during both visual stimulation (optical-flow/motion) and at resting state (i.e., absence of stimulus). We then applied the spike time-tiling (STTC) coefficient [3] to estimate the pairwise correlations of the neuronal firing and form the functional connectivity at the cell resolution. We then comparatively analyzed the functional connections within area AL and V1 under both stimulus-driven and resting-state conditions. The functional connectivity within AL remains consistently more robust over time than in area V1. Moreover, the structure of the functional connectivity in AL exhibits a smaller change between these two conditions compared to V1, indicating that functional connectivity derived from spontaneous activity more faithfully reflects the functional network architecture elicited by visual stimulation in this higher-order area. Finally, during the resting state, AL activity and functional connectivity are less dependent on pupil size than those of V1, indicating that arousal exerts a weaker modulatory effect on AL compared to V1.

neuroscience↗

bioRxiv2025

Disentangling Stimulus & Population Dynamics in Mouse V1: Orthogonal Subspace Decomposition for Neural Representation

Understanding how the primary visual cortex of mice represents the external sensory input separately from the internal states is a fundamental challenge in systems neuroscience. Our work contributes to the problem of decoupling the stimulus-driven and internally generated components of neural activity in the primary visual cortex. Internally generated (or intrinsic) activity refers to neural dynamics that are not directly driven by sensory stimuli, reflecting the brains ongoing, endogenous processes. Neuronal activity encodes both external stimuli and internal cortical states. The internally modulated activity, though not directly observable, can be inferred from the shared structure in population responses, and thus, serves as a proxy for the internal cortical state. We developed a two-phase Partial Least Squares Regression (PLSR) framework that decomposes neural activity into two orthogonal low-dimensional subspaces: (1) a "population" sub-space capturing global variability shared across neurons, and (2) a "stimulus" subspace containing dimensions that discriminate between stimulus conditions while being linearly uncorrelated with the population subspace. We focus on the granular (L4) and supragranular (L2/3) layers of awake mice exposed to visual stimuli consisting of optical flow directions, using mesoscopic two-photon calcium imaging. In both L4 and L2/3 layers, many components individually yield above-chance decoding accuracy, yet a small low-dimensional subspace preserves nearly the full decoding performance of the high-dimensional population. Stimulus-driven components exhibit strong cross-mouse correlations, indicating a conserved coding scheme present in both L4 and L2/3. These components are stable across the entire recording session, reflecting robustness of the underlying representation over time. Removing the global modulation did not abolish stimulus discriminability in either layer, suggesting that information about stimulus direction is not dependent on this global signal. Both L4 and L2/3 stimulus components exhibit comparable decoding performance as well as similar tuning representations, suggesting common encoding of stimulus direction across layers.

neuroscience↗

bioRxiv2025

Direction of motion decoding in mouse V1: Neuron predictive power relates to functional connectivity organization

Variability in single neuron responses presents a challenge in establishing reliable representations of visual stimuli essential for driving behavior. To enhance accuracy, integration of responses from multiple neurons is imperative. This study leverages simultaneous recordings from a large population (tens of hundreds) of neurons, achieved through in vivo mesoscopic 2-photon calcium imaging of the primary visual cortex (V1) in mice, under visual stimulus conditions as well as in resting state (absence of stimulus). The visual stimulus consisted of 16 distinct randomly shuffled directions of motion presented to the mice. We employed mutual information to identify neurons that contain the most significant information about the stimulus direction. As expected, neurons displaying high predictive power (HPP) in stimulus decoding exhibit elevated firing event rates during stimulus presentation. Furthermore, functional connectivity among HPP neurons during visual stimulation is denser and stronger compared to functional connectivity among other visually responsive neurons. Functional connections among HPP neurons appear to form independently of distance, suggesting a distributed yet highly coordinated network. In contrast, HPP neuronal activity and functional connectivity differed significantly at resting state. Specifically, during the resting state, HPP neurons exhibited lower event rates and functional connectivity structure that was not significantly different from that of other visually responsive neurons. This suggests that HPP neurons are less susceptible to being driven simultaneously by internal brain states in the absence of a stimulus. Finally, the tuning properties of HPP neurons were unexpectedly diverse: while some were sharply tuned, others conveyed a similar amount of mutual information, despite exhibiting much weaker tuning. This study sheds light on the organization of neuronal ensembles important for decoding visual motion direction in mouse area V1, contributing to the understanding of information processing in mouse visual cortex.

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bioRxiv2024

Brain orchestra under spontaneous conditions: Identifying communication modules from the functional architecture of area V1

While single-neuron responses in mouse V1 are well characterized, less is known about how functional ensembles-- groups of neurons that co-activate more frequently than expected by chance--emerge as computational units within laminar V1 circuits. Even with increasingly detailed knowledge of structural connectivity, the rules governing ensemble organization and interactions remain unclear. We imaged pyramidal neurons across granular (L4) and supragranular (L2/3) layers of mouse V1 and applied pairwise functional connectivity analysis to identify multi-neuronal ensembles as putative information-processing modules. In the absence of visual stimulation, 19-34% of pyramidal pairs within 300{micro}m were functionally connected, declining to 10% at 1 mm. Layer 2 to 4 laminar networks exhibited a small-world architecture, L4 displaying slightly denser connectivity and a near-uniform degree-of-connectivity distribution. We propose that neurons together with their first-order functionally connected (1FC) partners constitute putative elementary units of cortical computation. The firing probability of layer 2/3 neurons exhibits a ReLU-like nonlinearity, emerging when [≥] 13% of L4-1FC "putative inputs" co-fire, yielding sparse yet reliable responses. Moreover, L2/3 neuronal responses depend on the count (N), not the identity, of co-active L4-1FC partners, with response sensitivity scaling as a power law in N. These properties persist during visual stimulation and across different states of alertness. Interestingly, L2/3 neurons with L4-1FC modules of different sizes exhibit distinct coupling to brain-state and different computational signatures. This framework yields mechanistic insight into cortical circuit organization, complementary to structural connectivity, helping to link biological circuitry to deep-learning models of artificial intelligence.

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bioRxiv2022

Increased reliability of visually-evoked activity in area V1 of the MECP2-duplication mouse model of autism

Atypical sensory processing is now thought to be a core feature of the autism spectrum. Influential theories have proposed that both increased and decreased neural response reliability within sensory systems could underlie altered sensory processing in autism. Here, we report evidence for abnormally increased reliability of visual-evoked responses in layer 2/3 neurons of adult primary visual cortex in the MECP2-duplication syndrome animal model of autism. Increased response reliability was due in part to decreased response amplitude, decreased fluctuations in endogenous activity, and decreased neuronal coupling to endogenous activity. Similarly to what was observed neuronally, the optokinetic reflex occurred more reliably at low contrasts in mutant mice compared to controls. Retinal responses did not explain our observations. These data suggest that the circuit mechanisms for convolution of sensory-evoked and endogenous signal and noise may be altered in this form of syndromic autism.

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bioRxiv2021

Visual Motion Coherence Responses in Human Visual Cortex

1Random dot kinematograms (RDKs) have recently been used to train subjects with cortical scotomas to perform direction of motion discrimination, partially restoring visual motion perception. To study recovery of visual perception, it is important to understand how visual areas in normal subjects and subjects with cortical scotomas respond to RDK stimuli. Studies in normal subjects have shown that Blood Oxygen Level Dependent (BOLD) responses in human area hV5/MT+ increase monotonically with coherence, in general agreement with electrophysiology studies in primates. However, RDK responses in prior studies were obtained while the subject was performing fixation, not a motion discrimination condition. Furthermore, BOLD responses were gauged against a baseline condition of uniform illumination or static dots, potentially decreasing the specificity of responses for the spatial integration of local motion signals (motion coherence). Here we revisit this question starting from a baseline RDK condition of no coherence, thereby isolating the component of BOLD response due specifically to the spatial integration of local motion signals. In agreement with prior studies, we found that responses in area hV5/MT+ of healthy subjects were monotonically increasing when subjects fixated without performing a motion discrimination task. In contrast, when subjects were performing an RDK direction of motion discrimination task, responses in area hV5/MT+ remained flat, changing minimally, if at all, as a function of motion coherence. A similar pattern of responses was seen in area hV5/MT+ of subjects with dense cortical scotomas performing direction of motion discrimination for RDKs presented inside the scotoma. Passive RDK presentation within the scotoma elicited no significant hV5/MT+ responses. These observations shed further light on how visual cortex responses behave as a function of motion coherence, helping to prepare the ground for future studies using these methods to study visual system recovery after injury.

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bioRxiv2019

MeCP2 deletion impaired layer 2/3-dominant dynamic reorganization of cortical circuit during motor skill learning

Rett Syndrome (RTT) is a severe neurodevelopmental disorder caused by loss of function of the X-linked Methyl-CpG-binding protein 2 (MECP2). Several case studies report that gross motor function can be improved in children with RTT through treadmill walking, but whether the MeCP2-deficient motor circuit can support actual motor learning remains unclear. We used two-photon calcium imaging to simultaneously observe layer (L) 2/3 and L5a excitatory neuronal activity in the motor cortex (M1) while mice adapted to changing speeds on a computerized running wheel. Despite circuit hypoactivity and weakened functional connectivity across L2/3 and L5a, the Mecp2-null circuits firing pattern evolved with improved performance over two weeks. Moreover, trained mice became less anxious and lived 20% longer than untrained mice. Since motor deficits and anxiety are core symptoms of Rett, which is not diagnosed until well after symptom onset, these results underscore the benefit of motor learning.

neuroscience↗

bioRxiv2019

Contribution of Apical and Basal Dendrites of L2/3 Pyramidal Neurons to Orientation Encoding in Mouse V1

Pyramidal neurons integrate synaptic inputs from basal and apical dendrites to generate stimulus-specific responses. It has been proposed that feed-forward inputs to basal dendrites drive a neurons stimulus preference, while feedback inputs to apical dendrites sharpen selectivity. However, how a neurons dendritic domains relate to its functional selectivity has not been demonstrated experimentally. We performed 2-photon dendritic micro-dissection on layer-2/3 pyramidal neurons in mouse primary visual cortex. We found that removing the apical dendritic tuft did not alter orientation-tuning. Furthermore, orientation-tuning curves were remarkably robust to the removal of basal dendrites: ablation of 2-3 basal dendrites was needed to cause a small shift in orientation preference, without significantly altering tuning width. Computational modeling corroborated our results and put limits on how orientation preferences among basal dendrites differ in order to reproduce the post-ablation data. In conclusion, neuronal orientation-tuning appears remarkably robust to loss of dendritic input.

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bioRxiv2018

Measuring single neuron visual receptive field sizes by fMRI

The non-invasive measurements of neuronal receptive field (RF) properties in-vivo allow a detailed understanding of brain organization as well as its plasticity by longitudinal following of potential changes. Visual RFs measured invasively by electrophysiology in animal models have traditionally provided a great extent of our current knowledge about the visual brain and its disorders. Voxel based estimates of population RF (pRF) by functional magnetic resonance imaging (fMRI) in humans revolutionized the field and have been used extensively in numerous studies. However, current methods cannot estimate single-neuron RF sizes as they reflect large populations of neurons with individual RF scatter. Here, we introduce a new approach to estimate RF size using spatial frequency selectivity to checkerboard patterns. This method allowed us to obtain non-invasive, single-unit, RF estimates in human V1 for the first time. These estimates were significantly smaller compared to prior pRF methods. Further, fMRI and electrophysiological experiments in non-human primates demonstrated an exceptional match validating the approach.

neuroscience↗

bioRxiv2018

Inhibitory Units: An Organizing Nidus for Feature-Selective Sub-Networks in Area V1.

Sensory stimuli are encoded by the joint firing of neuronal groups composed of pyramidal cells and interneurons, rather than single isolated neurons (Uhlhaas et al, 2009, Buzsaki, 2010). However, the principles by which these groups are organized to encode information remain poorly understood. A leading hypothesis is that similarly tuned pyramidal cells that preferentially connect to each other may form multi-cellular encoding units yoked to a similar purpose. The existence of such groups would be reflected on the profile of spontaneous events observed in neocortical networks. We used 2-photon calcium imaging to study spontaneous population-burst events in layer 2/3 of mouse area V1 during postnatal maturation (postnatal day 8-52). Throughout the period examined both size and duration of spontaneously occurring population-bursts formed scale-free distributions obeying a power law. The same was true for the degree of \"functional connectivity,\" a measure of pairwise synchrony across cells. These observations are consistent with a hierarchical small-world-net architecture, characterized by groups of cells with high local connectivity (\"small worlds\", cliques) connected to each other via a restricted number of \"hub\" cells\" (Bonifazi et al., 2009, Sporns, 2011, Luce & Perry, 1949). To identify candidate \"small world\" groups we searched for cells whose calcium events had a consistent temporal relationship to events recorded from local inhibitory interneurons. This was guided by the intuition that groups of neurons whose synchronous firing represents a \"temporally coherent computational unit\" (or feature) ought to be inhibited together. This strategy allowed us to identify clusters of pyramidal neurons whose firing is temporally \"linked\" to one or more local interneurons. These \"small-world\" clusters did not remain static, during postnatal development: both cluster size and overlap with other clusters decreased over time as pyramidal neurons became progressively more selective, \"linking\" to fewer neighboring interneurons. Notably, pyramidal neurons in a cluster show higher tuning function similarity than expected with each other and with their \"linked\" interneurons. Our findings suggest that spontaneous population events in the visual cortex are shaped by \"small-world\" networks of pyramidal neurons that share functional properties and work in concert with one or more local interneurons. We argue that such groups represent a fundamental neocortical unit of computation at the population level.

neuroscience↗

bioRxiv2018

Organization of Area hV5/MT+ in Subjects with Homonymous Visual Field Defects

Damage to the primary visual cortex (V1) leads to a visual field loss (scotoma) in the retinotopically corresponding part of the visual field. Nonetheless, a small amount of residual visual sensitivity persists within the blind field. This residual capacity has been linked to activity observed in the middle temporal area complex (V5/MT+). However, it remains unknown whether the organization of hV5/MT+ changes following V1 lesions. We studied the organization of area hV5/MT+ of five patients with dense homonymous defects in a quadrant of the visual field as a result of partial V1+ or optic radiation lesions. To do so, we developed a new method, which models the boundaries of population receptive fields directly from the BOLD signal of each voxel in the visual cortex. We found responses in hV5/MT+ arising inside the scotoma for all patients and identified two possible sources of activation: 1) responses might originate from partially lesioned parts of area V1 corresponding to the scotoma, and 2) responses can also originate independent of area V1 input suggesting the existence of functional V1-bypassing pathways. Apparently, visually driven activity observed in hV5/MT+ is not sufficient to mediate conscious vision. More surprisingly, visually driven activity in corresponding regions of V1 and early extrastriate areas including hV5/MT+ did not guarantee visual perception in the group of patients with post-geniculate lesions that we examined. This suggests that the fine coordination of visual activity patterns across visual areas may be an important determinant of whether visual perception persists following visual cortical lesions.

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bioRxiv2017

Increased axonal bouton stability during learning in the mouse model of MECP2 duplication syndrome

MECP2-duplication syndrome is an X-linked form of syndromic autism caused by genomic duplication of the region encoding Methyl-CpG-binding protein 2. Mice overexpressing MECP2 demonstrate altered patterns of learning and memory, including enhanced motor learning. Previous work associated this enhanced motor learning to abnormally increased stability of dendritic spine clusters formed in the apical tuft of corticospinal, area M1, neurons during rotarod training. In the current study, we measure the structural plasticity of axonal boutons in Layer 5 (L5) pyramidal neuron projections to layer 1 of area M1 during motor learning. In wild-type mice we find that during rotarod training, bouton formation rate changes minimally, if at all, while bouton elimination rate doubles. Notably, the observed upregulation in bouton elimination with learning is absent in MECP2-duplication mice. This result provides further evidence of imbalance between structural stability and plasticity in this form of syndromic autism. Furthermore, the observation that axonal bouton elimination doubles with motor learning in wild-type animals contrasts with the increase of dendritic spine consolidation observed in corticospinal neurons at the same layer. This dissociation suggests that different area M1 microcircuits may manifest different patterns of structural synaptic plasticity during motor learning.\n\nSIGNIFICANCE STATEMENTAbnormal balance between synaptic stability and plasticity is a feature of several autism spectrum disorders, often corroborated by in vivo studies of dendritic spine turnover. Here we provide the first evidence that abnormally increased stability of axonal boutons, the presynaptic component of excitatory synapses, occurs during motor learning in the MECP2 duplication syndrome mouse model of autism. In contrast, in normal controls, axonal bouton elimination in L5 pyramidal neuron projections to layer 1 of area M1 doubles with motor learning. The fact that axonal projection boutons get eliminated, while corticospinal dendritic spines get consolidated with motor learning in layer 1 of area M1, suggests that structural plasticity manifestations differ across different M1 microcircuits.

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bioRxiv2017

Excessive ERK-dependent synaptic clustering with enhanced motor learning in the MECP2 duplication syndrome mouse model of autism

Autism-associated genetic mutations may produce altered learning abilities by perturbing the balance between stability and plasticity of synaptic connections in the brain. Here we report an increase in the stabilization of dendritic spines formed during repetitive motor learning in the mouse model of MECP2-duplication syndrome, a high-penetrance form of syndromic autism. This increased stabilization is mediated entirely by spines that form cooperatively in clusters. The number of clusters formed and stabilized predicts the mutants enhanced motor learning and memory phenotype, reminiscent of savant-like behaviors occasionally associated with autism.\n\nThe ERK signaling pathway, which promotes cooperative plasticity between spines, was found to be hyperactive in MECP2-duplication motor cortex specifically after training. Inhibition of ERK signaling normalizes clustered spine stabilization and rescues motor learning behavior in mutants. We conclude that learning-associated dendritic spine clustering stabilized by hyperactive ERK signaling drives abnormal motor learning and memory consolidation in this model of syndromic autism.

neuroscience↗