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Sejnowski, T. J.

Publications and source records attributed to Sejnowski, T. J..

At least 19 recordsLinked to original sources

Balancing Stability and Flow in Hippocampal Networks via Inductive Bias and Learned Symmetry Breaking

The hippocampus must balance stable memory representations with internally generated sequential dynamics underlying replay and prediction. How hippocampal circuitry achieves both remains unclear. Here, we show that recurrent neural networks trained on prediction tasks converge to a mixed-symmetry dynamical regime, in which dominant symmetric recurrence stabilizes an attractor while a weaker antisymmetric component induces directed flow. This structure accelerates learning and supports robust replay and prediction. We further show that such symmetry breaking can arise from biologically plausible spike-timing-dependent plasticity (STDP) rules, yielding a tilted Mexican-hat connectivity profile without explicit architectural constraints. Initializing networks with CA3-like structured connectivity biases learning toward this regime, and improves optimization efficiency and performance. These results suggest that hippocampal computation reflects an interaction between biologically constrained circuit structure and task-driven learning, with partial symmetry breaking providing a low-dimensional control principle for balancing stability and flow in sequence generation. Subject Areascomputational neuroscience, systems neuroscience, neural dynamics, learning, memory

neuroscience↗

Presynaptic vesicles supply membrane for axonal bouton enlargement during LTP

Long-term potentiation (LTP) induces presynaptic bouton enlargement and a reduction in the number of synaptic vesicles. To understand the relationship between these events, we performed 3D analysis of serial section electron micrographs in rat hippocampal area CA1, 2 hours after LTP induction. We observed a high vesicle packing density in control boutons, contrasting with a lower density in most LTP boutons. Notably, the summed membrane area of the vesicles lost in low-density LTP boutons is comparable to the surface membrane required for the observed bouton enlargement when compared to high-density control boutons. These novel findings suggest that presynaptic vesicle density provides a new structural indicator of LTP that supports a local mechanism of bouton enlargement.

neuroscience↗

The presynaptic vesicle cluster transitions from a compact to loose organization during long-term potentiation

Functional and structural elements of synaptic plasticity are tightly coupled, as has been extensively shown for dendritic spines. Here, we interrogated structural features of presynaptic terminals in 3DEM reconstructions from CA1 hippocampal axons that had undergone control stimulation or theta-burst stimulation (TBS) to produce long-term potentiation (LTP). We reveal that after LTP induction, the synaptic vesicle (SV) cluster is less dense, and SVs are more dispersed. The distances between neighboring SVs are greater in less dense terminals and have more SV-associated volume. We characterized the changes to the SV cluster by measuring distances between neighboring SVs, distances to the active zone, and the dispersion of the SV cluster. Furthermore, we compared the distribution of SVs with randomized ones and provided evidence that SVs gained mobility after LTP induction. With a computational model, we can predict the increment of the diffusion coefficient of the SVs in the cluster. Moreover, using a machine learning approach, we identify presynaptic terminals that were potentiated after LTP induction. Lastly, we show that the local SV density is a volume-independent property under strong regulation. Altogether, these results provide evidence that the SV cluster is undergoing a transition during LTP.

neuroscience↗

A spatial model of autophosphorylation of CaMKII in a glutamatergic spine suggests a network-driven kinetic mechanism for bistable changes in synaptic strength.

Long-term potentiation (LTP) is a biochemical process that underlies learning in excitatory glutamatergic synapses in the Central Nervous System (CNS). The critical early driver of LTP is autophosphorylation of the abundant postsynaptic enzyme, Ca2+/calmodulin-dependent protein kinase II (CaMKII). Autophosphorylation is initiated by Ca2+ flowing through NMDA receptors activated by strong synaptic activity. Its lifetime is ultimately determined by the balance of the rates of autophosphorylation and of dephosphorylation by protein phosphatase 1 (PP1). Here we have modeled the autophosphorylation and dephosphorylation of CaMKII during synaptic activity in a spine synapse using MCell4, an open source computer program for creating particle-based stochastic, and spatially realistic models of cellular microchemistry. The model integrates four earlier detailed models of separate aspects of regulation of spine Ca2+ and CaMKII activity, each of which incorporate experimentally measured biochemical parameters and have been validated against experimental data. We validate the composite model by showing that it accurately predicts previous experimental measurements of effects of NMDA receptor activation, including high sensitivity of induction of LTP to phosphatase activity in vivo, and persistence of autophosphorylation for a period of minutes after the end of synaptic stimulation. We then use the model to probe aspects of the mechanism of regulation of autophosphorylation of CaMKII that are difficult to measure in vivo. We examine the effects of "CaM-trapping," a process in which the affinity for Ca2+/CaM increases several hundred-fold after autophosphorylation. We find that CaM-trapping does not increase the proportion of autophosphorylated subunits in holoenzymes after a complex stimulus, as previously hypothesized. Instead, CaM-trapping may dramatically prolong the lifetime of autophosphorylated CaMKII through steric hindrance of dephosphorylation by protein phosphatase 1. The results provide motivation for experimental measurement of the extent of suppression of dephosphorylation of CaMKII by bound Ca2+/CaM. The composite MCell4 model of biochemical effects of complex stimuli in synaptic spines is a powerful new tool for realistic, detailed dissection of mechanisms of synaptic plasticity.

neuroscience↗

Long-Term Potentiation Produces a Sustained Expansion of Synaptic Information Storage Capacity in Adult Rat Hippocampus

Long-term potentiation (LTP) has become a standard model for investigating synaptic mechanisms of learning and memory. Increasingly, it is of interest to understand how LTP affects the synaptic information storage capacity of the targeted population of synapses. Here, structural synaptic plasticity during LTP was explored using three-dimensional reconstruction from serial section electron microscopy. Storage capacity was assessed by applying a new analytical approach, Shannon information theory, to delineate the number of functionally distinguishable synaptic strengths. LTP was induced by delta-burst stimulation of perforant pathway inputs to the middle molecular layer of hippocampal dentate granule cells in adult rats. Spine head volumes were measured as predictors of synaptic strength and compared between LTP and control hemispheres at 30 min and 2 hr after the induction of LTP. Synapses from the same axon onto the same dendrite were used to determine the precision of synaptic plasticity based on the similarity of their physical dimensions. Shannon entropy was measured by exploiting the frequency of spine heads in functionally distinguishable sizes to assess the degree to which LTP altered the number of bits of information storage. Outcomes from these analyses reveal that LTP expanded storage capacity; the distribution of spine head volumes was increased from 2 bits in controls to 3 bits at 30 min and 2.7 bits at 2 hr after the induction of LTP. Furthermore, the distribution of spine head volumes was more uniform across the increased number of functionally distinguishable sizes following LTP, thus achieving more efficient use of coding space across the population of synapses. SignificanceEstablishing relationships between structure, function, and information storage capacity provides a new approach to assessing network strength from structural measurements. Long term potentiation (LTP) is a standard model for investigating synaptic mechanisms of learning and memory. Information is a retrievable quantity that is being stored in synapses as synaptic strength and is correlated with multiple structural components of synaptic strength. Structural synaptic plasticity was measured in 3D reconstructions from serial section electron microscopy of spine head volume, as a proxy for synapse strength, at 30 min and 2 hr after LTP induction. Outcomes indicate that LTP enhances information storage capacity for at least 2 hr by increasing the precision of the synaptic structure and expanding the range of synapse sizes.

neuroscience↗

An open-access EEG dataset for speech decoding: Exploring the role of articulation and coarticulation

Electroencephalography (EEG) holds promise for brain-computer interface (BCI) devices as a non-invasive measure of neural activity. With increased attention to EEG-based BCI systems, publicly available datasets that can represent the complex tasks required for naturalistic speech decoding are necessary to establish a common standard of performance within the BCI community. Effective solutions must overcome various kinds of noise in the EEG signal and remain reliable across sessions and subjects without overfitting to a specific dataset or task. We present two validated datasets (N=8 and N=16) for classification at the phoneme and word level and by the articulatory properties of phonemes. EEG signals were recorded from 64 channels while subjects listened to and repeated six consonants and five vowels. Individual phonemes were combined in different phonetic environments to produce coarticulated variation in forty consonant-vowel pairs, twenty real words, and twenty pseudowords. Phoneme pairs and words were presented during a control condition and during transcranial magnetic stimulation targeted to inhibit or augment the EEG signal associated with specific articulatory processes.

neuroscience↗

Regional and LTP-Dependent Variation of Synaptic Information Storage Capacity in Rat Hippocampus

Connectomics is generating an ever-increasing deluge of data, which challenges us to develop new methods for analyzing and extracting insights from these data. We introduce here a powerful method for analyzing three-dimensional reconstruction from serial section electron microscopy (3DEM) to measure synaptic information storage capacity (SISC) and apply it to data following in vivo long-term potentiation (LTP). Connectomic researchers have focused on the pattern of connectivity between neurons. The strengths of synapses have also been studied by quantifying the sizes of synapses. Importantly, synapses from the same axon onto the same dendrite have a common history of coactivation, making them a candidate for measuring the precision of synaptic plasticity based on the similarity of their dimensions. Quantifying precision is fundamental to understanding information storage and retrieval in neural circuits. We quantify this precision with Shannon information theory, which is a more reliable estimate than prior analyses based on signal detection theory because there is no overlap between states, and outliers do not artificially bias the outcome. Spine head volumes are well correlated with other measures of synaptic weight, thus SISC can be determined by identifying the non-overlapping clusters of dendritic spine head volumes to determine the number of distinguishable synaptic weights. SISC analysis of spine head volumes in the stratum radiatum of hippocampal area CA1 revealed 24 distinguishable states (4.1 bits). In contrast, spine head volumes in the middle molecular layer of control dentate gyrus occupied only 5 distinguishable states (2 bits). Thus, synapses in different hippocampal regions had significantly different SISCs. Moreover, these were not fixed properties but increased by 30 min following induction of LTP in the dentate gyrus to occupy 10 distinguishable states (3 bits), and this increase lasted for at least 2 hours. We also observed a broader and nearly uniform distribution of spine head volumes across the increased number of states, suggesting the distribution evolved towards the theoretical upper bound of SISC following LTP. For dentate granule cells these findings show that the spine size range was broadened by the interplay among synaptic plasticity mechanisms. SISC provides a new analytical measure to probe these mechanisms in normal and diseased brains.

neuroscience↗

A thermodynamically-consistent model for ATP production in mitochondria

AO_SCPLOWBSTRACTC_SCPLOWLife is based on energy conversion. In particular, in the nervous system significant amounts of energy are needed to maintain synaptic transmission and homeostasis. To a large extent, neurons depend on oxidative phosphorylation in mitochondria to meet their high energy demand (Pekkurnaz and Wang, 2022). For a comprehensive understanding of the metabolic demands in neuronal signaling, accurate models of ATP production in mitochondria are required. Here, we present a thermodynamically consistent model of ATP production in mitochondria based on previous work (Pietrobon and Caplan, 1985; Magnus and Keizer, 1997; Metelkin et al., 2006; Garcia et al., 2019). The significant improvement of the model is that the reaction rate constants are set such that detailed balance is satisfied. Moreover, using thermodynamic considerations, the dependence of the reaction rate constants on membrane potential, pH, and substrate concentrations are explicitly provided. These constraints assure the model is physically plausible. Furthermore, we explore different parameter regimes to understand in which conditions ATP production or its export are the limiting steps in making ATP available in the cytosol. The outcomes reveal that, under the conditions used in our simulations, ATP production is the limiting step and not its export. Finally, we performed spatial simulations with nine 3D realistic mitochondrial reconstructions and linked the ATP production rate in the cytosol with morphological features of the organelles. 1. SO_SCPLOWUMMARYC_SCPLOWIn this work, Garcia et al present a thermodynamically consistent model for ATP production in mitochondria, in which reaction rate constants are set such that detailed balance is satisfied. Simulations revealed that ATP production, but not its export, is the limiting step, and simulations with 3D mitochondrial reconstructions linked the ATP production rate in the cytosol with the morphological features of the organelles.

cell biology↗

Hippocampus as a generative circuit for predictive coding of future sequences

The hippocampus receives sequences of sensory inputs from the cortex during exploration and encodes the sequences with millisecond precision. We developed a predictive autoencoder model of the hippocampus including the trisynaptic and monosynaptic circuits from the entorhinal cortex (EC). CA3 was trained as a self-supervised recurrent neural network to predict its next input. We confirmed that CA3 is prediction ahead by analyzing the spike coupling between simultaneously recorded neurons in the dentate gyrus, CA3 and CA1 of the mouse hippocampus. In the model, CA1 neurons signal prediction errors by comparing the prediction from CA3 to the next input directly from the EC. The model exhibits the rapid appearance and the slow fading of CA1 place cells, and displays replay and phase precession from CA3. The model could be learnt in a biologically plausible way with the help of error-encoding neurons. Similarities between the circuits in the hippocampus and thalamocortical circuits suggest that such computation motif could also underlie self-supervised sequence learning in the cortex.

neuroscience↗

MCell4 with BioNetGen: A Monte Carlo Simulator of Rule-Based Reaction-Diffusion Systems with Python Interface

Biochemical signaling pathways in living cells are often highly organized into spatially segregated volumes, membranes, scaffolds, subcellular compartments, and organelles comprising small numbers of interacting molecules. At this level of granularity stochastic behavior dominates, well-mixed continuum approximations based on concentrations break down and a particle-based approach is more accurate and more efficient. We describe and validate a new version of the open-source MCell simulation program (MCell4), which supports generalized 3D Monte Carlo modeling of diffusion and chemical reaction of discrete molecules and macromolecular complexes in solution, on surfaces representing membranes, and combinations thereof. The main improvements in MCell4 compared to the previous versions, MCell3 and MCell3-R, include a Python interface and native BioNetGen reaction language (BNGL) support. MCell4s Python interface opens up completely new possibilities for interfacing with external simulators to allow creation of sophisticated event-driven multiscale/multiphysics simulations. The native BNGL support, implemented through a new open-source library libBNG (also introduced in this paper), provides the capability to run a given BNGL model spatially resolved in MCell4 and, with appropriate simplifying assumptions, also in the BioNetGen simulation environment, greatly accelerating and simplifying model validation and comparison.

biophysics↗

Exploratory methods for high-performance EEG speech decoding

State-of-the-art technologies in neural speech decoding utilize data collected from microwires or microarrays implanted directly into the cerebral cortex. Yet as a tool accessible only to individuals with implanted electrodes, speech decoding from devices of this nature is severely limited in its implementation, and cannot be considered a viable solution for widespread application. Speech decoding from non-invasive EEG signals can achieve relatively high accuracy (70-80%), but only from very small classification tasks, with more complex tasks typically yielding a limited (20-50%) classification accuracy. We propose a novel combination of technologies in which transcranial magnetic stimulation (TMS) is first applied to augment the neural signals of interest, producing a greater signal-to-noise ratio in the EEG data. Next, delay differential analysis (DDA) - a cutting-edge computational method based on nonlinear dynamics - is implemented to capture the widest range of information available in the neural signal, by incorporating both linear and nonlinear dynamics.

neuroscience↗

Functional connectivity of fMRI using differential covariance predicts structural connectivity and behavioral reaction times

Recordings from resting state functional magnetic resonance imaging (rs-fMRI) reflect the influence of pathways between brain areas. A wide range of methods have been proposed to measure this functional connectivity (FC), but the lack of "ground truth" has made it difficult to systematically validate them. Most measures of FC produce connectivity estimates that are symmetrical between brain areas. Differential covariance (dCov) is an algorithm for analyzing FC with directed graph edges. Applied to synthetic datasets, dCov-FC was more effective than covariance and partial correlation in reducing false positive connections and more accurately matching the underlying structural connectivity. When we applied dCov-FC to resting state fMRI recordings from the human connectome project (HCP) and anesthetized mice, dCov-FC accurately identified strong cortical connections from diffusion Magnetic Resonance Imaging (dMRI) in individual humans and viral tract tracing in mice. In addition, those HCP subjects whose rs-fMRI were more integrated, as assessed by a graph-theoretic measure, tended to have shorter reaction times in several behavioral tests. Thus, dCov-FC was able to identify anatomically verified connectivity that yielded measures of brain integration causally related to behavior.

neuroscience↗

Dynamical differential covariance recovers directional network structure in multiscale neural systems

Investigating neural interactions is essential to understanding the neural basis of behavior. Many statistical methods have been used for analyzing neural activity, but estimating the direction of network interactions correctly and efficiently remains a difficult problem (1). Here, we derive dynamical differential covariance (DDC), a new method based on dynamical network models that detects directional interactions with low bias and high noise tolerance under nonstationarity conditions. The method was first validated and compared with other methods on networks with false positive motifs and multiscale neural simulations where the ground truth connectivity was known. When applied to recordings of resting-state functional magnetic resonance imaging (rs-fMRI) recordings, DDC consistently detected regional interactions with strong structural connectivity in over 1,000 individual subjects obtained by diffusion MRI (dMRI). DDC is a promising new family of methods for estimating functional connectivity that can be generalized to a wide range of dynamical models and recording techniques and to other applications where system identification from sparse data is needed. Significance StatementThrough dynamical interactions with each other, neurons make it possible for us to sense, move and think. It is now possible to simultaneously record from many individual neurons and brain regions. Methods for analyzing these large-scale recordings are needed that can reveal how the patterns of activity give rise to behavior. We developed an efficient, intuitive and robust way to analyze these recordings and validated it on simulations of model neural networks where the ground truth was known. We called this method dynamical differential covariance (DDC) because it can estimate not only the presence of a connection but also which direction the information is flowing in a network between neurons or cortical areas. We also successfully applied DDC to brain imaging data from functional Magnetic Resonance Imaging.

neuroscience↗

Brain network dynamics codify heterogeneity in seizure propagation

Dynamic functional brain connectivity facilitates adaptive cognition and behavior. Abnormal alterations within such connectivity could result in disrupted functions observed across various neurological conditions. As one of the most common neurological disorders, epilepsy is defined by the seemingly random occurrence of spontaneous seizures. A central but unresolved question concerns the mechanisms by which extraordinarily diverse dynamics of seizures emerge. Here, we apply a graph-theoretical approach to assess dynamic reconfigurations in the functional brain connectivity before, during, and after seizures that display heterogeneous propagation patterns despite sharing similar origins. We demonstrate unique reconfigurations in globally-defined network properties preceding seizure onset that predict propagation patterns of impending seizures, and in locally-defined network properties that differentiate post-onset dynamics. These results characterize quantitative network features underlying the heterogeneity of seizure dynamics and the accompanying clinical manifestations. Decoding these network properties could improve personalized preventative treatment strategies for epilepsy as well as other neurological disorders.

neuroscience↗

Neuromodulators enable overlapping synaptic memory regimes and nonlinear transition dynamics in recurrent neural networks

Neuromodulators are critical controllers of neural states, with dysfunctions linked to various neuropsychiatric disorders. Although many biological aspects of neuromodulation have been studied, the computational principles underlying how neuromodulation of distributed neural populations controls brain states remain unclear. Compared with specific contextual inputs, neuromodulation is a single scalar signal that is broadcast broadly to many neurons. We model the modulation of synaptic weight in a recurrent neural network model and show that neuromodulators can dramatically alter the function of a network, even when highly simplified. We find that under structural constraints like those in brains, this provides a fundamental mechanism that can increase the computational capability and flexibility of a neural network. Diffuse synaptic weight modulation enables storage of multiple memories using a common set of synapses that are able to generate diverse, even diametrically opposed, behaviors. Our findings help explain how neuromodulators "unlock" specific behaviors by creating task-specific hyperchannels in the space of neural activities and motivate more flexible, compact and capable machine learning architectures. SignificanceNeuromodulation through the release of molecules like serotonin and dopamine provides a control mechanism that allows brains to shift into distinct behavioral modes. We use an artificial neural network model to show how the action of neuromodulatory molecules acting as a broadcast signal on synaptic connections enables flexible and smooth behavioral shifting. We find that individual networks exhibit idiosyncratic sensitivities to neuromodulation under identical training conditions, highlighting a principle underlying behavioral variability. Network sensitivity is tied to the geometry of network activity dynamics, which provides an explanation for why different types of neuromodulation (molecular vs direct current modulation) have different behavioral effects. Our work suggests experiments to test biological hypotheses and paths forward in the development of flexible artificial intelligence systems.

neuroscience↗

Multiscale modeling of presynaptic dynamics from molecular to mesoscale

Chemical synapses exhibit a diverse array of internal mechanisms that affect the dynamics of transmission efficacy. Many of these processes, such as release of neurotransmitter and vesicle recycling, depend strongly on activity-dependent influx and accumulation of Ca2+. To model how each of these processes may affect the processing of information in neural circuits, and how their dysfunction may lead to disease states, requires a computationally efficient modelling framework, capable of generating accurate phenomenology without incurring a heavy computational cost per synapse. Constructing a phenomenologically realistic model requires the precise characterization of the timing and probability of neurotransmitter release. Difficulties arise in that functional forms of instantaneous release rate can be difficult to extract from noisy data without running many thousands of trials, and in biophysical synapses, facilitation of per-vesicle release probability is confounded by depletion. To overcome this, we obtained traces of free Ca2+ concentration in response to various action potential stimulus trains from a molecular MCell model of a hippocampal mossy fiber axon. Ca2+ sensors were placed at varying distance from a voltage-dependent calcium channel (VDCC) cluster, and Ca2+ was buffered by calbindin. Then, using the calcium traces to drive deterministic state vector models of synaptotagmin 1 and 7 (Syt-1/7), which respectively mediate synchronous and asynchronous release in excitatory hippocampal synapses, we obtained high-resolution profiles of instantaneous release rate, to which we applied functional fits. Synchronous vesicle release occurred predominantly within half a micron of the source of spike-evoked Ca2+ influx, while asynchronous release occurred more consistently at all distances. Both fast and slow mechanisms exhibited multi-exponential release rate curves, whose magnitudes decayed exponentially with distance from the Ca2+ source. Profile parameters facilitate on different time scales according to a single, general facilitation function. These functional descriptions lay the groundwork for efficient mesoscale modelling of vesicular release dynamics. Author SummaryMost information transmission between neurons in the brain occurs via release of neurotransmitter from synaptic vesicles. In response to a presynaptic spike, calcium influx at the active zone of a synapse can trigger the release of neurotransmitter with a certain probability. These stochastic release events may occur immediately after a spike or with some delay. As calcium accumulates from one spike to the next, the probability of release may increase (facilitate) for subsequent spikes. This process, known as short-term plasticity, transforms the spiking code to a release code, underlying much of the brains information processing. In this paper, we use an accurate, detailed model of presynaptic molecular physiology to characterize these processes at high precision in response to various spike trains. We then apply model reduction to the results to obtain a phenomenological model of release timing, probability, and facilitation, which can perform as accurately as the molecular model but with far less computational cost. This mesoscale model of spike-evoked release and facilitation helps to bridge the gap between microscale molecular dynamics and macroscale information processing in neural circuits. It can thus benefit large scale modelling of neural circuits, biologically inspired machine learning models, and the design of neuromorphic chips.

neuroscience↗

Morphological principles of neuronal mitochondria

In the highly dynamic metabolic landscape of a neuron, mitochondrial membrane architectures can provide critical insight into the unique energy balance of the cell. Current theoretical calculations of functional outputs like ATP and heat often represent mitochondria as idealized geometries and therefore can miscalculate the metabolic fluxes. To analyze mitochondrial morphology in neurons of mouse cerebellum neuropil, 3D tracings of complete synaptic and axonal mitochondria were constructed using a database of serial TEM tomography images and converted to watertight meshes with minimal distortion of the original microscopy volumes with a granularity of 1.6 nanometer isotropic voxels. The resulting in silico representations were subsequently quantified by differential geometry methods in terms of the mean and Gaussian curvatures, surface areas, volumes, and membrane motifs, all of which can alter the metabolic output of the organelle. Finally, we identify structural motifs that are present across this population of mitochondria; observations which may contribute to future modeling studies of mitochondrial physiology and metabolism in neurons.

neuroscience↗

Towards Biophysically-Based Neuromorphic Computing at Scale: Markov Abstractions of Electrochemical Reaction-Diffusion in Synaptic Transmission

Progress in computational neuroscience towards understanding brain function is challenged both by the complexity of molecular-scale electrochemical interactions at the level of individual neurons and synapses and the dimensionality of network dynamics across the brain covering a vast range of spatial and temporal scales. Our work abstracts an existing highly detailed, biophysically realistic 3D reaction-diffusion model of a chemical synapse to a compact internal state space representation that maps onto parallel neuromorphic hardware for efficient emulation at a very large scale and offers near-equivalence in input-output dynamics while preserving biologically interpretable tunable parameters.

neuroscience↗