Neuroscience: New tricks and old spines

Myelin: A gatekeeper of activity-dependent circuit plasticity?

[Figure: see text].

Emergence of Stable Synaptic Clusters on Dendrites Through Synaptic Rewiring

The connectivity structure of neuronal networks in cortex is highly dynamic. This ongoing cortical rewiring is assumed to serve important functions for learning and memory. We analyze in this article a model for the self-organization of synaptic inputs onto dendritic branches of pyramidal cells. The model combines a generic stochastic rewiring principle with a simple synaptic plasticity rule that depends on local dendritic activity. In computer simulations, we find that this synaptic rewiring model leads to synaptic clustering, that is, temporally correlated inputs become locally clustered on dendritic branches. This empirical finding is backed up by a theoretical analysis which shows that rewiring in our model favors network configurations with synaptic clustering. We propose that synaptic clustering plays an important role in the organization of computation and memory in cortical circuits: we find that synaptic clustering through the proposed rewiring mechanism can serve as a mechanism to protect memories from subsequent modifications on a medium time scale. Rewiring of synaptic connections onto specific dendritic branches may thus counteract the general problem of catastrophic forgetting in neural networks.

Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory

The bipartite network representation of the drug–target interactions (DTIs) in a biosystem enhances understanding of the drugs’ multifaceted action modes, suggests therapeutic switching for approved drugs and unveils possible side effects. As experimental testing of DTIs is costly and time-consuming, computational predictors are of great aid. Here, for the first time, state-of-the-art DTI supervised predictors custom-made in network biology were compared—using standard and innovative validation frameworks—with unsupervised pure topological-based models designed for general-purpose link prediction in bipartite networks. Surprisingly, our results show that the bipartite topology alone, if adequately exploited by means of the recently proposed local-community-paradigm (LCP) theory—initially detected in brain-network topological self-organization and afterwards generalized to any complex network—is able to suggest highly reliable predictions, with comparable performance with the state-of-the-art-supervised methods that exploit additional (non-topological, for instance biochemical) DTI knowledge. Furthermore, a detailed analysis of the novel predictions revealed that each class of methods prioritizes distinct true interactions; hence, combining methodologies based on diverse principles represents a promising strategy to improve drug–target discovery. To conclude, this study promotes the power of bio-inspired computing, demonstrating that simple unsupervised rules inspired by principles of topological self-organization and adaptiveness arising during learning in living intelligent systems (like the brain) can efficiently equal perform complicated algorithms based on advanced, supervised and knowledge-based engineering.

Functional Brain Network Topology Discriminates between Patients with Minimally Conscious State and Unresponsive Wakefulness Syndrome

Consciousness arises from the functional interaction of multiple brain structures and their ability to integrate different complex patterns of internal communication. Although several studies demonstrated that the fronto-parietal and functional default mode networks play a key role in conscious processes, it is still not clear which topological network measures (that quantifies different features of whole-brain functional network organization) are altered in patients with disorders of consciousness. Herein, we investigate the functional connectivity of unresponsive wakefulness syndrome (UWS) and minimally conscious state (MCS) patients from a topological network perspective, by using resting-state EEG recording. Network-based statistical analysis reveals a subnetwork of decreased functional connectivity in UWS compared to in the MCS patients, mainly involving the interhemispheric fronto-parietal connectivity patterns. Network topological analysis reveals increased values of local-community-paradigm correlation, as well as higher clustering coefficient and local efficiency in UWS patients compared to in MCS patients. At the nodal level, the UWS patients showed altered functional topology in several limbic and temporo-parieto-occipital regions. Taken together, our results highlight (i) the involvement of the interhemispheric fronto-parietal functional connectivity in the pathophysiology of consciousness disorders and (ii) an aberrant connectome organization both at the network topology level and at the nodal level in UWS patients compared to in the MCS patients.

Modelling Self-Organization in Complex Networks Via a Brain-Inspired Network Automata Theory Improves Link Reliability in Protein Interactomes

Protein interactomes are epitomes of incomplete and noisy networks. Methods for assessing link-reliability using exclusively topology are valuable in network biology, and their investigation facilitates the general understanding of topological mechanisms and models to draw and correct complex network connectivity. Here, I revise and extend the local-community-paradigm (LCP). Initially detected in brain-network topological self-organization and afterward generalized to any complex network, the LCP is a theory to model local-topology-dependent link-growth in complex networks using network automata. Four novel LCP-models are compared versus baseline local-topology-models. It emerges that the reliability of an interaction between two proteins is higher: (i) if their common neighbours are isolated in a complex (local-community) that has low tendency to interact with other external proteins; (ii) if they have a low propensity to link with other proteins external to the local-community. These two rules are mathematically combined in C1*: a proposed mechanistic model that, in fact, outperforms the others. This theoretical study elucidates basic topological rules behind self-organization principia of protein interactomes and offers the conceptual basis to extend this theory to any class of complex networks. The link-reliability improvement, based on the mere topology, can impact many applied domains such as systems biology and network medicine.

A Dynamic Connectome Supports the Emergence of Stable Computational Function of Neural Circuits through Reward-Based Learning

Synaptic connections between neurons in the brain are dynamic because of continuously ongoing spine dynamics, axonal sprouting, and other processes. In fact, it was recently shown that the spontaneous synapse-autonomous component of spine dynamics is at least as large as the component that depends on the history of pre- and postsynaptic neural activity. These data are inconsistent with common models for network plasticity and raise the following questions: how can neural circuits maintain a stable computational function in spite of these continuously ongoing processes, and what could be functional uses of these ongoing processes? Here, we present a rigorous theoretical framework for these seemingly stochastic spine dynamics and rewiring processes in the context of reward-based learning tasks. We show that spontaneous synapse-autonomous processes, in combination with reward signals such as dopamine, can explain the capability of networks of neurons in the brain to configure themselves for specific computational tasks, and to compensate automatically for later changes in the network or task. Furthermore, we show theoretically and through computer simulations that stable computational performance is compatible with continuously ongoing synapse-autonomous changes. After reaching good computational performance it causes primarily a slow drift of network architecture and dynamics in task-irrelevant dimensions, as observed for neural activity in motor cortex and other areas. On the more abstract level of reinforcement learning the resulting model gives rise to an understanding of reward-driven network plasticity as continuous sampling of network configurations.

Comparison of Local Information Indices Applied in Resting State Functional Brain Network Connectivity Prediction

Anatomical distance has been widely used to predict functional connectivity because of the potential relationship between structural connectivity and functional connectivity. The basic implicit assumption of this method is “distance penalization.” But studies have shown that one-parameter model (anatomical distance) cannot account for the small-worldness, modularity, and degree distribution of normal human brain functional networks. Two local information indices–common neighbor (CN) and preferential attachment index (PA), are introduced into the prediction model as another parameter to emulate many key topological of brain functional networks in the previous study. In addition to these two indices, many other local information indices can be chosen for investigation. Different indices evaluate local similarity from different perspectives. Currently, we still have no idea about how to select local information indices to achieve higher predicted accuracy of functional connectivity. Here, seven local information indices are chosen, including CN, hub depressed index (HDI), hub promoted index (HPI), Leicht-Holme-Newman index (LHN-I), Sørensen index (SI), PA, and resource allocation index (RA). Statistical analyses were performed on eight network topological properties to evaluate the predictions. Analysis shows that different prediction models have different performances in terms of simulating topological properties and most of the predicted network properties are close to the real data. There are four topological properties whose average relative error is less than 5%, including characteristic path length, clustering coefficient, global efficiency, and local efficiency. CN model shows the most accurate predictions. Statistical analysis reveals that five properties within the CN-predicted network do not differ significantly from the real data (P > 0.05, false-discovery rate method corrected for seven comparisons). PA model shows the worst prediction performance which was first applied in models of growth networks. Our results suggest that PA is not suitable for predicting connectivity in a small-world network. Furthermore, in order to evaluate the predictions rapidly, prediction power was proposed as an evaluation metric. The current study compares the predictions of functional connectivity with seven local information indices and provides a reference of method selection for construction of prediction models.

Can local-community-paradigm and epitopological learning enhance our understanding of how local brain connectivity is able to process, learn and memorize chronic pain?

The mystery behind the origin of the pain and the difficulty to propose methodologies for its quantitative characterization fascinated philosophers (and then scientists) from the dawn of our modern society. Nowadays, studying patterns of information flow in mesoscale activity of brain networks is a valuable strategy to offer answers in computational neuroscience. In this paper, complex network analysis was performed on the time-varying brain functional connectomes of a rat model of persistent peripheral neuropathic pain, obtained by means of local field potential and spike train analysis. A wide range of topological network measures (14 in total, the code is publicly released at: https://github.com/biomedical-cybernetics/topological_measures_wide_analysis) was employed to quantitatively investigate the rewiring mechanisms of the brain regions responsible for development and upkeep of pain along time, from three hours to 16 days after nerve injury. The time trend (across the days) of each network measure was correlated with a behavioural test for rat pain, and surprisingly we found that the rewiring mechanisms associated with two local topological measure, the local-community-paradigm and the power-lawness, showed very high statistical correlations (higher than 0.9, being the maximum value 1) with the behavioural test. We also disclosed clear functional connectivity patterns that emerged in association with chronic pain in the primary somatosensory cortex (S1) and ventral posterolateral (VPL) nuclei of thalamus. This study represents a pioneering attempt to exploit network science models in order to elucidate the mechanisms of brain region re-wiring and engram formations that are associated with chronic pain in mammalians. We conclude that the local-community-paradigm is a model of complex network organization that triggers a local learning rule, which seems associated to processing, learning and memorization of chronic pain in the brain functional connectivity. This rule is based exclusively on the network topology, hence was named epitopological learning.

The stability of memories during brain remodeling: A perspective

One of the most important features of the nervous system is memory: the ability to represent and store experiences, in a manner that alters behavior and cognition at future times when the original stimulus is no longer present. However, the brain is not always an anatomically stable structure: many animal species regenerate all or part of the brain after severe injury, or remodel their CNS toward a new configuration as part of their life cycle. This raises a fascinating question: what are the dynamics of memories during brain regeneration? Can stable memories remain intact when cellular turnover and spatial rearrangement modify the biological hardware within which experiences are stored? What can we learn from model species that exhibit both, regeneration and memory, with respect to robustness and stability requirements for long-term memories encoded in living tissues? In this Perspective, we discuss relevant data in regenerating planaria, metamorphosing insects, and hibernating ground squirrels. While much remains to be done to understand this remarkable process, molecular-level insight will have important implications for cognitive science, regenerative medicine of the brain, and the development of non-traditional computational media in synthetic bioengineering.

Neural model for learning-to-learn of novel task sets in the motor domain

During development, infants learn to differentiate their motor behaviors relative to various contexts by exploring and identifying the correct structures of causes and effects that they can perform; these structures of actions are called task sets or internal models. The ability to detect the structure of new actions, to learn them and to select on the fly the proper one given the current task set is one great leap in infants cognition. This behavior is an important component of the child's ability of learning-to-learn, a mechanism akin to the one of intrinsic motivation that is argued to drive cognitive development. Accordingly, we propose to model a dual system based on (1) the learning of new task sets and on (2) their evaluation relative to their uncertainty and prediction error. The architecture is designed as a two-level-based neural system for context-dependent behavior (the first system) and task exploration and exploitation (the second system). In our model, the task sets are learned separately by reinforcement learning in the first network after their evaluation and selection in the second one. We perform two different experimental setups to show the sensorimotor mapping and switching between tasks, a first one in a neural simulation for modeling cognitive tasks and a second one with an arm-robot for motor task learning and switching. We show that the interplay of several intrinsic mechanisms drive the rapid formation of the neural populations with respect to novel task sets.

From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks

Growth and remodelling impact the network topology of complex systems, yet a general theory explaining how new links arise between existing nodes has been lacking, and little is known about the topological properties that facilitate link-prediction. Here we investigate the extent to which the connectivity evolution of a network might be predicted by mere topological features. We show how a link/community-based strategy triggers substantial prediction improvements because it accounts for the singular topology of several real networks organised in multiple local communities - a tendency here named local-community-paradigm (LCP). We observe that LCP networks are mainly formed by weak interactions and characterise heterogeneous and dynamic systems that use self-organisation as a major adaptation strategy. These systems seem designed for global delivery of information and processing via multiple local modules. Conversely, non-LCP networks have steady architectures formed by strong interactions, and seem designed for systems in which information/energy storage is crucial.

[Progress in activity-dependent structural plasticity of neural circuits in cortex]

Neural circuits of mammalian cerebral cortex have exhibited amazing abilities of structural and functional plasticity in development, learning and memory, neurological and psychiatric diseases. With the new imaging techniques and the application of molecular biology methods, observation neural circuits' structural dynamics within the cortex in vivo at the cellular and synaptic level was possible, so there were many great progresses in the field of the activity-dependent structural plasticity over the past decade. This paper reviewed some of the aspects of the experimental results, focused on the characteristics of dendritic structural plasticity in individual growth and development, rich environment, sensory deprivation, and pathological conditions, as well as learning and memory, especially the dynamics of dendritic spines on morphology and quantity; after that, we introduced axonal structural plasticity, the molecular and cellular mechanisms of structural plasticity, and proposed some future problems to be solved at last.

Time scales of memory, learning, and plasticity

After only about 10 days would the storage capacity of our nervous system be reached if we stored every bit of input. The nervous system relies on at least two mechanisms that counteract this capacity limit: compression and forgetting. But the latter mechanism needs to know how long an entity should be stored: some memories are relevant only for the next few minutes, some are important even after the passage of several years. Psychology and physiology have found and described many different memory mechanisms, and these mechanisms indeed use different time scales. In this prospect we review these mechanisms with respect to their time scale and propose relations between mechanisms in learning and memory and their underlying physiological basis.

Brain plasticity, memory and neurological disorders: an epigenetic perspective

Epigenomic settings control gene regulation in both developing and postmitotic tissue, whereas abnormal regulation of epigenomic settings has been implicated in many developmental and neurological disorders. Evidence is emerging for the roles of epigenetic mechanisms in the mature nervous system, in the dynamic processes of learning and memory. The discovery of the involvement of DNA methylation and histone acetylation and methylation in neuronal processing provides a possible answer to the long-standing riddle of how memories persist in a biological system whose cellular composition is in a constant state of flux and renewal. This mini review focuses on present research in DNA methylation and histone posttranslational modifications in learning and memory, age-related cognitive decline, and related pathological disorders.

Learning new color names produces rapid increase in gray matter in the intact adult human cortex

The human brain has been shown to exhibit changes in the volume and density of gray matter as a result of training over periods of several weeks or longer. We show that these changes can be induced much faster by using a training method that is claimed to simulate the rapid learning of word meanings by children. Using whole-brain magnetic resonance imaging (MRI) we show that learning newly defined and named subcategories of the universal categories green and blue in a period of 2 h increases the volume of gray matter in V2/3 of the left visual cortex, a region known to mediate color vision. This pattern of findings demonstrates that the anatomical structure of the adult human brain can change very quickly, specifically during the acquisition of new, named categories. Also, prior behavioral and neuroimaging research has shown that differences between languages in the boundaries of named color categories influence the categorical perception of color, as assessed by judgments of relative similarity, by response time in alternative forced-choice tasks, and by visual search. Moreover, further behavioral studies (visual search) and brain imaging studies have suggested strongly that the categorical effect of language on color processing is left-lateralized, i.e., mediated by activity in the left cerebral hemisphere in adults (hence "lateralized Whorfian" effects). The present results appear to provide a structural basis in the brain for the behavioral and neurophysiologically observed indices of these Whorfian effects on color processing.