Brain-wide mapping reveals that engrams for a single memory are distributed across multiple brain regions

On robust learning of memory attractors with noisy deep associative memory networks

Developing the computational mechanism for memory systems is a long-standing focus in machine learning and neuroscience. Recent studies have shown that overparameterized autoencoders (OAEs) implement associative memory (AM) by encoding training data as attractors. However, the learning of memory attractors requires that the norms of all eigenvalues of the input-output Jacobian matrix are strictly less than one. Motivated by the observed strong negative correlation between the attractor robustness and the largest singular value of the Jacobian matrix, we develop the noisy overparameterized autoencoders (NOAEs) for learning robust attractors by injecting random noises into their inputs during the training procedure. Theoretical demonstrations show that the training objective of the NOAE approximately minimizes the upper bound of the weighted sum of the reconstruction error and the square of the largest singular value. Extensive experiments in terms of numerical and image-based datasets show that NOAEs not only increase the success rate of the training samples becoming attractors, but also improve the attractor robustness. Codes are available at https://github.com/RaoXuan-1998/neural-netowrk-journal-NOAE.

Voices from the water(s): Developing a salutogenic trace through swimming

Within geographies of health and wellbeing research, there is ongoing interest in how health-enabling spaces and places are assembled, maintained and reproduced through occupation and practice. Set within a specific blue space practice, swimming, this paper develops the concept of the salutogenic trace, as a new way to consider health and wellbeing in place. Trace is initially introduced as a concept that augments place and space, to consider how relational geographies are understood, using swimmers and the water they swim in, as an empirical example. In the study, swimming traces are also characterised as identifiably salutogenic, a key idea in both health promotion and recent writing on health-enabling spaces and places. Salutogenesis sees health as a braided stream traced across the lifecourse, where 'upstream' health is underpinned by a sense of coherence (SOC), with three dimensions, comprehensibility, manageability and meaningfulness. A well-developed SOC in-turn prevents or reduces ill-health 'downstream'. To better understand how the salutogenic trace works, the three core dimensions of SOC were examined from the point of view of Irish swimmers in three different types of water, river, lake and sea. Each dimension was identified and described as specific components that enabled swimmer's health and wellbeing. While these varied by swimmer and type of water, what emerged were important insights into key health enabling/promoting traces across swimmer' lives, and how these were enacted and reproduced in blue space. In addition, other key critical components of trace, including flows, blockages and accretion, spoke to the life-course dimensions of salutogenesis.

Neurocounter - A deep learning framework for high-fidelity spatial localization of neurons

BACKGROUND

Many neuroscientific applications require robust and accurate localization of neurons. It is still an unsolved problem because of the enormous variation in intensity, texture, spatial overlap, morphology, and background artifacts. In addition, curating a large dataset containing complete manual annotation of neurons from high-resolution images for training a classifier requires significant time and effort. In this work, we presented Neurocounter, a deep learning network to detect and localize neurons.

NEW METHOD

Neurocounter contains an encoder, a decoder and an attention module. It is trained on images containing incompletely-annotated neurons having highly varied morphology, and control images containing artifacts and background structures. During training, Neurocounter progressively labels the un-annotated neurons in the training data. It detects centers of neuron soma as the output.

RESULTS

Neurocounter's self-learning ability reduces the need for time-intensive complete annotation and ensures high accuracy in the localization of neurons across various brain regions (approximately 94 % F1 score). Comparison with existing methods Neurocounter shows its efficacy over the state of the arts by significantly reducing false-positive detection (by at least 3 %).

CONCLUSIONS

Neurocounter offers precise neuron soma detection in various scenarios, such as with background artifacts, clutter and overlapped cell soma. This tool can be potentially used to reconstruct brain-wide 3D maps of activated neurons from 2D localization of neurons.

Targeted NMDA receptor knockdown in recall-activated neuronal ensembles impairs remote fear extinction

Fear extinction training in rodents decreases fear responses, providing a model for the development of post-traumatic stress disorder therapeutics. Fear memory recall reactivates the consolidated fear memory trace across multiple brain regions, and several studies have suggested that these recall-activated neurons are re-engaged during extinction. However, the molecular mechanisms linking this reactivation to extinction remain largely elusive. Here, we investigated the role of N-Methyl-D-Aspartate receptors (NMDARs) in remote memory recall-activated neurons within the basolateral amygdala and the medial prefrontal cortex during extinction training in mice. We found that Grin1 knockdown in these specific ensembles impaired extinction of remote fear memory, but did not reduce their reactivation during retrieval of the extinguished memory. These data suggest that while reactivation of these neuronal populations persists, their NMDARs are crucial for driving the synaptic plasticity needed to extinguish remote fear memories.

Integrating Aversive Memories in the Basolateral Amygdala

Decades of research have established a critical role of the basolateral complex of the amygdala (BLA) in the encoding and storage of aversive memories. Much of this work has utilized Pavlovian fear conditioning procedures in which animals experience a single aversive event. Although this effort has produced great insight into the neural mechanisms that support fear memories for an isolated aversive experience, much less is known about how amygdala circuits encode and integrate multiple emotional experiences. The emergence of methods to label and record neuronal ensembles over days allows a deeper understanding of how amygdala neurons encode and integrate distinct aversive episodes over time. Here, we review evidence that the BLA is an essential site for the persistent storage of long-term fear memory. As a long-term storage site for fear memory, a challenge for encoding multiple fear memories is the mechanisms by which BLA neurons allocate, integrate, and discriminate distinct experiences from one another. In this review, we discuss the historical evidence supporting the BLA as a critical site for long-term memory storage, as well as new evidence that stems from technological advances that allow researchers to simultaneously study the encoding and storage of multiple memory traces, including recent versus remote experiences. We explore the possibility that dysfunction in ensemble coding schemes contributes to the pathophysiology of posttraumatic stress disorder and argue that future studies should place increased emphasis on potential subregional differences in memory coding schemes in the amygdala to deepen our understanding of both normal and pathological emotional memory.

Synaptic architecture of a memory engram in the mouse hippocampus

Memory engrams are formed through experience-dependent plasticity of neural circuits, but their detailed architectures remain unresolved. Using three-dimensional electron microscopy, we performed nanoscale reconstructions of the hippocampal CA3-CA1 pathway after chemogenetic labeling of cellular ensembles recruited during associative learning. Neurons with a remote history of activity coinciding with memory acquisition showed no strong preference for wiring with each other. Instead, their connectomes expanded through multisynaptic boutons independently of the coactivation state of postsynaptic partners. The rewiring of ensembles representing an initial engram was accompanied by input-specific, spatially restricted upscaling of individual synapses, as well as remodeling of mitochondria, smooth endoplasmic reticulum, and interactions with astrocytes. Our findings elucidate the physical hallmarks of long-term memory and offer a structural basis for the cellular flexibility of information coding.

Key-value memory in the brain

Classical models of memory in psychology and neuroscience rely on similarity-based retrieval of stored patterns, where similarity is a function of retrieval cues and the stored patterns. Although parsimonious, these models do not allow distinct representations for storage and retrieval, despite their distinct computational demands. Key-value memory systems, in contrast, distinguish representations used for storage (values) and those used for retrieval (keys). This allows key-value memory systems to optimize simultaneously for fidelity in storage and discriminability in retrieval. We review the computational foundations of key-value memory, its role in modern machine-learning systems, related ideas from psychology and neuroscience, applications to a number of empirical puzzles, and possible biological implementations.

Amygdalo-cortical dialogue underlies memory enhancement by emotional association

Emotional arousal plays a critical role in determining what is remembered from experiences. It is hypothesized that activation of the amygdala by emotional stimuli enhances memory consolidation in its downstream brain regions. However, the physiological basis of the inter-regional interaction and its functions remain unclear. Here, by adding emotional information to a perceptual recognition task that relied on a frontal-sensory cortical circuit in mice, we demonstrated that the amygdala not only associates emotional information with perceptual information but also enhances perceptual memory retention via amygdalo-frontal cortical projections. Furthermore, emotional association increased reactivation of coordinated activity across the amygdalo-cortical circuit during non-rapid eye movement (NREM) sleep but not during rapid eye movement (REM) sleep. Notably, this increased reactivation was associated with amygdala high-frequency oscillations. Silencing of amygdalo-cortical inputs during NREM sleep selectively disrupted perceptual memory enhancement. Our findings indicate that inter-regional reactivation triggered by the amygdala during NREM sleep underlies emotion-induced perceptual memory enhancement.

Engram and behavior: How memory is stored in the brain

During the processing of information in humans, activated neurons behave in a specific way. The activity of these neurons leaves traces on the neurons, such as changes in synaptic or intrinsic properties. Formation of the memory traces is associated with molecular changes in the neurons. Hence, monitoring collective neural activities and following the trace of neural activities are important to neuroscience research. This collective or group of neurons is described as a 'neural ensemble', while the neural trace is described as a 'neural engram'. Both terms have been used and studied by neuroscientists for a long time. In this article, we discuss the development of these concepts, current research methods, and future areas of development.

Brain-wide immunolabeling and tissue clearing applications for engram research

In recent years, there has been significant progress in memory research, driven by genetic and imaging technological advances that have given unprecedented access to individual memory traces or engrams. Although Karl Lashley argued since the 1930s that an engram is not confined to a particular area but rather distributed across the entire brain, most current studies have focused exclusively on a single or few brain regions. However, this compartmentalized approach overlooks the interactions between multiple brain regions, limiting our understanding of engram mechanisms. More recently, several studies have begun to investigate engrams across the brain, but research is still limited by a lack of standardized techniques capable of reconstructing multiple ensembles at single-cell resolution across the entire brain. In this review, we guide researchers through the latest technological advancements and discoveries in immediate early gene (IEG) techniques, tissue clearing methods, microscope modalities, and automated large-scale analysis. These innovations could propel the field forward in building brain-wide engram maps of normal and disease states, thus, providing unprecedented new insights. Ultimately, this review aims to bridge the gap between research focused on single brain regions and the need for a comprehensive understanding of whole-brain engrams, revealing new approaches for exploring the neuronal mechanisms underlying engrams.

Structural synaptic signatures of contextual memory retrieval-reactivated hippocampal engram cells

Learning enhances hippocampal engram cell synaptic connectivity which is crucial for engram reactivation and recall to natural cues. Memory retrieval engages only a subset of the learning-activated ensemble, indicating potential differences in synaptic connectivity signatures of reactivated and non-reactivated cells. We probed these differences in structural synaptic connectivity patterns after recent memory retrieval, 72 h after either neutral Context Exploration (CE) or aversive Contextual Fear Conditioning (CFC). Using a combination of eGRASP (enhanced green fluorescent protein (GFP) reconstitution across synaptic partners) and viral-TRAP (targeted recombination in activated populations) to label CA3 synapses onto CA1 engram cells, we investigated differences in spine density, clusters, and morphology between the reactivated and non-reactivated population of the learning ensemble. In doing so, we developed a pipeline for reconstruction and analysis of dendrites and spines, taking nested data structure into account. Our data demonstrate an interplay between reactivation status, context valence or both factors on the number, distribution, and morphology of CA1 engram cell synapses. Despite a lack of differences in spine density, reactivated engram cells encoding an aversive context were characterised by a higher probability of forming spine clusters and a more dynamic spine type signature compared to their non-reactivated counterparts or engram cells encoding a neutral context. Together, our data indicate that the learning-activated ensemble undergoes different trajectories in structural synaptic connectivity during engram refinement.

Emotional influences on remembering and forgetting explained by frontal and parietal dynamics

Based on item-method directed forgetting (DF) task, 60 participants were recruited to explore the influence of emotion (negative, neutral, and positive) on memory encoding processing, with all data referring to the encoding phase of the task. Behavioral results showed that participants were more successful at remembering negative pictures that needed to be forgotten, with both higher recognition rates and discrimination accuracy (Pr) compared with neutral pictures. In the brain, parietal activities reflected preferential processing during negative picture viewing through enhanced late parietal positive potentials (LPP) relative to neutral ones. In addition, "Remember" (R) instruction evoked a larger parietal P3 component, whereas "Forget" (F) instruction evoked a stronger frontal N2 component, each of which component was significantly associated with the DF effect (i.e., more recognized items of R-cue than that of F-cue), reflecting the fact that inhibitory control and selective rehearsal mechanisms were jointly responsible for the directed forgetting of emotional materials. Finally, we showed the presence of instruction-evoked low-frequency phase synchronization between frontal and parietal regions, and that these synchronization patterns differed between R-cue and F-cue in an emotion-dependent manner. Together, these findings reveal cognitive mechanisms and specific patterns of large-scale phase synchronization underlying active forgetting of emotional memories, deepening our comprehension of the interplay between cognition and emotion.NEW & NOTEWORTHY This study provides experimental evidence that emotional memories, especially negative ones, are more difficult to intentionally forget than neutral memories within the item-method directed forgetting paradigm. It explores the cognitive mechanisms underlying this process, highlighting the role of selective rehearsal and inhibitory control. In addition, it reveals emotion-dependent low-frequency phase synchronization between frontal and parietal regions, offering new insights into active forgetting of emotional memories.

Engrams across diseases: Different pathologies - unifying mechanisms?

Memories are our reservoir of knowledge and thus, are crucial for guiding decisions and defining our self. The physical correlate of a memory in the brain is termed an engram and since decades helps researchers to elucidate the intricate nature of our imprinted experiences and knowledge. Given the importance that memories have for our lives, their impairment can present a tremendous burden. In this review we aim to discuss engram malfunctioning across diseases, covering dementia-associated pathologies, epilepsy, chronic pain and psychiatric disorders. Current neuroscientific tools allow to witness the emergence and fate of engram cells and enable their manipulation. We further suggest that specific mechanisms of mnemonic malfunction can be derived from engram cell readouts. While depicting the way diseases act on the mnemonic component - specifically, on the cellular engram - we emphasize a differentiation between forms of amnesia and hypermnesia. Finally, we highlight commonalities and distinctions of engram impairments on the cellular level across diseases independent of their pathogenic origins and discuss prospective therapeutic measures.

Cortex-Specific Tmem169 Deficiency Induces Defects in Cortical Neuron Development and Autism-Like Behaviors in Mice

The development of the nervous system is a complex process, with many challenging scientific questions yet to be resolved. Disruptions in brain development are strongly associated with neurodevelopmental disorders, such as intellectual disability and autism. While the genetic basis of autism is well established, the precise pathological mechanisms remain unclear. Variations on chromosome 2q have been linked to autism, yet the specific genes responsible for the disorder have not been identified. This study investigates the role of the transmembrane protein 169 (TMEM169) gene, located on human chromosome 2q35, which has not been previously characterized. Our findings indicate that Tmem169 is highly expressed in the nervous system, and its deletion in the male mouse dorsal forebrain results in neuronal morphological abnormalities and synaptic dysfunction. Notably, Tmem169-deficient mice, irrespective of sex, display behavioral traits resembling those observed in individuals with autism. These results suggest that Tmem169 interacts with several key neuronal proteins, many of which are implicated in neurodevelopmental diseases. Furthermore, we demonstrate that Tmem169 promotes neuronal process and synapse development through its interaction with Shank3.

Calcium levels in ASER neurons determine behavioral valence by engaging distinct neuronal circuits in C. elegans

The valence of stimuli is shaped by various factors, including environmental cues, internal states, genetic variability, and past experience. However, the mechanisms behind this flexibility remain elusive. In the nematode C. elegans, we found that ethanol, an olfactory stimulus, can elicit opposite chemotaxis responses - attraction vs. aversion - depending on NaCl concentration, demonstrating the role of environmental factors in altering valence. Remarkably, a single chemosensory neuron, ASER, orchestrate this bidirectional ethanol chemotaxis by integrating information from both stimuli - ethanol and NaCl - into its neuronal activity dynamics. Specifically, different calcium dynamics in the ASER neuron differentially activate the signaling molecule CMK-1, thereby engaging different downstream interneurons and leading to opposite chemotaxis directions. Consistently, optogenetic manipulations of the ASER neuron reverse the chemotaxis directions, by altering its calcium dynamics. Our findings reveal a mechanism by which a single neuron integrates multisensory inputs to determine context-dependent behavioral valence, contributing to our current understanding of valence encoding.

A SMARTTR workflow for multi-ensemble atlas mapping and brain-wide network analysis

In the last decade, activity-dependent strategies for labelling multiple immediate early gene (IEG) ensembles in mice have generated unprecedented insight into the mechanisms of memory encoding, storage, and retrieval. However, few strategies exist for brain-wide mapping of multiple ensembles, including their overlapping population, and none incorporate capabilities for downstream network analysis. Here, we introduce a scalable workflow to analyze traditionally coronally-sectioned datasets produced by activity-dependent tagging systems. Intrinsic to this pipeline is simple multi-ensemble atlas registration and statistical testing in R (SMARTTR), an R package which wraps mapping capabilities with functions for statistical analysis and network visualization, and support for import of external datasets. We demonstrate the versatility of SMARTTR by mapping the ensembles underlying the acquisition and expression of learned helplessness (LH), a robust stress model. Applying network analysis, we find that exposure to inescapable shock (IS), compared to context training (CT), results in decreased centrality of regions engaged in spatial and contextual processing and higher influence of regions involved in somatosensory and affective processing. During LH expression, the substantia nigra emerges as a highly influential region which shows a functional reversal following IS, indicating a possible regulatory function of motor activity during helplessness. We also report that IS results in a robust decrease in reactivation activity across a number of cortical, hippocampal, and amygdalar regions, indicating suppression of ensemble reactivation may be a neurobiological signature of LH. These results highlight the emergent insights uniquely garnered by applying our analysis approach to multiple ensemble datasets and demonstrate the strength of our workflow as a hypothesis-generating toolkit.

Deconstruction of a Memory Engram Reveals Distinct Ensembles Recruited at Learning

How are associative memories formed? Which cells represent a memory, and when are they engaged? By visualizing and tagging cells based on their calcium influx with unparalleled temporal precision, we identified non-overlapping dorsal CA1 neuronal ensembles that are differentially active during associative fear memory acquisition. We dissected the acquisition experience into periods during which salient stimuli were presented or certain mouse behaviors occurred and found that cells associated with specific acquisition periods are sufficient alone to drive memory expression and contribute to fear engram formation. This study delineated the different identities of the cell ensembles active during learning, and revealed, for the first time, which ones form the core engram and are essential for memory formation and recall.

Neurobiological mechanisms of forgetting across timescales

Every species in the animal kingdom that learns, also forgets. Despite this balance between learning and forgetting, most neuroscientific explorations of memory have focused on how learning occurs, with recent studies identifying engrams as putative biological substrates for memory. Here we review an emerging literature that, in contrast, explores how our brains forget. These studies reveal that forgetting engages a broad collection of mechanisms that function to reduce engram accessibility. However, changes in accessibility emerge on vastly different timescales. At short timescales, forgetting is modulated by fluctuations in brain states that alter engram accessibility in a moment-to-moment fashion. In the intermediate- and long-term, forgetting depends, in part, on mechanisms that rewire engrams, rendering them gradually harder to access. Viewed this way, forgetting encompasses a family of plasticity mechanisms that modulate engram accessibility, perhaps in order to prioritize those memories that are most timely or relevant to the situation at hand.

Uniform volumetric single-cell processing for organ-scale molecular phenotyping

Extending single-cell analysis to intact tissues while maintaining organ-scale spatial information poses a major challenge due to unequal chemical processing of densely packed cells. Here we introduce Continuous Redispersion of Volumetric Equilibrium (CuRVE) in nanoporous matrices, a framework to address this challenge. CuRVE ensures uniform processing of all cells in organ-scale tissues by perpetually maintaining dynamic equilibrium of the tissue's gradually shifting chemical environment. The tissue chemical reaction environment changes at a continuous, slow rate, allowing redispersion of unevenly distributed chemicals and preserving chemical equilibrium tissue wide at any given moment. We implemented CuRVE to immunologically label whole mouse and rat brains and marmoset and human tissue blocks within 1 day. We discovered highly variable regionalized reduction of parvalbumin immunoreactive cells in wild-type adult mice, a phenotype missed by the commonly used genetic labeling. We envision that our platform will advance volumetric single-cell processing and analysis, facilitating comprehensive single-cell level investigations within their spatial context in organ-scale tissues.

An "Engram-Centric" Approach to Transient Global Amnesia (TGA) and Other Acute-Onset Amnesias

The differential diagnosis of acute-onset amnesia includes transient global amnesia (TGA), transient epileptic amnesia (TEA), and functional (or psychogenic) amnesia. The most common of these, TGA, is a rare but well-described condition characterised by a self-limited episode of dense anterograde amnesia with variable retrograde amnesia. Although the clinical phenomenology of TGA is well described, its pathogenesis is not currently understood, thus preventing the development of evidence-based therapeutic recommendations. Here, TGA, TEA, and functional amnesia are considered in light of the historical engram conception of memory, now informed by recent experimental research, as disturbances in distributed ensembles of engram neurones active during memory formation and recall. This analysis affords therapeutic implications for these conditions, should interventions to reactivate latent or silent engrams become available.

Memory engram synapse 3D molecular architecture visualized by cryoCLEM-guided cryoET

Memory is incorporated into the brain as physicochemical changes to engram cells. These are neuronal populations that form complex neuroanatomical circuits, are modified by experiences to store information, and allow for memory recall. At the molecular level, learning modifies synaptic communication to rewire engram circuits, a mechanism known as synaptic plasticity. However, despite its functional role on memory formation, the 3D molecular architecture of synapses within engram circuits is unknown. Here, we demonstrate the use of engram labelling technology and cryogenic correlated light and electron microscopy (cryoCLEM)-guided cryogenic electron tomography (cryoET) to visualize the in-tissue 3D molecular architecture of engram synapses of a contextual fear memory within the CA1 region of the mouse hippocampus. Engram cells exhibited structural diversity of macromolecular constituents and organelles in both pre- and postsynaptic compartments and within the synaptic cleft, including in clusters of membrane proteins, synaptic vesicle occupancy, and F-actin copy number. This 'engram to tomogram' approach, harnessing in vivo functional neuroscience and structural biology, provides a methodological framework for testing fundamental molecular plasticity mechanisms within engram circuits during memory encoding, storage and recall.

Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits

Animals need to rapidly learn to recognize and avoid predators. This ability may be especially important for young animals due to their increased vulnerability. It is unknown whether, and how, nascent vertebrates are capable of such rapid learning. Here, we used a robotic predator-prey interaction assay to show that 1 week after fertilization-a developmental stage where they have approximately 1% the number of neurons of adults-zebrafish larvae rapidly and robustly learn to recognize a stationary object as a threat after the object pursues the fish for ∼1 min. Larvae continue to avoid the threatening object after it stops moving and can learn to distinguish threatening from non-threatening objects of a different color. Whole-brain functional imaging revealed the multi-timescale activity of noradrenergic neurons and forebrain circuits that encoded the threat. Chemogenetic ablation of those populations prevented the learning. Thus, a noradrenergic and forebrain multiregional network underlies the ability of young vertebrates to rapidly learn to recognize potential predators within their first week of life.

Learning-associated astrocyte ensembles regulate memory recall

The physical manifestations of memory formation and recall are fundamental questions that remain unresolved1. At the cellular level, ensembles of neurons called engrams are activated by learning events and control memory recall1-5. Astrocytes are found in close proximity to neurons and engage in a range of activities that support neurotransmission and circuit plasticity6-10. Moreover, astrocytes exhibit experience-dependent plasticity11-13, although whether specific ensembles of astrocytes participate in memory recall remains obscure. Here we show that learning events induce c-Fos expression in a subset of hippocampal astrocytes, and that this subsequently regulates the function of the hippocampal circuit in mice. Intersectional labelling of astrocyte ensembles with c-Fos after learning events shows that they are closely affiliated with engram neurons, and reactivation of these astrocyte ensembles stimulates memory recall. At the molecular level, learning-associated astrocyte (LAA) ensembles exhibit elevated expression of nuclear factor I-A, and its selective deletion from this population suppresses memory recall. Taken together, our data identify LAA ensembles as a form of plasticity that is sufficient to provoke memory recall and indicate that astrocytes are an active component of the engram.

Decade of TRAP progress: Insights and future prospects for advancing functional network research in epilepsy

Targeted Recombination in Active Populations (TRAP) represents an effective and extensively applied technique that has earned significant utilization in neuroscience over the past decade, primarily for identifying and modulating functionally activated neuronal ensembles associated with diverse behaviors. As epilepsy is a neurological disorder characterized by pathological hyper-excitatory networks, TRAP has already been widely applied in epilepsy research. However, the deployment of TRAP in this field remains underexplored, and there is significant potential for further application and development in epilepsy-related investigations. In this review, we embark on a concise examination of the mechanisms behind several TRAP tools, introduce the current applications of TRAP in epilepsy research, and collate the key advantages as well as limitations of TRAP. Furthermore, we sketch out perspectives on potential applications of TRAP in future epilepsy research, grounded in the present landscape and challenges of the field, as well as the ways TRAP has been embraced in other neuroscience domains.

Comprehension of gut microbiota and microRNAs may contribute to the development of innovative treatment tactics against metabolic disorders and psychiatric disorders

Metabolic syndrome is a group of pathological disorders increasing the risk of serious diseases including cardiovascular disease, stroke, type 2 diabetes. Global widespread of the metabolic syndrome has put a heavy social burden. Interestingly, a crucial link between the metabolic syndrome and a psychiatric disorder may frequently coexist, in which certain shared mechanisms might play a role for the pathogenesis. In fact, some microRNAs (miRNAs) have been detected in the overlap pathology, suggesting a common molecular mechanism for the development of both disorders. Subsequent studies have revealed that these miRNAs and several metabolites of gut microbiota such as short chain fatty acids (SCFAs) might be involved in the development of both disorders, in which the association between gut and brain might play key roles with engram memory for the modulation of immune cells. Additionally, the correlation between brain and immunity might also influence the development of several diseases/disorders including metabolic syndrome. Brain could possess several inflammatory responses as an information of pathological images termed engrams. In other words, preservation of the engram memory might be achieved by a meta-plasticity mechanism that shapes the alteration of neuron linkages for the development of immune-related diseases. Therefore, it might be rational that metabolic syndrome and psychiatric disorders may belong to a group of immune-related diseases. Disrupting in gut microbiota may threaten the body homeostasis, leading to initiate a cascade of health problems. This concept may contribute to the development of superior therapeutic application with the usage of some functional components in food against metabolic and psychiatric disorders. This paper reviews advances in understanding the regulatory mechanisms of miRNAs with the impact to gut, liver and brain, deliberating the probable therapeutic techniques against these disorders.

Dorsal raphe to basolateral amygdala corticotropin-releasing factor circuit regulates cocaine-memory reconsolidation

Environmental stimuli elicit drug craving and relapse in cocaine users by triggering the retrieval of strong cocaine-related contextual memories. Retrieval can also destabilize drug memories, requiring reconsolidation, a protein synthesis-dependent storage process, to maintain memory strength. Corticotropin-releasing factor (CRF) signaling in the basolateral amygdala (BLA) is necessary for cocaine-memory reconsolidation. We have hypothesized that a critical source of CRF in the BLA is the dorsal raphe nucleus (DR) based on its neurochemistry, anatomical connectivity, and requisite involvement in cocaine-memory reconsolidation. To test this hypothesis, male and female Sprague-Dawley rats received adeno-associated viruses to express Gi-coupled designer receptors exclusively activated by designer drugs (DREADDs) selectively in CRF neurons of the DR and injection cannulae directed at the BLA. The rats were trained to self-administer cocaine in a distinct environmental context then received extinction training in a different context. Next, they were briefly re-exposed to the cocaine-predictive context to destabilize (reactivate) cocaine memories. Intra-BLA infusions of the DREADD agonist deschloroclozapine (DCZ; 0.1 mM, 0.5 µL/hemisphere) immediately after memory reactivation attenuated cocaine-memory strength, relative to vehicle infusion. This was indicated by a selective, DCZ-induced and memory reactivation-dependent decrease in drug-seeking behavior in the cocaine-predictive context in DREADD-expressing males and females at test compared to respective controls. Notably, BLA-projecting DR CRF neurons that exhibited increased c-Fos expression during memory reconsolidation co-expressed the glutamatergic neuronal marker, vesicular glutamate transporter 3. Together, these findings suggest that the DRCRF → BLA circuit is engaged to maintain cocaine-memory strength after memory destabilization, and this phenomenon may be mediated by DR CRF and/or glutamate release in the BLA.

Rectified activity-dependent population plasticity implicates cortical adaptation for memory and cognitive functions

Cortical network undergoes rewiring everyday due to learning and memory events. To investigate the trends of population adaptation in neocortex overtime, we record cellular activity of large-scale cortical populations in response to neutral environments and conditioned contexts and identify a general intrinsic cortical adaptation mechanism, naming rectified activity-dependent population plasticity (RAPP). Comparing each adjacent day, the previously activated neurons reduce activity, but remain with residual potentiation, and increase population variability in proportion to their activity during previous recall trials. RAPP predicts both the decay of context-induced activity patterns and the emergence of sparse memory traces. Simulation analysis reveal that the local inhibitory connections might account for the residual potentiation in RAPP. Intriguingly, introducing the RAPP phenomenon in the artificial neural network show promising improvement in small sample size pattern recognition tasks. Thus, RAPP represents a phenomenon of cortical adaptation, contributing to the emergence of long-lasting memory and high cognitive functions.

A brainstem circuit amplifies aversion

Dynamic gain control of aversive signals enables adaptive behavioral responses. Although the role of amygdalar circuits in aversive processing is well established, the neural pathway for amplifying aversion remains elusive. Here, we show that the brainstem circuit linking the interpeduncular nucleus (IPN) with the nucleus incertus (NI) amplifies aversion and promotes avoidant behaviors. IPN GABA neurons are activated by aversive stimuli and their predicting cues, with their response intensity closely tracking aversive values. Activating these neurons does not trigger aversive behavior on its own but rather amplifies responses to aversive stimuli, whereas their ablation or inhibition suppresses such responses. Detailed circuit dissection revealed anatomically distinct subgroups within the IPN GABA neuron population, highlighting the NI-projecting subgroup as the modulator of aversiveness related to fear and opioid withdrawal. These findings unveil the IPN-NI circuit as an aversion amplifier and suggest potential targets for interventions against affective disorders and opioid relapse.

Involvement of a lateral entorhinal cortex engram in episodic-like memory recall

Episodic memory relies on the entorhinal cortex (EC), a crucial hub connecting the hippocampus and sensory processing regions. This study investigates the role of the lateral EC (LEC) in episodic-like memory in mice. Here, we employ the object-place-context-recognition task (OPCRT), a behavioral test used to study episodic-like memory in rodents. Electrophysiology in brain slices reveals that OPCRT specifically induces a shift in the threshold for the induction of synaptic plasticity in LEC superficial layer II. Additionally, a dual viral system is used to express chemogenetic receptors coupled to the c-Fos promoter in neurons recruited during the learning. We demonstrate that the inhibition of LEC neurons impairs the performance of the mice in the memory task, while their stimulation significantly facilitates memory recall. Our findings provide evidence for an episodic-like memory engram in the LEC and emphasize its role in memory processing within the broader network of episodic memory.

Time-dependent neural arbitration between cue associative and episodic fear memories

After traumatic events, simple cue-threat associative memories strengthen while episodic memories become incoherent. However, how the brain prioritises cue associations over episodic coding of traumatic events remains unclear. Here, we developed an original episodic threat conditioning paradigm in which participants concurrently form two memory representations: cue associations and episodic cue sequence. We discovered that these two distinct memories compete for physiological fear expression, reorganising overnight from an overgeneralised cue-based to a precise sequence-based expression. With multivariate fMRI, we track inter-area communication of the memory representations to reveal that a rebalancing between hippocampal- and prefrontal control of the fear regulatory circuit governs this memory maturation. Critically, this overnight re-organisation is altered with heightened trait anxiety. Together, we show the brain prioritises generalisable associative memories under recent traumatic stress but resorts to selective episodic memories 24 h later. Time-dependent memory competition may provide a unifying account for memory dysfunctions in post-traumatic stress disorders.

Nedl1 knockout impaired the learning and memory of mice

BACKGROUND

Protein ubiquitination is a common post-translational modification involved in protein degradation and various life processes in cells. NEDL1 is a ubiquitin ligase that is highly expressed primarily in the brain. However, the functions of NEDL1 in social approach/novelty preference, anxiety, learning and memory remain poorly understood.

METHODS

Nedl1 knockout mice (Nedl1-/-) and wild-type mice (Nedl1+/+) were tested using three-chamber test, elevated plus maze, and Barnes maze. Then, brain tissue was stained, and blood was collected for metabolic analysis.

RESULTS

Compared with Nedl1+/+ mice, Nedl1-/- mice showed no differences in social approach/novelty preference and anxiety behavior. Nedl1-/- mice displayed impaired learning and memory. Nedl1 knockout did not affect the number of neurons and oligodendrocytes in the hippocampus. Astrocytes proliferated in the hippocampus of Nedl1-/- mice. The amino acid metabolism of Nedl1+/+and Nedl1-/- mice is different, especially the increase in proline and tryptophan.

CONCLUSION

This study showed that Nedl1 knockout impaired learning and memory, which may be related to astrocyte proliferation and amino acid metabolism change. Nedl1 knockout did not affect social style/novelty preference and anxiety behavior in mice. The preliminary study of NEDL1 in neurobehavioral function could help understand the role of NEDL1 in the nervous system.

Dentate gyrus is needed for memory retrieval

The hippocampus is crucial for acquiring and retrieving episodic and contextual memories. In previous studies, the inactivation of dentate gyrus (DG) neurons by chemogenetic- and optogenetic-mediated hyperpolarization led to opposing conclusions about DG's role in memory retrieval. One study used Designer Receptors Exclusively Activated by Designer Drugs (DREADD)-mediated clozapine N-oxide (CNO)-induced hyperpolarization and reported that the previously formed memory was erased, thus concluding that denate gyrus is needed for memory maintenance. The other study used optogenetic with halorhodopsin induced hyperpolarization and reported and dentate gyrus is needed for memory retrieval. We hypothesized that this apparent discrepancy could be due to the length of hyperpolarization in previous studies; minutes by optogenetics and several hours by DREADD/CNO. Since hyperpolarization interferes with anterograde and retrograde neuronal signaling, it is possible that the memory engram in the dentate gyrus and the entorhinal to hippocampus trisynaptic circuit was erased by long-term, but not with short-term hyperpolarization. We developed and applied an advanced chemogenetic technology to selectively silence synaptic output by blocking neurotransmitter release without hyperpolarizing DG neurons to explore this apparent discrepancy. We performed in vivo electrophysiology during trace eyeblink in a rabbit model of associative learning. Our work shows that the DG output is required for memory retrieval. Based on previous and recent findings, we propose that the actively functional anterograde and retrograde neuronal signaling is necessary to preserve synaptic memory engrams along the entorhinal cortex to the hippocampal trisynaptic circuit.

High frequency oscillations in human memory and cognition: a neurophysiological substrate of engrams?

Despite advances in understanding the cellular and molecular processes underlying memory and cognition, and recent successful modulation of cognitive performance in brain disorders, the neurophysiological mechanisms remain underexplored. High frequency oscillations beyond the classic electroencephalogram spectrum have emerged as a potential neural correlate of fundamental cognitive processes. High frequency oscillations are detected in the human mesial temporal lobe and neocortical intracranial recordings spanning gamma/epsilon (60-150 Hz), ripple (80-250 Hz) and higher frequency ranges. Separate from other non-oscillatory activities, these brief electrophysiological oscillations of distinct duration, frequency and amplitude are thought to be generated by coordinated spiking of neuronal ensembles within volumes as small as a single cortical column. Although the exact origins, mechanisms and physiological roles in health and disease remain elusive, they have been associated with human memory consolidation and cognitive processing. Recent studies suggest their involvement in encoding and recall of episodic memory with a possible role in the formation and reactivation of memory traces. High frequency oscillations are detected during encoding, throughout maintenance, and right before recall of remembered items, meeting a basic definition for an engram activity. The temporal coordination of high frequency oscillations reactivated across cortical and subcortical neural networks is ideally suited for integrating multimodal memory representations, which can be replayed and consolidated during states of wakefulness and sleep. High frequency oscillations have been shown to reflect coordinated bursts of neuronal assembly firing and offer a promising substrate for tracking and modulation of the hypothetical electrophysiological engram.

Mesocorticolimbic circuit mechanisms of social dominance behavior

Social animals, including rodents, primates, and humans, partake in competition for finite resources, thereby establishing social hierarchies wherein an individual's social standing influences diverse behaviors. Understanding the neurobiological underpinnings of social dominance is imperative, given its ramifications for health, survival, and reproduction. Social dominance behavior comprises several facets, including social recognition, social decision-making, and actions, indicating the concerted involvement of multiple brain regions in orchestrating this behavior. While extensive research has been dedicated to elucidating the neurobiology of social interaction, recent studies have increasingly delved into adverse social behaviors such as social competition and hierarchy. This review focuses on the latest advancements in comprehending the mechanisms of the mesocorticolimbic circuit governing social dominance, with a specific focus on rodent studies, elucidating the intricate dynamics of social hierarchies and their implications for individual well-being and adaptation.

Amygdala and Cortex Relationships during Learning of a Sensory Discrimination Task

During learning of a sensory discrimination task, the cortical and subcortical regions display complex spatiotemporal dynamics. During learning, both the amygdala and cortex link stimulus information to its appropriate association, for example, a reward. In addition, both structures are also related to nonsensory parameters such as body movements and licking during the reward period. However, the emergence of the cortico-amygdala relationships during learning is largely unknown. To study this, we combined wide-field cortical imaging with fiber photometry to simultaneously record cortico-amygdala population dynamics as male mice learn a whisker-dependent go/no-go task. We were able to simultaneously record neuronal populations from the posterior cortex and either the basolateral amygdala (BLA) or central/medial amygdala (CEM). Prior to learning, the somatosensory and associative cortex responded during sensation, while amygdala areas did not show significant responses. As mice became experts, amygdala responses emerged early during the sensation period, increasing in the CEM, while decreasing in the BLA. Interestingly, amygdala and cortical responses were associated with task-related body movement, displaying significant responses ∼200 ms before movement initiation which led to licking for the reward. A correlation analysis between the cortex and amygdala revealed negative and positive correlation with the BLA and CEM, respectively, only in the expert case. These results imply that learning induces an involvement of the cortex and amygdala which may aid to link sensory stimuli with appropriate associations.

Sex differences in nucleus accumbens core circuitry engaged by binge-like ethanol drinking

Growing parity in Alcohol Use Disorder (AUD) diagnoses in men and women necessitates consideration of sex as a biological variable. In humans and rodents, the nucleus accumbens core (NAcc) regulates alcohol binge drinking, a risk factor for developing AUD. We labeled NAcc inputs with a viral retrograde tracer and quantified whole-brain c-Fos to determine the regions and NAcc inputs differentially engaged in male and female mice during binge-like ethanol drinking. We found that binge-like ethanol drinking females had 129 brain areas with greater c-Fos than males. Moreover, ethanol engaged more NAcc inputs in binge-like ethanol drinking females (as compared with males), including GABAergic and glutamatergic inputs. Relative to water controls, ethanol increased network modularity and decreased connectivity in both sexes and did so more dramatically in males. These results demonstrate that early-stage binge-like ethanol drinking engages brain regions and NAcc-inputs and alters network dynamics in a sex-specific manner.

Divergent recruitment of developmentally defined neuronal ensembles supports memory dynamics

Memories are dynamic constructs whose properties change with time and experience. The biological mechanisms underpinning these dynamics remain elusive, particularly concerning how shifts in the composition of memory-encoding neuronal ensembles influence the evolution of a memory over time. By targeting developmentally distinct subpopulations of principal neurons, we discovered that memory encoding resulted in the concurrent establishment of multiple memory traces in the mouse hippocampus. Two of these traces were instantiated in subpopulations of early- and late-born neurons and followed distinct reactivation trajectories after encoding. The divergent recruitment of these subpopulations underpinned gradual reorganization of memory ensembles and modulated memory persistence and plasticity across multiple learning episodes. Thus, our findings reveal profound and intricate relationships between ensemble dynamics and the progression of memories over time.

An arginine-rich nuclear localization signal (ArgiNLS) strategy for streamlined image segmentation of single cells

High-throughput volumetric fluorescent microscopy pipelines can spatially integrate whole-brain structure and function at the foundational level of single cells. However, conventional fluorescent protein (FP) modifications used to discriminate single cells possess limited efficacy or are detrimental to cellular health. Here, we introduce a synthetic and nondeleterious nuclear localization signal (NLS) tag strategy, called "Arginine-rich NLS" (ArgiNLS), that optimizes genetic labeling and downstream image segmentation of single cells by restricting FP localization near-exclusively in the nucleus through a poly-arginine mechanism. A single N-terminal ArgiNLS tag provides modular nuclear restriction consistently across spectrally separate FP variants. ArgiNLS performance in vivo displays functional conservation across major cortical cell classes and in response to both local and systemic brain-wide AAV administration. Crucially, the high signal-to-noise ratio afforded by ArgiNLS enhances machine learning-automated segmentation of single cells due to rapid classifier training and enrichment of labeled cell detection within 2D brain sections or 3D volumetric whole-brain image datasets, derived from both staining-amplified and native signal. This genetic strategy provides a simple and flexible basis for precise image segmentation of genetically labeled single cells at scale and paired with behavioral procedures.

Molecular tools to capture active neural circuits

To understand how neurons and neural circuits function during behaviors, it is essential to record neuronal activity in the brain in vivo. Among the various technologies developed for recording neuronal activity, molecular tools that induce gene expression in an activity-dependent manner have attracted particular attention for their ability to clarify the causal relationships between neuronal activity and behavior. In this review, we summarize recently developed activity-dependent gene expression tools and their potential contributions to the study of neural circuits.

The thalamic reticular nucleus orchestrates social memory

Social memory has been developed in humans and other animals to recognize familiar conspecifics and is essential for their survival and reproduction. Here, we demonstrated that parvalbumin-positive neurons in the sensory thalamic reticular nucleus (sTRNPvalb) are necessary and sufficient for mice to memorize conspecifics. sTRNPvalb neurons receiving glutamatergic projections from the posterior parietal cortex (PPC) transmit individual information by inhibiting the parafascicular thalamic nucleus (PF). Mice in which the PPCCaMKII→sTRNPvalb→PF circuit was inhibited exhibited a disrupted ability to discriminate familiar conspecifics from novel ones. More strikingly, a subset of sTRNPvalb neurons with high electrophysiological excitability and complex dendritic arborizations is involved in the above corticothalamic pathway and stores social memory. Single-cell RNA sequencing revealed the biochemical basis of these subset cells as a robust activation of protein synthesis. These findings elucidate that sTRNPvalb neurons modulate social memory by coordinating a hitherto unknown corticothalamic circuit and inhibitory memory engram.

Reactivation of encoding ensembles in the prelimbic cortex supports temporal associations

Fear conditioning is encoded by strengthening synaptic connections between the neurons activated by a conditioned stimulus (CS) and those activated by an unconditioned stimulus (US), forming a memory engram, which is reactivated during memory retrieval. In temporal associations, activity within the prelimbic cortex (PL) plays a role in sustaining a short-term, transient memory of the CS, which is associated with the US after a temporal gap. However, it is unknown whether the PL has only a temporary role, transiently representing the CS, or is part of the neuronal ensembles that support the retrieval, i.e., whether PL neurons support both transient, short-term memories and stable, long-term memories. We investigated neuronal ensembles underlying temporal associations using fear conditioning with a 5-s interval between the CS and US (CFC-5s). Controls were trained in contextual fear conditioning (CFC), in which the CS-US overlaps. We used Robust Activity Marking (RAM) to selectively manipulate PL neurons activated by CFC-5s learning and Targeted Recombination in Active Populations (TRAP2) mice to label neurons activated by CFC-5s learning and reactivated by memory retrieval in the amygdala, medial prefrontal cortex, hippocampus, perirhinal cortices (PER) and subiculum. We also computed their co-reactivation to generate correlation-based networks. The optogenetic reactivation or silencing of PL encoding ensembles either promoted or impaired the retrieval of CFC-5s but not CFC. CFC-5s retrieval reactivated encoding ensembles in the PL, PER, and basolateral amygdala. The engram network of CFC-5s had higher amygdala and PER centralities and interconnectivity. The same PL neurons support learning and stable associative memories.

The mesopontine tegmentum in reward and aversion: From cellular heterogeneity to behaviour

The mesopontine tegmentum, comprising the pedunculopontine tegmentum (PPN) and the laterodorsal tegmentum (LDT), is intricately connected to various regions of the basal ganglia, motor systems, and limbic systems. The PPN and LDT can regulate the activity of different brain regions of these target systems, and in this way are in a privileged position to modulate motivated behaviours. Despite recent findings, the PPN and LDT have been largely overlooked in discussions about the neural circuits associated with reward and aversion. This review aims to provide a timely and comprehensive resource on past and current research, highlighting the PPN and LDT's connectivity and influence on basal ganglia and limbic, and motor systems. Seminal studies, including lesion, pharmacological, and optogenetic/chemogenetic approaches, demonstrate their critical roles in modulating reward/aversive behaviours. The review emphasizes the need for further investigation into the associated cellular mechanisms, in order to clarify their role in behaviour and contribution for different neuropsychiatric disorders.

Current and future applications of light-sheet imaging for identifying molecular and developmental processes in autism spectrum disorders

Autism spectrum disorder (ASD) is identified by a set of neurodevelopmental divergences that typically affect the social communication domain. ASD is also characterized by heterogeneous cognitive impairments and is associated with cooccurring physical and medical conditions. As behaviors emerge as the brain matures, it is particularly essential to identify any gaps in neurodevelopmental trajectories during early perinatal life. Here, we introduce the potential of light-sheet imaging for studying developmental biology and cross-scale interactions among genetic, cellular, molecular and macroscale levels of circuitry and connectivity. We first report the core principles of light-sheet imaging and the recent progress in studying brain development in preclinical animal models and human organoids. We also present studies using light-sheet imaging to understand the development and function of other organs, such as the skin and gastrointestinal tract. We also provide information on the potential of light-sheet imaging in preclinical drug development. Finally, we speculate on the translational benefits of light-sheet imaging for studying individual brain-body interactions in advancing ASD research and creating personalized interventions.

Memory Trace for Fear Extinction: Fragile yet Reinforceable

Fear extinction is a biological process in which learned fear behavior diminishes without anticipated reinforcement, allowing the organism to re-adapt to ever-changing situations. Based on the behavioral hypothesis that extinction is new learning and forms an extinction memory, this new memory is more readily forgettable than the original fear memory. The brain's cellular and synaptic traces underpinning this inherently fragile yet reinforceable extinction memory remain unclear. Intriguing questions are about the whereabouts of the engram neurons that emerged during extinction learning and how they constitute a dynamically evolving functional construct that works in concert to store and express the extinction memory. In this review, we discuss recent advances in the engram circuits and their neural connectivity plasticity for fear extinction, aiming to establish a conceptual framework for understanding the dynamic competition between fear and extinction memories in adaptive control of conditioned fear responses.

Engram mechanisms of memory linking and identity

Memories are thought to be stored in neuronal ensembles referred to as engrams. Studies have suggested that when two memories occur in quick succession, a proportion of their engrams overlap and the memories become linked (in a process known as prospective linking) while maintaining their individual identities. In this Review, we summarize the key principles of memory linking through engram overlap, as revealed by experimental and modelling studies. We describe evidence of the involvement of synaptic memory substrates, spine clustering and non-linear neuronal capacities in prospective linking, and suggest a dynamic somato-synaptic model, in which memories are shared between neurons yet remain separable through distinct dendritic and synaptic allocation patterns. We also bring into focus retrospective linking, in which memories become associated after encoding via offline reactivation, and discuss key temporal and mechanistic differences between prospective and retrospective linking, as well as the potential differences in their cognitive outcomes.

Modulation of learning safety signals by acute stress: paraventricular thalamus and prefrontal inhibition

Distinguishing between cues predicting safety and danger is crucial for survival. Impaired learning of safety cues is a central characteristic of anxiety-related disorders. Despite recent advances in dissecting the neural circuitry underlying the formation and extinction of conditioned fear, the neuronal basis mediating safety learning remains elusive. Here, we showed that safety learning reduces the responses of paraventricular thalamus (PVT) neurons to safety cues, while activation of these neurons controls both the formation and expression of safety memory. Additionally, the PVT preferentially activates prefrontal cortex somatostatin interneurons (SOM-INs), which subsequently inhibit parvalbumin interneurons (PV-INs) to modulate safety memory. Importantly, we demonstrate that acute stress impairs the expression of safety learning, and this impairment can be mitigated when the PVT is inhibited, indicating PVT mediates the stress effect. Altogether, our findings provide insights into the mechanism by which acute stress modulates safety learning.

Integrating and fragmenting memories under stress and alcohol

Stress can powerfully influence the way we form memories, particularly the extent to which they are integrated or situated within an underlying spatiotemporal and broader knowledge architecture. These different representations in turn have significant consequences for the way we use these memories to guide later behavior. Puzzlingly, although stress has historically been argued to promote fragmentation, leading to disjoint memory representations, more recent work suggests that stress can also facilitate memory binding and integration. Understanding the circumstances under which stress fosters integration will be key to resolving this discrepancy and unpacking the mechanisms by which stress can shape later behavior. Here, we examine memory integration at multiple levels: linking together the content of an individual experience, threading associations between related but distinct events, and binding an experience into a pre-existing schema or sense of causal structure. We discuss neural and cognitive mechanisms underlying each form of integration as well as findings regarding how stress, aversive learning, and negative affect can modulate each. In this analysis, we uncover that stress can indeed promote each level of integration. We also show how memory integration may apply to understanding effects of alcohol, highlighting extant clinical and preclinical findings and opportunities for further investigation. Finally, we consider the implications of integration and fragmentation for later memory-guided behavior, and the importance of understanding which type of memory representation is potentiated in order to design appropriate interventions.

Updating functional brain units: Insights far beyond Luria

This paper reviews Luria's model of the three functional units of the brain. To meet this objective, several issues were reviewed: the theory of functional systems and the contributions of phylogenesis and embryogenesis to the brain's functional organization. This review revealed several facts. In the first place, the relationship/integration of basic homeostatic needs with complex forms of behavior. Secondly, the multi-scale hierarchical and distributed organization of the brain and interactions between cells and systems. Thirdly, the phylogenetic role of exaptation, especially in basal ganglia and cerebellum expansion. Finally, the tripartite embryogenetic organization of the brain: rhinic, limbic/paralimbic, and supralimbic zones. Obviously, these principles of brain organization are in contradiction with attempts to establish separate functional brain units. The proposed new model is made up of two large integrated complexes: a primordial-limbic complex (Luria's Unit I) and a telencephalic-cortical complex (Luria's Units II and III). As a result, five functional units were delineated: Unit I. Primordial or preferential (brainstem), for life-support, behavioral modulation, and waking regulation; Unit II. Limbic and paralimbic systems, for emotions and hedonic evaluation (danger and relevance detection and contribution to reward/motivational processing) and the creation of cognitive maps (contextual memory, navigation, and generativity [imagination]); Unit III. Telencephalic-cortical, for sensorimotor and cognitive processing (gnosis, praxis, language, calculation, etc.), semantic and episodic (contextual) memory processing, and multimodal conscious agency; Unit IV. Basal ganglia systems, for behavior selection and reinforcement (reward-oriented behavior); Unit V. Cerebellar systems, for the prediction/anticipation (orthometric supervision) of the outcome of an action. The proposed brain units are nothing more than abstractions within the brain's simultaneous and distributed physiological processes. As function transcends anatomy, the model necessarily involves transition and overlap between structures. Beyond the classic approaches, this review includes information on recent systemic perspectives on functional brain organization. The limitations of this review are discussed.

Overnight neuronal plasticity and adaptation to emotional distress

Expressions such as 'sleep on it' refer to the resolution of distressing experiences across a night of sound sleep. Sleep is an active state during which the brain reorganizes the synaptic connections that form memories. This Perspective proposes a model of how sleep modifies emotional memory traces. Sleep-dependent reorganization occurs through neurophysiological events in neurochemical contexts that determine the fates of synapses to grow, to survive or to be pruned. We discuss how low levels of acetylcholine during non-rapid eye movement sleep and low levels of noradrenaline during rapid eye movement sleep provide a unique window of opportunity for plasticity in neuronal representations of emotional memories that resolves the associated distress. We integrate sleep-facilitated adaptation over three levels: experience and behaviour, neuronal circuits, and synaptic events. The model generates testable hypotheses for how failed sleep-dependent adaptation to emotional distress is key to mental disorders, notably disorders of anxiety, depression and post-traumatic stress with the common aetiology of insomnia.

Mystery of the memory engram: History, current knowledge, and unanswered questions

The quest to understand the memory engram has intrigued humans for centuries. Recent technological advances, including genetic labelling, imaging, optogenetic and chemogenetic techniques, have propelled the field of memory research forward. These tools have enabled researchers to create and erase memory components. While these innovative techniques have yielded invaluable insights, they often focus on specific elements of the memory trace. Genetic labelling may rely on a particular immediate early gene as a marker of activity, optogenetics may activate or inhibit one specific type of neuron, and imaging may capture activity snapshots in a given brain region at specific times. Yet, memories are multifaceted, involving diverse arrays of neuronal subpopulations, circuits, and regions that work in concert to create, store, and retrieve information. Consideration of contributions of both excitatory and inhibitory neurons, micro and macro circuits across brain regions, the dynamic nature of active ensembles, and representational drift is crucial for a comprehensive understanding of the complex nature of memory.