bioRxiv Subject Collection: Neuroscience's Journal

Temporal shift in task factor influence across the stretch reflex
Mechanical perturbations applied to the arm can elicit reflexive actions. These rapid corrective responses include the stretch reflex, which consists of different components: the short-latency reflex (SLR) as well as the early and late long-latency reflex (LLR). In this study, we explore how different task factors dynamically influence these reflex components in the context of a specific delayed-reach paradigm. Using multiple linear regression (MLR), we analysed reflex responses from seven muscles actuating the right arm to examine the effects of mechanical load, preparatory delay, perturbation and target direction, as well as their two-factor interactions. The MLR analysis shows that our delayed-reach tasks engaged shoulder girdle muscles, whereas the biceps and triceps primarily acted as stabilizing muscles, with rapid responses triggered regardless of perturbation direction. Specifically, our analyses show that the earliest corrective response, the SLR, exhibited some task/target-dependent modulation particularly in muscles of the shoulder girdle, although background (pre-)loading decreased this modulation. The SLR was primarily influenced by the main factors Load and Perturbation, along with the interaction Load x Perturbation. Perturbations aligned with the load direction were associated with increased electromyographic (EMG) activity across all examined muscles. While there was a small but significant effect of load during the early LLR, this effect diminished by the late LLR epoch. Task-dependent modulation was most pronounced at the late LLR epoch, suggesting greater top-down modulation of this reflex component. In particular, the late LLR was shaped by the factors Perturbation and Target, as well as the interaction Perturbation x Target. Targets and perturbations in opposing directions resulted in heightened EMG activity, and shoulder muscles exhibited stronger LLR responses for targets located farther along the muscle shortening direction. Across all reflex epochs, a longer preparatory delay (750 ms) was associated with higher EMG activity.

Relationship between Brain and Body Temperature in Anesthetized Animals Measured by Ultralocal Thermometry
Temperature is one of the least studied biophysical characteristics of the brain, although both the rate of biochemical reactions and the electrical activity of nervous tissue directly depend on it. The purpose of this study was to analyze the relationship between brain and body temperatures in anesthetized animals. Simultaneous measurement of brain and body temperature (rectally) was carried out at ambient temperature controlled with a thermal mat. The temperature of the deep layers of the somatosensory cortex was measured by ultralocal thermometry using a diamond thermometer. Under anesthesia, the body and brain temperature dropped to 27 C (4 degrees above ambient temperature). When the thermal mat was turned on, the brain and body began to heat up synchronously. The brain initially lagged behind, but when the critical temperature was reached, it began to release heat in quantities exceeding the influx from the blood, reaching physiological values of 37C. A reverse experiment with decreasing the temperature of the thermal mat showed a similar picture: a synchronous start of the decrease, but with reverse dynamics. Thus, we can distinguish two phases of the brain's reaction to external heating: passive - when neuronal activity is decreased, and active - after internal regulatory mechanisms are triggered, which, in its turn, slows down the temperature drop. In general, the data obtained in the present work indicate that the temperature of neural tissue is not linearly related to body temperature.

Biophysical modeling of thalamic reticular nucleus subpopulations and their differential contribution to network dynamics
The burst firing mode of thalamic reticular neurons plays a pivotal role in the generation and maintenance of sleep rhythms and is implicated in sleep-related deficits characteristic of neurodevelopmental disorders. Although several models of reticular neurons have been developed to date, we currently lack a biophysically detailed model able to accurately reproduce the heterogeneity of burst firing observed experimentally. Using electrophysiology recordings of patch-clamped fluorescently tagged Spp1+ and Ecel1+ reticular neurons, we leverage a previously established statistical framework to introduce differentiation of cell types in model thalamic reticular neurons. We developed a population of biophysically detailed models of thalamic reticular neurons that capture the diversity of their firing properties, particularly their ability to generate rebound bursts. These models incorporate key ion channels, such as T-type Ca and small conductance potassium channels (SK), and enable systematic investigations into the impact of these channels on single-cell dynamics. By integrating these models into a thalamic microcircuit, we demonstrate that T-type Ca and SK channel conductances have opposing effects on spindle oscillations. We identify a simple relationship between these conductances and the peak firing frequency of spindles, maintained across circuits with mixed reticular neuron populations, providing a framework for understanding how ion channel expression influences thalamic network dynamics. Collectively, these models establish a foundation for relating intrinsic cellular properties of reticular cell populations to network-level activity in both healthy and pathological conditions.

Goal-Directed Learning in Cortical Organoids
Experimental neuroscience techniques are advancing rapidly, with major recent developments in high-density electrophysiology and targeted electrical stimulation. In combination with these techniques, cortical organoids derived from pluripotent stem cells show great promise as in vitro models of brain development and function. Although sensory input is vital to neurodevelopment in vivo, few studies have explored the effect of meaningful input to in vitro neural cultures over time. In this work, we demonstrate the first example of goal-directed learning in brain organoids. We developed a closed-loop electrophysiology framework to embody mouse cortical organoids into a simulated dynamical task (the inverted pendulum problem known as "Cartpole") and evaluate learning through specific training signals. Longitudinal experiments enabled by this framework illuminate how different methods of selecting training signals enable improvement on the tasks. We found that for most organoids, training signals chosen by artificial reinforcement learning yield better performance on the task than randomly chosen training signals or the absence of a training signal. This systematic approach to studying learning mechanisms in vitro opens new possibilities for therapeutic interventions and biological computation.

Behavioral and genetic markers of susceptibility to escalate fentanyl intake.
BackgroundThe "loss of control" over drug consumption, present in opioid use disorder (OUD) and known as escalation of intake, is well-established in preclinical rodent models. However, little is known about how antecedent behavioral characteristics, such as valuation of hedonic reinforcers prior to drug use, may impact the trajectory of fentanyl intake over time. Moreover, it is unclear if distinct escalation phenotypes may be driven by genetic markers predictive of OUD susceptibility.

MethodsMale and female Sprague-Dawley rats (n=63) were trained in a sucrose reinforcement task using a progressive ratio schedule. Individual differences in responsivity to sucrose were hypothesized to predict escalation of fentanyl intake. Rats underwent daily 1-h acquisition sessions for i.v. fentanyl self-administration (2.5 {micro}g/kg; FR1) for 7 days, followed by 21 6-h escalation sessions, then tissue from prefrontal cortex was collected for RNA sequencing and qPCR. Latent growth curve and group-based trajectory modeling were used, respectively, to evaluate the association between sucrose reinforcement and fentanyl self-administration and to identify whether distinct escalation phenotypes can be linked to gene expression patterns.

ResultsSucrose breakpoints were not predictive of fentanyl acquisition nor change during escalation, but did predict fentanyl intake on the first day of extended access to fentanyl. Permutation analyses did not identify associations between behavior and single gene expression when evaluated overall, or between our ascertained phenotypes. However, weighted genome correlation network analysis (WGCNA) and gene set enrichment analysis (GSEA) determined several gene modules linked to escalated fentanyl intake, including genes coding for voltage-gated potassium channels, calcium channels, and genes involved in excitatory synaptic signaling. Transcription factor analyses identified EZH2 and JARID2 as potential transcriptional regulators associated with escalated fentanyl intake. Genome-wide association study (GWAS) term categories were also generated and positively associated with terms relating to substance use disorders.

DiscussionEscalation of opioid intake is largely distinct from motivation for natural reward, such as sucrose. Further, the gene networks associated with fentanyl escalation suggest that engagement of select molecular pathways distinguish individuals with "addiction prone" behavioral endophenotypes, potentially representing druggable targets for opioid use disorder. Our extended in silico identification of SNPs and transcription factors associated with the "addiction prone" high escalating rats highlights the importance of integrating findings from translational preclinical models. Through a precision medicine approach, our results may aid in the development of patient-centered treatment options for those with OUD.

Perceptual choice and motor signals in mouse somatosensory cortex
Somatosensory cortex activity relates both to sensation and movement, reflecting their intimate relationship, but the extent and nature of sensory-motor interactions in the somatosensory cortex remain unclear. Here, we investigated perception-related sensory and motor signals in the whisker areas of mouse primary (wS1) and secondary (wS2) somatosensory cortices. We recorded neuronal activity while mice performed a whisker detection task using two alternative lickports, one each to indicate the presence or absence of a whisker deflection on a given trial. One group of mice reported the presence of the whisker stimulus by licking at the port on the same ("congruent") side of the animal as the stimulated whisker, whereas a second group of mice did so by licking at the opposite ("incongruent") side. Activity of single neurons in wS1 and wS2 correlated with perceptual choice. This choice-related activity was enhanced when responding to the congruent side. wS2 neurons projecting along two output pathways--to wS1 or to whisker secondary motor cortex, wM2--also showed choice-related activity, but differed in their dependence on congruence and in the effects of optogenetic manipulation. Thus, somatosensory cortex contains pathway- and action-specific choice-related activity.

Multimodal single-cell analyses reveal molecular markers of neuronal senescence in human drug-resistant epilepsy
The histopathological neurons in the brain tissue of drug-resistant epilepsy exhibit aberrant cytoarchitecture and imbalanced synaptic circuit function. However, the gene expression changes of these neurons remain unknown, making it difficult for the diagnosis or to dissect the mechanism of drug-resistant epilepsy. By integrating whole-cell patch clamp recording and single-cell RNA sequencing approaches, we identified a transcriptionally distinct subset of cortical pyramidal neurons. These neurons highly expressed genes CDKN1A (P21), CCL2 and NFKBIA that associated with mTOR pathway, inflammatory response and cellular senescence. We confirmed the expression of senescent marker genes in a subpopulation of cortical pyramidal neurons with enlarged soma size in the brain tissue of drug-resistant epilepsy. We further revealed the expression of senescent cell markers P21, P53, COX2, {gamma}-H2AX, {beta}-Gal and reduction of nuclear integrity marker Lamin B1 in histopathological neurons in the brain tissue of drug-resistant epilepsy patients with different pathologies, but not in control brain tissue with no history of epilepsy. Additionally, chronic, but not acute, epileptic seizures induced senescent markers expression in cortical neurons in mouse models of drug-resistant epilepsy. These results provide important molecular markers for histopathological neurons and new insights into the pathophysiological mechanisms of drug-resistant epilepsy.

Hypocretin receptor 1 blockade early in abstinence reduces future demand for cocaine
Relapse to cocaine use after abstinence remains a significant challenge for treating cocaine use disorder. While the mechanisms of relapse are still under investigation, adaptations in mesolimbic dopamine systems may contribute to cocaine craving and propensity for relapse. Current pharmacological treatments targeting dopamine systems are often intolerable and may have abuse potential. Therefore, identifying novel pharmacological targets for cocaine use disorder is crucial. The hypocretin/orexin system has been shown to regulate cocaine-associated behavior and dopamine transmission. Our previous studies indicated that the hypocretin receptor 1 antagonist, RTIOX-276, reduced motivation for cocaine and attenuated dopamine responses to cocaine. Importantly, the effects of RTIOX-276 on dopamine transmission persisted for at least 24 hours, suggesting lasting effects of hypocretin receptor antagonism. Here, we hypothesized that a single RTIOX-276 treatment would reduce motivation for cocaine and normalize dopamine transmission after abstinence. Rats were pre-assessed for cocaine consumption and motivation using a within-session threshold schedule before intermittent access exposure to cocaine. Rats were subsequently treated with RTIOX-276 on the first day of a 7-day abstinence period, after which they were reassessed for cocaine consumption and motivation or examined for dopamine transmission using fast-scan cyclic voltammetry in nucleus accumbens core slices. We found that a single treatment with RTIOX-276 on the first day of abstinence reduced motivation for cocaine and normalized aberrant dopamine uptake observed following intermittent access to cocaine. These findings suggest that hypocretin receptor 1 may be a viable target for reducing motivation for cocaine through alterations in dopamine transmission in the nucleus accumbens.

Development of a real-time neural controller using an EMG-driven musculoskeletal model
Here we present our development of a novel real-time neural controller based on an EMG-driven musculoskeletal model, designed for volitional control of robots and computers. Our controller uniquely enables motion control during both isometric and non-isometric muscle contractions. We address several key challenges in EMG control system design, including accuracy, latency, and robustness. Our approach combines EMG signal processing, neural activation dynamics, and Hill-type muscle modeling to translate neural commands into muscle forces, which can enhance robustness against electrode variability and signal noise. Additionally, we integrate muscle activation dynamics with impedance control, inspired by the human motor control system, for smooth and adaptive interactions. As an initial proof of concept, we demonstrated that our system could control a robot actuator across a range of movements, both static and dynamic, and at different operating speeds, achieving high reference tracking performance and state-of-the-art processing times of 2.9 ms, important for real-time embedded computing. This research helps lay the groundwork for next-generation neural-machine interfaces that are fast, accurate, and adaptable to diverse users and control applications.

Exercise-induced differential transcriptional output of AMPK signalling improves axon regeneration and functional recovery
In adulthood, the regenerative capacity of the injured brain circuit is poor preventing functional restoration. Rehabilitative physical exercise is a promising approach to overcome such functional impairment and the metabolic sensor AMPK has emerged to be a critical mediator for this. However, the mechanistic understanding of upstream and downstream components of AMPK signalling in the physical exercise-mediated enhancement of axon regeneration is not clear. We combined swimming exercise with laser axotomy of posterior lateral microtubule (PLM) neurons of Caenorhabditis elegans to address this question. We found that direct activation of AMPK through AICAR treatment is sufficient to improve axon regeneration and functional recovery. The PAR-4/Liver kinase B1 (LKB1) acts upstream of AMPK to enhance functional recovery following swimming exercise. Using genetics, tissue-specific RNAi, and AICAR treatment, we found that the transcriptional regulators DAF-16 and MDT-15 act downstream of AMPK in mediating the positive effects of swimming. We found that MDT-15 acts in neuron to mediate the benefit of AMPK activation in axon regeneration, whereas DAF-16 acts both in neuron and muscle to promote regrowth downstream to AMPK. We also showed that swimming exercise induces nuclear localization of DAF-16 in an AMPK-dependent manner. Our results showed that neuronal and non-neuronal arms of AMPK signalling play an integrative role in response to physical exercise to promote functional recovery after axon injury.

Significance statementFinding ways to promote functional recovery after accidental damage to the nervous system has been challenging as adult neurons lose the capability to regenerate. Rehabilitation therapy is the most promising approach to improve the health condition of patients with nervous system injury. Even in the roundworm C. elegans, axon regeneration could be enhanced through swimming exercise, which is mediated by the metabolic energy sensor AMP Kinase. In this study, using sensory neurons in worm, we found that PAR-4/ Liver kinase B1 acts upstream of AMPK. Whereas, the transcription factor DAF-16/ FOXO and the transcriptional co-regulator MDT-15 act as downstream signalling arms in muscle and neuron tissues. Excitingly, both of these arms could be harnessed through agonist-mediated activation of AMPK to promote functional recovery in adulthood.

Cross-sectional and longitudinal changes in category-selectivity in visual cortex following pediatric cortical resection
The topographic organization of category-selective responses in human ventral occipitotemporal cortex (VOTC) and its relationship to regions subserving language functions is remarkably uniform across individuals. This arrangement is thought to result from the clustering of neurons responding to similar inputs, constrained by intrinsic architecture and tuned by experience. We examined the malleability of this organization in individuals with unilateral resection of VOTC during childhood for the management of drug-resistant epilepsy. In cross-sectional and longitudinal functional imaging studies, we compared the topography and neural representations of 17 category-selective regions in individuals with a VOTC resection, a control patient with resection outside VOTC, and typically developing matched controls. We demonstrated both adherence to and deviation from the standard topography and uncovered fine-grained competitive dynamics between word- and face-selectivity over time in the single, preserved VOTC. The findings elucidate the nature and extent of cortical plasticity and highlight the potential for remodeling of extrastriate architecture and function.

TeaserAfter pediatric cortical resection, deviations from the constraints of standard topography in visual cortex reflect plasticity.

Hearing in Two Closely Related Peromyscus Species (Peromyscus maniculatus and P. leucopus)
The genus Peromyscus has been extensively used as a model for ecological, behavioral, and evolutionary investigations. We used auditory brainstem responses (ABRs), craniofacial morphology, and pinna measurements to compare characteristics that impact hearing in two wild-caught species, P. leucopus P. maniculatus. We observed significant statistical differences in craniofacial and pinna attributes between species with P. leucopus overall exhibiting larger features than P. maniculatus. ABR recordings indicated that both species showed similar best frequency thresholds between 8-24 kHz. We found significant effects of intensity on amplitude ratio of wave I and IV for P. maniculatus, but not P. leucopus and effects of wave number on slope of the latency-intensity function with higher wave IV and shorter wave I slope of latency intensity function in P. leucopus. Finally, the data showed significant differences in latency shift of the DN1 component of the BIC in relation to ITD between species, while no significant differences were observed across relative DN1 amplitude. This study supports the used of P. leucopus and P. maniculatus as future model species for auditory research.

Sneezing in response to bright light exposure: A case study in a photic sneezer
Background: The photic sneeze reflex (PSR) is a widespread, yet understudied phenomenon characterised by sneezing in response to bright-light exposure, reportedly affecting around 30% of the general population. Our goals were to collect real-world data to characterise PSR-inducing naturalistic light conditions, and to develop an indoor protocol to reliably induce the PSR in affected subjects using parametric stimuli. Methods: This study was carried out on one male adult affected by photic sneezing (n=1). To characterise naturalistic light conditions eliciting photic sneezing, real-world light exposure was measured over a 30-day period, while logging PSR events. To study photic sneezing in response to artificial stimuli, a setup including a multi-primary LED source and an integrating sphere was used to present 30-second light stimuli to the subject while collecting pupillometric data with an eye-tracker. Results: 82 photic sneeze events were recorded, with an average of 2.73 sneezes per day and a range of 1 to 6 sneezes per event. At a sneeze event, illuminance is on average ten times bigger than five minutes before the sneeze event. A significant increase in illuminance is observed around 2 minutes before the sneeze event. Light levels go back down to pre-sneeze levels within 10 minutes after sneezing. Despite exposure to more than 150 stimuli, no sneeze could be artificially induced in the subject. However, a strong tickling sensation was consistently reported, especially for high illuminance settings. Conclusions: Real-world light data confirmed that a sudden increase in environmental lighting conditions can induce photic sneezing. Further analysis could be relevant on instances of illuminance increments not eliciting a photic sneeze. The experimental setup only elicited tickling sensations, but with further testing and optimisation, it is reasonable to assume that it would reliably induce photic sneezes, thereby opening further mechanistic study of this intriguing phenomenon.

Age-related decline in neural phase-locking to envelope and temporal fine structure revealed by frequency following responses: A potential signature of cochlear synaptopathy impairing speech intelligibility
Assessing the contribution of cochlear synaptopathy (CS) to the variability in speech-in-noise intelligibility among individuals remains a challenge. While several studies have proposed biomarkers for CS based on neural phase-locking to the temporal envelope (ENV), fewer have investigated how CS affects the coding of temporal fine structure (TFS), despite its crucial role in speech-in-noise perception. In this study, we specifically examined whether TFS-based markers of CS could be derived from electrophysiological responses and psychophysical detection thresholds of spectral modulation (SM) in a complex tone, which serves as a parametric model of speech. We employed an integrated approach, combining psychophysical testing with frequency-following response (FFR) measurements in three groups of participants: young normal-hearing (yNH), older normal-hearing (oNH), and older hearing-impaired (oHI) individuals. We expanded on previous work by assessing phase-locking to both ENV, using a 4 kHz rectangular amplitude-modulated (RAM) tone, and TFS, using a low-frequency (<1.5 kHz) SM complex tone. Overall, FFR results showed significant reductions in neural phase-locking to both ENV and TFS components with age and hearing loss. Specifically, the strength of TFS-related FFRs, particularly the component corresponding to the harmonic closest to the peak of the spectral envelope (~500 Hz), was negatively correlated with age, even after adjusting for audiometric thresholds. This TFS marker also correlated with ENV-related FFRs derived from the RAM tone, suggesting a shared decline in phase-locking capacity across low and high cochlear frequencies. Computational simulations of the auditory periphery indicated that the observed FFR strength reduction with age is consistent with approximately 50% loss of auditory nerve fibers, aligning with histopathological data. However, the TFS-based FFR marker did not account for variability in speech intelligibility observed in the same participants. Psychophysical measurements showed no age-related effects and were unrelated to the TFS-based FFR marker, highlighting the need for further psychophysical research to establish a behavioral counterpart. Altogether, our results demonstrate that FFRs to vowel-like stimuli can serve as a complementary electrophysiological marker for assessing neural coding fidelity to stimulus TFS. This approach could provide a valuable tool for better understanding the impact of CS on an important coding dimension for speech-in-noise perception.

Selective Targeting of a Defined Subpopulation of Corticospinal Neurons using a Novel Klhl14-Cre Mouse Line Enables Molecular and Anatomical Investigations through Development into Maturity
The corticospinal tract (CST) facilitates skilled, precise movements, which necessitates that subcerebral projection neurons (SCPN) establish segmentally specific connectivity with brainstem and spinal circuits. Developmental molecular delineation enables prospective identification of corticospinal neurons (CSN) projecting to thoraco-lumbar spinal segments; however, it remains unclear whether other SCPN subpopulations in developing sensorimotor cortex can be prospectively identified in this manner. Such molecular tools could enable investigations of SCPN circuitry with precision and specificity. During development, Kelch-like 14 (Klhl14) is specifically expressed by a specific SCPN subpopulation, CSNBC-lat, that reside in lateral sensorimotor cortex with axonal projections exclusively to bulbar-cervical targets. In this study, we generated Klhl14-T2A-Cre knock-in mice to investigate SCPN that are Klhl14+ during development into maturity. Using conditional anterograde and retrograde labeling, we find that Klhl14-Cre is specifically expressed by CSNBC-lat only at specific developmental time points. We establish conditional viral labeling in Klhl14-T2A-Cre mice as a new approach to reliably investigate CSNBC-lat axon targeting and confirm that this identifies known molecular regulators of CSN axon targeting. Therefore, Klhl14-T2A-Cre mice can be used as a novel tool for identifying molecular regulators of CST axon guidance in a relatively high-throughput manner in vivo. Finally, we demonstrate that intersectional viral labeling enables precise targeting of only Klhl14-Cre+ CSNBC-lat in the adult central nervous system. Together, our results establish that developmental molecular delineation of SCPN subpopulations can be used to selectively and specifically investigate their development, as well as anatomical and functional organization into maturity.

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.

What are you talking about? Representation of the Topic of Speech in the Human Brain
A sentence outside the context provides very restricted information to the listener. Real understanding requires one to be able to place it within the sequence of sentences forming a coherent story and just as importantly, within ones general knowledge of the topic. Here, we demonstrate the existence of functional brain networks that are robustly sensitive to the topic of ca. 6-minute-long coherent newspaper articles. The main network hubs are located in the parietal and temporal brain regions. These networks changed very slowly during the course of the article, consistent with their involvement in representing the topic rather than the story aspect of the context. Because even the meaning of words can depend on the topic (see, e.g., the word shuttle in transportation and weaving), the topic-sensitive network must also be intimately linked with the mental lexicon underlying language comprehension.

Cognitive effort and reward. Functional imaging of time on task and the involvement of dopaminergic and cholinergic substrates
Numerous neuroimaging studies have identified the cortical network associated with sustained cognitive efforts and control and its modulation by rewards. Different lines of evidence implicate the prefrontal cortex (especially the anterior cingulum, ACC), dopaminergic, and cholinergic substrates in this modulation. To inquire about involvement of these substrates, we studied their activity at increasing time on task (providing increasing levels of cognitive effort) in trial blocks with differing reward levels. In the cortex, while peaking in the ACC, activity associated with time on task was found to be extensive, also including activity decrements outside the default mode network, primarily involving motor and somatosensory regions. Information about reward levels was carried in the ventral tegmental area and ventral striatum, consistent with their motivational role and previous studies, but did not reflect increasing time on task. Instead, parts of the ventral forebrain corresponding to the location of cholinergic Ch4 nuclei increased in activity with time on task and were sensitive to reward levels. This finding is consistent with a cholinergic role in driving compensatory efforts modulated by reward levels, while dopaminergic substrates track levels of expected rewards irrespective of required sustained attention efforts. These findings identify a distinct neuroimaging phenotype associated with sustaining task sets and cognitive efforts.

All ribosomal RNAs and 45S spacers from humans to worms are packed with organism-specific motifs whose other copies are found predominantly in numerous nervous system genes including many associated with human disorders
The nucleotide sequences of ribosomal RNAs (rRNAs) and the spacers of 45S are tuned to fulfill optimally their respective roles during ribosome biosynthesis and function. We report that these sequences satisfy additional genome-wide constraints in humans, mice, fruit flies, and worms. In all four organisms, the rRNAs and 45S spacers are densely packed with organism-specific nucleotide motifs with many additional identical copies throughout the genome. The human rRNAs and 45S spacers contain 1,723 motifs whose sequences are unique to the rRNAs/spacers of primates. These motifs have numerous additional exact intronic and exonic copies whose genomic placement is also unique to primates. Specific combinations of the motifs appear exclusively in 3,430 human nervous system and developmental genes, including 1,046 risk genes for autism, schizophrenia, and bipolar disorder. RNA/RNA crosslinking experiments show that the rRNA/spacer motifs are contact points for rRNA-mRNA and mRNA-mRNA heteroduplexes. RNA binding protein (RBP) assays show that these motifs are also in the binding sites of 113 RBPs. RNA sequencing reveals that rRNAs and spacers produce endogenous small non-coding RNAs (sncRNAs) that carry the same primate-specific motifs. Lastly, the motifs' intergenic and intronic copies overlap 131 GWAS polymorphisms associated with neuropathologies (p-val<3.9e-12). The findings suggest that the motifs facilitate RNA/RNA and RBP/RNA interactions that are affected by polymorphisms and modulated by rRNA- and spacer-derived sncRNAs carrying the same motifs. Our study also genetically links for the first time rRNAs and 45S spacers to autism and other typically human neurological disorders. Mutation panels based on these motifs can lead to new molecular diagnostics for these disorders, whereas snRNAs carrying these motifs can serve as drugs or potential therapeutic targets.

Cell type mapping of mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy using single-nucleus multiomics
Objective Mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE) are brain lesions associated with focal epilepsy and characterized by increased oligodendroglial density, heterotopic neurons, and hypomyelination in the white matter. While previous studies have implicated somatic mutations in the SLC35A2 gene, the cellular and molecular mechanisms underlying MOGHE pathogenesis remain elusive. To address this gap, this study aimed to systematically characterize the cell type composition and molecular alterations of MOGHE lesions at cellular resolution using single-nucleus multiomics profiling. Methods We performed single-nucleus multiomics sequencing to obtain paired gene expression and chromatin accessibility profiles of > 31,000 nuclei from gray matter and white matter regions of MOGHE lesions, and compared the results with publicly available neurotypical control datasets. Results The analysis of gray and white matter regions from two MOGHE patients revealed significant cellular composition alterations, including an oligodendrocyte expansion and heterotopic neurons within the subcortical white matter. We identified a distinct population of MOGHE-associated oligodendrocytes characterized by expressing genes related to immune response, myelination disruption, and epilepsy-related pathways. These oligodendrocytes shared a common transcriptional signature with oligodendrocytes in other neurological conditions involving white matter abnormalities. Further analysis of heterotopic neurons in MOGHE revealed the upregulation of genes associated with neuronal migration and the Wnt signaling pathway, suggesting a mechanism underlying their atypical localization. Significance This high-resolution cell type mapping of MOGHE lesions in clinical samples unveils neuronal and glial populations affected by the disease, and provides novel insights into the pathophysiological mechanisms of MOGHE.