iScience

Instrumental learning typically requires hundreds to thousands of trials in which subjects learn to link motor responses to sensory cues. In standard rodent protocols, response accuracy is reported only at trial end, preventing subjects from correcting erroneously initiated responses. We hypothesized that within-trial, closed-loop sensory feedback would accelerate instrumental learning by providing real-time information about response correctness. Head-fixed mice performed a two-alternative forced-choice task by rotating a choice wheel in response to sensory cues. Mice received either no feedback (n = 18), auditory feedback (n = 16), or audiovisual feedback (n = 4) coupled to wheel movements. Feedback-receiving mice required significantly fewer trials to reach 70 % accuracy criterion (median: 3186, 4918 and 7329 trials for multimodal, unimodal and no feedback, respectively; p = 0.0245) and showed higher accuracy when modifying choices (expert stage: 17 %, 11 % and 9 % accuracy in trials with modified choices for multimodal, unimodal and no feedback, respectively; p=1.04x10-). Only feedback mice displayed movement refinements across training (p = 8.02x10-, p = 4.07x10-{superscript 1} and p = 0.2602 for multimodal, unimodal and no feedback, respectively). In summary, closed-loop sensory feedback accelerated instrumental acquisition, demonstrating its value as routine training protocol. HIGHLIGHTSO_LIMice provided with feedback require fewer trials to reach expert stage in an instrumental learning task C_LIO_LIMice provided with feedback perform with higher accuracy in trials involving changes of mind C_LIO_LIMovement trajectories of mice provided with feedback undergo refinement as training advances C_LIO_LISensory feedback can be used as a training aid to accelerate instrumental learning C_LI

The intrauterine environment has traditionally been viewed as a privileged site protected by the placental barrier. However, emerging evidence suggests that early in utero microbial exposure may prime the developing fetal immune system. Here, using target-enriched metagenomics and high-dimensional proteomics, we characterized the intra-amniotic viral landscape and immune networks in 114 healthy pregnancies including both normal and anomalous fetuses. We identify a sparse yet heterogeneous human viral signature in 26% of samples, predominantly composed of Herpesviridae, Polyomaviridae, and Picornaviridae. Although viral reads abundance was associated with fetal abnormalities, viral detection generally did not induce overt inflammatory activation, supporting a state of immune homeostasis within the amniotic cavity. Instead, viral presence was associated with subtle and selective immune modulation, including altered inducible antimicrobial peptide expression (HBD-2 and HBD-3), coupled with an attenuation of regulatory cytokines. Our results further reveal that the amniotic immune environment is primarily governed by gestational age, transitioning from a Th1-predominant "alert" phase to innate-readiness preceding parturition. These findings suggest that fragments of viral genetic material within the amniotic cavity may contribute to fetal immune instruction without triggering overt inflammation, providing a foundational framework for understanding how "silent" viral-exposure during gestation influences the developmental origins of neonatal immunity.

The neural system at the periphery is a frontline for embodied cognition, yet an acute, mild perturbation to dissect functional causality is hard to achieve. Peripheral neural processes and the central nervous system may work in concert to generate sophisticated representations regarding self and environments in the brain. This hypothesis, together with the underlying mechanisms, is particularly difficult to test for certain sensory inputs due to the lack of reversible manipulation techniques. Long postulated as a component for path integration, proprioception is one of such modalities. In this study, we developed a murine experimental system to manipulate proprioceptive inputs during memory-dependent localization task (which required precise operant-conditioned licks) in spatial virtual reality (VR). Through bioluminescent optogenetics (luminopsin) selectively expressed in the parvalbumin-positive neurons of the dorsal root ganglia in mice, proprioceptive processing was compromised directly from the periphery to bypass the bottleneck of specific central targeting, which results from the lack of anatomically or genetically dedicated proprioceptive circuits in the brain. In-vivo IVIS imaging and behavior suggested the effects of luminopsin last for roughly 20 minutes. While mice exhibited normal performance in tasks relying on gross motor skills, they showed subtle deficits in challenging spatial tasks that required integration of past movements. These observations support a task-specific role for proprioception, and demonstrate a potential of chemogenetics-like, rapidly reversible strategies for characterizing peripherally defined sensory contribution to spatial cognition. Future work will optimize this approach; for instance, to activate opsins by light with millisecond precision. To our knowledge, this is a first causal demonstration for acute participation of proprioception in path-integration biomechanics, enabling the first temporally defined method for mild perturbation of path-integration mechanisms.

In mammalian cells, under normal circumstances, the p53 protein exhibits oscillatory dynamics in response to DNA damage and maintains the cells in a cell-cycle-arrested state. Intriguingly, some cells can escape this cell-cycle-arrested state even after prolonged DNA damage, and often undergo mitotic catastrophe. In this context, the precise role of p53 dynamics and its complex interplay with cell-cycle regulation remain poorly understood. Herein, by constructing a comprehensive network model, we have identified crucial crosstalk regulations between the p53 protein and key cell-cycle regulators that enable some cells to escape cell-cycle arrest during prolonged DNA damage. The model further illustrates a probable cellular mechanism underlying mitotic catastrophe and predicts ways to induce it in a therapeutically relevant manner.

Cellular adaptation to nutrient fluctuation is a fundamental biological process, crucial to cell fate, function, and survival. The choice between aerobic glycolysis and oxidative phosphorylation does not merely satisfy energetic requirements but actively shapes the cellular stress responses. Here we report that during the complex metabolic programming of CD8+ T cells, glucose utilization pathways correlate with the speed and nature of the response to glucose withdrawal. By quantitating systematic RNA-protein interactions in response to glucose withdrawal, we found that effector T cells mount acute transcriptional and post-transcriptional responses to the stress, while memory T cells exhibit slower, more limited responses. The functional dichotomy observed in T cells - between highly glycolytic cytotoxic effector cells and respiratory memory cells - exemplifies how distinct glucose utilization pathways impact immunological fate and function. Understanding the intricate interplay between metabolic modality, glucose pathways, and post-transcriptional control is crucial for deciphering environment adaptations and developing interventions in contexts ranging from immunotherapy to cancer biology.

Human neurons develop more slowly than non-human primate (NHP) neurons, a phenomenon called neoteny, but research has primarily focused on neuron-intrinsic drivers. We hoped to further elucidate any species-specific divergence in function and the astrocytes role in influencing species-specific neurodevelopment rate. In this study, we identified a delayed onset of gliogenesis in human versus NHP organoid models. Transcriptomic and 13C metabolic flux analyses of iPSC-derived astrocytes revealed distinct metabolic profiles: NHP astrocytes exhibit increased serine and glycine synthesis, whereas human astrocytes show elevated lactate secretion, suggesting a change in the metabolic role of astrocytes across primate evolution. We then assessed the impact of these different species astrocytes on neuronal development. We observed an increase in electrophysiological maturation and a change in transcriptomic neuronal development trajectory in human neurons cultured with rhesus astrocyte conditioned media as opposed to human astrocyte conditioned media. Human astrocyte secretomes were enriched for synaptogenic and axon-growth proteins, which could indicate they play a greater role in supporting structural complexity and dendritic arborization over rapid maturation when compared to NHP astrocytes. Finally, chemical inhibition of PHGDH demonstrated that these changes in neuronal differentiation are partially mediated by the different metabolic roles that astrocytes play in humans versus NHPs. Collectively, our results reveal a cell-extrinsic role for astrocyte metabolism in shaping human-specific neurodevelopmental timing and trajectories. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/737608v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@ad88f4org.highwire.dtl.DTLVardef@fa5cf5org.highwire.dtl.DTLVardef@ecf0eborg.highwire.dtl.DTLVardef@1bcf078_HPS_FORMAT_FIGEXP M_FIG C_FIG

Herbivore insects are on an evolutionary tug-of-war with plants. An important part of the plant-herbivore insect interaction is the exchange of molecules, in particular proteins (in the form of effectors) and RNA. Among RNAs, small RNAs have been identified as important molecules shaping the communication between different pests/parasites and their host, but the role of these molecules in the interaction between aphids and plants is not well understood. Here, we explored the role of aphid-derived sRNAs in the interaction between Arabidopsis thaliana and the green peach aphid, Myzus persicae. Using sRNA sequencing, we identified a significant amount of bona-fide aphid-derived sRNAs within Arabidopsis tissues. Using immunoprecipitation followed by sRNA sequencing and degradome sequencing we determined that these sRNAs are incorporated into endogenous AGO proteins, in particular AGO1, and induce the cleavage of transcripts involved in the modulation of the immune response against the aphid. Our results indicate that aphid sRNAs attenuate the immune response of Arabidopsis thaliana and can improve aphid performance. In addition, we identified that aphid-derived sRNAs are commonly injected into other aphid-host combinations. Accordingly, our work indicates that aphid-derived sRNAs are active players in aphid-host interactions.

Coordinated dynamics between individuals are a hallmark of social interaction, yet the temporal structure and physiological basis of such coupling beyond human species remain poorly understood. Here, we investigated cross-species biobehavioral synchrony by simultaneously quantifying motion dynamics and autonomic activity with hyperscanning of human-canine dyads. We observed both spontaneous and task-related synchrony across motion dynamics, heart rate, and heart rate variability at multiple timescales. Importantly, synchrony was modulated by individual and relational factors. Task-related autonomic synchrony was affected by the human temperament, whereas greater familiarity within the dyad altered the leader-follower dynamics, shifting directional influence from human-led toward canine-driven coordination. Motion synchrony emerged with minimal delay, whereas cardiac synchrony unfolded across longer timescales, suggesting coordinated processes underlying the shared activity, arousal, and autonomic regulation. Our findings extend current models of social synchrony beyond human interactions and reveal that regulatory dynamics underlying coordinated behavior operate across species boundaries.

Primates are distinguished by large brains relative to body size, with humans showing the greatest expansion. This increase in brain size evolved alongside advanced cognitive abilities as well as an elevated energetic demand. Importantly, allometric scaling alone does not explain this increased metabolic requirement, suggesting that other cellular mechanisms may be driving the unique energetic capacity of the human brain. Brain metabolism is critical for neurological function by providing the energy necessary for neuron firing. Much of metabolism in the brain is carried out by astrocytes: a type of glial cell that have long been viewed as passive support cells for neurons. More recent research has highlighted the unique roles of astrocytes in many critical neurological processes; however, it is less understood how astrocytes differ among species. To better characterize this, we developed a cross-species co-culture model of astrocytes and neurons from human or chimpanzee-derived iPSCs. This co-culture system allowed us to assess cell-type specific effects as well as species-specific differences in cellular interactions that may be driving overall differences in brain metabolism. We conducted single-cell RNA-sequencing as well as Seahorse XF Mitochondrial Stress tests and observed that human neural co-cultures are more metabolically active than chimpanzee neural co-cultures. Cross-species co-culture systems also highlight that astrocytes are driving major species differences in metabolism, whereas neurons are highly responsive to astrocytic activity. We conclude that both neurons and astrocytes have evolved differently across primates, and that metabolic interactions between these cell types are key contributors in primate brain evolution.

Social hierarchies are a nearly universal feature of animal groups, but whether dominance reflects a single generalized trait or a collection of context-specific competitive abilities remains unclear. Here, we assess social hierarchy in three strains of laboratory mice (BALB/c, C57BL/6, and Shank3B knockouts) of both sexes using three established paradigms: the tube test, the warm spot assay, and the void spot assay. Hierarchies emerged in all strains and both sexes across all three assays, but how animals established rank differed markedly by strain and sex. In the tube test, Shank3b-/- knockout females, but not males, lacked the winner effects seen in wild-type mice, indicating that the ability to build a winning streak depends on social recognition in a sex-specific manner. In the warm spot assay, females formed stronger hierarchies than males, particularly among mice on a C57BL/6 background, with high-ranking females actively displacing others from the warm platform. In the void spot assay, BALB/c mice of both sexes frequently displayed territory-marking behavior, a pattern that was less common in the other strains. Overall, individual rank rarely generalized across domains, despite high trial-to-trial repeatability for individuals within each assay. Together, these findings indicate that mice behave as dominance specialists rather than generalists, with strain- and sex-specific strategies for establishing rank in different competitive contexts, suggesting that distinct neural circuits likely underlie these separable components of competitive ability.

Evolutionary success in mammals requires coordinated regulation of cognitive functions and reproductive capacity. Such coordination must involve shared genes and molecular pathways between the brain and germ cells, yet direct evidence linking cognition to reproduction across species remains limited. Here, proteomic and transcriptomic analyses were performed experimentally in Ovis aries and Rattus norvegicus, while transcriptomic datasets from Mus musculus, Macaca mulatta, and Homo sapiens were analyzed in silico. We identified 8,464 protein-coding genes shared between the brain and sperm/testis and conserved across five species. In rats, 8,444 of these genes were also shared between the brain and the ovary. Functional annotation classified 3,890 genes as associated with both neurological and reproductive functions, and 1,752 as uncharacterized in these contexts, highlighting candidates for future studies on reproductive and neurological disorders. These findings reveal a deeply conserved genetic network linking neurological and reproductive systems, underscoring the evolutionary interplay that supports mammalian fitness.

The blood brain barrier (BBB) tightly regulates the interface between the central nervous system and the systemic circulation. The function of the BBB is the output of an architecturally complex, multicellular neurovascular unit that consists of brain microvascular endothelial cells, pericytes, astrocytes, microglia and parenchymal neurons. Dysfunction of the BBB has been linked to numerous neurological diseases, such as multiple sclerosis, Alzheimers Disease, traumatic brain injury/chronic traumatic encephalopathy and stroke. Also, the control of the BBB over permeability makes it an ongoing interest and target for pharmaceutical development. Herein we present Blood Brain Barrier Agent-based Model (BBBABM), the first computational model that mechanistically represents the cellular components of the neurovascular unit and the molecular interactions that govern the response of the BBB to injury/activation, including the restorative functions that provide baseline homeostasis regarding the health of the BBB. Simulation experiments with the BBBABM replicate expected dynamics of disruption and restoration that demonstrate a dose responsiveness to the severity of the initial insult. The development of the BBBABM provided insight into the contribution of various forms of cellular-molecular responses to overall BBB dysfunction, including integrating across time scales from minutes to weeks. This initial implementation of the BBBABM offers numerous future paths for development, including being able to mechanistically represent the long time scales (years/decades) present in the pathophysiology of chronic neurological diseases and providing a platform to enhance therapeutic development via in silico trials and as the basis for mechanistic cellular-molecular Digital Twins.

The circadian clock regulates diverse cellular processes, including intestinal epithelial cell (IEC) proliferation. However, mechanisms regulating clock-dependent IEC differentiation remain unknown. We performed a time course RNA-Seq using the mouse small intestine and identified NOTCH signaling, a key mechanism regulating IEC differentiation, as one of the pathways under the control of circadian rhythms. Using mouse enteroids, we discovered that a NOTCH reporter, Hes1-luciferase, exhibits both ultradian or circadian oscillations depending on the stemness of mouse enteroids. Furthermore, single-cell analysis of Hes1-mCherry revealed that the period of Hes1 oscillations varies widely, but circadian rhythms modulate the number of Hes1-mCherry+ cells in the population. Finally, we show that Paneth cell numbers fluctuate over the circadian cycle, suggesting that circadian clock-regulated Hes1 drives the circadian dynamics of IEC composition. Our study provides a deeper insight into circadian regulation of IEC differentiation, which will be critical for applications of chronotherapies for digestive diseases.

Drosophila connectomic datasets provide increasingly comprehensive maps of neuronal morphology and synaptic connectivity, offering an unprecedented opportunity to explore the structural organization of its neural circuits. This calls for designing automated tools to interact with connectomic datasets at scale for efficiently exploring structural features embedded in the vast amount of data. Yet the central challenge remains the understanding of the functional logic of neural circuits. In order to understand how elements of the functional logic may emerge from this structural organization, it is critical to (i) characterize the objects in the natural environment in which brain circuits operate, and (ii) formulate how brain circuits represent and process the defined objects in the natural environment. To develop and demonstrate a methodology for these requirements, we focus on the Drosophila looming-evoked escape pathway. We modeled the trajectory of looming objects that are on a collision course (direct-hits) or pass-by the fly (near-misses): their projected images on the retina can be characterized by the solid angle (angular size) and elevation. We then analyzed the pathway's morphology across the OpticLobe, Hemibrain, and FlyWire connectome datasets. By abstracting their sub-neuronal structure and retinotopic organization, we constructed an executable circuit model that maps each structural element to a processing block. We demonstrate that this model separates direct hits from near misses well before the angular size could tell them apart. To accelerate the connectomic analysis step, we developed a Python toolset with an agentic, code-free workspace interface called NeuroGraphBench (NGB). NGB provides four composable morphology-analysis primitives and an AI agent that composes them to interactively respond to natural-language queries aided by visualization on an interactive 3D canvas. Thus, NGB automates tedious and repetitive tasks to enable faster and scalable connectomic exploration, keeping human reasoning, instead of writing code, at the center of an open-ended research inquiry.

Neutrophil swarming enables the coordinated recruitment of large numbers of cells to sites of infection. Although reactive oxygen species (ROS) are key mediators of neutrophil function, their dynamics during collective behavior remain poorly defined. Here, we developed a 3D ex vivo swarming system combined with HyPer7-expressing dHL-60 cells to visualize intracellular hydrogen peroxide (H2O2) dynamics in real time at single-cell resolution. This approach enabled us to reliably measure NADPH oxidase 2 (NOX2) activity during neutrophil swarming, revealing dynamic H2O2 production. We show that H2O2 production is spatially confined to cells at the stimulation site and temporally coupled to swarming initiation and distal cell recruitment. ROS production depends on NOX2 activity and calcium signaling but is not required for swarm formation or amplification. Notably, H2O2 accumulation was detected throughout activated cells rather than being restricted to phagosomes, suggesting a broader intracellular oxidative response. Together, these findings reveal a coordinated oxidative program associated with neutrophil swarm initiation and raise the possibility that ROS contribute to signaling functions beyond their established role in phagocytosis.

Caenorhabditis elegans, like other animals, relies on attractive odours for foraging and on aversive odours for avoidance of pathogens. An odour produced by pathogenic bacterium Pseudomonoas aeruginosa induces immune response as well as avoidance in C. elegans via AWB olfactory neurons. We asked whether AWB neurons provide broader immunity to a wide range of pathogens. We activated AWB neurons using three chemically distinct bacterial odours and found that activation indeed induces protective immunity. Conversely, silencing of AWB neurons early during infection enhances susceptibility to infections. Mechanistic investigation revealed that the activation of AWB using odours upregulates detoxification pathways and other protective pathways in non-neuronal tissues. Specifically, odour exposure activates UDP-glucuronosyltransferase UGT-18 in the intestine that protects worms from the phenazine toxin of Pseudomonas aeruginosa and promotes broader immunity to Gram-negative bacteria (P. aeruginosa and Salmonella enterica), Gram-positive bacteria, (Enterococcus faecalis and Staphylococcus aureus), and yeast (Cryptococcus neoformans). Altogether, our findings highlights microbial odours as non-canonical molecular patterns for activating immune responses.

Scaffold-organized multi-protein complexes are major drivers of cellular regulatory pathways, but how the expression of their constituent genes is coordinated to support efficient assembly and cell-to-cell homeostasis remains poorly understood. Using snapTotal-seq data, this study addresses this issue at the transcription level through comparative analyses of stochastic transcription bursting - a major driver of expression level and primary source of its intrinsic cell-to-cell noise. We compared scaffold proteins and their effector partners in major regulatory multi-protein complexes: TNRC6A/B/C (in the miRISC complex) and CNOT1/2 (in the CCR4-NOT complex) in mRNA regulation; and AXIN1, APC, KSR2, AKAPs, DLG1, PATJ, HOMER1/2, and SQSTM1 in signal transduction. Our analyses reveal a shared strategy: compared to genes for active effector partner proteins and the general transcriptome, genes for structural scaffold proteins consistently utilize more frequent and smaller-sized bursting to achieve the fine tuning of a homeostatic expression level. This finding establishes a fundamental link between a proteins physical role within a regulatory complex and the transcriptional bursting kinetics of its gene.

Spaceflight imposes unique physiological stresses on mammals, including microgravity and cosmic radiation, which drive complex molecular adaptations. However, the systemic and temporal dynamics of space-induced epigenetic regulation remain poorly understood. We constructed a comprehensive DNA methylome BodyMap across 12 organs or tissues from mice exposed to long-duration spaceflight across three time points using Reduced Representation Bisulfite Sequencing (RRBS). We also performed RNA-seq for five organs and integrated with DNA methylome. We mapped the methylome and transcriptome landscapes and found that spaceflight induces limited but highly tissue-specific differentially methylated CpGs (DMCs). Most spaceflight-induced methylation changes were reverted toward baseline within one to six months of post-flight. Functional enrichment analysis of DMCs highlighted metabolic and mitochondrial dysregulation commonly across organs, while developmental responses in immune, reproductive, and structural tissues were tissue-specific. Transcriptome data revealed that spaceflight suppressed immune and increased inflammatory responses at the multi-organ level, triggering a phenomenon resembling aging. Our study provides a comprehensive DNA methylome BodyMap across 12 organs/tissues in spaceflight mice, elucidating the tissue specificity of epigenetic changes. These insights are essential for developing biomarkers and countermeasures to safeguard astronaut health during extended missions.

Spontaneous behaviors, e.g., walking and speaking, are thought to rely on an internal sense of time that provides a scaffold for precise temporal coordination. Yet the endogenous rates of many behavioral processes often diverge from the arbitrarily defined unit of objective time (Chronos), raising a fundamental question: what temporal reference frame coordinates behavior? Recent theoretical work (Buzsaki, 2026) proposed the rich repertoire of subjective time (Kairos) to fluctuate in function of a dynamic cross-frequency architecture linking body-brain periodicities along a lognormal linear progression in the frequency domain. Withing this framework, an emergent sense of time may regulate the rate of semi-periodic behaviors. Using high temporal resolution multimodal recordings, we show that endogenous body-brain periodicities, including pupil fluctuations, saccadic eye movements, respiration, cardiac activity and neural oscillations, as well as spontaneous behaviors such as tapping, walking, and speaking, are organized as an arithmetic progression in a natural logarithmic frequency space. This observation suggests that a unified scaling law may coordinate complex, multi-scale interactions across biological and behavioral timescales. We propose that such organization may provide an emergent temporal reference frame that scaffolds perception and action.

Circadian rhythms temporally regulate immune cell trafficking, abundance, and immune responsiveness in adults, yet how this rhythmic organization emerges during postnatal development remains unknown. Here, we systematically investigated the establishment and development of circadian immune regulation across multiple biological levels. Leukocyte rhythmicity was not present at birth but was gradually established and strengthened during postnatal development in a leukocyte subset-dependent manner. In parallel, promigratory markers displayed dynamic and heterogeneous developmental trajectories, indicating progressive coordination of rhythmic promigratory programs. At the systemic level, peripheral clocks matured and synchronized during development, with tissue- and clock-gene-dependent differences in the acquisition timing, peak phase, and amplitude of circadian oscillations. This multi-level analysis identifies postnatal development as a dynamic period during which circadian immunity is progressively consolidated through leukocyte rhythmicity, regulation of promigratory factors, and peripheral clocks.