Biology subjects

Deisseroth, K.

Publications and source records attributed to Deisseroth, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Coevolutionary mining of prokaryotic non-coding elements with a genome language model

Microbial genomes encode compact molecular machines and diverse non-coding RNAs (ncRNAs) essential to gene regulation, pathogenesis, and many foundational biotechnologies. However, annotation remains largely protein-centric and homology-driven. Here, we introduce Minerva, a framework for coevolutionary mining that uses genome language models to predict local interactions directly from sequence as two-dimensional maps. Introducing two complementary techniques, categorical Jacobian fingerprinting and interaction heads, we demonstrate fast, accurate, alignment-free prediction of ncRNA base-pairing, monomeric protein contacts, and repetitive sequence motifs. Applied to 150 bacterial genomes, Minerva recovers known systems and predicts that 84.3% of predicted intergenic base-pairing falls outside of known annotations. In Pseudomonas, we find that the widespread TwoAYGGAY ncRNA family carries large secondary-structure extensions and is often flanked by short upstream repetitive motifs and larger downstream genomic repeats. Interpreting the coevolution maps, we find that Minerva emergently detects open-reading-frame (ORF) signatures at the DNA level despite never being trained to do so. In prophages within these genomes, we discover that Unknown Group 27 (UG27) reverse transcriptase systems encode arrays of structurally conserved yet sequence-diverse ncRNAs that template complementary DNA (cDNA) hairpin products. Together, these results establish coevolutionary mining as a scalable route to genome annotation and biological discovery across the rapidly expanding microbial universe.

bioinformatics↗

bioRxiv2026

Diffusion MRI Tractography Predicts Electrophysiological Connectivity and Explains Spectral Signatures of Evoked Potentials in the Human Brain

White matter fiber bundles are the structural conduits of information flow in the human brain and thereby mediate the spatial trajectories and timings of the electrophysiological signaling. Here, we combined diffusion magnetic resonance imaging (dMRI) and stereoelectroencephalography (SEEG) recordings in neurosurgical patients to develop an integrated framework for predicting and interpreting causal electrophysiological connectivity patterns between pairs of brain regions. We used repeated single-pulse electrical stimulation in 40 participants implanted with a total of 5794 intracranial electrodes throughout the human brain, encompassing both cortical and multiple thalamic nuclei. A nonlinear, time-frequency manifold learning approach was used to define electrophysiological connectivity, which was then compared with subject-specific and atlas-based structural connectivity. Across 150,000 electrode pairs, we found that the presence of a structural connection predicted causal electrophysiological connectivity with a probability of ~0.95; and its absence predicted the lack of the direct electrophysiological connectivity with a probability of ~0.8. We also show evidence of indirect/polysynaptic pathways supported by both modalities and reported neural features from time-frequency decomposition that distinguished between direct and indirect signaling. We demonstrated that an early phase-locked broadband component (10-70 ms) marked direct structural pathways, whereas delayed and slower components reflected indirect propagation. Notably, we reported that thalamic involvement within an indirect pathway results in increased latency (> 200 ms) and enhanced late oscillatory behavior, despite increased conduction velocity measures along thalamo-cortical pathways. Therefore, our multimodal framework maps human brain connectivity, bridging structural architecture, causal electrophysiological dynamics, and network-level communication.

neuroscience↗

bioRxiv2026

Hippocampo-septal inhibitory feedback controls the medial septal circuit as a function of brain state, pyramidal cell activity and movement speed.

Encoding novel experiences and retrieving stored information rely on the hippocampal theta rhythm in several mammalian species. Coordination of putative pacemakers in the medial septum (MS) by the GABAergic hippocampo-septal (HS) feedback is hypothesized to be essential for theta genesis. In order to reveal how the HS-feedback controls the MS circuit, and through it hippocampal oscillations in general, we set out to uncover the behavior-related activity of HS neurons as well as how different components of the MS network are regulated by the HS-feedback. Utilizing computational modelling and in vivo optogenetic manipulation of the HS pathway, we show that the HS feedback is not required for theta generation, which is primarily governed by intra-MS connections. HS blockade did not alter the phase coupling of MS neurons to hippocampal theta rhythm nor the synchrony between rhythmic MS neurons but augmented ongoing theta and coupled mid-gamma oscillations in the hippocampus. By contrast, correlated activity between non-rhythmic MS neurons was sensitive to HS blockade. Moreover, the HS feedback scaled with hippocampal activity and running speed. In turn, modulation of MS neurons by running and ripples was diminished by the transient suppression of HS terminals. These findings suggest that the HS feedback exerts inhibitory control of the MS depending upon hippocampal output and movement speed.

neuroscience↗

bioRxiv2026

AAV delivered lysosome-targeting chimeras mediate sustained antibody depletion in vivo

Immunoglobulin G (IgG) is a critical effector of the adaptive immune system, but IgG autoantibodies against self-antigens drive pathology across a wide range of autoimmune diseases. Lowering circulating IgG is a validated and promising therapeutic avenue. Here we developed genetically-encoded lysosome targeting chimeras (GELYTACs) that target circulating IgGs for clearance and degradation. The GELYTACs comprised two protein modules derived from insulin-like growth factor 2 (IGF2) and an IgG-binding nanobody, respectively, and mediated clearance of plasma IgG via the lysosomal trafficking receptor IGF2R. To achieve long-lasting IgG depletion, we encoded GELYTACs in an AAV gene therapy vector and established continuous expression in mice. We also developed conditional GELYACs that are activatable with disease-specific proteases or small molecule drugs and show that GELYTACs can be secreted from cellular therapies. This work establishes GELYTACs as a possible therapeutic modality that is deliverable using genetic medicine approaches.

synthetic biology↗

bioRxiv2026

Ultrasensitive voltage imaging reveals distinct electrical microdomains in neurons

For the brain to compute, electrical signals must propagate over the membranes of individual neurons, connecting synaptic inputs to synaptic outputs1. Complex neuronal morphologies coupled with the spatial organization of synaptic inputs and outputs enable diverse voltage transformations that underlie cell-type specific computations2,3. However, measuring these transformations in vivo has remained challenging, leaving a crucial gap in our mechanistic understanding of single neuron computation. Here, we develop ASAP7y, a genetically encoded voltage indicator with unprecedented subthreshold sensitivity and expanded excitation compatibility in both mice and flies. We leveraged ASAP7y combined with two-photon random-access microscopy to record sensory stimulus-evoked voltage dynamics with millisecond, subcellular, and subthreshold resolution along the neurites of individual neurons in Drosophila. We found remarkable heterogeneity in voltage propagation across cell-types, delineating a fundamental axis of electrical diversity. Leveraging a nanoscale EM reconstruction of the visual system4, we modeled the electrotonic properties of single neurons spanning 717 cell types, revealing how morphology shapes voltage transformations. Finally, we demonstrate that confined voltage propagation creates substrates for local computation, producing subcellular domains with distinct feature selectivity across multiple cell types. These results provide mechanistic insight into how critical single neuron computations arise and reveal parallel processing in single neurons.

neuroscience↗

bioRxiv2026

Intrinsic space-time couplings governing multi-scale cortical dynamics

The neocortex covers a vast expanse of the mammalian brain and represents the principal target of clinical neuromodulation; however, the global principles of neocortical operation have been challenging to identify. In this regard, a limitation has been tracking activity with cortex-wide spatial coverage while maintaining access to the millisecond temporal resolution of neuronal firing-- a crucial combination not achievable with existing recording technologies. Here we introduce and apply conformal immersion microscopy, enabling activity tracking across the entire dorsal cortex with millisecond temporal resolution and 100 {micro}m spatial resolution (thus spanning five orders of magnitude in time and four in space), at sufficient sensitivity to resolve single-trial activity beyond 100 Hz. Drawing on physics-based frameworks, we apply multiscale analysis to identify a fundamental frequency-dependent coherence length that partitions the neocortex into discrete dynamical elements with well-defined propagation speeds, boundaries, and scale-invariant dynamics. These dynamical elements were found to be conserved from sub-threshold to suprathreshold (neuronal firing) regimes of neural activity, and were robust to diverse pharmacological, optogenetic, and genetic interventions. However, it was possible to identify and establish conditions allowing elemental boundaries to be selectively overridden, and to allow perturbation of specific elements even while conserving global dynamical architecture. Together, these findings enable measurement of intrinsic spatiotemporal parameters governing the dynamical organization of neocortex, which may provide a foundation for mechanistically-informed basic and translational understanding.

neuroscience↗

bioRxiv2026

Causal and directional elements of global brain dynamics

Mammalian cognition appears to involve coordinated neural activity within and across brain-spanning networks. However, the governing principles of large-scale integration remain largely unknown. Here we developed an approach to record spontaneous cortex-wide neural activity (including with novel genetically encoded activity sensors), over very long timescales, and applied unbiased computation to capture conserved spatiotemporal regularities in these data. Initial screening extracted a set of directional elements: consistent spatiotemporal patterns of cortical activity that generalized across excitatory and inhibitory neuronal cell types as revealed by genetic targeting of activity sensors. In particular, novel genetically encoded voltage-sensing strategies revealed that the directional elements were not only highly conserved, but also were represented across the full neural activity frequency spectrum including the fastest timescales (gamma rhythms) enabled by voltage-sensing. Exploiting the spatiotemporal structure revealed by these directional elements, we tested for causal rules governing cortical network activation, using patterned optogenetic stimulation combined with activity imaging. We found that the directional propagation structure of these elements encoded a causal control hierarchy, as source regions (but not sink regions) sufficed to drive full element recruitment--a principle that held across all tested directional elements. Employing a panel of psychotropic drugs, we showed that directional element structure and excitability were robust to manipulations of neural and behavioral state, even as spontaneous network dynamics were reshaped in compound-specific ways. Finally, we developed and applied an all-optical sensing/control approach targeting the directional elements in a behavioral visual detection paradigm, revealing contributions of these conserved large-scale dynamics to elevated sensorimotor behavioral performance.

neuroscience↗

bioRxiv2026

Functional remodeling of the parasubthalamic nucleus drives alcohol drinking escalation in dependence

The neurocircuitry changes mediating the development and maintenance of an alcohol use disorder are complex and dynamic. The parasubthalamic nucleus (PSTN), a small nucleus of the posterior lateral hypothalamus best known for suppressing appetite, is interconnected with brain regions disrupted in addiction; yet its potential role in the regulation of alcohol consumption had never been examined. Here we show that the PSTN exerts potent control over alcohol drinking in mice. Remarkably, the influence of endogenous PSTN activity on voluntary alcohol consumption switches from inhibitory to stimulatory upon induction of alcohol dependence. Among PSTN cells, Crh neurons represent a unique subpopulation that promotes alcohol drinking and fires more in dependent mice. Alcohol intake escalation driven by PSTN Crh neurons involves thalamic output and behavioral disinhibition. Based on our results, PSTN Crh neurons could represent a critical node in the brain circuitry overactive in alcohol addiction driven by reward seeking in humans.

neuroscience↗

bioRxiv2025

Serotonergic neuron-glioma interactions drive high-grade glioma pathophysiology

High-grade gliomas are lethal brain cancers that are powerfully regulated by glutamatergic neurons through activity-dependent paracrine factors and functional neuron-to-glioma synapses. Here, we report that serotonergic neurons promote the proliferation of high-grade gliomas throughout the brain. Serotonergic neuronal activity drives circuit-specific increases in high-grade glioma proliferation, calcium transients, and reduced survival. This growth-promoting effect is chiefly mediated by activation of the serotonin (5-hydroxytryptamine; 5HT) receptor 5HT2A on glioma cells. Knock out or pharmacological blockade of 5HT2A receptors in glioma abrogated the glioma growth-promoting effects of serotonergic neuronal activity, while serotonergic psychedelic drugs robustly promote malignant cell proliferation. Gliomas alter serotonergic neuronal activity patterns, resulting in elevated serotonin release into the tumor microenvironment. Together, these findings uncover pathogenic, feed-forward interactions between serotonergic neurons and glioma cells.

neuroscience↗

bioRxiv2025

Experience-Dependent Plasticity of Thalamoprefrontal Circuitry Characterizes Learning Across Species

Learning is an adaptive process which is thought to require precise coordination among multiple brain regions over time. Thalamoprefrontal circuitry is central to multiple domains of cognitive control and executive function, yet its evolution during learning is not characterized. In this study, we explored thalamoprefrontal circuit signaling in mice and connectivity dynamics in humans over the course of learning a homologous psychomotor task. In mice, we targeted a genetically encoded Ca2+indicator to the mediodorsal-prefrontal (MdT-dmPFC) projection and used fiber photometry to record synaptic dorsomedial PFC (dmPFC) activity. As learning sessions progressed, all mice demonstrated a decrease in reaction time (RT) performance on successful trials (p<0.001). In concomitant synaptic MdT-dmPFC circuit activity across sessions, we observed a significant increase in activity during the anticipatory (p<0.01) and reward retrieval (p<0.01) periods, and a non-significant trend towards an increase in preparatory activity (p<0.15). However, following the learning period, during task re-exposure, we observed a significant shift in circuit activity, away from anticipatory (p<0.001) and towards the preparatory period (p<0.001) over the course of re-exposure sessions. Furthermore, we observed an emergence of a learner (decrease in RT) and a non-learner group (increase in RT) during the task re-exposure period. Over the course of a single analogous task session in humans, we also observed a learner and a non-learner group. When analyzing the thalamoprefrontal regional connectivity dynamics of early and late trials for learners, we observed a significant increase in low frequency and decrease in high frequency synchrony (connectivity tilt) in thalamoprefrontal pathways during preparatory and anticipatory periods. Interestingly, pairwise interactions specifically between the anterior corona radiata (ACR) and superior frontal gyrus (SFG), the human homolog to the genetically targeted MdT-dmPFC circuitry in mice, in fact demonstrated a robustly opposite connectivity tilt effect distinguishing learners from non-learners (Cohens d > 2). Overall, these findings may provide cross-species evidence of novel, conserved thalamoprefrontal circuit mechanisms of adaptive learning.

neuroscience↗

bioRxiv2025

Life-long behavioral screen reveals an architecture of vertebrate aging

Mapping behavior of individual vertebrate animals across lifespan is challenging, but if achieved, could provide an unprecedented view into the life-long process of aging. We created the first platform for high-resolution continuous behavioral tracking of a vertebrate animal across natural lifespan from adolescence to death--here, of the African killifish. This behavioral screen revealed that animals follow distinct individual aging trajectories. The behaviors of long-lived animals differed markedly from those of short-lived animals, even relatively early in life, and were linked to organ-specific transcriptomic shifts. Machine learning models accurately predicted age and even forecasted an individuals future lifespan, given only behavior at a young age. Finally, we found that animals progressed through adulthood in a sequence of stable and stereotyped behavioral stages with abrupt transitions suggesting a novel structure for the architecture of vertebrate aging.

animal behavior and cognition↗

bioRxiv2025

Quantitative profiling of whole-brain connectomes at single-axon resolution using deep learning and high-resolution light sheet microscopy

Revealing how individual axons create a brain-wide connectome would be indispensable for understanding brain function and behavior, yet remains technically challenging. We introduce MAPL3, an end-to-end pipeline that integrates self-supervised learning with an innovative deep architecture to capture local and global brain-wide axonal projections. MAPL3 enables subject- and population-level quantitative laminar analysis, generalizes across experiments, and outperforms state-of-the-art methods. We showcase its ability to map the circuitry of the orbitofrontal cortex from single axons to whole-brain projectome.

neuroscience↗

bioRxiv2025

Environmental Novelty Modulates Rapid Cortical Plasticity During Navigation

In novel environments, animals quickly learn to navigate, and position-correlated spatial representations rapidly emerge in both the retrosplenial cortex (RSC) and primary visual cortex (V1). However, the role of plasticity in building these spatial representations, and how experience modulates this process, are not well understood. Here, we investigated the plasticity of spatial representations with real-time, cellular-resolution read and write control of neural activity using two-photon calcium imaging combined with holographic optogenetic stimulation in mice navigating virtual reality environments. Targeted stimulation of individual layer 2/3 neurons rapidly biased neural activity towards stimulation-paired locations in novel, but not familiar, environments. In contrast, RSC layer 5 neurons exhibited stimulation-induced plasticity regardless of environmental familiarity. These findings reveal a layer-specific, experience-dependent modulation of plasticity and offer a framework for how neocortical spatial representations strike a balance between stability of familiar environments with flexibility for continuous updates of relevant context information. HighlightsO_LIAll optical read-write approach reveals experience-dependent plasticity in cortex C_LIO_LIStimulating layer 2/3 neurons biases activity in novel but not familiar environments C_LIO_LILayer 5 neurons exhibit plasticity regardless of environmental familiarity C_LI

neuroscience↗

bioRxiv2025

Large-scale cellular-resolution read/write of activity enables discovery of cell types defined by complex circuit properties

The complexity of the mammalian brains vast population of interconnected neurons poses a formidable challenge to elucidate its underlying mechanisms of coordination and computation. A key step forward will be technologies that can perform large-scale, cellular-resolution monitoring and interrogation of distributed brain circuit activity in behaving animals. Here, we present an all-optical strategy for precise optogenetic activity control of [~]103 neurons and simultaneous activity monitoring of [~]104 neurons within and across areas of mouse cortex--an order-of-magnitude leap beyond previous capabilities. Tracking population responses following delivery of precisely-defined widely-distributed activity patterns to the visual cortex of awake mice, we were surprised to identify neurons robustly responsive to stimulation of diverse ensembles, defying conventional like-to-like wiring rules. These cells were primarily deep L2/3 somatostatin-positive (SST) interneurons with functional properties distinct from other SST neurons, and appeared to play a role in brain dynamics that could only have been identified through broad cellular-resolution circuit interrogation. Our work reveals the value of measuring large-scale circuit-dynamical properties of functionally-resolved single cells, beyond genetic and anatomical classification, to define and explore the roles of cell types in brain function.

neuroscience↗

bioRxiv2025

Evidence for age-related vulnerability in dopamine-glutamate projections to the lateral entorhinal cortex

The lateral entorhinal cortex (LEC) supports novelty detection and episodic memory and is selectively vulnerable to aging. Dopamine signals novelty in LEC, but how aging alters this input is unclear. Using intersectional viral strategies to distinguish ventral tegmental area (VTA) dopamine neurons with or without glutamate co-release, we find that co-releasing neurons are a minority ([~]30%) in the VTA, yet provide [~]93% of the dopaminergic projections to LEC. In aged mice, dopamine-glutamate labeling in VTA and LEC decreases [~]80%, whereas pan-dopaminergic labeling of LEC axons remains, consistent with functional silencing rather than degeneration. In LEC dopaminergic axons, dopamine synthesis is reduced while glutamate vesicular packaging is relatively spared. Optogenetic stimulation combined with a dopamine sensor reveals diminished dopamine release at high frequencies, when synthesis demand is greatest. These findings identify selective vulnerability of dopamine-glutamate neurons as a cell- and circuit-specific mechanism that weakens dopamine signaling within memory circuits.

neuroscience↗

bioRxiv2025

Convergent state-control of endogenous opioid analgesia

Pain is a dynamic and nonlinear experience shaped by injury and contextual factors, including expectations of future pain or relief1. While {micro} opioid receptors are central to the analgesic effects of opioid drugs, the endogenous opioid neurocircuitry underlying pain and placebo analgesia remains poorly understood. The ventrolateral column of the posterior periaqueductal gray is a critical hub for nociception and endogenous analgesia mediated by opioid signaling2. However, significant gaps remain in understanding the cell-type identities, the sub-second neural dynamics involved in pain modulation, the role of endogenous peptide neuromodulators, and the contextual factors influencing these processes. Using spatial mapping with single-nuclei RNA sequencing of pain-active neurons projecting to distinct long-range brain targets, alongside cell type-specific and activity-dependent genetic tools for in vivo optical recordings and modulation of neural activity and opioid peptide release, we identified a functional dichotomy in the ventrolateral periaqueductal gray. Neurons expressing {micro} opioid receptors encode active nociceptive states, whereas enkephalin-releasing neurons drive pain relief during recovery from injury, in response to learned fear predictions, and during placebo analgesia. Finally, by leveraging the functional effects of placebo analgesia, we used direct optogenetic activation of vlPAG enkephalin neurons to drive opioid peptide release, resulting in a robust reduction in pain. These findings show that diverse need states converge on a shared midbrain circuit that releases endogenous opioids with high spatiotemporal precision to suppress nociceptive activity and promote analgesia.

neuroscience↗

bioRxiv2024

Cholinergic Neuronal Activity Promotes Diffuse Midline Glioma Growth through Muscarinic Signaling

Neuronal activity promotes the proliferation of healthy oligodendrocyte precursor cells (OPC) and their malignant counterparts, gliomas. Many gliomas arise from and closely resemble oligodendroglial lineage precursors, including diffuse midline glioma (DMG), a cancer affecting midline structures such as the thalamus, brainstem and spinal cord. In DMG, glutamatergic and GABAergic neuronal activity promotes progression through both paracrine signaling and through bona-fide neuron-to-glioma synapses. However, the putative roles of other neuronal subpopulations - especially neuromodulatory neurons located in the brainstem that project to long-range target sites in midline anatomical locations where DMGs arise - remain largely unexplored. Here, we demonstrate that the activity of cholinergic midbrain neurons modulates both healthy OPC and malignant DMG proliferation in a circuit-specific manner at sites of long-range cholinergic projections. Optogenetic stimulation of the cholinergic pedunculopontine nucleus (PPN) promotes glioma growth in pons, while stimulation of the laterodorsal tegmentum nucleus (LDT) facilitates proliferation in thalamus, consistent with the predominant projection patterns of each cholinergic midbrain nucleus. Reciprocal signaling was evident, as increased activity of cholinergic neurons in the PPN and LDT was observed in pontine DMG-bearing mice. In co-culture, hiPSC-derived cholinergic neurons form neuron-to-glioma networks with DMG cells and robustly promote proliferation. Single-cell RNA sequencing analyses revealed prominent expression of the muscarinic receptor genes CHRM1 and CHRM3 in primary patient DMG samples, particularly enriched in the OPC-like tumor subpopulation. Acetylcholine, the neurotransmitter cholinergic neurons release, exerts a direct effect on DMG tumor cells, promoting increased proliferation and invasion through muscarinic receptors. Pharmacological blockade of M1 and M3 acetylcholine receptors abolished the activity-regulated increase in DMG proliferation in cholinergic neuron-glioma co-culture and in vivo. Taken together, these findings demonstrate that midbrain cholinergic neuron long-range projections to midline structures promote activity-dependent DMG growth through M1 and M3 cholinergic receptors, mirroring a parallel proliferative effect on healthy OPCs. HIGHLIGHTSO_LIActivity of midbrain cholinergic neuron long-range projections increases proliferation of both healthy oligodendrocyte precursor cells (OPC) and malignant diffuse midline glioma (DMG) cells. C_LIO_LIOptogenetic stimulation of cholinergic midbrain nuclei promotes growth in thalamic and pontine glioma in a circuit-dependent manner. C_LIO_LIReciprocally, DMG cells increase cholinergic neuronal activity in cholinergic midbrain nuclei. C_LIO_LIThe muscarinic receptors CHRM1 and CHRM3 are identified as therapeutic targets in DMG. C_LI

neuroscience↗

bioRxiv2024

Food and water uptake are regulated by distinct central amygdala circuits revealed using intersectional genetics

The central amygdala (CeA) plays a crucial role in defensive and appetitive behaviours. It contains genetically defined GABAergic neuron subpopulations distributed over three anatomical subregions, capsular (CeC), lateral (CeL), and medial (CeM). The roles that these molecularly- and anatomically-defined CeA neurons play in appetitive behavior remain unclear. Using intersectional genetics, we found that neurons driving food or water consumption are confined to the CeM. Separate CeM subpopulations exist for water only versus water or food consumption. In vivo calcium imaging revealed that CeMHtr2a neurons promoting feeding are responsive towards appetitive cues with little regard for their physical attributes. CeMSst neurons involved in drinking are sensitive to the physical properties of salient stimuli. Both CeM subtypes receive inhibitory input from CeL and send projections to the parabrachial nucleus to promote appetitive behavior. These results suggest that distinct CeM microcircuits evaluate liquid and solid appetitive stimuli to drive the appropriate behavioral responses.

neuroscience↗