Biology subjects

Cai, D. J.

Publications and source records attributed to Cai, D. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Grooming as a window into the post-stress recuperative process

Alterations in rodent self-grooming have been used to model various facets of neuropsychiatric illness. In the context of affective behavior, increases in grooming have been proposed as a sign of stress. This is because grooming has been observed to increase in close temporal proximity to stressful events. However, in other situations, stress appears to suppress grooming, complicating the utility of measuring grooming in the study of stress and mental health. Here, we show that this discrepancy can be resolved by considering time and experimental context. We found that in initial response to stress, grooming declined in proportion to stressor intensity. Moreover, stress-related cues and anxiogenic stimuli similarly suppressed grooming. Conversely, optogenetic inhibition of the amygdala in a stress-associated context decreased threat-elicited freezing, consistent with a reduction in stress, and increased grooming. These results indicate that the immediate response to stress is a suppression of grooming. However, when stressed mice were returned to their homecage environment, grooming increased. Similarly, mice increased grooming when they returned to the safe zone in an anxiety assay. Accordingly, rather than being a defensive response to signs of danger, increased grooming seems to reflect a post-stress response that occurs once animals detect the absence of danger. These findings suggest that post-stress grooming could provide a window into the neurobiology of post-stress recuperative processes.

neuroscience↗

bioRxiv2026

Simultaneous brain-wide single-cell recording resolves spatiotemporal memory architecture

Many fundamental mammalian brain functions emerge from the coordinated activity of cells distributed across large, brain-wide networks. To understand these processes in healthy and diseased states, ideally one would simultaneously measure and analyze single-cell activity at the brain-wide scale, an enduring challenge for live-measurement approaches that often face an inherent tradeoff between spatial resolution and scale. Here, we present GLOBE (sinGle-cell spatiotemporaL recOrding Brain-widE), a technology for brain-wide single-cell recording of cellular activity in vivo with spatiotemporal resolution, physiological sensitivity, and parallelization-accelerated readout. GLOBE leverages genetically encoded intracellular protein tape recorders and a high-throughput computational platform for integrated image and signal analysis. GLOBE records analog signal amplitudes across a continuous time axis, requires only standard light microscopy for in situ readout, and is compatible with expansion microscopy and RNA readouts. We applied GLOBE to simultaneously record transcriptional activity of the immediate early gene Fos in up to 219,703 neurons simultaneously across a single mouse brain over 5.5 continuous days, with a timestamp precision of 3.1-6.7 hours (median absolute error), a local recording density of 69-90% of neurons per imaging field of view, and a post-mortem imaging readout speed of 2.9 seconds per neuron on average. GLOBE resolves the brain-wide spatiotemporal structure of single-cell activity, revealing that Fos transcriptional dynamics associated with fear learning and memory retrieval are distributed across the brain with region-specific temporal heterogeneity, and that the variance of this structure scales down as the number of sampled cells increases. We envision GLOBE to have broad applications for dissecting and decoding physiological and pathological processes at the brain-wide scale.

neuroscience↗

bioRxiv2026

State-dependent geometric transformations in the mouse hippocampus support fear generalization without loss of discriminability

Learning from aversive experiences often generalizes beyond the context in which they occurred. In rodents, a strong aversive event can induce retrospective memory linking (RLI), whereby fear generalizes to a previously neutral context encountered days earlier. Although prior work has shown that RLI is associated with increased co-activity of hippocampal CA1 neurons across neutral and aversive contexts, it remains unclear how broader representational changes support generalization without affecting the ability to discriminate between contexts. Here, we reanalyzed calcium imaging data from dorsal CA1 during RLI to examine how hippocampal representational geometry changes during fear generalization. Using robust, non-parametric measures of population similarity, we show that in mice exhibiting RLI, the representation of the neutral context not only changes over time but becomes more similar to the aversive context during recall. Beyond this similarity increase, we provide evidence for a higher-dimensional geometric transformation consistent with a shared "fear" operation that can be applied across contexts while preserving their identity. Crucially, these two representational signatures dissociate by behavioral state: similarity to the aversive context emerges during freezing, whereas a shared transformation is expressed during active exploration. Together, these findings demonstrate that hippocampal representations support retrospective fear generalization through state-dependent geometric transformations, highlighting representational geometry as a key computational mechanism to resolve the apparent tension between generalization and discriminability.

neuroscience↗

bioRxiv2025

Interneuron theta phase locking controls seizure susceptibility

The timing of neuronal activity is highly precise and often organized by brain-wide oscillations. Many neurons modulate their firing rates at specific phases of theta (known as theta phase locking), creating discrete windows for information processing. Disrupted theta phase locking has been found across several neurological and psychiatric disorders (e.g., epilepsy), but gaps in technology have prevented its causal influence from being tested. Here, we developed PhaSER, a closed-loop optogenetic system designed to control the phase locking of specific interneurons, and demonstrate a causal role for inhibitory phase locking in seizure susceptibility. We first found that parvalbumin (PV+) and somatostatin (SOM+) expressing interneurons in the dentate gyrus (DG) show distinct theta phase locking profiles and are differentially impacted in a mouse model of chronic temporal lobe epilepsy. In healthy mice, PV+ interneurons have extremely consistent phase-locked firing near the trough of CA1 theta, aligned with excitatory inputs to DG. However, in epileptic mice, PV+ interneuron activity is dispersed across the theta cycle, suggesting that altered inhibitory phase locking could be a causal mediator of seizure susceptibility in epilepsy. To test this hypothesis, we applied PhaSER to directly control the phase locking of DG interneurons during an acute test of seizure susceptibility. In epileptic mice, re-aligning DG PV+ interneuron theta phase locking reduced seizure susceptibility, while in healthy mice, disrupting normal phase locking of PV+ interneurons increased seizure susceptibility. Together, this provides the first causal evidence that inhibitory theta phase locking can directly control network function by shifting seizure susceptibility in the healthy and epileptic brain.

neuroscience↗

bioRxiv2025

Multiplexed, scalable analog recording of gene regulation dynamics over weeks using intracellular protein tapes

Gene expression is constantly regulated by gene regulatory networks that consist of multiple regulatory components to mediate cellular functions. An ideal tool for analyzing gene regulation processes would provide simultaneous measurements of the dynamics of many components in the gene regulatory network, but existing methodologies fall short of simultaneously tracking the dynamics of components over long periods of time. Here, we present CytoTape--a genetically encoded, modular, and scalable analog recorder for continuous, multiplexed in situ recording of gene regulation dynamics over multiple days and weeks at single-cell resolution. CytoTape consists of a flexible, thread-like, elongating intracellular protein self-assembly engineered via AI-guided rational design. Gene regulation dynamics, together with timestamps for reconstruction of the continuous time axis, are directly encoded via distinct molecular tags distributed along single CytoTape assemblies in live cells, to be readout at scale after fixation via standard immunofluorescence imaging. CytoTape recorders are modularly designed to record gene expression driven by a variety of activity-dependent promoters. We demonstrated the utility of CytoTape in mammalian embryonic kidney cells, cancer cells, glial cells, and neurons, achieving simultaneous recording of five cell plasticity-associated transcription factor activities and immediate early gene expression levels, namely CREB, c-fos, Arc, Egr1, and Npas4 activities, within single cells in a spatiotemporally scalable manner. CytoTape revealed complex waveforms and nonlinear temporal couplings among these cellular activities, enabling investigations of how gene regulation histories and intrinsic signaling states shape transcriptional logics. We envision CytoTape to have broad applications in both basic and disease-related cell biology research.

synthetic biology↗

bioRxiv2025

Medial entorhinal-hippocampal desynchronization parallels the emergence of memory impairment in a mouse model of Alzheimer's disease pathology

Alzheimers disease (AD) is a neurodegenerative disease characterized by progressive impairments in episodic and spatial memory, as well as circuit and network-level dysfunction. While functional impairments in medial entorhinal cortex (MEC) and hippocampus (HPC) have been observed in patients and rodent models of AD, it remains unclear how communication between these regions breaks down in disease, and what specific physiological changes are associated with the onset of memory impairment. We used silicon probes to simultaneously record neural activity in MEC and hippocampus before or after the onset of spatial memory impairment in the 3xTg mouse model of AD pathology. We found that reduced hippocampal theta power, reduced MEC-CA1 theta coherence, and altered phase locking of MEC and hippocampal neurons all coincided with the emergence of spatial memory impairment in 3xTg mice. Together, these findings indicate that disrupted temporal coordination of neural activity in the MEC-hippocampal system parallels the emergence of memory impairment in a model of AD pathology. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/633171v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@11606a5org.highwire.dtl.DTLVardef@10e5d0borg.highwire.dtl.DTLVardef@1feabe1org.highwire.dtl.DTLVardef@c646ed_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHICAL ABSTRACTC_FLOATNO C_FIG HighlightsO_LISpatial memory impairments in 3xTg mice emerge between 6 and 8 months of age C_LIO_LIMemory deficits emerge alongside reduced HPC theta power and reduced CA1-MEC theta coherence C_LIO_LIMemory deficits emerge alongside disrupted timing of MEC and HPC neural activity C_LIO_LIInterneuron loss in MEC and interneuron desynchronization in HPC occur prior to memory impairment C_LI

neuroscience↗

bioRxiv2024

Chemotagging: a chemogenetic approach for identifying cell types with in vivo calcium imaging

The ability to monitor the activity of specific cell types in vivo is critical for understanding the complex interplay between various neuronal populations driving freely moving behavior. Existing methods, such as optogenetic tagging (i.e., Optotagging1), have proven useful for identifying cell types in in vivo electrophysiological recordings during freely moving behavior. However, electrophysiological recordings are limited in their capacity to track the same neuronal populations across long periods of time (days to weeks). Single-photon miniscope imaging offers the advantage of tracking the same cells across weeks to months; however, it is difficult to distinguish different cell types within the recorded population. Here, we present "chemotagging," a technique that allows for the identification of specific cell types in in vivo calcium imaging recordings. This protocol offers a method for tagging cell types with chemogenetic tools like Designer Receptors Exclusively Activated by Designer Drugs (DREADDs)2, while simultaneously recording calcium activity from a pan-neuronal population with calcium indicators. We highlight the key advantages and limitations of chemotagging and its potential implications for neuroscience research.

neuroscience↗

bioRxiv2024

An anterior hypothalamic circuit gates stress vulnerability

Prior adversity increases susceptibility to subsequent stressful events, but the causal underlying changes in brain circuitry are poorly understood. We harnessed unbiased whole-brain activity mapping to identify circuits that are functionally remodeled by prior adversity. This revealed that the anterior hypothalamic nucleus (AHN) displays heightened stress reactivity in previously stressed mice. This was accompanied by increased functional connectivity between the AHN and a threat-related limbic network. Using in vivo Miniscope imaging, we found that neuronal activity in the AHN encodes stressor valence. Moreover, stimulating AHN neurons enhanced, and inhibiting their activity mitigated, reactivity to stressful events. Lastly, silencing amygdala inputs to the AHN abolished the ability of prior adversity to increase stress sensitivity. These findings define a key role of the AHN in gating stress vulnerability by scaling valence signals from the amygdala.

neuroscience↗

bioRxiv2024

Simultaneous dual-color calcium imaging in freely-behaving mice

Miniaturized fluorescence microscopes (miniscopes) enable imaging of calcium events from a large population of neurons in freely behaving animals. Traditionally, miniscopes have only been able to record from a single fluorescence wavelength. Here, we present a new open-source dual-channel Miniscope that simultaneously records two wavelengths in freely behaving animals. To enable simultaneous acquisition of two fluorescent wavelengths, we incorporated two CMOS sensors into a single Miniscope. To validate our dual-channel Miniscope, we imaged hippocampal CA1 region that co-expressed a dynamic calcium indicator (GCaMP) and a static nuclear signal (tdTomato) while mice ran on a linear track. Our results suggest that, even when neurons were registered across days using tdTomato signals, hippocampal spatial coding changes over time. In conclusion, our novel dual-channel Miniscope enables imaging of two fluorescence wavelengths with minimal crosstalk between the two channels, opening the doors to a multitude of new experimental possibilities. TeaserNovel open-source dual-channel Miniscope that simultaneously records two wavelengths with minimal crosstalk in freely behaving animals.

neuroscience↗

bioRxiv2024

Distinct changes to hippocampal and medial entorhinal circuits emerge across the progression of cognitive deficits in epilepsy

Temporal lobe epilepsy (TLE) causes pervasive and progressive memory impairments, yet the specific circuit changes that drive these deficits remain unclear. To investigate how hippocampal-entorhinal dysfunction contributes to progressive memory deficits in epilepsy, we performed simultaneous in vivo electrophysiology in hippocampus (HPC) and medial entorhinal cortex (MEC) of control and epileptic mice 3 or 8 weeks after pilocarpine-induced status epilepticus (Pilo-SE). We found that HPC synchronization deficits (including reduced theta power, coherence, and altered interneuron spike timing) emerged within 3 weeks of Pilo-SE, aligning with early-onset, relatively subtle memory deficits. In contrast, abnormal synchronization within MEC and between HPC-MEC emerged later, by 8 weeks after Pilo-SE, when spatial memory impairment was more severe. Furthermore, a distinct subpopulation of MEC layer 3 excitatory neurons (active at theta troughs) was specifically impaired in epileptic mice. Together, these findings suggest that hippocampal-entorhinal circuit dysfunction accumulates and shifts as cognitive impairment progresses in TLE.

neuroscience↗

bioRxiv2023

Chronotate: An open-source tool for manual timestamping and quantification of animal behavior

A core necessity to behavioral neuroscience research is the ability to accurately measure performance on behavioral assays, such as the novel object location and novel object recognition tasks. These tasks are widely used in neuroscience research and measure a rodents instinct for investigating novel features as a proxy to test their memory of a previous experience. Automated tools for scoring behavioral videos can be cost prohibitive and often have difficulty distinguishing between active investigation of an object and simply being in close proximity to an object. As such, many experimenters continue to rely on hand scoring interactions using stopwatches which makes it difficult to review scoring after-the-fact and results in the loss of temporal information. Here, we introduce Chronotate, a free, open-source tool to aid in manually scoring novel object behavior videos. The software consists of an interactive video player with keyboard integration for marking timestamps of behavioral events during video playback, making it simple to quickly score and review bouts of rodent-object interaction. In addition, Chronotate outputs detailed interaction bout data, allowing for nuanced behavioral performance analyses. Using this detailed temporal information, we demonstrate that novel object location performance peaks within the first 3 seconds of interaction time and preference for the novel location becomes reduced across the test session. Thus, Chronotate can be used to determine the temporal structure of interactions on this task and can provide new insight into the memory processes that drive this behavior. Chronotate is available for download at: https://github.com/ShumanLab/Chronotate.

neuroscience↗

bioRxiv2023

Progressive excitability changes in the medial entorhinal cortex in the 3xTg mouse model of Alzheimer's disease pathology

Alzheimers disease (AD) is a chronic neurodegenerative disorder that is characterized by memory loss and progressive cognitive impairments. In mouse models of AD pathology, studies have found neuronal and synaptic deficits in the hippocampus, but less is known about what happens in the medial entorhinal cortex (MEC), which is the primary spatial input to the hippocampus and an early site of AD pathology. Here, we measured the neuronal intrinsic excitability and synaptic activity in MEC layer II (MECII) stellate cells, MECII pyramidal cells, and MEC layer III (MECIII) excitatory neurons at early (3 months) and late (10 months) time points in the 3xTg mouse model of AD pathology. At 3 months of age, prior to the onset of memory impairments, we found early hyperexcitability in MECII stellate and pyramidal cells intrinsic properties, but this was balanced by a relative reduction in synaptic excitation (E) compared to inhibition (I), suggesting intact homeostatic mechanisms regulating activity in MECII. Conversely, MECIII neurons had reduced intrinsic excitability at this early time point with no change in the synaptic E/I ratio. By 10 months of age, after the onset of memory deficits, neuronal excitability of MECII pyramidal cells and MECIII excitatory neurons was largely normalized in 3xTg mice. However, MECII stellate cells remained hyperexcitable and this was further exacerbated by an increased synaptic E/I ratio. This observed combination of increased intrinsically and synaptically generated excitability suggests a breakdown in homeostatic mechanisms specifically in MECII stellate cells at this post-symptomatic time point. Together, these data suggest that the breakdown in homeostatic excitability mechanisms in MECII stellate cells may contribute to the emergence of memory deficits in AD.

neuroscience↗

bioRxiv2023

A double-hit of social and economic stress in mice precipitates changes in decision-making strategies

Economic stress can serve as a "second-hit" for those who already accumulated a history of adverse life experiences. How one recovers from a setback is a core feature of resilience but is seldom captured in animal studies. We challenged mice in a novel two-hit stress model by exposing animals to chronic social defeat stress (first-hit) and then testing how mice adapt to reward scarcity on a neuroeconomic task (second-hit). Mice were tested longitudinally across months on the Restaurant Row task during which mice foraged daily for their sole source of food while on a limited time budget. An abrupt transition into a reward-scarce environment on this task elicits an economic crisis, precipitating a massive drop in food intake and body weight to which mice must respond in order to survive. We found that mice with a history of social defeat mounted a robust behavioral response to this economic challenge. This recovery was achieved through a complex redistribution of how time was allocated among competing opportunities via multiple valuation algorithms. Interestingly, we found that mice with a history of social defeat displayed changes in the development of decision-making policies during the recovery process important for not only ensuring food security necessary for survival but also prioritizing subjective value. These findings indicate that an individuals capacity to "bounce back" from economic stress depends on ones prior history of stress and can affect multiple aspects of subjective well-being, highlighting a motivational balance that may be altered in stress-related disorders such as depression. In BriefDurand-de Cuttoli et al. found that after chronic social defeat stress, when mice were subsequently challenged on a neuroeconomic foraging task, an economic stressor can serve as a "second hit" and reveal changes in the development of complex decision-making strategies important for maintaining the balance between food security and subjective well-being.

animal behavior and cognition↗

bioRxiv2023

Drift of neural ensembles driven by slow fluctuations of intrinsic excitability

Representational drift refers to the dynamic nature of neural representations in the brain despite the behavior being seemingly stable. Although drift has been observed in many different brain regions, the mechanisms underlying it are not known. Since intrinsic neural excitability is suggested to play a key role in regulating memory allocation, fluctuations of excitability could bias the reactivation of previously stored memory ensembles and therefore act as a motor for drift. Here, we propose a rate-based plastic recurrent neural network with slow fluctuations of intrinsic excitability. We first show that subsequent reactivations of a neural ensemble can lead to drift of this ensemble. The model predicts that drift is induced by co-activation of previously active neurons along with neurons with high excitability which leads to remodeling of the recurrent weights. Consistent with previous experimental works, the drifting ensemble is informative about its temporal history. Crucially, we show that the gradual nature of the drift is necessary for decoding temporal information from the activity of the ensemble. Finally, we show that the memory is preserved and can be decoded by an output neuron having plastic synapses with the main region.

neuroscience↗

bioRxiv2023

Aversive experience drives offline ensemble reactivation to link memories across days

Memories are encoded in neural ensembles during learning and stabilized by post-learning reactivation. Integrating recent experiences into existing memories ensures that memories contain the most recently available information, but how the brain accomplishes this critical process remains unknown. Here we show that in mice, a strong aversive experience drives the offline ensemble reactivation of not only the recent aversive memory but also a neutral memory formed two days prior, linking the fear from the recent aversive memory to the previous neutral memory. We find that fear specifically links retrospectively, but not prospectively, to neutral memories across days. Consistent with prior studies, we find reactivation of the recent aversive memory ensemble during the offline period following learning. However, a strong aversive experience also increases co-reactivation of the aversive and neutral memory ensembles during the offline period. Finally, the expression of fear in the neutral context is associated with reactivation of the shared ensemble between the aversive and neutral memories. Taken together, these results demonstrate that strong aversive experience can drive retrospective memory-linking through the offline co-reactivation of recent memory ensembles with memory ensembles formed days prior, providing a neural mechanism by which memories can be integrated across days.

neuroscience↗

bioRxiv2023

Dissociable contributions of the amygdala and ventral hippocampus to stress-induced changes in defensive behavior

BackgroundSevere stress can produce multiple persistent changes in defensive behavior relevant to psychiatric illness. While much is known about the circuits supporting stress-induced associative fear, how stress-induced circuit plasticity supports non-associative changes in defensive behavior remains unclear. MethodsMice were exposed to an acute severe stressor, and subsequently, both associative and non-associative defensive behavioral responses were assessed. A mixture of local protein synthesis inhibition, pan-neuronal chemogenetic inhibition, and projection-specific chemogenetic inhibition were utilized to isolate the roles of the basolateral amygdala (BLA) and ventral hippocampus (vHC) to the induction and expression of associative and non-associative defensive behavioral changes. ResultsStress-induced protein synthesis in the BLA was necessary for enhancements in stress sensitivity but not enhancements in anxiety-related behaviors, whereas protein synthesis in the vHC was necessary for enhancements in anxiety-related behavior but not enhancements in stress sensitivity. Like protein synthesis, neuronal activity of the BLA and vHC were found to differentially support the expression of these same defensive behaviors. Additionally, projection-specific inhibition of BLA-vHC connections failed to alter these behaviors, indicating that these defensive behaviors are regulated by distinct BLA and vHC circuits. Lastly, contributions of the BLA and vHC to stress sensitivity and anxiety-related behavior were independent of their contributions to associative fear. ConclusionsStress-induced plasticity in the BLA and vHC were found to support dissociable non-associative behavioral changes, with BLA supporting enhancements in stress sensitivity and vHC supporting increased anxiety-related behavior. These findings demonstrate that independent BLA and vHC circuits are critical for stress-induced defensive behaviors, and that differential targeting of BLA and vHC circuits may be needed in disease treatment.

neuroscience↗

bioRxiv2022

Ensemble-specific deficit in neuronal intrinsic excitability in aged mice

With the prevalence of age-related cognitive deficits on the rise, it is essential to identify cellular and circuit alterations that contribute to age-related memory impairment. Increased intrinsic neuronal excitability after learning is important for memory consolidation, and changes to this process could underlie memory impairment in old age. Some studies find age-related deficits in hippocampal neuronal excitability that correlate with memory impairment but others do not, possibly due to selective changes only in activated neural ensembles. Thus, we tagged CA1 neurons activated during learning and recorded their intrinsic excitability 5 hours or 7 days post-training. Adult mice exhibited increased neuronal excitability 5 hours after learning, specifically in ensemble (learning-activated) CA1 neurons. As expected, ensemble excitability returned to baseline 7 days post-training. In aged mice, there was no ensemble-specific excitability increase after learning, which was associated with impaired hippocampal memory performance. These results suggest that CA1 may be susceptible to age-related impairments in post-learning ensemble excitability and underscore the need to selectively measure ensemble-specific changes in the brain.

neuroscience↗

bioRxiv2022

Ensemble remodeling supports memory-updating

Memory-updating is critical in dynamic environments because updating memories with new information promotes versatility. However, little is known about how memories are updated with new information. To study how neuronal ensembles might support memory-updating, we used a hippocampus-dependent spatial reversal task to measure hippocampal ensemble dynamics when mice switched navigational goals. Using Miniscope calcium imaging, we identified neuronal ensembles (co-active neurons) in dorsal CA1 that were spatially tuned and stable across training sessions. When reward locations were moved during a reversal session, a subset of these ensembles decreased their activation strength, correlating with memory-updating. These "remodeling" ensembles were a result of weakly-connected neurons becoming less co-active with their peers. Middle-aged mice were impaired in reversal learning, and the prevalence of their remodeling ensembles correlated with their memory-updating performance. Therefore, we have identified a mechanism where the hippocampus breaks down ensembles to support memory-updating.

neuroscience↗