Biology subjects

Sabatini, B. L.

Publications and source records attributed to Sabatini, B. L..

At least 19 recordsLinked to original sources

bioRxiv2026

SPOUT: An open-source hardware and software platform to study decision making while manipulating and recording from neural activity

Recording and manipulating brain activity during behavior is critical to understanding the underlying mechanisms of decision-making. Linking neural activity to behavior requires behavioral hardware and software tightly integrated with recording and perturbation systems on a shared clock. We built SPOUT (State-machine Platform for Operant Uni/dual-spout Tasks), an open-source, Teensy-driven state-machine platform with a MATLAB interface that runs 10 unique decision-making tasks (with dozens of variations available through user-friendly settings) to study behavior in head-restrained mice. The platform is built on several custom hardware devices: a dual-lick detector, headplate designs for optogenetics and two-photon calcium imaging, a three-axis motorized spout manipulator, and an optogenetics power modulator. The firmware differentiates between one and two lick spout tasks and can be controlled by a user-friendly interface. Task settings can be selected through the interface or by loading predefined settings files. We validated the clock speed and lick detection against an independent, external acquisition system and identified highly precise, sub-millisecond detection of single licks. Using a pseudo-random synchronization pulse generated by SPOUT, we corrected for missing data due to glitches in the acquisition system and clock drift. We showcase the versatility of SPOUT by training mice on an uninstructed lick-left/lick-right task in which the rewarded side switches unexpectedly and found that mice use history-dependent action-outcome associations to guide future behavior. Transiently inhibiting the anterior lateral motor cortex (ALM) during cue presentation induced contralateral deficits, without affecting ipsilateral trials. Finally, two-photon imaging of ALM neurons revealed stronger population responses during contralateral choice licks compared to ipsilateral ones. Together, SPOUT offers an open-source, affordable platform to study decision-making in head-restrained mice while combining neural recordings and manipulations.

neuroscience↗

bioRxiv2026

Reward predictability shapes decision making states and exploitative control in marmosets

Animals navigating dynamic environments must transition between behavioral states dominated by exploitation of known rewards or exploration of alternatives. Understanding this flexibility requires characterizing not only choices and outcomes but also how reward information updates strategy. Common marmosets offer a unique combination of genetic tractability and frontal cortical complexity, yet scalable behavioral platforms for studying flexible decision making in this species remain limited. Here, we developed an automated home-cage touchscreen platform that enables voluntary behavioral testing across extended periods without water restriction. We trained marmosets on a series of reversal learning tasks of increasing complexity, culminating in a fully uncued probabilistic two-armed bandit task, and applied reinforcement learning models to examine how reward predictability shapes adaptive choice in marmosets. A Q-learning model with choice perseveration captured trial-by-trial dynamics, with choice variability consistent with stochastic sampling from the fitted policy. A trial-level behavioral state classifier identified distinct and persistent modes of exploitation and exploration that differed in their sensitivity to reward history and their transition structure. Comparing behavioral patterns within probabilistic and deterministic reward contingencies revealed that reward predictability reorganized state occupancy and sharpened error correction within predominately exploitative states, with animals responding to single negative outcomes more rapidly under deterministic feedback. These findings establish both a behavioral and computational framework to dissect the computations and circuits underlying adaptive decision making in marmosets.

animal behavior and cognition↗

bioRxiv2026

Striatal activity maintains a short-term action-outcome memory to guide future choice

Adaptive behavior requires animals to use the outcomes of recent actions (action-outcomes) to guide future decisions. While the striatum is critical for decision-making, it is currently unclear how it is involved in the storage and retrieval of short-term associative memories. Here, we implemented a head-fixed memory-guided decision-making task in which mice use the outcome of a previous choice to determine whether to repeat or switch their next action. We show that dopamine fluctuations in the ventrolateral striatum are modulated by reward receipt or omission and recent outcome history, while the activity of direct and indirect pathway striatal projection neurons encodes recent action-outcome associations and predicts future switch/repeat choices. Closed-loop optogenetic activation and inhibition of direct and indirect pathway neurons during either the action-outcome association period or the delay preceding the next choice bidirectionally biased future actions away from those favored by reward history. Together, these findings suggest that striatal activity maintains a short-term action-outcome associative memory that links completed actions to future motor plans during adaptive decision-making.

neuroscience↗

bioRxiv2026

Branch-specific plasticity explains distal enrichment of retinotopically displaced inputs in visual cortex

Neurons distribute synaptic inputs across their dendritic tree. In layer 2/3 pyramidal cells of primary visual cortex, spines on distal dendrites share somatic orientation preference but have receptive fields displaced in retinotopic space, which supports tuning to visual edges. However, it is not known how synaptic plasticity rules can lead to specialization of tuning properties across dendritic compartments. We demonstrate an experimentally grounded model of compartment-specific spike-timing dependent plasticity (STDP) that accounts for the enrichment of retinotopically-displaced inputs on distal branches. Our previous experimental work revealed compartment-specific calcium signals that predict reduced STDP-mediated depression but preserved potentiation. Based on these findings, we built an STDP model with compartment-specific properties, in which some distal branches are relatively resistant to STDPmediated depression. Synapses on these branches are more likely to stabilize inputs with weaker correlations to postsynaptic spiking. Using a visual input model, we show that compartment-specific reduction in STDP-mediated depression recapitulates in vivo experimental measurements of spine tuning. Furthermore, our experimental results show that reduced STDP-mediated depression is restricted to distal dendritic compartments with complex branching structure and not observed in other distal branches. Therefore, our model makes an untested prediction that complex branches will be hotspots for retinotopically-displaced inputs.

neuroscience↗

bioRxiv2025

Rapid fluorescence lifetime sensor development of LifeCamp enables transient and baseline absolute calcium measurements

Genetically encoded calcium sensors (GECIs) have been instrumental for studying neuronal activity and intracellular signaling. GECIs are typically fluorescence-intensity sensors that change brightness upon calcium binding. Iterative improvements in GECIs have yielded indicators that report action potential-evoked calcium entry with high sensitivity and temporal resolution, enabling measurement of network activity across thousands of neurons. However, fluorescence intensity-based measurements generally cannot report baseline or absolute calcium levels and may confound neuromodulatory regulation of calcium handling with changes in action potential firing. Fluorescence lifetime sensors are insensitive to many artifacts that plague intensity-based measures and report absolute substrate levels, including those at rest. However, relatively few lifetime sensors for neuronal signals exist, and developing new sensors is typically difficult and low-yield. Here, we introduce a new rapid lifetime sensor development (RALISED) platform, which we use to build a new GCaMP8m-based high-speed lifetime calcium sensor, termed LifeCamp. We show that LifeCamp enables comparison of baseline calcium signals in cell culture, brain slices, and mice. In addition, we show that LifeCamp enables the detection of fast action potential-evoked calcium transients in single neurons from brain slices and in behaving mice. Using LifeCamp, we discovered calcium baseline changes associated with neuronal activity in brain slices and behaving mice, as well as slow average calcium changes in neuronal populations of freely moving mice. Altogether, this study highlights the utility of the RALISED method to rapidly develop new lifetime sensors and the application of the LifeCamp calcium lifetime sensor to study fast and slow calcium signaling. Significance statementWe developed a new high-speed, sensitive calcium lifetime sensor (LifeCamp) using a novel rapid lifetime sensor development (RALISED) platform. LifeCamp has high sensitivity and a large substrate-dependent lifetime change (<1ns), allowing for the capture of baseline calcium levels, transient calcium changes, and neuronal firing in vitro and behaving animals. LifeCamp lifetime measurement is insensitive to artifacts that plague conventional intensity imaging and enables absolute comparison of baseline and transient calcium changes across cells, brain regions, and experimental conditions. Hence, LifeCamp is a powerful tool that enables a more accurate and in-depth understanding of neuronal activity and calcium signaling.

neuroscience↗

bioRxiv2025

A silent Kv channel subunit shapes PV neuron action potential waveform and short-term synaptic plasticity during high-frequency firing

Fast-spiking parvalbumin-positive (PV) neurons provide precisely timed, context-dependent inhibition within cortical circuits. PV neuron firing properties are specialized among cortical neurons, suggesting that they express a unique complement of ion channels. Here, we identify the PV-specific silent voltage-gated potassium (Kv) channel subunit Kv6.4 (encoded by Kcng4), whose role in cortical PV neuron physiology was previously unknown, as a modulator of both intrinsic and synaptic properties. Kv6.4 does not form functional channels on its own but, as shown in prior work, assembles with Kv2 subunits to create heterotetrameric channel complexes, effectively reducing Kv2-mediated delayed rectifier current. We find that Kcng4 expression is enriched within a distinct Pvalb-expressing subclass in primary somatosensory (S1) and motor (M1) cortex and emerges during postnatal development. In PV neurons, Kv6.4 loss reduces action potential (AP) height and width, hyperpolarizes the threshold and interspike potential, and accelerates AP upstroke particularly during repetitive firing. Kv6.4 loss, potentially due to the changes in AP waveform, also alters GABA release and paired-pulse depression at synapses made by PV onto pyramidal (PYR) neurons. The effects of Kv6.4 loss are amplified during high-frequency firing, within the physiological range of fast-spiking PV neurons, likely due to altered repolarization dynamics that accumulate across successive APs. These findings are thus consistent with the function of Kv6.4 in modifying Kv2-mediated delayed rectifier currents. Hence, Kv6.4 tunes the temporal precision of PV inhibitory output, a feature that may be critical for stable excitation-inhibition ratios and adaptive circuit function underlying learning and behavior. Significance StatementVoltage-gated ion channels are broadly expressed yet serve cell-type-specific functions. We demonstrate that the Kv6.4 silent subunit is selectively expressed by fast-spiking parvalbumin-positive (PV) inhibitory neurons among cortical neurons. In PV neurons, Kv6.4 modulates action potential (AP) waveform and GABA release onto excitatory neurons in a frequency-dependent manner, well within the physiological range of PV firing. This mechanism is likely important for preserving the temporal precision of inhibition, which is particularly critical for fast-spiking interneuron output. By shaping short-term synaptic plasticity during high-frequency firing, Kv6.4 provides a molecular and cell-type-specific mechanism for context-dependent tuning of inhibition within cortical circuits. This function may be especially relevant for sensory processing, experience-dependent plasticity, and the maintenance of excitation-inhibition ratios in vivo.

neuroscience↗

bioRxiv2025

Spectral envelopes of rhythmic facial movements predict intention and motor cortical representations

1Animals, including humans, use coordinated facial movements to sample the environment, ingest nutrients, and communicate. Rodents, in particular, produce rhythmic facial movements during spontaneous behavior and cognitive tasks. Measuring these movements precisely and linking them to neural activity remains challenging. We introduce face-rhythm, an unsupervised pipeline that combines markerless pointtracking, spectral analysis, and non-negative tensor component analysis to decompose facial video into a small set of interpretable components. Applied to videos of mice during a Pavlovian odor-reward task, a brain-machine interface (BMI) task, and free behavior, face-rhythm recovers human-interpretable behaviors such as whisking, sniffing, licking, and subtler motifs. The resulting components are consistent across animals, are sufficient to decode task variables or internal belief states, and explain cortical activity using a low-rank representation. We also find that the activity of neurons in face-associated primary motor cortex (M1) is predicted well by a phase-invariant spectral transformation of facial movements above [~]0.5 Hz, while slower movements retain a phase-variant representation better predicted by the instantaneous position of the face; individual neurons can show either or both forms of tuning. A systematic comparison against deeplearning point-tracking models, contrastive-learning embeddings, and vision-transformer features places face-rhythm competitively across tasks while also achieving the goal of producing a low-dimensional, interpretable description of rodent facial behavior that is closely linked to cortical activity.

neuroscience↗

bioRxiv2025

Synaptic sign switching mediates online dopamine updates

In the mammalian brain, excitatory and inhibitory synapses are generally distinct and have fixed synaptic signs. Therefore, unlike in artificial neural networks, learning in biological networks is thought to be manifested by plasticity mechanisms that modify synaptic weights but not signs. Here, we demonstrate experience-dependent sign switching at synapses between glutamate and GABA co-releasing neurons of the entopedunculus (EP) and their targets in the lateral habenula (LHb). Pairing of reward or punishment with activation of EP co-releasing neurons makes EP-LHb synapses relatively more inhibitory or excitatory, respectively. Synaptic sign switching modulates downstream dopaminergic signaling, correlates with recent dopamine updates, and contributes to reinforcement learning. These data unveil a plasticity mechanism that alters both synaptic signs and weights to rapidly update dopamine release and drive learning.

neuroscience↗

bioRxiv2025

Absolute measurement of fast and slow neuronal signals with fluorescence lifetime photometry at high temporal resolution

The concentrations of extracellular and intracellular signaling molecules, such as dopamine and cAMP, change over both fast and slow timescales and impact downstream pathways in a cell-type specific manner. Fluorescence sensors currently used to monitor such signals in vivo are typically optimized to detect fast, relative changes in concentration of the target molecule. They are less well suited to detect slowly-changing signals and rarely provide absolute measurements of either fast and slow signaling components. Here, we developed a system for fluorescence lifetime photometry at high temporal resolution (FLIPR) that utilizes frequency-domain analog processing to measure the absolute fluorescence lifetime of genetically-encoded sensors at high speed but with long-term stability and picosecond precision in freely moving mice. We applied FLIPR to investigate dopamine signaling in two functionally distinct regions in the striatum, the nucleus accumbens core (NAC) and the tail of striatum (TOS). We observed higher tonic dopamine levels at baseline in the TOS compared to the NAC and detected differential and dynamic responses in phasic and tonic dopamine to appetitive and aversive stimuli. Thus, FLIPR enables simple monitoring of fast and slow time-scale neuronal signaling in absolute units, revealing previously unappreciated spatial and temporal variation even in well-studied signaling systems.

neuroscience↗

bioRxiv2024

Hunger modulates exploration through suppression of dopamine signaling in the tail of striatum

Caloric depletion leads to behavioral changes that help an animal find food and restore its homeostatic balance. Hunger increases exploration and risk-taking behavior, allowing an animal to forage for food despite risks; however, the neural circuitry underlying this change is unknown. Here, we characterize how hunger restructures an animals spontaneous behavior as well as its directed exploration of a novel object. We show that hunger-induced changes in exploration are accompanied by and result from modulation of dopamine signaling in the tail of the striatum (TOS). Dopamine signaling in the TOS is modulated by internal hunger state through the activity of agouti-related peptide (AgRP) neurons, putative "hunger neurons" in the arcuate nucleus of the hypothalamus. These AgRP neurons are poly-synaptically connected to TOS-projecting dopaminergic neurons through the lateral hypothalamus, the central amygdala, and the periaqueductal grey. We thus delineate a hypothalamic-midbrain circuit that coordinates changes in exploration behavior in the hungry state.

neuroscience↗

bioRxiv2024

Projections between the globus pallidus externa and cortex span motor and non-motor regions

The globus pallidus externa (GPe) is a heterogenous nucleus of the basal ganglia, with intricate connections to other basal ganglia nuclei, as well as direct connections to the cortex. The anatomic, molecular and electrophysiologic properties of cortex-projecting pallidocortical neurons are not well characterized. Here we show that pallidocortical neurons project to diverse motor and non-motor cortical regions, are organized topographically in the GPe, and segregate into two distinct electrophysiological and molecular phenotypes. In addition, we find that the GPe receives direct synaptic input back from deep layers of diverse motor and non-motor cortical regions, some of which form reciprocal connections onto pallidocortical neurons. These results demonstrate the existence of a fast, closed-loop circuit between the GPe and the cortex which is ideally positioned to integrate information about behavioral goals, internal states, and environmental cues to rapidly modulate behavior.

neuroscience↗

bioRxiv2024

Elevated synaptic PKA activity and abnormal striatal dopamine signaling in Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder

AbstractLoss-of-function mutations in AKAP11 (a protein kinase A (PKA)-binding protein) greatly increase the risk of bipolar disorder and schizophrenia. To determine the neurobiological functions of AKAP11, we conduct multi-omic and neurobiological analyses of Akap11 mutant mouse brains. We find that AKAP11 is a key regulator of PKA proteostasis in the brain whose loss leads to dramatically increased levels of PKA subunits and phosphorylated PKA substrates, especially in synapses. Akap11 mutant mice show extensive transcriptomic changes throughout the brain, including prominent decreases in synapse-related genes sets. Gene expression is highly impacted in spiny projection neurons of the striatum, a brain region implicated in motivation, cognition and psychotic disorders. Real-time measurements of PKA activity reveal elevated basal PKA activity in the striatum of Akap11-/- mice, with exaggerated additional response to dopamine receptor antagonists. Behaviorally, Akap11 mutant mice show abnormally prolonged locomotor response to amphetamine, deficits in associative learning and contextual discrimination, as well as depression-like behaviors. Our study connects molecular changes to circuit dysfunction and behavioral disturbance in a genetically valid animal model of psychotic disorder.

neuroscience↗

bioRxiv2024

Widespread Neuroanatomical Integration and Distinct Electrophysiological Properties of Glioma-Innervating Neurons

Gliomas are the most common malignant primary brain tumors and are often associated with severe neurological deficits and mortality. Unlike many cancers, gliomas rarely metastasize outside the brain, indicating a possible dependency on unique features of brain microenvironment. Synapses between neurons and glioma cells exist, suggesting that glioma cells rely on neuronal inputs and synaptic signaling for proliferation. Yet, the locations and properties of neurons that innervate gliomas have remained elusive. In this study, we utilized transsynaptic tracing with a pseudotyped, glycoprotein-deleted rabies virus to specifically infect TVA and glycoprotein-expressing human glioblastoma cells in an orthotopic xenograft mouse model, allowing us to identify the neurons that form synapses onto the gliomas. Comprehensive whole-brain mapping revealed that these glioma-innervating neurons (GINs) consistently arise at brain regions, including diverse neuromodulatory centers and specific cortical layers, known to project to the glioma locations. Molecular profiling revealed that these long-range cortical GINs are predominantly glutamatergic, and subsets express both glutamatergic and GABAergic markers, whereas local striatal GINs are largely GABAergic. Electrophysiological studies demonstrated that while GINs share passive intrinsic properties with cortex-innervating neurons, their action potential waveforms are altered. Our study introduces a novel method for identifying and mapping GINs and reveals their consistent integration into existing location-dependent neuronal network involving diverse neurotransmitters and neuromodulators. The observed intrinsic electrophysiological differences in GINs lay the groundwork for future investigations into how these alterations may correspond with the postsynaptic characteristics of glioma cells. SignificanceWe have developed a novel system utilizing rabies virus-based monosynaptic tracing to directly visualize neurons that synapse onto human glioma cells implanted in mouse brain. This approach enables the mapping and quantitative analysis of these glioma-innervating neurons (GINs) in the entire mouse brain and overcomes previous barriers of molecular and electrophysiological analysis of these neurons due to the inability to identify them. Our findings indicate that GINs integrate into existing neural networks in a location-specific manner. Long-range GINs are mostly glutamatergic, with a subset expressing both glutamatergic and GABAergic markers and local striatal GINs are GABAergic, highlighting a complex neuromodulatory profile. Additionally, GINs exhibit unique action potential characteristics, distinct from similarly selected neurons in non-tumor-bearing brains. This study provides new insights into neuronal adaptations in response to forming putative synapses onto glioma, elucidating the intricate synaptic relationship between GINs and gliomas.

cancer biology↗

bioRxiv2024

Mixed representations of choice and outcome by GABA/glutamate cotransmitting neurons in the entopeduncular nucleus

The basal ganglia (BG) are an evolutionarily conserved and phylogenetically old set of sub-cortical nuclei that guide action selection, evaluation, and reinforcement. The entopeduncular nucleus (EP) is a major BG output nucleus that contains a population of GABA/glutamate cotransmitting neurons (EPSst+) that specifically target the lateral habenula (LHb) and whose function in behavior remains mysterious. Here we use a probabilistic switching task that requires an animal to maintain flexible relationships between action selection and evaluation to examine when and how GABA/glutamate cotransmitting neurons contribute to behavior. We find that EPSst+neurons are strongly engaged during this task and show bidirectional changes in activity during the choice and outcome periods of a trial. We then tested the effects of either permanently blocking cotransmission or modifying the GABA/glutamate ratio on behavior in well-trained animals. Neither manipulation produced detectable changes in behavior despite significant changes in synaptic transmission in the LHb, demonstrating that the outputs of these neurons are not required for on-going action-outcome updating in a probabilistic switching task.

neuroscience↗

bioRxiv2024

Developmental maturation of frontal cortical circuits impacts decision-making

In humans, frontal cortical circuits mature in parallel with the development of higher cognitive functions over the course of 15-20 years. In mice, behavior and brain structure change rapidly until reaching sexual maturity ([~]8 weeks of age). In contrast, the degree to which frontal cortices and the behaviors they support continue to develop in mice after this period is unclear. Here, we uncover age-related changes in the acquisition and execution of a probabilistic reward reinforcement task. Both young and old mice complete a similar number of trials per session, but 16-30-week-old mice obtain higher reward rates than younger mice. The older mice adjust their behavior more readily after failing to receive a reward, suggesting that age-dependent changes to circuits relevant to forming action-outcome associations, such as those in frontal associative cortices (FACs). Indeed, we identified cell-type and input-specific refinements of FAC circuits over the first 24 weeks of age, including protracted reductions in excitatory drive and increases in inhibition onto pyramidal cells. Dampening inhibitory activity in FAC alters behavior in a manner that counteracts the age-related differences. Together, these reveal an extended period of synaptic maturation in FAC that directly impacts age-related changes in decision-making.

neuroscience↗

bioRxiv2023

Comment on 'Accumbens cholinergic interneurons dynamically promote dopamine release and enable motivation'

Acetylcholine is widely believed to modulate the release of dopamine in the striatum of mammals. Experiments in brain slices clearly show that synchronous activation of striatal cholinergic interneurons is sufficient to drive dopamine release via axo-axonal stimulation of nicotinic acetylcholine receptors. However, evidence for this mechanism in vivo has been less forthcoming. A recent paper in eLife (Mohebi et al., 2023) reported that, in awake behaving rats, optogenetic activation of striatal cholinergic interneurons with blue light readily evokes dopamine release measured with the red fluorescent sensor RdLight1. Here, we show that blue light alone alters the fluorescent properties of RdLight1 in a manner that may be misconstrued as phasic dopamine release, and that this artefactual photoactivation can account for the effects attributed to cholinergic interneurons. Our findings indicate that measurements of dopamine using the red-shifted fluorescent sensor RdLight1 should be interpreted with caution when combined with optogenetics. In light of this and other publications that did not observe large acetylcholine-evoked dopamine transients in vivo, the conditions under which such release occurs in behaving animals remain unknown.

neuroscience↗

bioRxiv2023

Striatum supports fast learning but not memory recall

Animals learn to carry out motor actions in specific sensory contexts to achieve goals. The striatum has been implicated in producing sensory-motor associations, yet its contribution to memory formation or recall is not clear. To investigate the contribution of striatum to these processes, mice were taught to associate a cue, consisting of optogenetic activation of striatum-projecting neurons in visual cortex, with forelimb reaches to access food pellets. As necessary to direct learning, striatal neural activity encoded both the sensory context and outcome of reaching. With training, the rate of cued reaching increased, but brief optogenetic inhibition of striatal activity arrested learning and prevented trial-to-trial improvements in performance. However, the same manipulation did not affect performance improvements already consolidated into short- (within an hour) or long-term (across days) memories. Hence, striatal activity is necessary for trial-to-trial improvements in task performance, leading to plasticity in other brain areas that mediate memory recall.

neuroscience↗

bioRxiv2023

A Cre-dependent reporter mouse for quantitative real-time imaging of Protein Kinase A activity dynamics

Intracellular signaling dynamics play a crucial role in cell function. Protein kinase A (PKA) is a key signaling molecule that has diverse functions, from regulating metabolism and brain activity to guiding development and cancer progression. We previously developed an optical reporter, FLIM-AKAR, that allows for quantitative imaging of PKA activity via fluorescence lifetime imaging microscopy and photometry. However, using viral infection or electroporation for the delivery of FLIM-AKAR is invasive, cannot easily target sparse or hard-to-transfect/infect cell types, and results in variable expression. Here, we developed a reporter mouse, FL-AK, which expresses FLIM-AKAR in a Cre-dependent manner from the ROSA26 locus. FL-AK provides robust and consistent expression of FLIM-AKAR over time. Functionally, the mouse line reports an increase in PKA activity in response to activation of both Gs and Gq-coupled receptors in brain slices. In vivo, FL-AK reports PKA phosphorylation in response to neuromodulator receptor activation. Thus, FL-AK provides a quantitative, robust, and flexible method to reveal the dynamics of PKA activity in diverse cell types.

neuroscience↗