Biology subjects

Arnold, D. B.

Publications and source records attributed to Arnold, D. B..

10 recordsLinked to original sources

bioRxiv2026

Protein-guided RNA barcoding links transcriptomes to synaptic architecture

Mammalian brain function relies on the precise synaptic architecture of diverse cell types, yet scalable methods for linking a neurons transcriptomic profile to its neuroanatomy remain limited. We present Synapse-seq, an in vivo strategy in which cell-identifying barcoded mRNAs are routed to subcellular compartments via targeting proteins and detected by single-cell and spatial genomics. Using AAV delivery for minimal perturbation of gene expression, we directed barcodes to presynaptic terminals (via synaptophysin) in four distinct circuits, or to postsynaptic sites (via nanobodies to endogenous PSD95) of hippocampal excitatory neurons. In the mouse primary visual cortex, presynaptic Synapse-seq recovered known long-range projections and discovered cortical layer subtypes with distinct thalamic innervation. In the anterior cortex, we elucidated simple topographic rules of corticostriatal innervation: intratelencephalic neurons followed a continuous depth-to-target gradient, while extratelencephalic neurons exhibited striatal collaterals that spatially correlated with medullary innervation. Finally, postsynaptic barcoding of excitatory neurons revealed cell type-specific variation in dendritic architectures across and within hippocampal subfields. These data establish Synapse-seq as a versatile, genomics-based approach for the integrated definition of molecular identity and synaptic organization across mammalian brains.

neuroscience↗

bioRxiv2026

Transsynaptic neural circuit mapping of ventral hippocampus motivational control systems

The ventral hippocampus contributes to food intake regulation and a range of motivational and memory processes, and its dysfunction is associated with several cognitive and behavioral disorders. However, its circuit-level organization remains incompletely understood. Ventral CA1 (CA1v) neurons send projections to several regions involved in motivational control. Here we focus on three major forebrain targets: the nucleus accumbens shell (ACBsh), medial prefrontal cortex (mPFC), and lateral hypothalamic area (LHA). We mapped the upstream and downstream circuitry of CA1v neurons defined by their projections to these target regions in rats using complementary transsynaptic anterograde and retrograde viral tracing approaches. Monosynaptic outputs to ACBsh, mPFC, and LHA were targeted using ATLAS, a novel transsynaptic anterograde viral approach that drives Cre recombinase in neurons receiving glutamatergic synaptic transmission from the CA1v. Second-order projections arising from these defined pathways were then mapped using a Cre-dependent anterograde viral tracing strategy. In parallel, upstream inputs to CA1v neurons projecting to each downstream target were mapped using a conditional retrograde glycoprotein-deleted rabies viral approach. Anterograde tracing revealed both shared and pathway-specific second-order targets, including bidirectional CA1v projections. Retrograde tracing confirmed expected inputs (e.g., CA3) and uncovered previously unrecognized cortical sources that differed across downstream projection-defined CA1v subpopulations. Together, these findings delineate pathway-specific, multinode circuits linking CA1v neurons to key motivational systems that may inform future therapeutic strategies for disorders involving ventral hippocampal dysfunction.

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bioRxiv2025

Negative-Valence Neurons in the Larval Zebrafish Pallium

An organisms survival depends on the rapid classification of sensory events as either harmful or beneficial. In mammals, this computation is partially performed by neurons in the amygdala that respond to signals with negative or positive valence. The larval zebrafish pallium is thought to contain homologs of the mammalian amygdala, isocortex, and hippocampus; however, the signals encoded by pallial neurons remain largely uncharacterized. Using two-photon light-sheet microscopy to image 7-9-day-old zebrafish that express pan-neuronal GCaMP6s, we recorded calcium dynamics throughout the brain while presenting a panel of strongly aversive stimuli including infrared heat, electric shock, and a whole-field looming shadow, together with milder threats including vibration, loud sound, light transitions, and a partial looming stimulus. A compact cluster of neurons in the rostrolateral dorsal pallium (Rl) responded vigorously to strongly noxious and fully looming stimuli, but not to the milder cues. In contrast, neurons in the ventromedial pallium and habenula responded to all stimuli tested. Rl neurons are characterized by high Tiam2a expression, suggesting they can be genetically accessed. Thus, our results identify a locus of negative valence neurons in the teleost pallium.

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bioRxiv2025

A ventral hippocampus to nucleus accumbens pathway regulates impulsivity

Heightened impulsivity is attributed with substance abuse disorders, gambling, and obesity. The ventral hippocampus (vHPC) has recently been linked with impulse control, yet the neurobiological and behavioral mechanisms through which this control occurs are unknown. A subset of vHPC neurons project to the nucleus accumbens (ACB), a brain region known for regulating reward and motivation. Here, we evaluated the role of vHPC-ACB signaling in food-directed impulsivity using fiber photometry and transsynaptic chemogenetic and behavioral approaches. Male and female rats were trained in the differential reinforcement of low rates of responding (DRL) test of impulsive action, where they learn to withhold lever presses for 20 seconds to obtain a palatable food reward. Photometry recordings during DRL revealed analogous elevations in calcium-dependent activity in the vHPC and ACB during the 5s immediately prior to a non-impulsive vs. an impulsive response. Chemogenetic silencing of ACB-projecting vHPC neurons elevated impulsive responses in DRL relative to vehicle treatment in males but not females, yet had no effect on home cage food intake, operant-based motivation to work for palatable food, impulsive choice, or anxiety-like behavior. To determine whether this impulse control circuit requires vHPC->ACB communication independent of collateral targets of ACB-projecting vHPC neurons, we utilized a novel transsynaptic viral approach to selectively silence ACB neurons that receive synaptic glutamatergic signaling from the vHPC. Results reveal that inhibition of ACB neurons receiving vHPC signaling elevates impulsive action in the DRL task relative to vehicle treatment. Collective results reveal a hippocampal-striatal circuit that regulates impulsive action in males.

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bioRxiv2024

A toolbox for ablating excitatory and inhibitory synapses

Recombinant optogenetic and chemogenetic proteins are potent tools for manipulating neuronal activity and controlling neural circuit function. However, there are few analogous tools for manipulating the structure of neural circuits. Here, we introduce three rationally designed genetically encoded tools that use E3 ligase-dependent mechanisms to trigger the degradation of synaptic scaffolding proteins, leading to functional ablation of synapses. First, we developed a constitutive excitatory synapse ablator, PFE3, analogous to the inhibitory synapse ablator GFE3. PFE3 targets the RING domain of the E3 ligase Mdm2 and the proteasome-interacting region of Protocadherin 10 to the scaffolding protein PSD-95, leading to efficient ablation of excitatory synapses. In addition, we developed a light-inducible version of GFE3, paGFE3, using a novel photoactivatable complex based on the photocleavable protein PhoCl2c. paGFE3 degrades Gephyrin and ablates inhibitory synapses in response to 400 nm light. Finally, we developed a chemically inducible version of GFE3, chGFE3, which degrades inhibitory synapses when combined with the bio-orthogonal dimerizer HaloTag ligand-trimethoprim. Each tool is specific, reversible, and capable of breaking neural circuits at precise locations.

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bioRxiv2024

Prefrontal Cortex subregions provide distinct visual and behavioral feedback modulation to the Primary Visual Cortex

The mammalian Prefrontal Cortex (PFC) has been suggested to modulate sensory information processing across multiple cortical regions via long-range axonal projections. These axonal projections arise from PFC subregions with unique brain-wide connectivity and functional repertoires, which may provide the architecture for modular feedback intended to shape sensory processing. Here, we used axonal tracing, axonal and somatic 2-photon calcium imaging, and chemogenetic manipulations in mice to delineate how projections from the Anterior Cingulate Cortex (ACA) and ventrolateral Orbitofrontal Cortex (ORB) of the PFC modulate sensory processing in the primary Visual Cortex (VISp) across behavioral states. Structurally, we found that ACA and ORB had distinct patterning of projections across cortical regions and layers, monosynaptically targeting both excitatory and inhibitory neuronal cell types in these areas. ACA axons in VISp had a stronger representation of visual stimulus information than ORB axons, but both projections showed non-visual, behavior-dependent activity. ACA input to VISp enhanced the encoding of visual stimuli by VISp neurons, and modulation of visual responses scaled with arousal. On the other hand, ORB input shaped movement and arousal related modulation of VISp visual responses, but surprisingly reduced the encoding of high-contrast visual stimuli. Thus, ACA and ORB feedback have separable projection patterns and encode distinct visual and behavioral information, putatively providing the substrate for their unique effects on visual representations and behavioral modulation in VISp. Our results offer a refined model of cortical hierarchy and its impact on sensory information processing, whereby specific PFC projections contribute uniquely to VISp activity during discrete behavioral states.

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bioRxiv2023

ATLAS: A rationally designed anterograde transsynaptic tracer

Neural circuits, which constitute the substrate for brain processing, can be traced in the retrograde direction, from postsynaptic to presynaptic cells, using methods based on introducing modified rabies virus into genetically marked cell types. These methods have revolutionized the field of neuroscience. However, similarly reliable, transsynaptic, and non-toxic methods to trace circuits in the anterograde direction are not available. Here, we describe such a method based on an antibody-like protein selected against the extracellular N-terminus of the AMPA receptor subunit GluA1 (AMPA.FingR). ATLAS (Anterograde Transsynaptic Label based on Antibody-like Sensors) is engineered to release the AMPA.FingR and its payload, which can include Cre recombinase, from presynaptic sites into the synaptic cleft, after which it binds to GluA1, enters postsynaptic cells through endocytosis and subsequently carries its payload to the nucleus. Testing in vivo and in dissociated cultures shows that ATLAS mediates monosynaptic tracing from genetically determined cells that is strictly anterograde, synaptic, and non-toxic. Moreover, ATLAS shows activity dependence, which may make tracing active circuits that underlie specific behaviors possible.

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bioRxiv2023

Molecular layer disinhibition unlocks climbing-fiber-instructed motor learning in the cerebellum

Climbing fibers supervise cerebellar learning by providing signals to Purkinje cells (PCs) that instruct adaptive changes to mistakenly performed movements. Yet, climbing fibers are regularly active, even during well performed movements, suggesting that a mechanism dynamically regulates the ability of climbing fibers to induce corrective plasticity in response to motor errors. We found that molecular layer interneurons (MLIs), whose inhibition of PCs powerfully opposes climbing-fiber-mediated excitation, serve this function. Optogenetically suppressing the activity of floccular MLIs in mice during the vestibulo-ocular reflex (VOR) induces a learned increase in gain despite the absence of performance errors. Suppressing MLIs when the VOR is mistakenly underperformed reveled that their inhibitory output is necessary to orchestrate gain-increase learning by conditionally permitting climbing fibers to instruct plasticity induction during ipsiversive head turns. Ablation of an MLI circuit for PC disinhibition prevents gain-increase learning during VOR performance errors which was rescued by re-imposing PC disinhibition through MLI activity suppression. Our findings point to a decisive role for MLIs in gating climbing-fiber-mediated learning through their context-dependent inhibition of PCs.

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bioRxiv2023

Basolateral amygdala oscillations enable fear learning in a biophysical model

The basolateral amygdala (BLA) is a key site where fear learning takes place through synaptic plasticity. Rodent research shows prominent low theta ([~]3-6 Hz), high theta ([~]6-12 Hz), and gamma (>30 Hz) rhythms in the BLA local field potential recordings. However, it is not understood what role these rhythms play in supporting the plasticity. Here, we create a biophysically detailed model of the BLA circuit to show that several classes of interneurons (PV, SOM, and VIP) in the BLA can be critically involved in producing the rhythms; these rhythms promote the formation of a dedicated fear circuit shaped through spike-timing-dependent plasticity. Each class of interneurons is necessary for the plasticity. We find that the low theta rhythm is a biomarker of successful fear conditioning. The model makes use of interneurons commonly found in the cortex and, hence, may apply to a wide variety of associative learning situations. SignificanceOur paper accounts for the experimental evidence showing that amygdalar rhythms exist, suggests network origins for these rhythms, and points to their central role in the mechanisms of plasticity involved in associative learning. It is one of the few papers to address high-order cognition with biophysically detailed models, which are sometimes thought to be too detailed to be adequately constrained. Our paper provides a template for how to use information about brain rhythms to constrain biophysical models. It shows in detail, for the first time, how multiple interneurons help to provide time scales necessary for some kinds of spike-timing-dependent plasticity (STDP). It spells out the conditions under which such interactions between interneurons are needed for STDP and why. Finally, our work helps to provide a framework by which some of the discrepancies in the fear learning literature might be reevaluated. In particular, we discuss issues about Hebbian plasticity in fear learning; we show in the context of our model how neuromodulation might resolve some of those issues. The model addresses issues more general than that of fear learning since it is based on interactions of interneurons that are prominent in the cortex, as well as the amygdala.

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bioRxiv2018

Quantitative synapse analysis for cell-type specific connectomics

Anatomical methods for determining cell-type specific connectivity are essential to inspire and constrain our understanding of neural circuit function. We developed new genetically-encoded reagents for fluorescence-synapse labeling and connectivity analysis in brain tissue, using a fluorogen-activating protein (FAP)-or YFP-coupled, postsynaptically-localized neuroligin-1 targeting sequence (FAP/YFPpost). Sparse viral expression of FAP/YFPpost with the cell-filling, red fluorophore dTomato (dTom) enabled high-throughput, compartment-specific localization of synapses across diverse neuron types in mouse somatosensory cortex. High-resolution confocal image stacks of virally-transduced neurons were used for 3D reconstructions of postsynaptic cells and automated detection of synaptic puncta. We took advantage of the bright, far-red emission of FAPpost puncta for multichannel fluorescence alignment of dendrites, synapses, and presynaptic neurites to assess subtype-specific inhibitory connectivity onto L2 neocortical pyramidal (Pyr) neurons. Quantitative and compartment-specific comparisons show that PV inputs are the dominant source of inhibition at both the soma and across all dendritic branches examined and were particularly concentrated at the primary apical dendrite, a previously unrecognized compartment of L2 Pyr neurons. Our fluorescence-based synapse labeling reagents will facilitate large-scale and cell-type specific quantitation of changes in synaptic connectivity across development, learning, and disease states.

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