Biology subjects

Park, P.

Publications and source records attributed to Park, P..

At least 19 recordsLinked to original sources

bioRxiv2026

AFIDs-Validator: An Open-Access AI-Guided Platform for Learning Anatomical Landmark Placement

Accurate localization of anatomical landmarks is a foundational skill in anatomy and imaging that is often taught informally through expert mentorship, requiring access to data and desktop software. There is no openly accessible, interactive resource that teaches neuroanatomy with quantitative feedback. We present the AFIDs-Validator (validator.afids.io), an open-access, browser-based platform that pairs guided instruction with quantitative assessment. The platform combines (1) a learning mode in which a language-model neuroanatomy tutor operates inside an MRI viewer, giving anatomy-first instruction that responds to the learner's current image slice, orientation, and cursor position; and (2) a validation engine that accepts a learner's landmark file and returns per-landmark Euclidean error against expert-annotated references spanning 21 brain templates. To make the feedback interpretable, we analyzed 15,000 landmark annotations across 132 human subjects and found that landmark difficulty varies fourfold (median error ranged from 0.37 mm at the anterior commissure to 1.50 mm at the temporal horns) with heavy-tailed distributions at every landmark. These distributions are compiled into per-landmark reliability priors, so learners are scored against the empirical spread of trained raters rather than an arbitrary threshold, and difficult landmarks are not mistaken for poor performance. The AFIDs-Validator requires no installation, licensed software, or local data, and all code, reference data, and tutor design are openly released.

scientific communication and education↗

bioRxiv2026

A CRISPR-Cas9 platform for primary human hepatocytes enables arrayed screening and in vivo validation of HBV host factors

More than two million deaths annually are attributed to liver-related conditions, making primary human hepatocytes (PHH) an invaluable in vitro model for studying liver pathophysiology and the molecular mechanisms underlying hepatic diseases. However, because PHH do not proliferate in culture, CRISPR gene editing has been highly inefficient. Here, we report lipofection- and lentivirus-mediated protocols for CRISPR-Cas9 delivery in mouse-passaged primary human hepatocytes (mpPHH), a system that enables PHH expansion in liver-humanized mice. We achieve robust gene editing efficiencies exceeding 90% in mpPHH while maintaining cell viability. We demonstrate the utility of these protocols by disrupting CYP3A4 to impair xenobiotic metabolism and by showing that edited mpPHH efficiently engraft and expand in mice, generating liver-humanized animals. We establish the feasibility of arrayed CRISPR screening in mpPHH using an 85-gene screen to identify host factors influencing hepatitis B virus (HBV) infection, and validate key findings in humanized mice by targeting the HBV entry receptor SLC10A1 (NTCP), which reduced viral infection in vivo. Our methodology enables scalable genetic manipulation of mpPHH, opening new avenues for HBV research and liver disease modeling.

genomics↗

bioRxiv2026

Synaptic engram underlies memory

Memory encoding cells, or engram cells, are sparsely distributed across the brain. Recent findings have shown that memory formation coincides with the strengthening of interregional synaptic connectivity between engram ensembles. However, whether this learning-induced synaptic reorganization causally supports memory, independently or in concert with heterosynaptic and intrinsic plasticity, remains elusive. Here we developed optically implemented spike-timing-dependent plasticity (oSTDP), which induces synaptic depression selectively at target synapses by controlling the relative timing of pre- and postsynaptic activity. In vivo application of oSTDP to the synapses between entorhinal cortex (EC) and dentate gyrus (DG) engram cells caused a significant synaptic depression and the resultant memory impairment. Our results demonstrate that plasticity of functional connectivity between memory-encoding ensembles causally underlies memory.

neuroscience↗

bioRxiv2026

Intranasal CRISPR- lipid nanoparticles targeting MAPK9 reduce neuroinflammation after traumatic brain injury

Traumatic brain injury (TBI) triggers a sustained neuroinflammatory response driven by activated microglia, which contributes to secondary injury and long-term neurological dysfunction. Therapeutic reprogramming of microglial activation from a pro-inflammatory (M1-like) to a reparative (M2-like) phenotype represents a promising strategy; however, the lack of cell-specific targeting within an injured brain has limited clinical translation. Here, we developed a targeted gene-editing nanotherapy to modulate post-traumatic innate immune responses. Lipid nanoparticles (LNPs) encapsulating CRISPR-Cas12a components were engineered to target mitogen-activated protein kinase-9 (MAPK9), a key regulator of pro-inflammatory signaling, and were conjugated with an Iba-1 antibody (Iba-1-CRISPR-LNPs) to enable selective targeting of microglia. In vitro, MAPK9 editing in primary macrophages inhibited M1 polarization and promoted an M2-like phenotype, leading to reduced production of pro-inflammatory cytokines. In a TBI mouse model, intranasal administration of Iba-1-CRISPR-LNPs achieved efficient delivery to the injured brain, with selective localization in Iba-1+ microglia. MAPK9 CRISPR targeting significantly attenuated microglial activation, reduced central and peripheral inflammatory responses, and decreased pro-inflammatory cytokine levels. Importantly, this approach demonstrated a favorable safety profile, with no detectable toxicity across major organs. Collectively, these findings establish a non-viral, intranasal CRISPR-based strategy for cell-specific modulation of neuroinflammation following TBI. Targeted genome editing of MAPK9 effectively reprograms microglial activation and attenuates acute inflammatory responses, highlighting its potential as a promising and translationally relevant therapeutic platform for TBI and related neuroinflammatory disorders.

neuroscience↗

bioRxiv2026

A dendrite-resolved, in vivo transfer function from spike patterns to dendritic Ca2+

Dendrites transform local electrical activity into intracellular Ca2+ signals that drive plasticity1,2, yet the voltage[->]Ca2+ mapping during natural behavior remains poorly defined. Here, we measure this transfer function via simultaneous voltage and Ca2+ imaging throughout the dendritic arbors of hippocampal CA2 pyramidal neurons in behaving mice. Dendritic Ca2+ exhibited a hierarchical activation pattern dominated by back-propagating action potentials: simple spikes primarily drove somatic and proximal Ca2+, whereas complex spikes produced larger somatic Ca2+ signals and propagated farther into distal dendrites, sometimes in a branch-selective manner. Dendrite-restricted co-activation of voltage and Ca2+ without concurrent somatic events was rare. A biophysics-inspired model accurately predicted local Ca2+ transients from local voltage waveforms. Our data and model provide a quantitative understanding of when - and why - dendritic Ca2+ signals in CA2 pyramidal cells arise during behavior.

neuroscience↗

bioRxiv2026

Dendritic excitations primarily mediate back-propagation in CA1 pyramidal neurons during behavior

Dendrites integrate synaptic inputs to trigger action potentials, and dendrites carry back-propagating action potentials (bAPs) to synapses where these signals contribute to plasticity. Despite strong evidence for a rich repertoire of nonlinear dendritic excitations, the in vivo roles of these excitations in dendritic integration and back-propagation remain uncertain. Here, we used high-speed voltage imaging through a chronically implanted microprism to map membrane potential dynamics from basal to apical dendrites of CA1 neurons in mice navigating in a virtual reality environment. Despite complex dendritic branch morphology, the dynamics were largely captured by 2 or 3 electrical compartments: basal, soma, and apical. Fast dendritic spikes almost always started from bAPs, indicating that dendritic spikes are primarily a consequence rather than a cause of somatic spiking. These fast spikes sometimes triggered slower apical dendritic plateau depolarizations, which drove complex spikes at the soma. We found that the biophysics of dendritic excitability determined the distribution of simple and complex spikes across a place field. Our results show how CA1 pyramidal neurons convert synaptic inputs to spiking outputs and suggest a primary role of dendritic nonlinearities in mediating activity-dependent plasticity.

neuroscience↗

bioRxiv2025

Telomerase mRNA-Lipid nanoparticles attenuate neuroinflammation after traumatic brain injury in mice

Traumatic brain injury (TBI) is a leading cause of chronic neurological disability, yet no disease-modifying therapy exists. Emerging evidence indicates that TBI activates cellular aging programs, including telomere erosion and persistent inflammation, that contribute to progressive neurodegeneration. Telomerase reverse transcriptase (TERT) preserves telomere homeostasis and provides cytoprotective effects in the central nervous system, but has not been therapeutically targeted after TBI. Here, we developed an mRNA nanotherapy consisting of mouse TERT mRNA encapsulated in lipid nanoparticles (mTERT-LNPs) and evaluated it in a controlled cortical impact model of moderate TBI. We first established that TBI transiently disrupts TERT biology, with reduced cortical TERT mRNA and shortened telomeres at 3 days post-injury (dpi), followed by partial recovery by 14 dpi. mTERT-LNPs were well tolerated in vitro and in vivo. Following intravenous delivery in the acute post-injury window, LNPs localized to the injured brain and displayed expected peripheral biodistribution. A single systemic dose increased cortical TERT mRNA and protein and partially restored telomere length at 3 dpi. TERT mRNA delivery significantly reduced Iba1+ microglial activation and suppressed pro-inflammatory cytokines, with modest increases in anti-inflammatory markers. Systemically, mTERT-LNPs lowered serum C-reactive protein and malondialdehyde, indicating reduced peripheral inflammation and oxidative stress, without adverse effects on body weight or peripheral organ histology. Several outcomes showed sex-dependent patterns. Collectively, these data provide the first in vivo evidence that telomerase therapy can modulate telomere biology and neuroinflammation after TBI, supporting mRNA-LNP-mediated TERT restoration as a scalable, mechanistically grounded strategy for disease modification in TBI and related disorders. Significant statementTraumatic brain injury (TBI) can initiate progressive brain changes that worsen long after the initial impact, and no therapy directly slows or prevents this decline. A key contributor may be "accelerated aging" in injured tissue, including telomere damage (protective chromosome ends) and persistent neuroinflammation driven by activated immune cells. This study is significant because it tests a targeted way to disrupt these processes by restoring telomerase reverse transcriptase (TERT), which helps maintain telomeres and cellular resilience. Using a clinically validated mRNA-lipid nanoparticle platform, a single intravenous dose increased brain TERT, partially restored telomere length, and reduced neuroinflammation and systemic oxidative stress without obvious toxicity. These findings connect telomere dysfunction to a scalable disease-modifying strategy for TBI and related neurodegenerative conditions.

neuroscience↗

bioRxiv2025

DENDRO: Recovery and denoising of whole-tree dendritic voltagefrom 2D voltage movies

The ability to image voltage at high spatiotemporal resolution across an entire dendritic tree would represent a major advance in systems and circuit neuroscience. Recent advances in genetically encoded voltage indicators (GEVIs) have brought this possibility closer to reality. However, due to fundamental tradeoffs between imaging speed, resolution, SNR, and volume, this goal has remained out of reach. Here we develop a computational method that fuses 3D anatomical information with 2D voltage video data, yielding full time-varying 3D voltage estimates. Our method, termed DENDRO, comprises two steps. In step one, we use the anatomical data to build a microscope model which maps from voltages along the tree to observed fluorescence at the imaging plane. By exploiting local spatial smoothness of the voltage signal, we parameterize the voltage signal using a set of local basis functions, which reduces the dimensionality of the problem and allows us to approximately invert the microscope model. This step leverages spatial but not temporal smoothness of the underlying signal and yields noisy 3D estimates. In step two, we train a lightweight self-supervised neural network to perform spatiotemporal denoising of the inferred voltages. On simulated data, we find that DENDRO is able to recover voltages at high accuracy across an entire dendritic tree. On real voltage movies from hippocampal slices, DENDRO recovers known dendritic phenomena at single trial resolution and millisecond time-scales, and allows visualization of backpropagating action potentials in 3D.

neuroscience↗

bioRxiv2025

Computational Design of Miniprotein Binders Targeting the Viral Entry in Chikungunya and Dengue, Neglected Tropical Diseases

Neglected Tropical Diseases (NTDs) continue to be a global health concern, affecting millions worldwide. Arboviruses such as Chikungunya virus (CHIKV) and Dengue virus (DENV) are particularly threatening due to the lack of specific antiviral treatments, the continual emergence of new variants, and their mosquito vectors. These challenges underscore the urgent need for novel antiviral strategies. Here, we apply computational methods to design miniprotein binders targeting critical viral entry components: the CHIKV envelope, and DENV fusion loop. Our protocol integrates classical and deep learning-based approaches and can be generalizable to other protein targets. Promising binder candidates were further evaluated through all-atom Molecular Dynamics simulations to assess structural stability and binding interactions. We provide complete transparency and a detailed rationale for each design step to facilitate adaptation of these protocols to other neglected disease targets. While the miniproteins presented here represent promising antiviral leads, experimental validation remains essential to confirm their biological activity.

biophysics↗

bioRxiv2025

The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data

The Data Distillery Knowledge Graph (DDKG) is a framework for semantic integration and querying of biomedical data across domains. Built for the NIH Common Fund Data Ecosystem, it supports translational research by linking clinical and experimental datasets in a unified graph model. Clinical standards such as ICD-10, SNOMED, and DrugBank are integrated through UMLS, while genomics and basic science data are structured using ontologies and standards such as HPO, GENCODE, Ensembl, STRING, and ClinVar. The DDKG uses a property graph architecture based on the UBKG infrastructure and supports ontology-based ingestion, identifier normalization, and graph-native querying. The system is modular and can be extended with new datasets or schema modules. We demonstrate its utility for informatics queries across eight use cases, including regulatory variant analysis, tissue-specific expression, biomarker discovery, and cross-species variant prioritization. The DDKG is accessible via a public interface, a programmatic API, and downloadable builds for local use.

bioinformatics↗

bioRxiv2024

GoMartini 3: From large conformational changes in proteins to environmental bias corrections

Coarse-grained modeling has become an important tool to supplement experimental measurements, allowing access to spatio-temporal scales beyond all-atom based approaches. The G[o]Martini model combines structure- and physics-based coarse-grained approaches, balancing computational efficiency and accurate representation of protein dynamics with the capabilities of studying proteins in different biological environments. This paper introduces an enhanced G[o]Martini model, which combines a virtual-site implementation of G[o] models with Martini 3. The implementation has been extensively tested by the community since the release of the new version of Martini. This work demonstrates the capabilities of the model in diverse case studies, ranging from protein-membrane binding to protein-ligand interactions and AFM force profile calculations. The model is also versatile, as it can address recent inaccuracies reported in the Martini protein model. Lastly, the paper discusses the advantages, limitations, and future perspectives of the Martini 3 protein model and its combination with G[o] models.

biophysics↗

bioRxiv2024

Photophysics-informed two-photon voltage imaging using FRET-opsin voltage indicators

Microbial rhodopsin-derived genetically encoded voltage indicators (GEVIs) are powerful tools for mapping bioelectrical dynamics in cell culture and in live animals. Forster resonance energy transfer (FRET)-opsin GEVIs use voltage-dependent changes in opsin absorption to modulate the fluorescence of an atached fluorophore, achieving high brightness, speed, and voltage sensitivity. However, the voltage sensitivity of most FRET-opsin GEVIs has been reported to decrease or vanish under two-photon (2P) excitation. Here we investigated the photophysics of the FRET-opsin GEVIs Voltron1 and 2. We found that the voltage sensitivity came from a photocycle intermediate, not from the opsin ground state. The voltage sensitivities of both GEVIs were nonlinear functions of illumination intensity; for Voltron1, the sensitivity reversed sign under low-intensity illumination. Using photocycle-optimized 2P illumination protocols, we demonstrate 2P voltage imaging with Voltron2 in barrel cortex of a live mouse. These results open the door to high-speed 2P voltage imaging of FRET-opsin GEVIs in vivo. TeaserVoltage sensitivity in FRET-opsin indicators comes from a photocycle intermediate, reachable via optimized 2P excitation.

neuroscience↗

bioRxiv2024

Solaris: a panel of bright and sensitive hybrid voltage indicators for imaging membrane potential in cultured neurons

Dynamic changes in the membrane potential underlie neuronal activities. Fluorescent voltage indicators allow optical recording of electrical signaling across a neuronal population with cellular precision and at millisecond-level temporal resolution. Here we report the design and characterization of a chemigenetic hybrid voltage indicator, Solaris, in which a circularly permuted HaloTag is inserted into the first extracellular loop of Acetabularia rhodopsin. Solaris is compatible with fluorogenic HaloTag ligands JF525, JF549, JF552, JF585, and JF635. The most sensitive conjugate, Solaris585, has more than 2-fold higher voltage sensitivity than the spectrally similar Voltron2585 ({Delta}F/F0 = -28.1 {+/-} 1.3% versus -12.3 {+/-} 0.7% per action potential in cultured neurons). Solaris585 supports the measurement of optogenetically evoked spike activity or dual-color imaging in conjunction with green-emitting calcium or glutamate indicators. Solaris indicators are also applicable to fluorescence lifetime imaging, which probes the absolute membrane potential. This new hybrid voltage indicator is a valuable tool for imaging neuronal electrophysiological activities in cultured cells with substantially improved dynamic range compared to previous hybrid indicators.

neuroscience↗

bioRxiv2023

All-optical mapping of cAMP transport reveals rules of sub-cellular localization

Cyclic adenosine monophosphate (cAMP) is a second messenger that mediates diverse intracellular signals. Studies of cAMP transport in cells have produced wildly different results, from reports of nearly free diffusion to reports that cAMP remains localized in nanometer-scale domains. We developed an all-optical toolkit, cAMP-SITES, to locally perturb and map cAMP transport. In MDCK cells and in cultured neurons, cAMP had a diffusion coefficient of [~]130 {micro}m2/s, similar to the diffusion coefficients of other small molecules in cytoplasm. In neuronal dendrites, a balance between diffusion and degradation led to cAMP domains with a length-scale of 27 {+/-} 11 {micro}m (mean {+/-} s.d.). Geometrical confinement by membranes led to subcellular variations in cAMP concentration, but we found no evidence of nanoscale domains or of distinct membrane-associated and cytoplasmic pools. We discuss the scaling relations which govern diffusible signaling in tube-shaped structures.

biophysics↗

bioRxiv2023

Dendritic voltage imaging reveals biophysical basis of associative plasticity rules

Dendrites on neurons support nonlinear electrical excitations, but the computational significance of these events is not well understood. We developed molecular, optical, and analytical tools to map sub-millisecond voltage dynamics throughout the dendritic trees of CA1 pyramidal neurons under diverse optogenetic and synaptic stimulus patterns, in acute brain slices. We observed history-dependent spike back-propagation in distal dendrites, driven by locally generated Na+ spikes (dSpikes). Dendritic depolarization created a transient window for dSpike propagation, opened by A-type KV channel inactivation, and closed by slow NaV inactivation. Collisions of dSpikes with synaptic inputs triggered calcium channel and N-methyl-D-aspartate receptor (NMDAR)-dependent plateau potentials, with accompanying complex spikes at the soma. This hierarchical ion channel network acts as a spike-rate accelerometer, providing an intuitive picture of how dendritic excitations shape associative plasticity rules.

neuroscience↗

bioRxiv2023

Voltage dynamics of dendritic integration and back-propagation in vivo

Neurons integrate synaptic inputs within their dendrites and produce spiking outputs, which then propagate down the axon and back into the dendrites where they contribute to plasticity. Mapping the voltage dynamics in dendritic arbors of live animals is crucial for understanding neuronal computation and plasticity rules. Here we combine patterned channelrhodopsin activation with dual-plane structured illumination voltage imaging, for simultaneous perturbation and monitoring of dendritic and somatic voltage in Layer 2/3 pyramidal neurons in anesthetized and awake mice. We examined the integration of synaptic inputs and compared the dynamics of optogenetically evoked, spontaneous, and sensory-evoked back-propagating action potentials (bAPs). Our measurements revealed a broadly shared membrane voltage throughout the dendritic arbor, and few signatures of electrical compartmentalization among synaptic inputs. However, we observed spike rate acceleration-dependent propagation of bAPs into distal dendrites. We propose that this dendritic filtering of bAPs may play a critical role in activity-dependent plasticity.

neuroscience↗

bioRxiv2023

Mapping memories: pulse-chase labeling reveals AMPA receptor dynamics during memory formation

A tool to map changes in synaptic strength during a defined time window could provide powerful insights into the mechanisms governing learning and memory. We developed a technique, Extracellular Protein Surface Labeling in Neurons (EPSILON), to map -amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) insertion in vivo by pulse-chase labeling of surface AMPARs with membrane-impermeable dyes. This approach allows for single-synapse resolution maps of plasticity in genetically targeted neurons during memory formation. We investigated the relationship between synapse-level and cell-level memory encodings by mapping synaptic plasticity and cFos expression in hippocampal CA1 pyramidal cells upon contextual fear conditioning (CFC). We observed a strong correlation between synaptic plasticity and cFos expression, suggesting a synaptic mechanism for the association of cFos expression with memory engrams. The EPSILON technique is a useful tool for mapping synaptic plasticity and may be extended to investigate trafficking of other transmembrane proteins.

neuroscience↗

bioRxiv2022

Magnetic resonance imaging datasets with anatomical fiducials for quality control and registration

Tools available for reproducible, quantitative assessment of brain correspondence have been limited. We previously validated the anatomical fiducial (AFID) placement protocol for point-based assessment of image registration with millimetric (mm) accuracy. In this data descriptor, we release curated AFID placements for some of the most commonly used structural magnetic resonance imaging templates and datasets. The release of our accurate placements allows for rapid quality control of image registration, teaching neuroanatomy, and clinical applications such as disease diagnosis and surgical targeting. We release placements on individual subjects from four datasets (n = 132 subjects for a total of 15,232 fiducials) and more than 10 brain templates (4,288 fiducials), compiling over 300 human rater hours of annotation. We also validate human rater accuracy of released placements to be within 1-2 mm (using a total of 50,336 Euclidean distances), consistent with prior studies. Our data is compliant with the Brain Imaging Data Structure (BIDS) allowing for facile incorporation into modern neuroimaging analysis pipelines. Data is accessible on GitHub (https://github.com/afids/afids-data).

neuroscience↗