Biology subjects

Sun, Y. J.

Publications and source records attributed to Sun, Y. J..

8 recordsLinked to original sources

bioRxiv2026

Inhibitory network predicts microstimulation-induced circuit changes in the awake mammalian cortex

Intracortical microstimulation is a powerful tool to perturb neural circuits, yet how circuit changes post-stimulation remains poorly understood. Using two-photon imaging in the awake mouse visual cortex, we tracked genetically identified neurons before, during, and after microstimulation. Even after a short 15-min microstimulation, there is pronounced suppression in excitatory neurons, accompanied by increased activity in inhibitory neurons, particularly those not recruited during microstimulation. Our findings highlight inhibition as a key player in shaping stimulation-induced circuit changes: the magnitude of plasticity in excitatory neurons is not only dependent on the level of recruitment during stimulation, but also shaped by the recruitment level of neighboring inhibitory cells, whereas the inhibitory plasticity is best explained by pre-stimulation population coupling.

neuroscience↗

bioRxiv2025

GABAergic signaling by VIP interneurons gates running-dependent visual recovery in the adult brain

Experience-dependent plasticity in the adult visual cortex is enhanced by locomotion, a process mediated by vasoactive intestinal peptide (VIP)-expressing interneurons. While VIP interneurons are known to signal through both Gamma-aminobutyric acid (GABA) and VIP peptide, the specific contributions of these pathways during different forms of plasticity remain unclear. Monocular deprivation (MD) in adult mice alters cortical responses, though more slowly and differently than during a critical period in early life. Here, we used two-photon calcium imaging in awake adult mice to dissect the roles of VIP and GABA release from VIP interneurons during adult MD and subsequent binocular recovery. We found comparable level of ocular dominance shifts after MD in mice deficient in either peptidergic or GABA signaling, but disrupting GABA signaling impaired recovery of binocular responses. We also showed that running preferentially enhances contralateral eye responses in binocular primary visual cortex. However, this eye-specific modulation of visual responses by running was altered during recovery from MD and was dependent on VIP signaling pathways. These findings highlight the GABA-mediated inhibition by VIP interneurons as a critical pathway for promoting visual restoration in the adult brain. Significance StatementUsing longitudinal two-photon imaging in awake adult mice with genetically altered signaling path-ways in VIP interneurons, we demonstrate that GABAergic, but not peptidergic, signaling from VIP interneurons is essential for the recovery of binocular vision following monocular deprivation. We further reveal that locomotion modulates cortical responses in an eye-specific manner, a property dynamically reshaped by plasticity and dependent on VIP interneuron function. These findings identify a discrete inhibitory circuit element that links behavioral state to sensory recovery and highlight GABA release from VIP cells as a potential therapeutic target for restoring visual function in adulthood.

neuroscience↗

bioRxiv2024

Type 2 diabetes remodels collateral circulation and promotes leukocyte adhesion following ischemic stroke

AbstractType 2 diabetes mellitus (T2DM) is associated with impaired leptomeningeal collateral compensation and poor stroke outcome. Neutrophils tethering and rolling on endothelium after stroke can also independently reduce flow velocity. However, the chronology and topological changes in collateral circulation in T2DM is not yet defined. Here, we describe the spatial and temporal blood flow dynamics and vessel remodeling in pial arteries and veins and leukocyte- endothelial adhesion following middle cerebral artery (MCA) stroke using two-photon microscopy in awake control and T2DM mice. Relative to control mice prior to stroke, T2DM mice already exhibited smaller pial vessels with reduced flow velocity. Following stroke, T2DM mice displayed persistently reduced blood flow in pial arteries and veins, resulting in a poor recovery of downstream penetrating arterial flow and a sustained deficit in microvascular flow. There was also persistent increase of leukocyte adhesion to the endothelium of veins, coincided with elevated neutrophils infiltration into brain parenchyma in T2DM mice compared to control mice after stroke. Our data suggest that T2DM-induced increase in chronic inflammation may contribute to the remodeling of leptomeningeal collateral circulation and the observed hemodynamics deficiency that potentiates poor stroke outcome. HighlightsO_LIBlood flow and leukocyte imaging in awake mice by two-photon microscopy before and after stroke under physiological conditions C_LIO_LIT2DM induces collateral remodeling prior to stroke C_LIO_LIT2DM reduces blood flow and impedes recovery in pial arteries and veins after ischemic stroke C_LIO_LIPoor recovery of penetrating arterial flow and sustained deficit in microvascular flow after ischemic stroke in T2DM mice C_LIO_LIT2DM increases persistent leukocyte adhesion to endothelium of veins and elevates neutrophils infiltration into the brain parenchyma after ischemic stroke. C_LI

neuroscience↗

bioRxiv2024

Artificial Intelligence's Contribution to Biomedical Literature Search: Revolutionizing or Complicating?

There is a growing number of articles about conversational AI (i.e., ChatGPT) for generating scientific literature reviews and summaries. Yet, comparative evidence lags its wide adoption by many clinicians and researchers. We explored ChatGPTs utility for literature search from an end-user perspective through the lens of clinicians and biomedical researchers. We quantitatively compared basic versions of ChatGPTs utility against conventional search methods such as Google and PubMed. We further tested whether ChatGPT user-support tools (i.e., plugins, web-browsing function, prompt-engineering, and custom-GPTs) could improve its response across four common and practical literature search scenarios: (1) high-interest topics with an abundance of information, (2) niche topics with limited information, (3) scientific hypothesis generation, and (4) for newly emerging clinical practices questions. Our results demonstrated that basic ChatGPT functions had limitations in consistency, accuracy, and relevancy. User-support tools showed improvements, but the limitations persisted. Interestingly, each literature search scenario posed different challenges: an abundance of secondary information sources in high interest topics, and uncompelling literatures for new/niche topics. This study tested practical examples highlighting both the potential and the pitfalls of integrating conversational AI into literature search processes, and underscores the necessity for rigorous comparative assessments of AI tools in scientific research. Author SummaryAs generative Artificial Intelligence (AI) tools become increasingly functional, the promise of this technology is creating a wave of excitement and anticipation around the globe including the wider scientific and biomedical community. Despite this growing excitement, researchers seeking robust, reliable, reproducible, and peer-reviewed findings have raised concerns about AIs current limitations, particularly in spreading and promoting misinformation. This emphasizes the need for continued discussions on how to appropriately employ AI to streamline the current research practices. We, as members of the scientific community and also end-users of conversational AI tools, seek to explore practical incorporations of AI for streamlining research practices. Here, we probed text-based research tasks--scientific literature mining-- can be outsourced to ChatGPT and to what extent human adjudication might be necessary. We tested different models of ChatGPT as well as augmentations such as plugins and custom GPT under different contexts of biomedical literature searching. Our results show that though at present, ChatGPT does not meet the level of reliability needed for it to be widely adopted for scientific literature searching. However, as conversational AI tools rapidly advance (a trend highlighted by the development of augmentations in this article), we envision a time when ChatGPT can become a great time saver for literature searches and make scientific information easily accessible.

scientific communication and education↗

bioRxiv2022

Spatiotemporal recruitment of inhibition and excitation in the mammalian cortex during electrical stimulation

Electrical stimulation has emerged as a powerful and precise treatment in which to modulate aberrant neural activity patterns common in neural dysfunction and disease; however, the physiological process involved in microstimulation is poorly understood, particularly regarding the contributions of inhibitory neurons to shaping stimulation-evoked activity. To address this issue, we used 2-photon imaging of transgenic mice to measure the widespread responses of inhibitory and excitatory neurons to electrical stimulation through a chronically-implanted cortical microelectrode. We found that increasing stimulation amplitude both raised the fraction of neurons that responded to a stimulus and increased the distance at which inhibitory and excitatory neurons were significantly modulated by stimulation; however, the lateral spread of inhibitory activity preceded that of excitatory activity. By 50 {micro}A, a significantly larger fraction of inhibitory neurons vs. excitatory neurons were modulated by stimulation. Increasing amplitude also shifted the temporal response properties of the population -- towards longer-latency excitation close to the electrode tip and strong inhibition of more distant neurons. Animal behavior, specifically their locomotion patterns, strongly correlated with trial-to-trial variability in stimulation-evoked responses. We conclude that changing electrical stimulation amplitude can shift the balance of excitation to inhibition in the brain in a manner that interact with ongoing animal behavior.

neuroscience↗

bioRxiv2021

TMPRSS2 structure-phylogeny repositions Avoralstat for SARS-CoV-2 prophylaxis in mice

Drugs targeting host proteins can act prophylactically to reduce viral burden early in disease and limit morbidity, even with antivirals and vaccination. Transmembrane serine protease 2 (TMPRSS2) is a human protease required for SARS-CoV-2 viral entry and may represent such a target.1-3 We hypothesized drugs selected from proteins related by their tertiary structure, rather than their primary structure, were likely to interact with TMPRSS2. We created a structure-based phylogenetic computational tool 3DPhyloFold to systematically identify structurally similar serine proteases with known therapeutic inhibitors and demonstrated effective inhibition of SARS-CoV-2 infection in vitro and in vivo.4,5 Several candidate compounds, Avoralstat, PCI-27483, Antipain, and Soybean-Trypsin-Inhibitor, inhibited TMPRSS2 in biochemical and cell infection assays. Avoralstat, a clinically tested Kallikrein-related B1 inhibitor,6 inhibited SARS-CoV-2 entry and replication in human airway epithelial cells. In an in vivo proof of principle,5 Avoralstat significantly reduced lung tissue titers and mitigated weight-loss when administered prophylactically to SARS-CoV-2 susceptible mice indicating its potential to be repositioned for COVID-19 prophylaxis in humans.

microbiology↗

bioRxiv2019

A physics-based energy function allows the computational redesign of a PDZ domain

A powerful approach to understand protein structure and evolution is to perform computer simulations that mimic aspects of evolution. In particular, structure-based computational protein design (CPD) can address the inverse folding problem, exploring a large space of amino acid sequences and selecting ones predicted to adopt a given fold. Previously, CPD has been used to entirely redesign several proteins: all or most of the protein sequence was allowed to mutate freely; among sampled sequences, those with low computed folding energy were selected, and a few percent of them did indeed adopt the correct fold. Those studies used an energy function that was partly or largely knowledge-based, with several empirical terms. Here, we show that a PDZ domain can be entirely redesigned using a \"physics-based\" energy function that combines standard molecular mechanics and a recent, continuum electrostatic solvent model. Many thousands of sequences were generated by Monte Carlo simulation. Among the lowest-energy sequences, three were chosen for experimental testing. All three could be overexpressed and had native-like circular dichroism and 1D-NMR spectra. Two exhibited an increase in their thermal denaturation curves when a peptide ligand was present, indicating binding and suggesting correctly folded proteins. Evidently, the physical principles that govern molecular mechanics and continuum electrostatics are sufficient to perform whole-protein redesign. This is encouraging, since these methods provide physical insights, can be systematically improved, and are transferable to other biopolymers and ligands of medical or technological interest.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC=\"FIGDIR/small/790667v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@145ea28org.highwire.dtl.DTLVardef@10ffa2forg.highwire.dtl.DTLVardef@1f2460eorg.highwire.dtl.DTLVardef@d5691c_HPS_FORMAT_FIGEXP M_FIG Table of Contents Graphic\n\nC_FIG

biophysics↗

bioRxiv2019

Experience-dependent structural plasticity at pre- and postsynaptic sites of layer 2/3 cells in developing visual cortex

The developing brain can respond quickly to altered sensory experience by circuit reorganization. During a critical period in early life, neurons in the primary visual cortex rapidly lose responsiveness to an occluded eye and come to respond better to the open eye. While physiological and some of the molecular mechanisms of this process have been characterized, its structural basis, except for the well-known changes in the thalamocortical projection, remains obscure. To elucidate the relationship between synaptic remodeling and functional changes during this experience-dependent process, we used 2-photon microscopy to image synaptic structures of sparsely labeled layer 2/3 neurons in the binocular zone of mouse primary visual cortex. Anatomical changes at presynaptic and postsynaptic sites in mice undergoing monocular visual deprivation (MD) were compared to those in control mice with normal visual experience. We found that postsynaptic spines remodeled quickly in response to MD, with neurons more strongly dominated by the deprived eye losing more spines. These postsynaptic changes parallel changes in visual responses during MD and their recovery after restoration of binocular vision. In control animals with normal visual experience, the formation of presynaptic boutons increased during the critical period and then declined. MD affected bouton formation, but with a delay, blocking it after 3 days. These findings reveal intracortical anatomical changes in cellular layers of the cortex that can account for rapid activity-dependent plasticity.\n\nSignificance statementThe operation of the cortex depends on the connections among its neurons. Taking advantage of molecular and genetic tools to label major proteins of the presynaptic and postsynaptic densities, we studied how connections of layer 2/3 excitatory neurons in mouse visual cortex were changed by monocular visual deprivation during the critical period, which causes amblyopia. The deprivation induced rapid remodeling of postsynaptic spines and impaired bouton formation. Structural measurement followed by calcium imaging demonstrated a strong correlation between changes in postsynaptic structures and functional responses in individual neurons after monocular deprivation. These findings suggest that anatomical changes at postsynaptic sites serve as a substrate for experience-dependent plasticity in the developing visual cortex.

neuroscience↗