Biology subjects

Wang, E. Y.

Publications and source records attributed to Wang, E. Y..

13 recordsLinked to original sources

bioRxiv2026

Tuning metaplasticity in the adult visual cortex using flickering light

Synaptic connections in the brain are refined by sensory experience during an early postnatal critical period, but by adulthood synaptic connectivity is resistant to further changes. A consequence of lost plasticity is limited recovery from brain injury, disease, and adverse sensory experience. Thus, there is great interest in treatments that can promote synaptic modifications in the adult brain. In a wide variety of contexts, it has been established that the qualities of synaptic plasticity are not fixed but rather vary depending on the recent history of cellular or synaptic activity1. This plasticity of plasticity, or metaplasticity2 explains why temporary manipulations of brain activity (e.g., by drugs3, transcranial stimulation4, or sensory deprivation5) can set the stage for subsequent, potentially therapeutic, long-lasting synaptic modifications6. Here we tested the hypothesis that plasticity in the adult mouse visual cortex is influenced by prior exposure to temporally modulated light and discovered that different flicker frequencies have qualitatively different effects. Exposure to 60 Hz stimulation increased microglia density, depleted perineuronal nets (PNNs), and restored ocular dominance plasticity in response to brief monocular deprivation (MD). Exposure to 40 Hz flicker also enabled ocular dominance plasticity, but it did so in a distinct way and without PNN remodeling. A key distinction is that unlike 60 Hz flicker, which enabled depression of synaptic strength by MD, 40 Hz flicker promoted synaptic strengthening. Indeed, we found that 40 Hz flicker primed a rapid and robust recovery from the effects of long-term MD that failed to occur after 60 Hz flicker. Thus, metaplasticity can be non-invasively "tuned" by light flickering at different frequencies to encourage different forms of synaptic plasticity in the cerebral cortex, including modifications that enable recovery of function.

neuroscience↗

bioRxiv2025

Intra-Abdominal Photodynamic Therapy in a Rabbit Model of Perforated Appendicitis

ImportancePerforated appendicitis is a common and morbid pediatric surgical condition frequently requiring prolonged antibiotic therapy. Adjunctive intraoperative strategies for local antimicrobial therapy are limited, and photodynamic therapy (PDT) may offer a targeted, resistance-independent approach. ObjectiveTo evaluate the feasibility, safety, and preliminary efficacy of laparoscopic methylene blue photodynamic therapy (MB-PDT) for intra-abdominal disinfection in a rabbit model of perforated appendicitis. DesignExperimental preclinical animal study conducted between 2023 and 2025. SettingSingle-center laboratory-based animal research facility affiliated with an academic medical center. ParticipantsNineteen New Zealand White rabbits underwent surgically induced perforated appendicitis with peritonitis via appendiceal ligation and electrocautery perforation. InterventionsRabbits received laparoscopic MB-PDT (n=9) or control conditions (methylene blue only, no light; n=10) 24 - 40 hours after appendiceal perforation. MB-PDT involved peritoneal lavage with 300 {micro}g/mL methylene blue, followed by 665 nm laser illumination to 25 J/cm2. Peritoneal aspirates were collected before and 24h after intervention. Bacterial burden was quantified, and isolated bacteria were submitted to in vitro PDT. Tissue samples from intraperitoneal organs were collected 24 hours post-intervention. Main Outcomes and MeasuresPrimary outcomes included feasibility of PDT delivery, safety (histologic evidence of off-target injury), and preliminary in vivo efficacy (change in bacterial burden pre-vs. post-intervention). Secondary outcomes included clinical parameter changes and in vitro MB-PDT efficacy. ResultsOf the 14 rabbits that developed peritonitis, 10 (age 5-6 months, weight 3.1-3.8 kg) completed follow-up. Laparoscopic MB-PDT delivery was feasible and caused no off-target histologic injury. Bacterial burden increased in MB-PDT animals relative to controls, though not significantly (p=0.18). Post-intervention, body temperature showed a trend toward reduction in MB-PDT animals (-0.37 {+/-} 1.32{degrees}C) vs controls (0.26 {+/-} 0.76{degrees}C; p=0.27). In vitro MB-PDT significantly reduced bacterial burden for all tested species (p<0.001), with greater efficacy in Gram-positive bacteria. Conclusions and RelevanceLaparoscopic MB-PDT was feasible and safe in a rabbit model of perforated appendicitis, with high in vitro antimicrobial efficacy. Although in vivo bacterial reduction was not demonstrated, these results support further investigation of MB-PDT as a novel intraoperative adjunct for treating intra-abdominal infection.

microbiology↗

bioRxiv2025

The Critical Role of the C-terminal Lobe of Calmodulin in Activating Eukaryotic Elongation Factor 2 Kinase

Eukaryotic elongation factor-2 kinase (eEF-2K), a member of the -kinase family, modulates translational rates by phosphorylating eEF-2, a GTPase that facilitates the translocation of the nascent chain on the ribosome during the elongation phase of protein synthesis. eEF-2K is regulated by diverse cellular cues, many of which sensitize it to the Ca2+-effector protein calmodulin (CaM). CaM, which binds and allosterically activates eEF-2K in the presence of Ca2+, contains two structural "lobes," each with a pair of Ca2+-binding EF-hands. Using kinetic analysis, we demonstrate that the isolated C-terminal lobe of CaM (CaMC) is sufficient to engage and fully activate eEF-2K in a Ca2+-dependent fashion. Genetically fusing CaMC to the N-terminus of eEF-2K, upstream of its critical CaM-targeting motif (CTM) via a flexible 2-glycine linker, results in a chimeric species (C-LiNK) that is constitutively active independent of external CaM and Ca2+. A structure of the C-LiNK functional core reveals no significant deviation in the overall conformations of the interacting modules and orientations of key catalytic-site residues relative to the heterodimeric complex between full-length CaM and eEF-2K. These observations demonstrate that, in contrast to other CaM-regulated kinases, CaMC alone is sufficient to activate eEF-2K fully. The proximity effect of CaMC in the context of C-LiNK removes the requirement for external Ca2+, whose apparent role is to enhance the CaM-affinity of eEF-2K and drive kinase activation. The responsiveness of eEF-2K to regulatory stimuli in cells appears to be lost in C-LiNK, presumably due to its permanently "on" state.

biochemistry↗

bioRxiv2025

Methylene Blue-Photodynamic Therapy Effectively Kills Antibiotic-Resistant Bacteria from Pediatric Patients with Perforated Appendicitis

ObjectivesPerforated appendicitis (PA) is the most common cause of intra-abdominal abscess in children and is associated with higher costs, extended hospitalizations, and worse postoperative outcomes compared to uncomplicated appendicitis. Photodynamic therapy (PDT) utilizes a photosensitizer and light to generate cytotoxic reactive species that are efficacious against bacteria. We sought to determine whether PDT could effectively eliminate bacteria isolated from the peritoneal cavities of pediatric patients with perforated appendicitis. HypothesisIn monoculture planktonic samples, PDT achieves a minimum of 99.9% bacterial cell kill (3 log10 growth reduction per mL). MethodsAfter IRB approval, bacterial subcultures from 30 pediatric surgical patients with PA were developed as planktonic monocultures. Samples were derived from standard clinical collection of peritoneal fluid in patients undergoing surgery for PA. Cultures were incubated with the photosensitizer methylene blue (MB) and exposed to a 665 nm laser to perform PDT. Control conditions were MB alone, laser alone, or no MB and no laser. Log reductions in bacterial growth between groups were compared using two-way ANOVA. ResultsBacteria were isolated from 28 (93.3%) specimens, and 26 (86.7%) were polymicrobial. The most prevalent organisms included Escherichia coli (76.7%), the Streptococcus anginosus group (56.7%), Bacteroides fragilis (46.6%), and Pseudomonas aeruginosa (26.7%), with antibiotic resistance common among E. coli isolates. For E. coli, MB-PDT caused a 5.86 {+/-} 0.39 log10 reduction compared to the no-treatment control (p<0.001). For S. anginosus and P. aeruginosa, MB-PDT resulted in reductions of 5.91 {+/-} 0.88 log10 and 2.23 {+/-} 0.64 log10, respectively (all p<0.001). PDT showed comparable efficacy in isolates with multiple antibiotic resistance relative to those that were antibiotic pan-susceptible for E. coli (p=0.760), S. anginosus group (p>0.999), and P. aeruginosa (p=0.991). ConclusionsPDT application to bacterial isolates from patients with perforated appendicitis achieved >99.9% bacterial kill in all isolated strains other than P. aeruginosa, regardless of antibiotic susceptibility, suggesting that PDT may be a viable adjunct to in vivo antimicrobial therapy.

microbiology↗

bioRxiv2025

Anti- and Pro-tumor Functions of Distinct Regulatory T Cell Subsets in Colorectal Cancer

Regulatory T (Treg) cells contribute to solid organ cancer progression, except in colorectal cancer (CRC) despite being abundantly present. Here, we demonstrate that two distinct tumoral IL-10 and IL-10- Treg cell subsets exert opposing functions by counteracting and promoting CRC tumor growth, respectively. The tumor restraining activity of IL-10 Treg cells was mediated by their suppression of effector CD4 T cell production of IL-17, which directly stimulates CRC tumor cell proliferation. Consistently, IL-10- Treg cells were more abundant in both mouse and human CRC tumors than in tumor-adjacent normal tissues, whereas IL-10+ Treg cells exhibited the opposite distribution. Furthermore, relative abundance of IL-10 and IL-10- Treg cells correlated with better and worse disease prognoses in human CRC, respectively. This functional dichotomy between Treg cell subsets provides a rationale for therapeutic strategies to selectively target pro-tumoral Treg cells while preserving their anti-tumoral counterparts across barrier tissue cancers that harbor both subsets.

immunology↗

bioRxiv2023

Flavonols improve thermotolerance in tomato pollen during germination and tube elongation by maintaining ROS homeostasis

Elevated temperatures impair pollen performance and reproductive success, resulting in lower crop yields. The Solanum lycopersicum anthocyanin reduced (are) mutant has a FLAVANONE 3 HYDROXYLASE (F3H) gene mutation resulting in impaired synthesis of flavonol antioxidants. The are mutant has reduced pollen performance and seed set relative to the VF36 parental line, which is accentuated at elevated temperatures. Transformation of are with the wild-type F3H gene, or chemical complementation with flavonols, prevented temperature-dependent ROS accumulation in pollen and reversed ares reduced viability, germination, and tube elongation to VF36 levels. VF36 transformed with an F3H overexpression construct prevented temperature driven ROS increases and impaired pollen performance, revealing thermotolerance results from elevated flavonol synthesis. Although stigmas of are had reduced flavonols and elevated ROS, the growth of are pollen tubes were similarly impaired in both are and VF36 pistils. RNA-Seq was performed at optimal and stress temperatures in are, VF36, and the VF36 F3H overexpression line at multiple timepoints across pollen tube elongation. Differentially expressed gene numbers increased with duration of elevated temperature in all genotypes, with the largest number in are. These findings suggest potential agricultural interventions to combat the negative effects of heat-induced ROS in pollen that leads to reproductive failure. One sentence summaryFlavonol antioxidants reduce the negative impacts of elevated temperatures on pollen performance by reducing levels of heat induced reactive oxygen species and modulation of heat-induced changes in the pollen transcriptome.

plant biology↗

bioRxiv2023

Myosin inhibitor reverses hypertrophic cardiomyopathy in pediatric iPSC-cardiomyocytes to mirror variant correction

Hypertrophic cardiomyopathy (HCM) is mainly caused by sarcomere gene variants in MYH7 and MYBPC3. Targeted drugs like myosin ATPase inhibitors have shown efficacy in adult HCM but have not been evaluated in children. We generated iPSC-cardiomyocytes (CMs) from four children with HCM harboring variants in MYH7 (V606M; R453C) or MYBPC3 (G148R; P955fs and TNNI3_A157P), variant-corrected controls, and a healthy individual. All CMs showed hypertrophy and sarcomere disorganization. All 3 single variant CMs showed higher contractility, slower relaxation, higher calcium transients and higher ATPase activity. Only MYH7 variant CMs showed stronger myosin-actinin binding. Targeted myosin ATPase inhibitor showed complete rescue of the phenotype in affected CMs and in cardiac Biowires to mirror isogenic controls. The response was stronger compared to verapamil or metoprolol, highlighting the need for clinical trials of myosin targeted therapy in pediatric HCM patients. The phenotype and response to drug therapy are influenced by the underlying genotype.

genetics↗

bioRxiv2023

Towards a Foundation Model of the Mouse Visual Cortex

The complexity of neural circuits makes it challenging to decipher the brains algorithms of intelligence. Recent break-throughs in deep learning have produced models that accurately simulate brain activity, enhancing our understanding of the brains computational objectives and neural coding. However, these models struggle to generalize beyond their training distribution, limiting their utility. The emergence of foundation models, trained on vast datasets, has introduced a new AI paradigm with remarkable generalization capabilities. We collected large amounts of neural activity from visual cortices of multiple mice and trained a foundation model to accurately predict neuronal responses to arbitrary natural videos. This model generalized to new mice with minimal training and successfully predicted responses across various new stimulus domains, such as coherent motion and noise patterns. It could also be adapted to new tasks beyond neural prediction, accurately predicting anatomical cell types, dendritic features, and neuronal connectivity within the MICrONS functional connectomics dataset. Our work is a crucial step toward building foundation brain models. As neuroscience accumulates larger, multi-modal datasets, foundation models will uncover statistical regularities, enabling rapid adaptation to new tasks and accelerating research.

neuroscience↗

bioRxiv2022

Advanced physiological maturation of iPSC-derived human cardiomyocytes using an algorithm-directed optimization of defined media components

Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) hold tremendous promise for in vitro modeling to assess native myocardial function and disease mechanisms as well as testing drug safety and efficacy. However, current iPSC- CMs are functionally immature, resembling in vivo CMs of fetal or neonatal developmental states. The use of targeted culture media and organoid formats have been identified as potential high-yield contributors to improve CM maturation. This study presents a novel iPSC-CM maturation medium formulation, designed using a differential evolutionary approach targeting metabolic functionality for iterative optimization. Relative to gold-standard reference formulations, our medium significantly matured morphology, Ca2+ handling, electrophysiology, and metabolism, which was further validated by multiomic screening, for cells in either pure or co-cultured microtissue formats. Together, these findings not only provide a reliable workflow for highly functional iPSC-CMs for downstream use, but also demonstrate the power of high-dimensional optimization processes in evoking advanced biological function in vitro.

bioengineering↗

bioRxiv2021

A type I interferon response defines a conserved microglial state required for effective phagocytosis

Microglia are brain resident phagocytes that can engulf synaptic components and extracellular matrix as well as whole neurons. However, whether there are unique molecular mechanisms that regulate these distinct phagocytic states is unknown. Here we define a molecularly distinct microglial subset whose function is to engulf neurons in the developing brain. We transcriptomically identified a cluster of Type I interferon (IFN-I) responsive microglia that expanded 20-fold in the postnatal day 5 somatosensory cortex after partial whisker deprivation, a stressor that accelerates neural circuit remodeling. In situ, IFN-I responsive microglia were highly phagocytic and actively engulfed whole neurons. Conditional deletion of IFN-I signaling (Ifnar1fl/fl) in microglia but not neurons resulted in dysmorphic microglia with stalled phagocytosis and an accumulation of neurons with double strand DNA breaks, a marker of cell stress. Conversely, exogenous IFN-I was sufficient to drive neuronal engulfment by microglia and restrict the accumulation of damaged neurons. IFN-I deficient mice had excess excitatory neurons in the developing somatosensory cortex as well as tactile hypersensitivity to whisker stimulation. These data define a molecular mechanism through which microglia engulf neurons during a critical window of brain development. More broadly, they reveal key homeostatic roles of a canonical antiviral signaling pathway in brain development.

neuroscience↗

bioRxiv2021

A human brain vascular atlas reveals diverse cell mediators of Alzheimer's disease risk

The human brain vasculature is of vast medical importance: its dysfunction causes disability and death, and the specialized structure it forms--the blood-brain barrier--impedes treatment of nearly all brain disorders. Yet, no molecular atlas of the human brain vasculature exists. Here, we develop Vessel Isolation and Nuclei Extraction for Sequencing (VINE-seq) to profile the major human brain vascular and perivascular cell types through 143,793 single-nucleus transcriptomes from 25 hippocampus and cortex samples of 17 control and Alzheimers disease (AD) patients. We identify brain region-enriched pathways and genes divergent between humans and mice, including those involved in disease. We describe the principles of human arteriovenous organization, recapitulating a gradual endothelial and punctuated mural cell continuum; but discover that many zonation and cell-type markers differ between species. We discover two subtypes of human pericytes, marked by solute transport and extracellular matrix (ECM) organization; and define perivascular versus meningeal fibroblast specialization. In AD, we observe a selective vulnerability of ECM-maintaining pericytes and gene expression patterns implicating dysregulated blood flow. With an expanded survey of brain cell types, we find that 30 of the top 45 AD GWAS genes are expressed in the human brain vasculature, confirmed in situ. Vascular GWAS genes map to endothelial protein transport, adaptive immune, and ECM pathways. Many are microglia-specific in mice, suggesting an evolutionary transfer of AD risk to human vascular cells. Our work unravels the molecular basis of the human brain vasculature, informing our understanding of overall brain health, disease, and therapy.

neuroscience↗

bioRxiv2021

REAP: A platform to identify autoantibodies that target the human exoproteome

Autoantibodies that recognize extracellular proteins (the "exoproteome") exert potent biological effects but have proven challenging to detect with existing screening technologies. Here, we developed Rapid Extracellular Antigen Profiling (REAP) as a technique for comprehensive, high-throughput discovery of exoproteome-targeting autoantibodies. With REAP, patient samples are applied to a genetically-barcoded library containing 2,688 human extracellular proteins displayed on the surface of yeast. Antibody-coated cells are isolated by magnetic selection and deep sequencing of their barcodes is used to identify the displayed antigens. To benchmark the performance of REAP, we screened 77 patients with autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED). REAP sensitively and specifically detected known autoantibody reactivities in APECED in addition to numerous previously unidentified reactivities. We further screened 106 patients with systemic lupus erythematosus (SLE) and identified novel autoantibody reactivities against a diverse set of antigens including growth factors, extracellular matrix components, cytokines, and immunomodulatory proteins. Several of these responses were associated with disease severity and specific clinical manifestations of SLE and exerted potent functional effects on cell signaling ex vivo. These findings demonstrate the utility of REAP to atlas the expansive landscape of exoproteome-targeting autoantibodies and their impacts on patient health outcomes.

immunology↗

bioRxiv2020

Cellular expression and functional roles of all 26 neurotransmitter GPCRs in the C. elegans egg-laying circuit

Maps of the synapses made and neurotransmitters released by all neurons in model systems such as C. elegans have left still unresolved how neural circuits integrate and respond to neurotransmitter signals. Using the egg-laying circuit of C. elegans as a model, we mapped which cells express each of the 26 neurotransmitter G protein coupled receptors (GPCRs) of this organism and also genetically analyzed the functions of all 26 GPCRs. We found that individual neurons express many distinct receptors, epithelial cells often express neurotransmitter receptors, and receptors are often positioned to receive extrasynaptic signals. The egg-laying circuit appears to use redundancy and compensation to achieve functional robustness, as receptor knockouts reveal few defects; however, increasing receptor signaling through overexpression more efficiently reveals receptor functions. This map of neurotransmitter GPCR expression and function in the egg-laying circuit provides a model for understanding GPCR signaling in other neural circuits.

neuroscience↗