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Biology subjects

Lee, L. P.

Publications and source records attributed to Lee, L. P..

11 recordsLinked to original sources

Chirality-Driven Photonic PCR Enables Label-Free Genetic Amplification

Photonic polymerase chain reaction (PCR) offers a rapid alternative to conventional thermal cycling for genetic amplification, but current platforms are limited by low photothermal conversion efficiencies and a dependence on bulky fluorescent monitoring systems. Here we report a chirality-driven photonic amplification paradigm that achieves both accelerated nucleic acid replication and direct, label-free detection. By leveraging chiral plasmonic nanoparticles, we exploit their elevated absorption cross-sections to achieve exceptional light-to-heat conversion and rapid thermal relaxation, significantly accelerating heating and cooling rates during cycling. We show that localized chiral near-fields generated by these chiral plasmonic nanoparticles optimize DNA polymerase conformational dynamics, lowering the activation energy barrier for synthesis and boosting amplification efficiency. Furthermore, by tracking the reaction with circular dichroism spectroscopy, we directly monitor the intrinsic chiroptical signature of amplifying DNA, completely eliminating the need for external fluorescent dyes or labeled probes. We validate this system using SARS-CoV-2 E-gene plasmid DNA templates, demonstrating rapid, label-free amplification and single-copy detection within clinically relevant timelines. By bridging asymmetric photothermal dynamics with chiral-field-induced enzymatic activation, this work translates chiroplasmonic materials from fundamental physics into high-performance, point-of-care molecular diagnostics.

bioengineering↗

Cascaded Nano-ring Dialyzer for Continuous Regenerative Peritoneal Dialysis

End-stage kidney disease (ESKD) requires lifelong kidney replacement therapy, yet conventional hemodialysis and peritoneal dialysis remain limited by intermittent treatment, restricted mobility, and repeated dialysate exchange. Here, we developed a continuous regenerative peritoneal dialysis platform based on a nano-ring-assisted nanoelectrokinetic dialyzer for portable artificial kidney applications. We first identified key geometric and electrokinetic parameters governing the removal performance of nano-ring meshes, including mesh dimension, nano-ring coating thickness, the number of cascaded nano-rings, and the relative orientation between fluid flow and the applied electric field. We then developed a single nano-ring dialyzer operating at 1.33 mL/min and scaled the treatment capacity to approximately 10 mL min/min through parallel integration of multiple modules. In a canine model, the closed-loop system achieved approximately 10 % reduction in circulating uremic toxin levels during continuous treatment. We further improved the biocompatibility of the regenerated dialysate by integrating plate-type electrodes, activated carbon, bicarbonate buffering, and UV-C treatment. In an unanesthetized canine model, the improved system sustained continuous toxin removal for 4 h while major hepatic and inflammatory markers remained within recoverable ranges. These results demonstrate that cascaded nano-ring enables continuous dialysate regeneration with scalable throughput, reduced dependence on fresh dialysate, and in vivo control of uremic toxins, providing a technological foundation for portable or wearable regenerative peritoneal dialysis systems.

bioengineering↗

Cryptic disease-prone states in human mesocortical assembloids revealed by multimodal profiling

Neurodegenerative diseases are characterized by synaptic failure, aberrant protein accumulation, and neuroglial dysfunction that emerge long before clinical onset. Although brain assembloids, which recapitulate interregional circuit connectivity beyond the scope of single organoids, significantly advance the modeling of circuit pathophysiology, they are predominantly evaluated through single-modality approaches that cannot resolve the functional and molecular heterogeneity underlying differential disease susceptibility. Here we show that morphologically identical human iPSC-derived dorso forebrain-midbrain mesocortical assembloids (MCAs) spontaneously bifurcate into disease-prone and non-prone states under identical culture conditions, revealing that MCA heterogeneity reflects intrinsic neurodegeneration susceptibility rather than stochastic culture variability. Using integrated electrophysiological, molecular, and spatial profiling, we find that disease-prone MCAs exhibit a temporally ordered molecular cascade in which neurofilament light chain elevation precedes tau dysregulation, mirroring the sequential biomarker trajectories observed in pre-symptomatic human neurodegeneration. Disease-prone MCAs further display selective cortical hyperexcitability and aberrant brainwave-like oscillatory dynamics that remain undetectable by any single modality. Spatially, a discrete junction-like neuronal population at the midbrain-forebrain interface shows transcriptional priming for synaptic overactivation alongside impaired astrocytic glutamate clearance, defining a spatially confined neuron-glial uncoupling as a candidate early origin of the disease-prone state. These findings reframe MCA heterogeneity as a biological window into pre-symptomatic neurodegeneration, with broad implications for disease modeling, risk stratification, and therapeutic discovery.

neuroscience↗

Antigenic Divergence of Cobra Short-chain α-Neurotoxins: Implications for Regional Antivenom Effectiveness in Southeast Asia

Short-chain -neurotoxins (SNTXs) are the principal neurotoxic components in several Asiatic cobras, including Naja atra, Naja philippinensis, and N. samarensis. Although structurally conserved, SNTXs exhibit marked antigenic variation that can limit the effectiveness of regional antivenoms used for snakebite envenoming in Asia. Here, we evaluated the immunoreactivity of the Philippine Cobra Antivenom (PCAV) and three regional products--Naja kaouthia Monovalent Antivenom (NkMAV), Neuro Bivalent Antivenom (NBAV), and Indonesian SABU--against a panel of cobra venoms and purified -neurotoxins. PCAV bound strongly to homologous N. philippinensis SNTX but showed weak cross-reactivity with SNTXs from N. kaouthia, N. sputatrix, and N. atra, and minimal recognition of marine elapid SNTXs and long-chain -neurotoxins (LNTXs) of Monocled Cobra as well as King Cobra. Conversely, NkMAV and NBAV recognized mainland Asian SNTXs more broadly but reacted poorly with the Philippine cobra toxin. Hierarchical clustering of normalized immunoreactivity delineated two major SNTX antigenic subtypes corresponding to Philippine versus continental Asian lineages. Peptide sequence analysis unmasked two distinct loop-II motifs (28WWS-TII37 and 28RWR-YRT37) associated with these divergent immunotypes. Phylogenetic reconstruction suggests that the Philippine cobras retain an ancestral SNTX motif, while Sundaic and East Asian cobras have diversified to employ another major SNTX form. Epitope prediction further revealed differences in surface exposure and accessibility that help explain the limited cross-neutralization across antivenoms. These findings demonstrate a clear antigenic dichotomy among Asian cobra SNTXs, which underlies species-specific antivenom effectiveness and highlights the need to incorporate representative SNTX variants into immunogen formulations to improve regional antivenom coverage.

biochemistry↗

EVscope: A Comprehensive Bioinformatics Pipeline for Accurate and Robust Analysis of Total RNA Sequencing from Extracellular Vesicles

MotivationExtracellular vesicle (EV) RNA sequencing has emerged as a powerful approach for studying RNA biomarkers and intercellular communication. Nevertheless, the extremely low abundance, fragmented nature and ubiquitous tissue origin of EV RNAs, alongside potential contamination from co-isolated materials, such as free DNA and bacterial RNA, pose substantial analytical challenges. These complexities highlight a pressing need for a standardized, computational workflow that ensures robust quality control and EV RNA characterization. ResultsHere, we present EVscope, an open-source bioinformatics pipeline designed specifically for processing EV RNA-seq datasets. EVscope employs an optimized genome-wide expectation-maximization (EM) algorithm that significantly improves multi-mapping read assignment at single-base resolution by effectively leveraging alignment scores (AS) and local read coverage, specifically tailored for fragmented and low-abundance EV RNAs. Notably, EVscope uniquely generates EM-based BigWig files for downstream analysis, a capability currently unavailable in existing EM-based BigWig quantification tools. The pipeline systematically integrates 27 major steps, including quality control, analysis of library structure, contamination assessment, read alignment, read strandedness detection, UMI-based deduplication, RNA quantification, genomic DNA (gDNA) contamination correction, cellular and tissue source inference and visualization with a comprehensive HTML report. EVscope incorporates a comprehensive, updated annotation covering 19 distinct RNA biotypes, encompassing protein-coding genes, lncRNAs, miRNAs, piRNAs, retrotransposons (LINEs, SINEs, ERVs), and additional non-coding RNAs (tRNAs, rRNAs, snoRNAs). Furthermore, it leverages two highly balanced circRNA detection algorithms for robust circular RNA identification. Notably, a downstream module enables the inference of the tissue/cellular origins of EV RNAs using bulk and single-cell RNA-seq reference datasets. EVscope is implemented as a convenient, single-command Bash pipeline leveraging Conda-managed standard software packages and custom scripts, ensuring reproducibility and straightforward deployment. Availability and implementationCode, documentation, and tutorials are available at GitHub (https://github.com/TheDongLab/EVscope) and archived on Zenodo (https://zenodo.org/records/15577789).

bioinformatics↗

Human Stem Cell-derived Kidney Collecting Duct Model via Epithelial Microphysiological Analysis Platform: Epi-MAP

The kidney epitheliums pivotal role in molecular filtration, metabolism, and excretion highlights the crucial importance of understanding kidney physiology in drug development. However, our knowledge is largely derived from non-human or non-physiological models, potentially limiting its applicability to humans. To address this significant gap, we have pioneered a human kidney epithelial microphysiological analysis platform (Epi-MAP) designed to establish, mature, and monitor renal functions of the human collecting epithelium within a physiologically relevant microenvironment. We first demonstrate the highly mature collecting duct physiology derived from human stem cells, enabled by the Epi-MAPs microenvironments that recapitulate in vivo asymmetries in fluidic and biochemical conditions. The integrated biosensors of the Epi-MAP provide long-term, time-resolved epithelial maturation trajectories, revealing advanced integrity and functional maturity with transepithelial metrics. Furthermore, Epi-MAPs electrophysiological analytics for measuring water flux, in conjunction with transepithelial potential and resistance, allow for real-time decoding of intricate epithelial responses to substance stimulation, showcasing its effectiveness as a robust pharmacological test model. This human cell-derived, physiologically advanced model on a chip stands as a robust in vitro tool, offering comprehensive insights into human kidney biology and significantly enhancing drug discovery process based on human physiology.

bioengineering↗

Dynamic Kidney Organoid Microphysiological Analysis Platform

Kidney organoids, replicating human development, pathology, and drug responses, are a promising model for advancing bioscience and pharmaceutical innovation. However, reproducibility, accuracy, and quantification challenges hinder their broader utility for advanced biological and pharmaceutical applications. Herein, we present a dynamic kidney organoid microphysiological analysis platform (MAP), designed to enhance organoid modeling and assays within physiologically relevant environments, thereby expanding their utility in advancing kidney physiology and pathology research. First, precise control of the dynamic microenvironment in MAP enhances the ability to fine-tune nephrogenic intricacies, facilitating high-throughput and reproducible human kidney organoid development. Also, MAPs miniaturization of kidney organoids significantly advances pharmaceutical research by allowing for detailed analysis of entire nephron segments, which is crucial for assessing the nephrotoxicity and safety of drugs. Furthermore, the MAPs application in disease modeling faithfully recapitulates pathological development and functions as a valuable testbed for therapeutic exploration in polycystic kidney diseases. We envision the kidney organoid MAP enhancing pharmaceutical research, standardizing processes, and improving analytics, thereby elevating the quality and utility of organoids in biology, pharmacology, precision medicine, and education.

bioengineering↗

Brainwaves Monitoring via Human Midbrain Organoids Microphysiological Analysis Platform: MAP

Understanding the development and pathogenesis of the human midbrain is critical for developing diagnostics and therapeutics for incurable neurological disorders including Parkinsons disease (PD)1-3. While organoid models are introduced to delineate midbrain-related pathogenesis based on experimental flexibility4-6, there is currently a lack of tools with high fidelity for tracing the long-term dynamics of intact brain networks-- an essential portrait of physiological states7,8. Here, we report a brain organoid microphysiological analysis platform (MAP) designed for long-term physiological development and in-situ real-time monitoring, akin to electroencephalogram (EEG), of midbrain organoids. We successfully achieved the on-chip homogeneous organogenesis of midbrain organoids and in-situ, non-disturbing electrophysiological tracking of the midbrain network activities. Throughout our long-term EEG monitoring via MAP, we captured the early-stage electrophysiological evolution of midbrain development, transitioning from discontinuous brief brainwave bursts to complex broadband activities. Furthermore, our midbrain organoid MAP facilitated the modeling and monitoring of neurotoxin-induced Parkinsonism, replicating the pathological dynamics of midbrain circuitry and exhibiting PD-like alterations in beta oscillation. We envision that the modeling and monitoring of brain organoid MAP will significantly enhance our understanding of human neurophysiology, neuropathogenesis, and drug discovery of neurodegenerative diseases.

bioengineering↗

Unveiling the Secrets of Extracellular Vesicles in Urban Water Systems: Understanding the Link Between Human and Environmental Health

It is crucial to gain valuable insights into the ecological health of rivers to inform management decisions and protect sustainable living conditions. Understanding biological information is vital to gaining insight into river ecosystem biodiversity, but reliable methods are challenging. Here, We investigate the potential impact of extracellular vesicles (EVs) in urban water systems on human and environmental health to promote urban sustainability. We used EXODUS to detect EVs and perform metaproteomic analysis on samples from an urban water system that contained human feces, wastewater, bacteria, plants, arthropods, and soil. We analyzed EVs collected from urban and green areas, observing taxonomic variations and discovering bacterial contributions to their protein content. According to our research, the abundance and expression levels of proteins in EVs can indicate how human activities affect microbial communities in rivers, potentially impacting public health. Our study offers a fresh perspective on the interconnectedness of urban sustainability, public health, and river ecosystem biodiversity.

ecology↗

Extracellular vesicles-based point-of-care testing for the diagnosis and monitoring of Alzheimer's disease

Alzheimers disease (AD) is a debilitating condition that affects millions of people worldwide. One promising strategy for detecting and monitoring AD early on is using extracellular vesicles (EVs)-based point-of-care testing; however, diagnosing AD using EVs poses a challenge due to the low abundance of EV-biomarkers. Here, we present a fully integrated organic electrochemical transistor (OECT) that enables high accuracy, speed, and convenience in the detection of EVs from AD patients. We incorporated self-aligned acoustoelectric enhancement of EVs on a chip that rapidly propels, enriches, and specifically binds EVs to the OECT detection area. With our enhancement of pre-concentration, we increased the sensitivity to a limit of detection of 500 EV particles/L and reduced the required detection time to just two minutes. We also tested the sensor on an AD mouse model to monitor AD progression, examined mouse A{beta} EVs at different time courses, and compared them with intraneuronal A{beta} cumulation using MRI. This innovative technology has the potential to diagnose Alzheimers and other neurodegenerative diseases accurately and quickly, enabling monitoring of disease progression and treatment response.

bioengineering↗

Understanding immune-driven brain aging by human brain organoid microphysiological analysis platform

The aging of the immune system drives systemic aging and the pathogenesis of age-related diseases. However, a significant knowledge gap remains in understanding immune-driven aging, especially in brain aging, due to the limited current in vitro models of neuro-immune interaction. Here we report the development of a human brain organoid microphysiological analysis platform (MAP) to discover the dynamic process of immune-driven brain aging. We create the organoid MAP by 3D printing that can confine organoid growth and perfuse oxygen and nutrients (and immune cells) to generate standardized human cortical organoids that promote viability, maturation, and commitment to human forebrain identity. Dynamic rocking flow is incorporated for the platform that allows us to perfuse primary monocytes from young (20 to 30-year-old) and aged (>60-year-old) donors and culture human cortical organoids for modeling and analyzing the aged immune cell interacting organoid tissues systematically. We discovered the aged monocytes had increased infiltration and promoted the expression of aging-related markers (e.g., p16 in astrocytes neighboring to monocytes) within human cortical organoids, indicating that aged monocytes may drive brain aging. We believe that our human brain organoid MAP provides promising solutions for basic research and translational applications in aging, neuroimmunological diseases, autoimmune disorders, and cancers.

bioengineering↗