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Biology subjects

Han, J. H.

Publications and source records attributed to Han, J. H..

7 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↗

AI-driven framework modeling perturbation in brain organoids reveals candidate genes for autism

Autism gene discovery is constrained by the rarity and heterogeneity of damaging variants, requiring large cohorts to identify susceptibility genes. Neural organoids and single-cell foundation models enable perturbation modeling in neurodevelopmental contexts. Here, we show that perturbation-informed foundation modeling of neural organoids can provide functional context for prioritizing candidate genes with genomic and clinical support. We constructed a 3.6-million-cell organoid atlas and trained models to predict genome-wide perturbation responses. Benchmarking 17 models identified a telencephalic neuron-specific model best preserving autism-relevant perturbation structure. Genome-wide profiling revealed two clusters associated with mid-fetal synaptic neuronal processes and early radial glia ubiquitin signaling. These clusters were supported by damaging-variant enrichment and clinical phenotypes across 89,916 family-based samples. Logistic-regression prioritization identified 343 candidates, including 167 in the key clusters, with convergence across TADA signals and recurrent evidence for NBEA and KLHDC10. This framework integrates predicted perturbation effects with genomic evidence to support autism candidate prioritization.

bioinformatics↗

Fasting is required for many of the benefits of calorie restriction in the 3xTg mouse model of Alzheimer&aposs disease

Caloric restriction (CR) is a widely recognized geroprotective intervention that slows or prevents Alzheimers disease (AD) in animal models. CR is typically implemented via feeding mice a single meal per day; as CR mice rapidly consume their food, they are subject to a prolonged fast between meals. While CR has been shown to improve metabolic and cognitive functions and suppress pathological markers in AD mouse models, the specific contributions of fasting versus calorie reduction remains unclear. Here, we investigated the contribution of fasting and energy restriction to the beneficial effects of CR on AD progression. To test this, we placed 6-month-old 3xTg mice on one of several diet regimens, allowing us to dissect the effects of calories and fasting on metabolism, AD pathology, and cognition. We find that energy restriction alone, without fasting, was sufficient to improve glucose tolerance and reduce adiposity in both sexes, and to reduce A{beta} plaques and improve aspects of cognitive performance in females. However, we find that a prolonged fast between meals is necessary for many of the benefits of CR, including improved insulin sensitivity, reduced phosphorylation of tau, decreased neuroinflammation, inhibition of mTORC1 signaling, and activation of autophagy, as well as for the full cognitive benefits of CR. Finally, we find that fasting is essential for the benefits of CR on survival in male 3xTg mice. Overall, our results demonstrate that fasting is required for the full benefits of a CR diet on the development and progression of AD in 3xTg mice, and suggest that both when and how much we eat influences the development and progress of AD.

physiology↗

MSH2 and MSH6 as size dependent cellular determinants for prime editing in human embryonic stem cells

Potential applications of precise genome editing in human pluripotent stem cells (hPSCs), not only for isogenic disease modeling but also for ex vivo stem cell therapy, have urged the application of diverse genome editing tools in hPSCs. However, unlike differentiated somatic cells, the unique cellular properties of hPSCs (e.g., high susceptibility to DNA damage and active DNA repair) largely determine the overall efficiency of editing tools. Considering high demand of prime editors (PE), mostly due to its broad editing coverage compared to base editors, it is important to characterize the key molecular determinants of PE efficiency in hPSCs. Herein, we showed that MSH2 and MSH6, two main components of the MutS complex of mismatch repair (MMR), are highly expressed in hPSCs and determine PE efficiency in an editing size-dependent manner. Importantly, loss of MSH2, which disrupts both MutS and MutS{beta} complexes, was found to dramatically improve the efficiency of PE from one base to 10 bases, up to 50 folds. In contrast, genetic perturbation of MSH6, which solely abrogates MutS activity, marginally improved the editing efficiency up to 3 base pairs. The size dependent effect of MSH2 or MSH6 on prime editing in hPSCs not only implies MMR is a major determinant of PE efficiency in hPSCs but also highlights the distinct roles of MutS and MutS{beta} in the outcome of genome editing.

molecular biology↗

Trimethylamine N-oxide reduces neurite density and plaque intensity in a murine model of Alzheimer disease

BackgroundAlzheimers disease (AD) is the most common aging-associated neurodegenerative disease; nevertheless, the etiology and progression of the disease is still incompletely understood. We have previously shown that the microbially-derived metabolite trimethylamine N-oxide (TMAO) is elevated in the cerebrospinal fluid (CSF) of individuals with cognitive impairment due to AD and positively correlates with increases in CSF biomarkers for tangle, plaque, and neuronal pathology. ObjectiveWe assessed the direct impact of TMAO on AD progression. MethodsTo do so, transgenic 5XFAD mice were supplemented with TMAO for 12 weeks. ResultsOral TMAO administration resulted in significantly reduced neurite density in several regions of the brain, as assessed through quantitative brain microstructure imaging with neurite orientation dispersion and density imaging (NODDI) magnetic resonance imaging (MRI). Amyloid-{beta} plaque mean intensity was reduced, while plaque count and size remained unaltered. Proteomics analysis of the cortex revealed that TMAO treatment impacted the expression of 31 proteins (1.5-fold cut-off) in 5XFAD mice, including proteins known to influence neuronal health and amyloid-{beta} precursor protein processing. TMAO treatment did not alter astrocyte and microglial response (as determined by histological analysis) nor cortical synaptic protein expression. ConclusionThese data suggest that elevated plasma TMAO impacts AD pathology via reductions in neurite density.

neuroscience↗

Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Aggression is a complex behavior that is observed across the animal kingdom, and plays roles in resource acquisition, defense, and reproductive success. While there are many individual differences in propensity to be aggressive within and between populations, the mechanisms underlying differences in aggression between individuals in natural populations are not well understood. We addressed this using the Mexican tetra, Astyanax mexicanus, a powerful model organism to understand behavioral evolution. A. mexicanus exists in two forms: a river-dwelling surface form and multiple populations of a blind cave form. We characterized aggression in surface fish and cavefish in a resident/intruder assay through quantifying multiple behaviors occurring during social interactions. Surface fish, which are aggressive, display multiple social behaviors in this context, which we characterized into two types of behaviors: aggression- associated and escape-associated behaviors. The majority of these behaviors were reduced or lost in Pachon cavefish. Further, both aggression-associated and escape-associated behaviors were not dependent on the presence of light, and both surface fish and cavefish remained aggressive or non-aggressive, respectively, when opposed to fish from a different population. Additionally, we found that within populations, levels of stress response were not correlated with aggression- or escape-associated behaviors. Finally, when we compared aggression- and escape- associated behaviors across four cavefish populations, we found that both types of behaviors are reduced in three cave populations, while still present in one. Together, these results reveal that multiple cavefish populations have repeatedly evolved reduced aggression through shared behavioral components, while other cavefish have retained aggression. Summary StatementComparison of aggression between surface fish and cavefish demonstrates that multiple complex behaviors compose aggression in surface fish and reveals heterogeneity in loss of aggression in cave populations.

evolutionary biology↗

Therapeutic adenine base editing corrects nonsense mutation and improves visual function in a mouse model of Leber congenital amaurosis

Leber congenital amaurosis (LCA) is an inherited retinal degeneration that causes severe visual dysfunction in children and adolescents. In patients with LCA, pathogenic variants are evident in specific genes, such as RPE65, which are related to the functions of retinal pigment epithelium and photoreceptors. Base editing confers a way to correct pathogenic substitutions without double-stranded breaks in contrast to the original Cas9. In this study, we prepared dual adeno-associated virus vectors containing the split adenine base editors with trans-splicing intein (AAV-ABE) for in vivo adenine base editing in retinal degeneration 12 (rd12) mice, an animal model of LCA, which possess a nonsense mutation of C to T transition in the Rpe65 gene (p.R44X). AAV-ABE induced an A to G transition in retinal pigment epithelial cells of rd12 mice when injected into the subretinal space. The on-target editing was sufficient to recover wild-type mRNA, RPE65 protein, and light-induced electrical responses of retinal tissues. We suggest adenine base editing to correct pathogenic variants in the treatment of LCA.

genetics↗