https://scholarworks.unist.ac.kr/handle/201301/6 Wed, 08 Apr 2026 00:40:30 GMT 2026-04-08T00:40:30Z https://scholarworks.unist.ac.kr/handle/201301/90880 Title: Surface Modificated and Multifunctional Iron Oxide Nanostructures Construction for Bioapplications Author(s): CHEN, NING Abstract: Magnetic iron oxide nanoparticles (Fe3O4 NPs, IONPs) represent a prominent class of multifunctional nanomaterials that have been increasingly explored for diverse biomedical applications, such as magnetic resonance imaging (MRI), biological catalysis (nanozyme), magnetic hyperthermia, magnetic targeting and separation, photothermal therapy, and drug transport. Owing to their large surface-to-volume ratio and high surface energy, IONPs have a natural tendency to aggregate in order to minimize the system’s surface energy. In addition, the uncoated particles are chemically reactive and readily oxidized in air. Therefore, surface modification of IONPs is essential—not only to enhance their stability by preventing aggregation and oxidation but also to create a versatile interface for further functionalization. This dissertation focuses on developing strategies for surface engineering and multifunctionalization of IONPs to enable biomolecular conjugation and broaden their biomedical applications. Chapter 2 presents the develop of a multidentate catechol-based copolymer for 7 nm-sized IONPs. Using an amine-assisted catechol nanocoating (ligand-exchange) approach, compact, monodisperse, and highly colloidally stable IONPs grafted with the designed multifunctional brush polymer were successfully obtained. Subsequently, the conjugation of DNA strands onto the IONP surface was demonstrated, achieving an average “valency” ranging from 1 to 26 per particle, which enabled precise control over their spatial assembly. Furthermore, a series of core-satellite nanostructures (AuNP-IONP assemblies) were constructed through DNA hybridization using single-DNA-valency IONPs as building blocks. Finally, the T2 relaxivity was modulated by the distinct assembly configurations, which was attributed to the spatial arrangement-dependent aggregation of IONPs, hybrid spin-coupling interactions and local magnetic field fluctuations arising from electron-transfer dynamics within the nanostructure. In Chapter 3, a petal-like catalytic colorimetric nanohybrid was fabricated by the in situ growth of sub-nanometer Ruthenium nanoparticles on poly(acrylic acid)-functionalized 45 nm-sized magnetic iron oxide nanoflower supports (referred to as Ru-IONFs) and subsequently applied to enhance the sensitivity of lateral flow immunoassays (LFIAs). The incorporation of RuNPs not only improved the brightness of the colorimetric signal but also lowered the activation energy barrier, leading to an increased maximum reaction rate and enhanced peroxidase-like catalytic activity. As a proof of concept, the as-prepared Ru-IONFs nanozyme was integrated into LFIAs (Ru-IONFs-LFIAs) for the detection of SARS-CoV-2 antigen. Compared with conventional gold nanoparticle (AuNP)-based LFIAs, the Ru- IONFs-LFIAs exhibited a 20.5-fold enhancement in sensitivity, enabling a visual detection limit as low as 78 ng/mL. Given the outstanding analytical performance, the Ru-IONFs-based LFIA presents a promising and reliable platform for the rapid and sensitive diagnosis of SARS-CoV-2. As discussed earlier, we have developed highly stable and multifunctional magnetic iron oxide nanostructures through surface modification, enabling efficient biomolecule conjugation (including DNA and antibodies) for subsequent self-assembly and immunoassay applications. We believe that our strategy can significantly promote the broader bioapplication of IONPs, owing to their versatile and tailorable surface properties. Major: Department of Biological Sciences Sat, 31 Jan 2026 15:00:00 GMT https://scholarworks.unist.ac.kr/handle/201301/90880 2026-01-31T15:00:00Z https://scholarworks.unist.ac.kr/handle/201301/90881 Title: The Mechanistic Role of ATAD5 in the Deubiquitination of Ub-PCNA Author(s): Yoo, Juyeong Abstract: Accurate regulation of DNA replication and replication-associated repair is crucial for maintaining genomic integrity. In these processes, PCNA functions as a molecular hub protein that tethers replication and repair factors to the site of DNA synthesis. Upon exposure to DNA damaging agents, PCNA is ubiquitinated to recruit TLS DNA polymerases for lesion bypass. Because dysregulation of PCNA leads to defects in DNA metabolism and genome instability, the tight control of PCNA dynamics is critical, and numerous studies have aimed to define its regulatory mechanisms. One of the key regulators of PCNA is ATAD5, a PCNA unloader that operates in association with RFC 2-5 subunits and is conserved from yeast to humans. In addition to its role in PCNA unloading, ATAD5 promotes the deubiquitination of Ub-PCNA with UAF1–USP1 complex. Excessive accumulation of Ub-PCNA leads to ssDNA gap formation and genomic instability. However, the detailed molecular mechanism by which ATAD5 contributes to Ub-PCNA deubiquitination has not been fully elucidated. Here, we identified the function of ATAD5 N-terminal domain in the deubiquitination of Ub-PCNA and its detailed regulatory mechanisms. Consistent with previous reports linking ATAD5 to the deubiquitinating enzyme UAF1–USP1, we confirmed that ATAD5 interacts with UAF1 and its substrate Ub-PCNA to promote efficient deubiquitination of Ub-PCNA in both In vivo and In vitro systems. Since the ATAD5 C-terminal domain functions as PCNA unloader, we sought to define the regulatory relationship between PCNA unloading and deubiquitination. Because ATAD5 preferentially acts on DNA-loaded Ub-PCNA, deubiquitination likely occurs prior to PCNA unloading by ATAD5. Furthermore, we showed that disrupting the interaction of ATAD5 with UAF1, Ub-PCNA, or DNA leads to genomic instability. In addition, ATAD5 associates with other deubiquitinating enzymes, USP7 and USP11, which display distinct deubiquitination specificities toward DNA-loaded or free Ub-PCNA compared with UAF1–USP1. These findings suggest that ATAD5 serves as a scaffold protein that coordinates multiple deubiquitinating enzymes for efficient PCNA recycling. Beyond mono-ubiquitinated PCNA, PCNA can also be poly-ubiquitinated for template switching or fork remodeling. ATAD5, together with UAF1–USP1, USP7 and USP11, catalyzes the deubiquitination of poly-Ub-PCNA, with each enzyme exhibiting distinct cleavage preferences within the polyubiquitin chain. Based on these mechanistic insights, the additional analyses with UAF1–USP1–ATAD5 complex and its substrate, Ub-PCNA were performed for structural determination of deubiquitination intermediate. We focused on the reconstitution of functional and stable deubiquitination ternary complex that retains functional deubiquitination activity toward Ub-PCNA. Major: Department of Biological Sciences Sat, 31 Jan 2026 15:00:00 GMT https://scholarworks.unist.ac.kr/handle/201301/90881 2026-01-31T15:00:00Z https://scholarworks.unist.ac.kr/handle/201301/90879 Title: Dopamine-Orchestrated Synaptic Plasticity through Circuit- and Cell-Type-Specific Mechanisms in the Basal Ganglia Author(s): Lee, Youngeun Abstract: The Basal Ganglia (BG) circuitry is the central hub for action selection, motor control, and reward- based learning. Dopamine (DA) is a key neuromodulator that flexibly regulates synaptic plasticity across BG circuits, enabling adaptive control of movement and learning. Although dopaminergic regulation has been extensively studied in the striatum, the precise mechanisms by which DA fine-tunes synaptic plasticity across distinct cellular and circuit domains remain largely unknown. Understanding this circuit- and cell-type-specific heterogeneity in DA signaling is essential for comprehending how BG output adapts to internal and external demands, and how its dysregulation contributes to movement disorders such as Parkinson’s disease (PD). In this dissertation, I investigate how DA orchestrates synaptic plasticity across multiple levels of the BG through distinct neuronal and astrocytic mechanisms. Specifically, I focused on two complementary pathways, the striatopallidal synapse in the external globus pallidus (GPe), which represents the first inhibitory relay of the indirect pathway, and the corticostriatal synapse, where DA and astrocytes cooperatively shape excitatory remodeling during motor learning. In Chapter 3, I demonstrate that DA modulates striatopallidal inhibitory transmission in a subregion- specific manner through distinct pre- and postsynaptic receptor mechanisms. I found that presynaptic D2 receptors and postsynaptic D4 receptors differentially shape short-term plasticity across GPe subregions exhibiting a pinwheel-like topographical organization. DA depletion reorganizes these regional patterns by altering D2R localization and calcium dynamics at striatopallidal terminals, revealing that dopaminergic signaling in the GPe is spatially heterogeneous yet functionally precise. In Chapter 4, I reveal that DA also governs long-term excitatory plasticity through astrocytic mechanisms. I find that DA-dependent astrocytic MEGF10 signaling drives synapse-specific engulfment of corticostriatal inputs during motor learning. Through ex vivo whole-cell recordings, I demonstrate that astrocytic MEGF10 is required for maintaining corticostriatal synaptic strength and quantal properties following motor learning. Using distinct paradigms of motor learning and chemogenetic DA modulation, I further reveal that astrocytic MEGF10 is required for learning-induced synaptic strengthening and DA-dependent regulation of corticostriatal transmission in D1- and D2- medium spiny neurons (MSNs). These electrophysiological findings establish the functional necessity of astrocyte-mediated synaptic remodeling for DA-driven circuit refinement and motor adaptation. In Chapter 5, I summarize the key findings of this dissertation and discuss their broader implications for BG function. Altogether, my research identifies DA as a key orchestrator of synaptic architecture— through highly structured regulation that coordinates fast, region-specific modulation of inhibitory transmission and slow, astrocyte-dependent remodeling of excitatory connections. This dual mechanism provides new insight into how DA confers both flexibility and stability to BG networks and suggests potential therapeutic targets for movement disorders associated with dopaminergic dysfunction. Major: Department of Biological Sciences Sat, 31 Jan 2026 15:00:00 GMT https://scholarworks.unist.ac.kr/handle/201301/90879 2026-01-31T15:00:00Z https://scholarworks.unist.ac.kr/handle/201301/90878 Title: Deciphering the molecular mechanisms of STIM1 and Orai1: coronavirus cleaves STIM1 to evade innate immune and Orai1 negatively regulates KLF1 in terminal erythropoiesis Author(s): Lee, Yoon Young Abstract: This dissertation consists of two independent studies centered on major component of SOCE, STIM1 and Orai1, which mediate distinct regulatory mechanisms in host–virus interaction and erythropoiesis. In the first study, I investigated how human coronaviruses exploit host cellular machinery to evade antiviral immunity. I identified STIM1, a key Ca²⁺ sensor in the endoplasmic reticulum, as a previously unrecognized substrate of the coronavirus 3CL protease. Cleavage of STIM1 at residue Q496 generates two fragments that acquire novel proviral functions. The STIM1 NT inhibits MAVS aggregation and MAVS–TRAF2–TBK1 signalosome formation, whereas the STIM1 CT interferes with IKKα-mediated p65 phosphorylation through its interaction with HSP70. Together, these mechanisms cooperatively suppress interferon-β production and attenuate host antiviral responses, revealing a new strategy by which coronaviruses subvert host immunity through targeted cleavage of STIM1. The second study focuses on the role of Orai1-mediated Ca²⁺ signaling in terminal erythroid maturation. Erythropoietin (EPO) and the master transcription factor Krüppel-like factor 1 (KLF1) orchestrate the progression of erythropoiesis; however, the contribution of Ca²⁺ signaling to this process has remained poorly defined. I found Orai1 as a novel EPO-responsive Ca²⁺ channel that functions as a dynamic regulatory toggle controlling KLF1 transcription. In early erythroid differentiation, EPO- induced Orai1 activity suppresses KLF1 expression via Ca²⁺-dependent NFAT2 activation, transiently pausing maturation. As differentiation proceeds, Orai1 expression declines, relieving NFAT2-mediated repression and allowing EPO–STAT5-dependent activation of KLF1 to promote terminal erythropoiesis. Functional disruption of Orai1, by R91W mutation or CRISPR/Cas9-mediated knockout, enhances KLF1 expression, globin synthesis, and enucleation efficiency in HUDEP-2, UCB-, and hPSC-derived erythroid cells. Collectively, this dissertation delineates two distinct molecular strategies—one utilized by viruses to undermine host immune defenses and another employed by developing erythroblasts to coordinate maturation—underscoring the versatility of calcium-related regulatory pathways in controlling cellular function and disease processes. Major: Department of Biological Sciences Sat, 31 Jan 2026 15:00:00 GMT https://scholarworks.unist.ac.kr/handle/201301/90878 2026-01-31T15:00:00Z