Biology subjects

Kim, T.

Publications and source records attributed to Kim, T..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Dissecting Molecular Origins of the Mechano-Adaptive Behaviors of Actomyosin Bundles

Actomyosin bundles, composed mainly of actin filaments, myosin II filaments, and actin cross-linking proteins, are central to force generation and maintenance in non-striated muscle cells. Actomyosin bundles exhibit diverse mechano-adaptive responses to external mechanical cues. However, the molecular mechanisms underlying such adaptability remain poorly understood. In this study, we employed experiments and agent-based simulations to illuminate how actomyosin bundles adapt to complex mechanical perturbations. Our experiments revealed that individual stress fibers isolated from cells, and thus operating independently of cellular regulation, exhibited buckling in response to rapid compressions following stretch, accompanied by gradual recovery to a straight configuration. Such buckling was not observed under slow compression, indicating that the bundles exhibit rate-dependent adaptive responses. These findings demonstrate that mechano-adaptive behavior is an intrinsic property of actomyosin bundles. Simulations successfully reproduced these rate-dependent behaviors intrinsic to actomyosin bundles and identified key factors determining the dependence. Bundle stiffness influenced the buckling-induced curvature but had little effect on the time required for recovery to straight configuration. Motor density did not alter the recovery time but significantly influenced the magnitude of tensile forces developed after full recovery. The recovery time was primarily governed by the motor walking rate and the applied compressive strain rate. This work reveals how intrinsic mechanics and motor activity drive actomyosin bundle behavior in cellular mechano-adaptation.

biophysics↗

bioRxiv2025

Agent-based computational modeling of the stochastic dynamic behavior of actin filaments recapitulates the homeostatic cortical array in plant epidermal cells

The homeostatic cortical actin array in plant cells plays important roles in fundamental processes, including intracellular transport, secretion, cell expansion, and cytoplasmic streaming. In response to diverse chemical and mechanical signals, the cortical array can remodel within minutes to assume new configurations or altered filament abundance. The homeostatic cortical actin array of some plant epidermal cells comprise sparsely distributed individual actin filaments and actin bundles, which enables tracking and quantitative analysis of dynamic properties over many minutes at high spatiotemporal resolution. Previous studies using quantitative live-cell imaging, small molecule inhibitors, and genetic mutations reveal the robust dynamic steady state of the cortical actin array, with individual filaments showing a behavior termed stochastic dynamics. Compared to experimental findings, computational efforts focused on the plant actin cytoskeleton are lacking, although computational models have the potential to define underlying mechanisms of actin array homeostasis and remodeling. Here, we used an agent-based computational model to reproduce the stochastic dynamic behavior of individual actin filaments in epidermal cells with consideration of key governing factors, including the nucleation, polymerization, depolymerization, severing, capping, and branching of filaments. Our model was able to reproduce experimental observations with respect to the abundance and length of filaments as well as the rates or frequencies of dynamic events. This model can be used to study the role of myosin motors and other actin-binding proteins, as well as the effects of signaling events and fluxes in cellular second messengers, on actin dynamics in plant cells.

plant biology↗

bioRxiv2025

Reconstitution of actomyosin networks in cell-sized liposomes reveals distinct mechanical roles of cytoskeletal organization in membrane shape remodeling

The actin cortex, a thin layer of actomyosin network beneath the plasma membrane, regulates various cell functions by generating active forces and inducing membrane deformations, including blebs. Although upstream signaling is involved in regulating cell shape, the extent to which downstream actomyosin molecules can control the shape remains elusive. Here, using a minimal reconstituted system with a combination of agent-based computational model, we show that while actin-membrane coupling strength determines the magnitude of membrane deformation, its balance with actin network connectivity governs the bleb initiation mechanism, either by detachment of the cortex from the membrane or by rupture of the cortex. This balance also regulates whether single or multiple blebs form. Furthermore, both experiments and simulations suggest that not only the dense cortical network but also the sparse volume-spanning network actively contributes to regulating bleb number. These findings provide mechanical insights into how cells tune actin network organization to control their shape.

biophysics↗

bioRxiv2025

Reversion of a RND transporter pseudogene uncovers latent stress resistance in Brucella ovis

Small-molecule screens can advance therapeutic discovery while yielding new insights into pathogen biology. Through a luminescence-based screen, we identified clinically approved dihydropyridines that reduced the fitness of the intracellular pathogen Brucella ovis within mammalian phagocytes. Given the established role of dihydropyridines as inhibitors of mammalian L-type calcium channels and our observation that drug treatment perturbed calcium and manganese levels in host phagocytes, we initially hypothesized a host-directed mechanism of action. However, dose-response assays in axenic medium revealed that these drugs can directly inhibit B. ovis growth. To investigate the genetic basis of B. ovis susceptibility to dihydropyridine treatment, we selected for mutants capable of growing in the presence of cilnidipine. Cilnidipine-resistant isolates carried single-base deletions in the bepE pseudogene that restored an open reading frame encoding an RND-family transporter subunit. B. ovis is an ovine venereal pathogen that has experienced significant pseudogenization in its recent evolutionary history. Frameshift mutations that restored bepE function in B. ovis increased its resistance not only to dihydropyridines but also to a broad range of membrane-disrupting agents, including bile acid. Conversely, deleting bepE in Brucella abortus, a related zoonotic species that retains an intact version of the gene, increased its sensitivity to bile acid in vitro and to cilnidipine in the intracellular niche. We conclude that bepE is a key determinant of chemical stress resistance in Brucella spp., and that its pseudogenization in B. ovis contributes to the documented hypersensitivity of this host-restricted lineage to chemical stressors. Author SummaryBrucella species are intracellular bacterial pathogens that infect diverse wildlife and livestock and can also cause disease in humans. We developed a high-throughput assay to identify compounds that reduce the intracellular fitness of Brucella ovis, a globally distributed pathogen of sheep. This screen identified two dihydropyridine-class hypertension drugs as inhibitors of B. ovis fitness within mammalian cells. While dihydropyridines are established inhibitors of calcium channels in mammals, our results revealed that they also directly inhibited B. ovis growth. The B. ovis genome contains over 300 pseudogenes, and we discovered that resistance to dihydropyridines and other chemical stressors can emerge through frameshift mutations that resurrect the function of bepE, a conserved pseudogene encoding a membrane transporter subunit. In other Brucella species, bepE remains intact, and we show that deleting this gene in the zoonotic pathogen Brucella abortus increases susceptibility to both dihydropyridine treatment and membrane-disrupting stress. Our study provides evidence that pseudogenes like bepE can serve as a latent reservoir of adaptive functions in B. ovis, including drug and stress resistance.

microbiology↗

bioRxiv2025

Microglia modulate concussion biomarkers and cognitive recovery in male mice

There is a critical unmet need for concussion biomarkers that predict cognitive recovery. Existing TBI biomarkers largely capture acute cellular damage rather than the multicellular repair processes that determine long-term outcome, and whether microglia causally shape divergent trajectories remains unclear. Here, we used PLX5622 to deplete microglia and other CSF1R-dependent myeloid cells in a male mouse model comparing concussion alone to concussion preconditioned by prior subconcussive impacts. Microglial depletion had no effect on cognitive outcome after concussion alone, but introduced a significant novel object recognition deficit specifically when concussion was preconditioned, revealing a history-dependent role for microglia in recovery. To identify the molecular substrates of this divergence, we profiled brain-derived GluA1/2+ extracellular vesicle (EV) miRNAs and single-nuclei transcriptomes from the injured brain. Diagnostic and injury-history EV miRNA biomarkers discriminated between concussion subtypes in microglia-intact animals but lost this discriminative power after depletion, indicating that these neuron-enriched biomarkers are influenced by microglia-dependent biology rather than injury alone. snRNA-seq further revealed that microglial depletion selectively induced transcriptional programs related to oligodendrocyte maturation after unconditioned concussion, a candidate substrate for this microglia-dependence. Finally, we identified a serum EV miRNA panel that estimated cognitive recovery across injury conditions. Together, these findings identify a history-dependent role for microglia in concussion outcome and characterize brain-derived EVs as a potentially promising tool for surveilling the neuroinflammatory processes influencing recovery.

bioengineering↗

bioRxiv2025

Improving RNA Secondary Structure Prediction Through ExpandedTraining Data

In recent years, deep learning has revolutionized protein structure prediction, achieving remarkable speed and accuracy. RNA structure prediction, however, has lagged behind. Although several methods have shown some success in predicting RNA secondary and tertiary structures, none have reached the accuracy observed with contemporary protein models. The lack of success of these RNA structure prediction models has been proposed to be due to limited high-quality structural information that can be used as training data. To probe this proposed limitation, we developed a large and diverse dataset comprising paired RNA sequences and their corresponding secondary structures. We assess the utility of this enhanced dataset by retraining on a deep learning model, SincFold. We find that SincFold exhibited improved generalization to some previously unseen RNA families, enhancing its capability to predict accurate de novo RNA secondary structures. The RNASSTR dataset provides a substantial advance for RNA structure modeling, laying a strong foundation for the development of future RNA secondary structure prediction algorithms.

bioinformatics↗

bioRxiv2025

Combined CSF1R Inhibition and Sensory Gamma Stimulation Provide Protective Effects in a Mouse Model of Alzheimers Disease

The CSF1R inhibitor PLX3397, an FDA-approved treatment for a rare cancer, has been shown to reduce microglia count, lower inflammation, and increase synaptic markers in mouse models of Alzheimers disease (AD). However, the effects of PLX3397 on neural function in AD remain largely unknown. Here, we characterized the effects of PLX3397 treatment in 5xFAD mice. While PLX3397 increased synaptic density, it reduced the percentage of neurons phase-locked to gamma oscillations. This neural decoupling was closely associated with gene expression changes related to synapse organization. We investigated whether Gamma ENtrainment Using Sensory (GENUS) stimulation could counterbalance the neural circuit alterations induced by PLX3397. GENUS + PLX3397 restored gamma phase-locking, reshaped gene expression signatures, and improved learning and memory better than either treatment alone in 5xFAD mice. These findings suggest that CSF1R inhibitors like PLX3397 may benefit from a multimodal approach combining microglial targeting with non-invasive sensory stimulation to support neural physiology and improve cognitive function in AD.

neuroscience↗

bioRxiv2025

Impact of exercise intervention on IGF-1 signaling related to muscle regeneration and physical performance in aged mice

Aging encompasses the natural processes of birth, growth, and aging, during which the functional ability of muscles gradually decreases, leading to the loss of muscle size and reduced exercise performance known as sarcopenia. This condition is closely associated with weakness, osteoporosis, and degenerative diseases, increasing the risk of falls, fractures, metabolic diseases, and mortality due to limitations in physical performance among the elderly. This study investigated the effects of exercise intervention on biological markers related to skeletal muscle mass and functions in conjunction with aging. At age of four or twenty, the C57BL/6 mice were assigned to Young control (Y-Con, n = 10) or exercise training (Y--Exe, n = 10), and Aged control (A-Con, n=10) or exercise training (A-Exe, n = 10). Exercise intervention was performed on a rodent motor-driven treadmill with a frequency of 5 days per week for 8 weeks. As a consequence, exercise intervention in mice resulted in positive changes in IGF-1 signaling and muscle phenotype compared to mice that did not undergo exercise intervention, specifically showing prominent effects in the A-Exe group compared to the A-Con group. The mitigating effects of exercise intervention on age-related skeletal muscle dysfunction were accompanied by enhanced exercise performance and muscle function, as assessed by grip strength and the rotarod test. The current findings support previous studies that have reported the positive effect of exercise intervention in alleviating age-related declines in exercise performance and muscle function in older adults.

physiology↗

bioRxiv2025

Neuronal cell adhesion molecule (NRCAM) variant defined by microexon skipping is an essential, antigenically distinct, and targetable surface proteoform in high-grade glioma

To overcome the paucity of known tumor-specific surface antigens in pediatric high-grade glioma (pHGG), we contrasted splicing patterns in pHGGs and normal brain samples. Among alternative splicing events affecting extracellular protein domains, the most pervasive alteration was the skipping of [≤]30 nucleotide-long exons. Several of these skipped microexons mapped to L1-IgCAM family members, such as NRCAM. Bulk and single-nuclei short- and long-read RNA-seq revealed uniform skipping of NRCAM microexons 5 and 19 in virtually every pHGG sample. Importantly, the {Delta}ex5{Delta}ex19 (but not the full-length) NRCAM proteoform was essential for pHGG cell migration and invasion in vitro and tumor growth in vivo. We developed a monoclonal antibody selective for {Delta}ex5{Delta}ex19 NRCAM and demonstrated that "painting" of pHGG cells with this antibody enables killing by T cells armed with an FcRI-based universal immune receptor. Thus, pHGG-specific NRCAM and possibly other L1-IgCAM proteoforms are promising and highly selective targets for adoptive immunotherapies.

cancer biology↗

bioRxiv2025

Fine-Tuning of Material Properties via Catch Bonds

Semiflexible polymer networks are ubiquitous in biological systems, including a scaffolding structure within cells called the actin cytoskeleton. The polymers in these networks are often interconnected by transient bonds. For example, actin filaments in the cytoskeleton are physically connected via cross-linkers. The mechanical and kinetic properties of the cross-linkers significantly affect the rheological properties of the actin cytoskeleton. Here, we employed an agent-based model to elucidate how the force-dependent behaviors of the cross-linkers determine the material properties of passive networks without molecular motors and the force generation of active networks with molecular motors. The cross-linkers are assumed to behave as a slip bond whose dissociation rate is proportional to forces or as a catch-slip bond whose dissociation rate is inversely proportional to forces at low force level but proportional to forces at high force level. We found that catch-slip-bond cross-linkers can increase both stress and strain at a yield point by forming force-bearing elements that turn over continuously, which is impossible to achieve without the catch-slip bonds. In addition, we demonstrated that the catch-slip-bond cross-linkers help myosin motors generate greater internal contractile forces by reinforcing the force-bearing parts of the active network.

biophysics↗

bioRxiv2025

Pathobiont-triggered induction of epithelial IDO1 drives regional susceptibility to Inflammatory Bowel Disease

The structure and function of the mammalian gut vary by region, yet why inflammatory diseases manifest in specific regions and not others remains unclear. We use a TNF-overexpressing Crohns disease (CD) model (Tnf{Delta}ARE/+), which typically presents in the terminal ileum (TI), to investigate how environmental factors interact with the hosts immune susceptibility to drive region-specific disease. We identified Chlamydia muridarum, an intracellular bacterium and murine counterpart to the human sexually transmitted C. trachomatis, as necessary and sufficient to trigger disease manifestation in the ascending colon (AC), another common site of human CD. Disease manifestation in the AC depends on indoleamine 2,3-dioxygenase (IDO1) activity induced by hypersensitive surface secretory cells in genetically susceptible hosts. Single-cell and microbial analyses of human specimens also implicates this pathobiont-epithelial IDO1 pathway in patients with a history of CD in the AC. Our findings demonstrate that genetic and microbial factors can independently drive region-specific disease and provide a unique model to study CD specific to the AC.

cell biology↗

bioRxiv2024

Cluster Formation and Phase Separation Driven by Mobile Myosin Motors in the Motility Assay

Interactions between F-actin and myosin are critically important for a wide range of biological processes, including cell migration, cytokinesis, and morphogenesis. The motility assay with myosin motors fixed on a surface has been utilized for understanding various phenomena emerging from the interactions between F-actin and myosin. For example, F-actin in the motility assay exhibited distinct collective behaviors when actin concentration was above a critical threshold. Recent studies have performed the myosin motility assay on a lipid bilayer, meaning that myosin motors anchored on the fluid-like membrane have mobility. Interestingly, mobile motors led to very different collective behaviors of F-actin compared to those induced by stationary motors. However, the dynamics and mechanism of the unique collective behaviors have remained elusive. In this study, we employed our cutting-edge computational model to simulate the motility assay with mobile myosin motors. We reproduced the formation of actin clusters observed in experiments and showed that F-actin within clusters exhibits strong polar ordering and leads to phase separation between myosin motors and F-actin. The cluster formation was highly dependent on the average length and concentration of F-actin. Our study provides insights into understanding the collective behaviors of F-actins that could emerge under more physiological conditions.

biophysics↗

bioRxiv2024

A female-specific RdDM-associated element guides de novo DNA methylation during rice gametophyte development

DNA methylation is crucial for regulating gene expression and silencing transposons. While the spatiotemporal specificity of DNA methylation controls organ formation and development, the molecular mechanisms underlying locus- or tissue-specific DNA methylation remain unclear. Previously, locus- or tissue-specific DNA methylation was thought to depend solely on the recognition of histone methylations. Here we show that high expression of 24-nucleotide small interfering RNAs (24-nt siRNAs) leads to incremental CHH methylation at specific loci via the RNA-directed DNA methylation (RdDM) pathway during female gametophyte development in rice. We also identify a DNA motif, the Female-specific RdDM-associated Element (FRE), which guides methylation to these loci. Furthermore, we show that the female-preferentially expressed protein OsCLSY3 directly interacts with FRE to regulate CHH methylation specifically in female reproductive tissues. These findings uncover a novel molecular mechanism necessary for tissue- and locus-specific de novo DNA methylation that might be conserved across diverse organisms including animals.

plant biology↗

bioRxiv2024

Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information

Molecular barcoding methods enable high-sensitivity detection of circulating tumor DNA that is rarely present in liquid biopsy samples. Many methods involve ligation of molecular barcodes to DNA prior to hybridization capture, enabling recovery of starting molecules. Development of polymerase chain reaction (PCR)-based methods could facilitate more cost- and labor- effective detection; however, tracking molecular identity can be difficult, as new barcodes overwrite old barcodes in each cycle. We developed a sensitive genotyping method based on a peer-to-peer network-derived identifier for error reduction in amplicon sequencing (SPIDER-seq) and enable molecular identity tracking with PCR-derived libraries using overwritten barcodes. SPIDER-seq detected mutations at frequences as low as 0.125% after only two consecutive general PCR cycles and systematically analyzed the error pattern in the peer-to-peer network. Our method could facilitate the rapid detection of mutations associated with various cancers.

bioinformatics↗

bioRxiv2024

Large-scale Signal Propagation Modes in the Human Brain

The brains large-scale temporal dynamics play a crucial role in understanding its operations, but developing a cohesive framework to integrate the potentially extensive array of spatiotemporal patterns remains elusive. Our work addresses this gap by identifying multiple large-scale signal propagation modes in resting-state fMRI time series under a unified methodological framework. We found five distinct modes that effectively predict future blood-oxygen-level-dependent (BOLD) signal dynamics, each reconciling transitions between well-known large-scale brain networks into coherent spatiotemporal units. By utilizing these coherent units, our approach circumvents the need to explore combinatorial explosion of transitions between potential states, enabling parsimonious modeling and effective prediction of whole-brain temporal evolution. Each mode captures specific operational dimensions of neural resource allocation, ensuring their interpretability. Importantly, we showed that complex spatiotemporal features emerge from the superposition of these few propagation modes, unifying a broad spectrum of well-known brain dynamics phenomena. Our results lay the groundwork for a unified framework to understand large-scale spatiotemporal brain organization. Moreover, individual differences in mode expression profiles correlate with general cognitive abilities, exhibit heritability, and demonstrate cross-task stability, underscoring their functional significance. This could lead to efficient methods for characterizing functional fingerprints and advancing diagnostic approaches for neurological disorders.

neuroscience↗

bioRxiv2024

The Mechanism of Dynamic Steady States in Lamellipodia

Lamellipodia are quasi-two-dimensional actin projections formed on the leading edge of the cell, playing an important role in sensing surrounding environments by forming focal adhesions. A branched actin network in the lamellipodia exhibits a stable, dynamic steady state characterized by a retrograde flow, which is attributed to a balance between network assembly at the leading edge and disassembly at the rear. Although the molecular players and architecture of the lamellipodia have been investigated extensively during recent decades, it still remains elusive how the dynamic steady state with continuous retrograde flow is achieved and robustly maintained. In this study, using an agent-based computational model, we probed how physical interactions between subcellular components in the lamellipodia lead to the dynamic steady state. We reproduced a steady retrograde flow induced by myosin activity and balance between network assembly and disassembly but hindered by resistances from adhesions formed on the underlying substrate. We demonstrated that different modes of dynamic steady states are possible, and that a network which failed to show the retrograde flow due to perturbations can be rescued by altering other factors. Our study provides insights into understanding how cells maintain the dynamic steady state of the lamellipodia in highly varying microenvironments.

biophysics↗

bioRxiv2024

Impacts of Structural Properties of Myosin II Filaments on Force Generation

Cells need intracellular forces for their physiological functions, such as migration, cytokinesis, and morphogenesis. The actin cytoskeleton generates a large fraction of the forces via interactions between cytoskeletal components, such as actin filament (F-actin), myosin, and actin cross-linking proteins (ACPs). Myosin II plays the most important role in cellular force generation. Myosin II molecules self-assemble into filaments with different structures depending on myosin II isoforms and other conditions such as pH and ionic concentration. It has remained elusive how force generation in actomyosin structures is affected by the architecture of myosin II filaments. In this study, we employed an agent-based model to investigate the effects of the structural properties of myosin II filaments on force generation in disorganized actomyosin structures. We demonstrated that the magnitude of forces and the efficiency of force generation can vary over a wide range depending on the number and spatial distribution of myosin II filaments. Further, we showed that the number of myosin heads and the length of a bare zone at the center of myosin II filaments without heads highly affect the force generation process in bundles and networks. Our study provides insights into understanding the roles of the structural properties of myosin II filaments in actomyosin contractility.

biophysics↗

bioRxiv2024

Understanding How Biopolymers Found in Marine Ecosystems Impact the Efficacy of Bacteriophages against Bacteria

Bacteriophages are abundant in Earths ecosystem and serve as valuable mediators in marine environments, regulating bacterial populations in oceans, hot springs, and salterns, among others. However, bacteriophages have high-specificity to their host, thus making it difficult to study bacteria-phage relationships. In this study, we observe whether naturally occurring biopolymers (coral mucin (from Stylophora pistillata), chitin, and sodium alginate) increase bacteriophage affinity to bacteria by recording the plaques formed throughout 15-minute time intervals. We use an isolated E. coli strain and its corresponding T7 phage, as well as isolated bacteria and phage strains from a coral sample (labeled Stylophora pistillata or "Coral 1"). The research conducted plaque assays using minimal media solution to quantify phage-forming units (PFUs) using 2 bacterial forms, Coral 1 and E. coli and Mucin, Sodium Alginate, and Chitin as biopolymers. Our research found that the biopolymers had an effective impact on the generation of PFUs in our bacterial cultures for all samples. While we were unable to conduct future plaque assays, the information we have now is important to discovering ways to increase phage efficiency in marine environments to help maintain nutrient resource levels in such ecosystems.

microbiology↗