Biology subjects

Kim, T.

Publications and source records attributed to Kim, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Within-host population structure, migration, and parallel adaptive evolution of Pseudomonas aeruginosa in cystic fibrosis lung disease

Pseudomonas aeruginosa infections in adults with cystic fibrosis (CF) are comprised of heterogeneous populations, most often tracing ancestry back to a single recent common ancestor. What is not clear is the physical spatial structure within the lung infection population, its stability over time and whether this physical structure leads to different evolutionary trajectories in different adaptive environments. To compare the P. aeruginosa populations across a single lung, we performed whole genome sequence analyses of 450 isolates recovered from lavage samples of the three different lobes of the right lung from a person with mild-to-moderate CF lung disease at three time points over the course of [~]1.5 years. We found that isolates fell into five distinct phylogenetic lineages with evidence for repeated translocation of isolates from different lineages across lobes and loss-of-function mutations in lasR and mucA were present in all 450 isolates. The well-resolved phylogenetic analyses revealed a structured population in which we find the coexistence of a slowly evolving lineage and more rapidly evolving lineages. There is also support for numerous migration events. Further, strong evidence for parallel adaptive mutations in multiple genes revealed distinct evolutionary paths affecting mucoid phenotypes and genetic variation in antibiotic resistance-associated pathways across coexisting populations within a single individual over time. These results provide an example of within-host evolution leading to microheterogeneity that may be useful to consider in future study of infection metapopulations dynamics over the course of chronic infection. IMPORTANCEIndividuals with cystic fibrosis (CF) commonly have chronic lung infections that contain clonally derived Pseudomonas aeruginosa populations with genotypic and phenotypic diversity. This study describes a substantial dataset containing 450 isolates from different lobes of the right lung across three timepoints from an individual with mild-to-moderate CF lung disease. Some regional enrichment for specific lineages with parallel mutations among individual lobes of the lung was observed, but longitudinal analysis also demonstrated that compartmentalization is not strictly maintained and that isolates migrate between lobes of the lung over time. Perspectives on within lung evolution will be important for understanding the pathogen populations in chronic respiratory infections in CF and other diseases.

microbiology↗

bioRxiv2026

Kinetic Control of Out-Of-Equilibrium Dynamics in the RhoA Signaling Cascade Shapes Actomyosin Contractility

Cellular functions rely on the precise timing of signal transmission through sequential activation cascades, yet the origin and functional role of signaling delays remain poorly understood. Here, we dissect the temporal organization of the RhoA signaling cascade during pulsed actomyosin contractility in the early C. elegans embryo. We uncover a stereotypical delay between upstream RhoA/ROCK activation and downstream myosin II recruitment. Using TIRF single-molecule microscopy, we show that this delay arises from binding and unbinding kinetics of myosin rather than from slow biochemical reactions. A simple and versatile kinetic model parameterized by these measurements accurately predicts the temporal evolution of myosin accumulation and reveals active control of the dynamic range of the cascade. Perturbing actin and myosin turnover experimentally confirms these predictions, and numerical simulations show that the delay between actin and myosin plays a critical role in force deployment during pulsed contraction. Together, our results indicate that kinetic delays in signaling cascades are not simply tolerated during morphogenesis, but actively shape force deployment in the cell.

developmental biology↗

bioRxiv2026

Intranasal Replicating Adenovirus type 4-SARS-CoV-2 Recombinants Induce Superior Immune Response Durability and Efficacy in Preclinical Testing Compared to Standard Intramuscular Vaccines

The portfolio of next generation COVID-19 vaccines would benefit from candidates that induce durable systemic and mucosal immune responses that would lessen person-to-person transmission. We constructed an intranasal (IN) replication-competent adenovirus type 4 recombinant platform to express SARS-CoV-2 Spike variants (Ad4-S) and assessed immunogenicity and efficacy in the Syrian hamster model. Although both IN Ad4-S and intramuscular (IM) vaccines (Ad26.CoV2.S and mRNA-1273) induced serum binding antibodies, only Ad4-S induced a robust mucosal response in the nasal cavity. IN Ad4-S vaccination induced serum neutralizing titers equivalent to or greater than IM vaccination but more durable up to 6 months. Upon challenge, IN immunization also resulted in less weight loss, greater breadth and durability of restriction of viral replication, and less lung pathology than IM immunization up to 268 days after immunization. These data support the potential of the IN Ad4 vaccine platform to reduce transmission of SARS-CoV-2 and other respiratory viruses with pandemic potential.

immunology↗

bioRxiv2026

Quantitative Optimization of Sensitivity and Specificity in Targeted and Whole-Exome Sequencing Using Reference-Standard DNA Mixtures

BackgroundWe previously developed a benchmarking strategy using mixtures of homozygote and heterozygote DNAs as reference standards to simultaneously assess sensitivity and false positive (FP) error rates in targeted next-generation sequencing (T-NGS) and whole-exome sequencing (WES), revealing substantial variability across commercial platforms. However, optimal analytic conditions for clinical application remain undefined. MethodsWe systematically evaluated multiple sequencing kits and bioinformatics pipelines across various variant allele fraction (VAF) thresholds to identify conditions that maximize both sensitivity and specificity. Recurrent error-prone alleles were defined and filtered to enhance specificity. ResultsOptimal performance was achieved using the DRAGEN pipeline with recurrent FP allele filtering. For T-NGS, a 1% VAF cutoff yielded a 95% detection threshold of 2.99% and 1.21 FPs per megabase (FP/Mb); for WES, a 2% cutoff yielded a 95% threshold of 5.02% and 1.15 FP/Mb. These settings improved sensitivity >3-fold and reduced FP rates >96% versus suboptimal pipelines. Notably, VAF thresholds flattened sensitivity differences across platforms, obscuring key performance disparities--challenging assumptions that T-NGS is inherently more sensitive than WES. In-house and conventional pipelines undercalled up to 10% of true variants. Restricting reporting of 1-4% VAF variants to [~]1,000 predefined actionable sites enabled recovery of clinically relevant mutations while reducing FP risk >99%. ConclusionsThis study provides a quantitative framework for optimizing NGS performance. Our findings support actionable strategies to improve diagnostic accuracy in clinical genomics through tailored pipeline selection, VAF thresholding, and artifact filtering.

bioinformatics↗

bioRxiv2026

Exact formula of the total quasi-steady state approximation in competitive target-mediated drug disposition

Competitive target-mediated drug disposition (competitive TMDD) arises when two drugs compete for the same target receptor. These dynamics can be characterized by the full competitive TMDD model; yet, its complexity motivated the use of a reduced model, which is invalid under high receptor concentrations. While this problem can be resolved by using the total quasi-steady state approximation (tQSSA), which remains valid for all receptor conditions, the exact formula of the tQSSA-based reduced model--competitive qTMDD--has remained unknown for 15 years, as it requires solving a cubic equation and the nontrivial task of identifying a biologically meaningful solution. Consequently, researchers have relied on numerical approximation methods, which impose substantial computational costs to maintain accuracy and thereby hinder their practical use in complex real-world applications. To address this problem, we derive--for the first time--a real-valued exact formula for competitive qTMDD by leveraging analytic properties of cubic equations and geometric characteristics of their roots in the complex plane. This exact formula improved computational speed by more than 11-fold compared to previous numerical approximation methods, thereby enabling Bayesian inference using competitive qTMDD, which had been impractical due to excessive computational time. When applied to real-world data from clinical trials, competitive qTMDD estimated pharmacological parameter estimates comparable to those from the full competitive TMDD model while requiring only 30-43% of the computation time. Importantly, this estimation using competitive qTMDD remained consistently accurate regardless of data sparsity, whereas the previous reduced model produced biased estimates under sparse sampling conditions. By ensuring precise biological interpretation of drug systems even in complex real-world scenarios, the exact formula of competitive qTMDD has the potential to significantly streamline the drug development and clinical testing process. Our exact formula also consists entirely of real-valued terms, allowing seamless integration into existing pharmacometrics software. Author SummaryCompetitive target-mediated drug disposition (competitive TMDD) occurs when two drugs compete for the same target receptor. Analyzing this interaction has faced a dilemma for 15 years: choosing between a full model that is accurate but computationally intensive, and a reduced model that is fast but often loses accuracy under real-world clinical conditions. Researchers tried to solve this dilemma by deriving an accurate reduced model; however, it was mathematically challenging. As a result, they had to rely on numerical approximations--which require substantial computational power to maintain the accuracy needed for clinical use, making them impractical in real-world scenarios. In this study, we derive a first-ever exact formula for the new reduced model that is accurate across all biological conditions. This formula computes more than 11 times faster than previous numerical methods, making advanced statistical analyses--such as Bayesian inference--feasible for the first time in this context. When applied to real-world clinical data for Anakinra and rhIL-7-hyFc, our method yielded parameter estimates as accurate as the full model but required significantly less computation time. This breakthrough provides a more accurate biological interpretation and better guidance for determining the right drug dose, potentially accelerating drug development and reducing associated costs.

pharmacology and toxicology↗

bioRxiv2026

Dual Oxygen-Partitioned Co-Culture Uncovers Microbe-Specific Epithelial Stress and Homeostatic Programs

Direct epithelial-microbial interactions occur across a steep aerobic-anaerobic interface in the intestine, yet mechanistic analysis has been limited by the difficulty of sustaining oxygen-dependent epithelial cells together with strictly anaerobic microbes in vitro. Here, we establish a dual oxygen-partitioned co-culture system that reproducibly maintains aerobic intestinal epithelial cells and obligate anaerobic gut bacteria, enabling controlled analysis of epithelial responses under physiologically relevant oxygen architecture. Using Mediterraneibacter gnavus and Lacticaseibacillus casei as contrasting microbial partners, we identify distinct epithelial programs. M. gnavus induces epithelial stress characterized by tight-junction disruption, suppression of mitochondrial respiration, and activation of chromatin-associated and innate immune regulatory pathways, whereas L. casei preserves barrier integrity and supports mitochondrial capacity with restrained immune modulation. Integrated transcriptomic and proteomic analyses reveal a shared epithelial energy-conserving response to microbial proximity, upon which microbe-specific stress or homeostatic programs are imposed. In vivo analysis using a dextran sodium sulfate-induced colitis model demonstrates that these epithelial programs become physiologically relevant under inflammatory conditions, with L. casei promoting epithelial repair and immune rebalancing. Together, these findings define oxygen-partitioned epithelial-microbial interactions as a determinant of microbe-specific epithelial states.

microbiology↗

bioRxiv2026

A single-cell transcriptomic atlas of the periventricular proliferative zone in the late gestation fetal brain in the pigtail macaque

BackgroundThe fetal brain undergoes rapid changes in late gestation, when waves of neurogenesis and gliogenesis shape cortical circuitry. The periventricular proliferative region and adjacent white matter are enriched in neuroprogenitor cells, newborn neurons, and interneurons, which is challenging to study in the late gestation human fetal brain. The nonhuman primate (NHP) provides a powerful translational model to overcome this limitation, given its close similarity to human neurodevelopmental trajectories. The study objective was to construct a single-cell RNA-Seq (scRNA-Seq) atlas of the late-gestation fetal brain of the pigtail macaque (Macaca nemestrina), focused on the periventricular proliferative zone. MethodsA sample of the lateral ventricular wall, subventricular zone, and overlying white/gray matter was dissociated into single cells and processed through the 10X Genomics pipeline, followed by SoupX removal of ambient RNA, and Seurats pipeline to aggregate, cluster and annotate single-cell populations. Monocle3 was used to determine pseudotime and map lineage progression. ResultsThis analysis captured diverse populations of neuroprogenitors, newborn neurons, developing lineages of excitatory and inhibitory neurons, oligodendrocyte and astrocyte lineages, and resident immune and endothelial cells. ConclusionsSingle-cell populations from the third-trimester nonhuman primate fetal brain are highly similar to those in the human fetus. This late-gestation single-cell atlas of the periventricular proliferative zone provides a unique reference for progenitor, neuronal, glial, vascular, and immune cell states during a critical window of primate neurodevelopment, enabling mechanistic interrogation of how inflammatory, infectious, or hypoxic insults disrupt vulnerable neurogenic niches.

genomics↗

bioRxiv2025

A multivalent mRNA-LNP therapeutic vaccine with broad cross-genotype immunogenicity elicits clearance of HBV infected hepatocytes

Chronic hepatitis B remains a major global health challenge, affecting over 254 million individuals and causing over 1 million deaths annually. Despite current antiviral therapies effectively suppressing viral replication, functional cure rates are low due to HBV-induced immune dysfunction and exhaustion. Therefore, new therapeutic approaches to achieve immune control of HBV infection are needed. Following the systematic evaluation of multiple HBV mRNA antigen designs, we developed mRNA-1965, a trivalent therapeutic mRNA vaccine encoding nanoparticle-displayed PreS1 and PreS2 domains of HBsAg to bypass the immune interference caused by HBV subviral particles, along with mutant forms of HBV Core and Polymerase. In HBV naive mice, mRNA-1965 immunization induced dose-dependent HBV-neutralizing antibodies and Th1-skewed CD4+ and IFN{gamma}+ CD8+ T cell responses to all three encoded HBV antigens. In non-human primates, mRNA-1965 elicited broad antibody and T cell responses across multiple HBV genotypes. Furthermore, vaccination with mRNA-1965 achieved a strong neutralizing antibody response and complete clearance of serum and liver HBV biomarkers in in an AAV-HBV mouse model with [~]100 IU/mL baseline HBsAg. Notably, combining mRNA-1965 with immune stimulatory co-modalities targeting PD-L1 and OX40 further enhanced therapeutic efficacy in mice with [~]1000 IU/mL baseline HBsAg. Clearance of HBV in AAV-HBV mice was associated with T cell response to mRNA-encoded antigens and with activation and differentiation of Core-specific CD8+ T cells. These findings support the potential of mRNA-1965 to promote a functional cure for chronic hepatitis B by overcoming immune dysfunction and subsequently enabling robust, functional immunity.

immunology↗

bioRxiv2025

Magneto-Photonic Gene Circuit for Minimally Invasive Control of Gene Expression in Mammalian Cells

Precise control of gene expression is one of the fundamental goals of synthetic biology. Whether the objective is to modify endogenous cellular function or induce the expression of molecules for diagnostic and therapeutic purposes, gene regulation remains a key aspect of biological systems. Over time, advances in protein engineering and molecular biology have led to the creation of gene circuits capable of inducing the expression of specific proteins in response to external stimulus such as light. These optogenetic, or light-activated circuits hold significant potential for gene therapy as a tool for regulating the expression of therapeutic genes within cells. However, the applications of optogenetic systems can be limited by the lack of efficient ways for light delivery inside cells or tissue. Our approach to address this challenge is to harness the power of bioluminescence to produce light directly inside cells using a luminescent enzyme. Combined with a photosensitive transcription factor, we report the development of a fully genetically encoded optogenetic circuit for control of gene expression. Furthermore, we utilized a magneto sensitive protein to engineer a split protein version of this luminescent enzyme, where its reconstitution is driven by a 50mT magnetic stimulus. Thus, resulting in a first-of-its-kind gene circuit activated by a combination of light and magnetic stimulus. We expect this work to advance the implementation of light-controlled systems without the need of external light sources, as well as serve as a basis for the development of future magneto-sensitive tools.

synthetic biology↗

bioRxiv2025

Unconventional linkers facilitate potent stabilized coronavirus stem antibody responses following nanoparticle vaccination

Vaccine technologies that protect against a range of related pathogens within viral families, such as human immunodeficiency virus (HIV), influenza, and coronaviruses (CoVs) represent the future of viral vaccine development. Towards developing broad-spectrum CoV and influenza vaccines, we and others previously designed and evaluated CoV and influenza stem antigens; but these elicited relatively weak and sub-neutralizing antibody (Ab) responses. Multivalent antigen display on nanoparticles (NPs) is an established strategy to enhance and shape immunogenicity. However, one facet of NP vaccines has been largely overlooked: the indispensable linker segment between the antigen and NP core. Here, we introduce de novo-designed rigid (L2) and rarely used long flexible (L6) linkers to optimally display antigens on NPs, target occluded epitopes, and enhance cross-reactive Ab responses, using prefusion-stabilized Middle East respiratory syndrome coronavirus (MERS-CoV) spike (S-2P) and stem (SS) antigens as prototype antigens. Antigenic characterization of L2-NPs confirmed enhanced Ab binding and exposure of cross-reactive epitopes compared with L6-NPs and soluble antigens. Immunization with SS-L2-NPs elicited broader, more potent cross-reactive Ab responses across the seven human-infecting CoVs and pandemic threat WIV1-CoV, whereas SS-L6-NPs induced stronger neutralizing Ab responses against MERS-CoV, SARS-CoV-2, and WIV1-CoV. Ab competition and systems serology analyses revealed that SS-L2-NPs elicit robust Fc-mediated effector functions. By improving CoV-targeting Ab functionality, these linker approaches have the potential to confer broad-spectrum CoV protection and represent a promising strategy against hypervariable influenza and HIV viruses - as well as other broad viral families with pandemic potential.

bioengineering↗

bioRxiv2025

Neural mechanisms of handedness for precision drawing: hand-dependent engagement of cortical networks for bimanual control and tool use

Neural mechanisms underlying handedness remain poorly understood. We used functional magnetic resonance imaging (fMRI) to study performance of a visually guided drawing task with each hand. We hypothesized that the left superior parietal lobule supports drawing with either hand, and individuals with chronic peripheral nerve injury (PNI) to the dominant hand use the same mechanism as healthy adults. Thirty-three right-handed adults (23 healthy, 10 patients) underwent fMRI while performing a precision drawing task, alternating between the right hand (RH) and left hand (LH). BOLD magnitude and functional connectivity (FC) modulation via generalized psychophysiological interaction were analyzed in 12 a priori regions of interest, followed by additional exploratory areas identified via whole brain magnitude analysis. During LH drawing (compared to RH drawing), contralateral primary motor cortex showed lower BOLD magnitude but greater FC with two networks: First, a left motor-premotor network with increased FC and equal-or-greater magnitude during LH drawing. Second, a right parietal network characterized by increased FC during LH drawing but increased magnitude during RH drawing. Exploratory whole-brain analyses supported and extended these motor and parietal networks, and additionally suggested that RH drawing may involve greater magnitude and FC within a bilateral parieto-premotor network centered on right paracingulate cortex. Patient group (PNI vs. control) did not interact with these effects. These results describe the first proposed mechanisms for LH precision drawing, both of which depend on differential engagement of bimanual control networks: a left hemisphere motor-premotor network for precision motor control, which engages intrahemispherically (directly) during RH drawing and interhemispherically (indirectly) during LH drawing; and a right hemisphere parietal network with greater distributed coordination during LH drawing. These mechanisms did not differ between PNI patients and healthy adults, highlighting these mechanisms potential as neuromodulatory targets to enhance LH performance after RH impairment.

neuroscience↗

bioRxiv2025

Human Norovirus NS7 Protein Activates Canonical Inflammasome Pathways via NLRP6 in Intestinal Epithelial Cells

Human norovirus (HNoV) is a leading cause of acute gastroenteritis, yet the mechanisms by which it interfaces with host innate immunity remain elusive. Here, we demonstrate that the HNoV NS7 protein, an RNA-dependent RNA polymerase, acts as a direct activator of canonical inflammasomes. Using reconstituted cell systems and human intestinal enteroids (HIEs), we found that NS7 interacts with both NLRP3 and NLRP6, promoting ASC speck formation, caspase-1 cleavage, and secretion of IL-1{beta} and IL-18. HNoV infection of HIEs recapitulated these events, including gasdermin D processing and robust IL-18 release. Importantly, CRISPR/Cas9-mediated NLRP6 deficiency abrogated inflammasome activation and markedly enhanced viral replication, underscoring the essential role of NLRP6 in epithelial antiviral defense. These findings identify NS7 as a novel inflammasome activator and establish NLRP6 as a key determinant of innate immune control of HNoV. Our study highlights inflammasome signaling as a potential therapeutic target for norovirus infection. Author summaryIn this study, we used human intestinal organoid models to explore how norovirus infection triggers a specific immune response known as inflammasome, which helps protect the gut from viral invaders. We focused on a viral protein called NS7 and discovered that it directly activates two types of inflammasome sensors, NLRP3 and NLRP6. We found that NLRP6, which is abundant in the gut lining, is especially important for detecting norovirus and launching an immune response. When we removed NLRP6 from intestinal cells, the virus was able to replicate more easily, and normal immune activation was lost. Our results reveal that norovirus uses its NS7 protein to interact with the bodys immune machinery in the intestine, and that NLRP6 plays a key role in controlling infection. This work highlights a new way in which the gut senses and responds to norovirus and may help guide future efforts to develop treatments that target these immune pathways.

immunology↗

bioRxiv2025

Functional clusters for shape, texture, and motion encoding in macaque V2

Macaque primary visual cortex (V1) exhibits exquisite columnar organization, while midlevel area V4 does not. Here we investigated the functional organization and representational bases of intervening area V2 with high-density Neuropixels recordings and a variety of visual stimuli--shape, texture, drifting grating, and translational motion patches. We observed dense clusters of similarly tuned neurons often spanning [~]500 {micro}m for shape and motion stimuli, and larger for texture stimuli, consistent with a columnar structure. In terms of representational bases, V2 responses were largely explained by stimulus features based on local image statistics: shape tuning is well-modeled by a linear combination of orientation filters, and direction selectivity is stronger with surface compared to object motion, in striking contrast to V4. Overall, our results support the progression from columns to sparse clusters as neuronal representations transform from encoding local features and feature conjunctions in V1/V2 to a high-dimensional object-based code in V4. Significance StatementBy recording hundreds of neurons simultaneously across layers of macaque visual area V2, we show the first evidence of exquisite fine-scale functional clusters that encode higher-order shape, texture, and motion features, extending well beyond the classic orientation-selective columns seen in area V1. Comparative analyses with V4 further reveal distinct representational bases and organization patterns between adjacent cortical areas, offering insights into how columnar organization is preserved in early visual areas (V1 and V2) but markedly attenuated in higher-order cortex such as V4.

neuroscience↗

bioRxiv2025

Evaluation of Paper-based Loop-Mediated Isothermal Amplification

Colorimetric loop-mediated isothermal amplification (LAMP) on microfluidic paper-based analytical devices (PADs) offers a low-cost, disposable, and equipment-free alternative to liquid LAMP assays. However, amplification on PADs is consistently slower, by 5-46%, than reactions in tubes. To identify the origin of this delay, we evaluated heat transfer, diffusion in porous cellulose, and nonspecific adsorption of LAMP components across both high- and low-copy input regimes. Our results show that once thermal equilibrium is reached, reduced effective diffusion is the dominant contributor to the kinetic lag at low copy numbers, whereas nonspecific adsorption becomes the primary barrier at higher template concentrations. Pre-coating the paper with bovine serum albumin (BSA) mitigates adsorption. It narrows the tube-to-paper gap, thereby accelerating amplification of the SARS-CoV-2 ORF7ab synthetic gene by an average of 6 minutes, from 1E3 to 1E5 copies per reaction. These findings provide a mechanistic basis for the copy-number-dependent behavior of PAD LAMP and offer simple, low-cost strategies to improve the speed and reliability of PAD nucleic acid assays.

bioengineering↗

bioRxiv2025

Spatially Organized DNA-templated Silver Nanoclusters as Potent Antimicrobial Agents for ESKAPE Infections

Antibiotic-resistant bacteria cause more than one million deaths annually worldwide. The rapid evolution and gene exchange among pathogens often render new antibiotic drugs ineffective soon after deployment, underscoring the urgent need for alternative therapeutic strategies. Nanoscale silver is well known for its innate bacteriostatic and bactericidal activity but typically requires high concentrations for efficacy that causes toxicities and limits broader clinical applications. To address this, we introduce programmable self-assembling DNA scaffolds that template, stabilize, and spatially organize multiple copies of monodisperse silver nanoclusters (DNA-AgNCs). These assemblies enhance antimicrobial potency of formulations while also exhibiting intrinsic fluorescence, providing dual functionality for therapeutic and bioimaging applications. Detailed characterization identified DNA-AgNC scaffolds with improved stability and enhanced activity against clinically relevant antibiotic-resistant planktonic ESKAPE pathogens. We also revealed the DNA-AgNC constructs that significantly lowered intracellular infections of human bone cells with Staphylococcus aureus. Collectively, the results highlight spatially organized DNA-AgNCs as a promising modular platform for next-generation antibacterial therapy and real-time bioimaging.

biochemistry↗

bioRxiv2025

Rational Design of Multiclade Coronavirus Spike Immunodominant Domain Nanoparticles Elicit Broad Antibody Responses

Four seasonal endemic human coronaviruses (EhCoVs), HKU1-CoV, OC43-CoV, 229E-CoV, and NL63-CoV, are culprits of mild upper respiratory and periodic severe diseases in vulnerable populations. Despite their prevalence, understanding EhCoVs antigenic and immune signatures remains elusive. SARS-CoV-2 has evolved as the fifth EhCoV, requiring seasonal vaccination in most parts of the world, and currently, no other EhCoV vaccines are available. SARS-CoV-2 co-infection with EhCoVs increases disease severity; thus, combined vaccination may provide increased protection against seasonal EhCoVs overall. Here, we explored Spike (S) receptor binding domain (RBD) vs. N-terminal domain (NTD) B-cell immunodominance in EhCoV-positive convalescent donors and immunogenicity in mice. We found that while antibody and B-cell isotypes were relatively dominant to S NTD, mice immunized with S RBD elicited significantly higher binding and neutralizing antibody (nAb) responses. With that knowledge, we used computational methods to infer that EhCoV S sequences evolve into two main clades and designed chimeric immunodominant domains (IDDs) from both clades for each EhCoV. IDDs were scaffolded onto two-component nanoparticles (NPs) displaying each IDD separately (monovalent IDD NP); three {beta}-EhCoV IDDs (Mosaic-3 IDD NP); or five EhCoVs IDDs (Mosaic-5 IDD NP). Mice immunized with mosaic IDD NPs, but not soluble IDD antigens nor monovalent IDD NPs, elicited potent, broadly cross-reactive binding and neutralizing antibody (Ab) responses against SARS-CoV-2 variants, other EhCoVs, and Sarbecoviruses. System serology revealed that all four IDD immunogens elicited distinct Ab subclasses and Fc-effector functions, with mosaic-5 IDD NPs eliciting the most de novo Ab subclasses, distributions, and broader Fc-mediated immune mechanisms. Dissection of vaccine-immune sera revealed polyclonal Ab responses against multiple non-overlapping cross-reactive S epitopes. Due to elicitation of broad Ab responses with combinatory functionality, IDD NPs open new horizons for developing first-in-class supraseasonal EhCoV vaccine candidates, with potential to decrease frequent SARS-CoV-2 sequence updates and protect against other EhCoVs. Moreover, elicitation of Ab breadth that spans pandemic-threat Sarbecoviruses gives mosaic IDD NPs promise towards pandemic preparedness.

bioengineering↗

bioRxiv2025

Computational Modeling of Motor-Driven Extension of Microtubule Bundles in Axons

In addition to actin assembly at the growth cone, neuronal axons elongate via interactions between microtubules and microtubule-associated proteins including dynein motor proteins and cross-linking proteins. Dynein translocates microtubules toward the growth cone to exert extensile forces for axonal outgrowth. During this process, microtubules are most likely to experience compressive loads, which can result in bending deformation on microtubules called buckling. Such buckled microtubules are impaired in their ability to bear compressive forces and may not contribute significantly to axonal outgrowth. If microtubules are interconnected by cross-linking proteins, they are less likely to be buckled and thus able to resist larger compressive loads. Despite the importance of the buckling and connectivity of microtubules, their effects on the axonal outgrowth have not been investigated to date. In this study, using an agent-based computational model, we created a microtubule bundle to simulate the microtubule system in axons. This bundle increased its length by interactions between dynein-like motors and microtubules against a mechanical load. We found that intermediate cross-linking density resulted in maximal elongation of the bundle, because microtubules were easily buckled at low cross-linking density, whereas the displacement of microtubules was inhibited at high cross-linking density. When individual microtubules were much stiffer, the bundle showed higher elongation even with lower cross-linking density, since stiff microtubules were less likely to be buckled by compressive loads. Our study provides new insights into the mechanisms driving axonal outgrowth.

biophysics↗

bioRxiv2025

Maternal IBD-related antibodies are associated with early life gut inflammatory status and microbiota composition: insights from cord blood

PurposeAntibodies in peripheral blood are used to aid in the diagnosis of inflammatory bowel disease (IBD), but their presence in neonatal cord blood and potential effects on early life development remain unknown. MethodsWe measured anti-CBir1, ANCA, anti-OmpC, ASCA IgA, and ASCA IgG levels in the cord blood of babies born to 78 mothers with or without IBD. Their association with fecal calprotectin (FC), and microbiota composition, characterized by 16S rRNA sequencing, was assessed throughout pregnancy and during the first 3 years of life using linear mixed-effects models. ResultsAntibodies were detected in cord blood, with significantly higher levels of anti-CBir1 and ASCA IgG in babies born to mothers with Crohns disease (p = 0.002) and higher abundance of ANCA and anti-OmpC in babies of mothers with ulcerative colitis (p = 0.002), compared to controls. ASCA IgG levels positively correlated with babies FC (p = 0.006), while babies microbiota Shannon diversity was negatively associated with ANCA, anti-OmpC, and ASCA IgA levels (p = 0.003, 0.04, and 0.008, respectively). Romboutsia spp., Citrobacter spp., Pseudomonas spp., Clostridiaceae, Clostridia, and Varibaculum spp. were positively correlated with either or both ANCA and anti-OmpC levels (all multiple testing adjusted q < 0.1). ConclusionOur findings suggest that maternal IBD-associated antibodies cross the placenta barrier and may be associated with intestinal inflammation and imbalanced microbiota colonization. Whether these serological profiles negatively influence the priming of the babys immune system or IBD risk later in life remains to be determined.

immunology↗