Biology subjects

Kim, D.

Publications and source records attributed to Kim, D..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Human Lymph Node Cellular Senescence Atlas Reveals Age-Dependent Alteration in Germinal Center B Cell Function and Niches

Immunosenescence, the age-associated decline in immune function, is a key feature of human aging. In human lymphoid organs, however, the specific immune cell populations that acquire senescence-associated phenotypes during aging and how they influence the surrounding tissue microenvironment remain poorly understood. A spatially resolved map of these senescence-associated immune states in human lymphoid tissues could help clarify their relationship with aging and their potential contributions to the progressive decline of immune function. Here, we integrated single-cell and spatial multi-omics to systematically characterize age-related senescence in human lymph nodes (LNs). Single-cell transcriptomics of lymphoid tissues from donors aged 18 to 100 years old identified 34 immune and stromal cell types and revealed age-associated upregulation of senescence signatures in specific populations. Spatial proteomic profiling of 99 LN sections from 51 donors (18-86 years) using high-plex immunofluorescence ([~]20 million cells) mapped senescence markers (p16, p21, HMGB1, -H2AX) at single-cell resolution, revealing diverse senescent-like cell types ("senotypes") and a stepwise shift from extrafollicular to germinal center (GC) localization with age. Notably, we observed focal clonal-like senescence in GC B cells in older donor LNs. Spatial transcriptomics, epigenomics, and metabolic imaging of selected samples further elucidate the multi-omics signatures and underlying mechanisms of functional impairment, metabolic remodeling, and distinct regulatory programs in senescent-like GC B cells. This study presents a comprehensive spatial atlas of senescence-associated immune states in human lymph nodes, revealing cell-type-specific and spatial heterogeneity that may contribute to immunosenescence and the decline of immune function during aging.

immunology↗

bioRxiv2026

Cultivation and genomic characterization of the first representative of the globally distributed marine UBA868 group

Members of the UBA868 group within the order Arenicellales are globally distributed marine Gammaproteobacteria predicted to participate in sulfur and carbon cycling, yet their physiology and ecological roles remain unknown due to the absence of cultured representatives. Here, we report the isolation and characterization of the first heterotrophic representative of the previously uncultured UBA868 group. Using dilution-to-extinction cultivation, we obtained four isolates from the Yellow Sea whose high-quality genomes represent a single UBA868 species. One strain, IMCC57338, maintained in axenic culture, exhibited small coccoid morphology and slow growth (doubling time [~]2.9 days), consistent with an oligotrophic lifestyle. Genome analysis revealed a predominantly aerobic chemoorganoheterotrophic lifestyle with a streamlined central carbon metabolism, including a complete glyoxylate shunt and limited carbohydrate utilization capacity, suggesting adaptation to low-nutrient conditions. The genome also encodes pathways for methylated amine oxidation coupled to formaldehyde assimilation via the serine cycle, indicating a capacity for methylotrophy. Genes encoding sulfur oxidation (Sox) and reverse dissimilatory sulfite reductase (rDsr) pathways further suggest a capacity for sulfur-based chemolithoheterotrophy. Global metagenomic and metatranscriptomic read recruitment showed that the species represented by IMCC57338 is widely distributed across ocean basins and pelagic depth layers, with higher abundance and transcriptional activity in mesopelagic waters. Our findings provide the first physiological and genomic insights into the UBA868 group and suggest that members of this lineage contribute to the cycling of organic carbon, C1 compounds, and sulfur in marine ecosystems.

microbiology↗

bioRxiv2026

The Computational and Neural Basis of Zero-Shot Control in Dynamic Pursuit

Biological agents flexibly adapt their behavior to novel goals and environmental demands without additional training, yet the computational principles enabling such control remain unclear. Here, we propose that three cognitive constructs constitute minimal computational motifs for flexible control: relational structure, spotlight attention, and affordance computation. We examine whether these constructs underpin flexible control in an embodied dynamic pursuit task requiring continuous integration of inter-entity relations, reward, and action feasibility, making it a suitable testbed for real-time control. By implementing these constructs within a multi-module graph convolutional network, we show that the model achieves zero-shot transfer across novel pursuit scenarios without additional training. Although not explicitly trained to do so, the model also exhibits change-of-mind behavior, a hallmark of flexible control exhibited by biological agents. Neural recordings from the primate dorsal anterior cingulate cortex revealed population-level signatures linking these constructs to neural dynamics, providing biological support for the proposed computational architecture.

neuroscience↗

bioRxiv2026

Phosphoserine aminotransferase SerC is a central metabolic checkpoint and druggable vulnerability in Mycobacterium tuberculosis

Serine metabolism is fundamental to the pathogenicity of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), yet its full metabolic scope and therapeutic potential remain unclear. Here we show that the phosphoserine aminotransferase serC is an essential metabolic node that coordinates central carbon and nitrogen flux and enables intracellular survival in the host. Deletion of serC caused severe growth defects across macrophage and murine infection models and rewired central carbon metabolism, reducing glycolytic, tricarboxylic-acid-cycle, and methylcitrate-cycle fluxes while altering one-carbon, branched-chain, and amino-acid biosynthetic pathways. Transposon sequencing identified sdaA-dependent serine deamination and the glycine cleavage system as key determinants of serine-based nitrogen assimilation, while revealing redundancy in serine transport. Our findings validate serine biosynthesis as a vulnerable, druggable metabolic target in Mtb and highlight it as a promising route for the development of urgently needed therapies against TB, which continues to kill millions of people each year.

microbiology↗

bioRxiv2026

Deep-learning-enabled morphodynamic analysis of drug responses in a biomimetic fibrin-based 3D glioblastoma invasion model

Glioblastoma (GBM) lethality arises from aggressive invasion and diffuse infiltration of brain tissue. Conventional GBM preclinical models often fail to predict clinical therapeutic efficacy because they do not recapitulate the pathological extracellular matrix (ECM) cues that drive tumor invasion. Here, we present an ECM mimetic 3D platform using a fibrin scaffold to recapitulate the hemorrhagic, pro-thrombotic tumor microenvironment characteristic of high-grade gliomas. This fibrin scaffold induces a pro-invasive phenotype in GBM spheroids by upregulating proliferation/cell cycle- (MYC, FOXOM1, CCND1) and invasion-associated-(CTSS, FOXM1, CCND1) genes. Traditional cell morphology quantification methods (e.g., circularity) distil complex shapes into singular metrics and cannot capture the nuances of invasion. To address this limitation, we have applied a deep-learning segmentation pipeline (MARS-Net) and high-content morphodynamic descriptors. By using the Preserving Heterogeneity (PHet) algorithm, the 3D platform accurately classifies invasiveness levels and captures the invasion-inhibitory effects of potential repurposable drug candidates. We demonstrate that our model can predict a spheroids long-term invasive fate with high accuracy using only partial image sets from early time-points, rather than the complete time-course images. Our work presents an in vivo-like, scalable 3D platform integrated with a quantitative high-throughput pipeline to elucidate GBM invasion mechanisms and to evaluate anti-invasive compounds.

bioengineering↗

bioRxiv2026

Modulating Innate Immune Responses to Curli Fibers Through Protein Engineering

Curli fibers produced by Escherichia coli are functional amyloids that activate Toll-like receptor 2 (TLR2), initiating innate immune responses at mucosal surfaces. While microbiome-derived curli contribute to host-microbe interactions, their intrinsic immunostimulatory activity limits their utility as programmable scaffolds for engineered probiotic systems, and dysregulated TLR2 activation has been linked to inflammatory bowel disease, systemic lupus erythematosus, neurodegeneration, and sepsis. Here, we engineered E. coli Nissle 1917 to produce modified curli fibers designed to inhibit TLR2 through two mechanistically distinct strategies: steric shielding via silk-elastin-like protein sequences, and direct receptor antagonism via a known TLR2 antagonist, staphylococcal superantigen-like protein 3 (SSL3). Both engineered variants assembled into structurally intact amyloid fibers and exhibited significantly reduced intrinsic TLR2-dependent NF-{kappa}B activation in reporter cells. In competitive inhibition assays against structurally diverse TLR2 agonists, the SSL3 fusion achieved near-complete inhibition maintained under rising agonist load, while steric shielding provided moderate, agonist-class-dependent inhibition. In primary human monocyte-derived dendritic cells, the SSL3 fusion robustly attenuated IL-8 secretion and transcriptional induction of IL-8, IL-6, and IL-1{beta}, whereas steric shielding produced only partial attenuation that did not translate to broad inflammatory suppression. These results establish engineered curli as a tunable platform for receptor-specific modulation of innate immune signaling and highlight the broader potential of modular microbial amyloids as programmable interfaces for engineering host-microbe interactions at mucosal surfaces. IMPORTANCEBacteria residing in the gut produce protein fibers called curli that potently activate the immune system through a receptor called Toll-like receptor 2 (TLR2). While TLR2 plays a beneficial role in maintaining gut health, its overactivation drives chronic inflammation in conditions including inflammatory bowel disease, autoimmune diseases, neurodegenerative diseases, and sepsis, and curli fibers have been directly implicated in several of these conditions. Here, we engineered curli fibers produced by the probiotic E. coli Nissle 1917 to inhibit TLR2 activation, transforming a naturally inflammatory bacterial fiber into a programmable immune modulator. We demonstrated that direct receptor antagonism, rather than steric shielding, is required for effective immune modulation in primary human immune cells, establishing a design principle for engineering bacteria-derived fibers as programmable interfaces with host immunity. The modularity of the curli scaffold positions this platform as a broader tool for programming interactions between probiotic bacteria and the mucosal immune system.

synthetic biology↗

bioRxiv2026

Programmable domestication of thermophilic bacteria through removal of non-canonical defense systems

Thermophilic bacteria offer major advantages for industrial biotechnology, yet most remain genetically intractable because cellular defense systems block efficient DNA acquisition. Here, we present a programmable domestication strategy that converts wild Geobacillus strains into genetically tractable thermophilic hosts. We developed the Domestication of Non-Model Bacteria (DNMB) Suite, a multi- omics-guided computational framework that systematically identifies genetic barriers to transformation. DNMB analysis revealed that non-canonical nuclease-based defense systems, including Wadjet II, constitute dominant barriers to DNA uptake in previously intractable Geobacillus strains. Targeted deletion of these loci increased transformation efficiency by up to six orders of magnitude. We further established a hierarchical thermophilic engineering toolkit that integrates plasmid artificial modification, conjugation-assisted DNA delivery, and genome editing using an endogenous CRISPR-Cas9 system. The resulting domesticated strains support stable heterologous expression and tunable genetic control at elevated temperatures. Together, these results establish a generalizable framework for transforming genetically intractable thermophiles into programmable industrial chassis.

bioengineering↗

bioRxiv2026

UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism

The ubiquitin-fold modifier 1 (UFM1) post-translational modification (PTM), or UFMylation, regulates protein homeostasis and is essential for human development. Yet the roles of the de-UFMylase, UFM1-specific peptidase 2 (UFSP2), which removes UFM1 from UFMylated proteins, remain poorly characterized. Here, we demonstrate that UFMylation and UFSP2 regulate mitochondrial metabolism. Quantitative proteomics in UFSP2-deficient cells revealed the accumulation of many proteins previously unknown to be impacted by UFMylation. These included components of the mitochondrial ribosome, electron transport chain (ETC), and pyruvate dehydrogenase (PDH) complex. Functional analyses demonstrated that excessive UFMylation in UFSP2-deficient cells increases mitochondrial respiration, glucose oxidation in the tricarboxylic acid (TCA) cycle, and PDH enzymatic activity. We identified dihydrolipoamide S-acetyltransferase (DLAT), the E2 component of PDH, as a direct UFMylation substrate, with lysine 118 (K118) as the primary conjugation site. Mutating K118 to arginine (K118R) abolished DLAT UFMylation and reduced pyruvate oxidation, identifying this modification as an activator of PDH. These findings reveal a UFMylation-based regulatory mechanism that controls mitochondrial function by inducing utilization of pyruvate as a TCA cycle fuel.

biochemistry↗

bioRxiv2026

POLQ-driven repair scars shape the immunogenic landscape of homologous recombination-deficient pancreatic cancer

Pancreatic cancer (PC) is broadly resistant to immune checkpoint blockade, although a subset of homologous recombination-deficient (HRD) tumors exhibits durable immune engagement. The genomic features that distinguish these immune-responsive tumors from immune-inert HRD tumors remain poorly understood. Here we identify a microhomology-mediated end joining (MMEJ) repair scar, the MMEJ Deletion Footprint (MDF), as a genomic readout of POLQ-associated error-prone repair that enriches for frameshift indels. Across the multi-omic discovery cohort integrating tumor genomics, single-nucleus transcriptomics and spatial immune profiling, MDF-high HRD PC exhibited increased frameshift-indel-derived neoantigens and interferon programs. MDF was further associated with remodeling of the myeloid compartment toward MHC II-high dendritic cell-like antigen-presenting macrophage states and the immune synapse architecture marked by increased spatial interaction between APC-like macrophages and cytotoxic CD8+ T cells. These tissue-level features aligned with a functional trajectory shift of CD8+ T cells, consistent with effective anti-tumor immunity and was associated with favorable clinical outcomes of patients. Together, our findings position MMEJ-linked repair scarring as actionable biology that connects an HRD genotype to immune organization and suggests rational immunotherapy combinations that may enhance antigen presentation and myeloid activation to extend durable benefit in HRD-lineage cancers.

cancer biology↗

bioRxiv2026

Fluorescence anisotropy structured illumination microscopy for quantitative super-resolved mapping of cell microenvironment and cytoskeletal dynamics

The crowded intracellular milieu shapes organelle architecture and dynamics, yet nanoscale heterogeneity in its physicochemical properties remains difficult to visualize with conventional fluorescence anisotropy (FA) imaging. Here, we develop fluorescence anisotropy structured illumination microscopy (FA-SIM), which employs orthogonal-polarization structured illumination with dual-angle detection to achieve [~]100-nm resolution and quantitative FA retrieval with 0.56% relative error, representing over 20-fold higher accuracy than conventional FA imaging. With low phototoxicity, FA-SIM enables dual-color, hour-long quantitative super-resolution imaging in cells. Using viscosity standards, defined nanoparticles and small-molecule drug binding assays, we validate FA-SIM as a quantitative reporter of rotational mobility and molecular interactions. In cells, FA-SIM resolves nanoscale crowding heterogeneity, correlates anisotropy landscapes with condensate dynamics, and uncovers a radial crowding gradient across the microtubule network and mitotic spindle. Long-term dual-color imaging further resolves coordinated actin-microtubule remodeling and associated microenvironmental changes. By enabling quantitative, super-resolved mapping of intracellular physical properties in living systems, FA-SIM provides a powerful platform for investigating the physical regulation of cellular organization and dynamics in health and disease.

cell biology↗

bioRxiv2026

Seasonal Dynamics of Nonstructural Carbon Compounds in Pine Forest

Non-structural carbon compounds (NSCs) serve to buffer short-term imbalances between carbon supply and demand in trees; however, their seasonal dynamics throughout the entire tree remain inadequately understood. We quantified year-round non-structural carbohydrate storage and fluxes in a temperate pine forest by integrating monthly measurements of soluble sugars, starch, and lipids across five tissues with biometric scaling to ecosystem stocks. Soluble sugars were consistently highest in canopy tissues and maintained a relatively stable concentration, even as sugar fluxes exhibited pronounced seasonal variations and reversals. In contrast, starch showed clear seasonality, increasing during the mid-growing season and decreasing later, whereas lipid pools remained relatively stable and contributed minimally to short-term fluctuations. Ecosystem-scale analyses indicated that sugars predominantly contributed to NSC turnover, accounting for approximately 80% of the total annual flux, while stored pools exhibited slower changes. The net annual NSC flux, approximately 65 g C m-2 yr-1, was relatively modest in comparison to biomass production, which totaled around 522g C m-2 yr -1. These findings indicate that seasonal changes in carbon balance are primarily driven by rapid redistribution of soluble carbon rather than by significant changes in overall NSC storage.

physiology↗

bioRxiv2026

Volumetric montaging of optical coherence tomography in human retinas

Optical coherence tomography (OCT) has transformed clinical eye care by providing high-resolution volumetric imaging of the retina. Recently, ultrawide-field-of-view (FOV) OCT played an increasingly significant clinical role; however, most clinical OCT systems offer only a rather limited FOV. We increased the FOV of clinical OCT by volumetrically montaging multiple OCT datasets in three dimensions (3D). We performed volumetric montaging by representing the internal limiting membrane (ILM) and retinal pigment epithelium (RPE) in each volume as point clouds and using these point clouds to compute transformations that map each volume to a common reference frame. We validated our methodology using datasets from three institutions with different OCT hardware and data-acquisition procedures. Using the mean surface distance between point clouds, we found the error in montaging was less than the lateral pixel size. Our method enabled existing clinical OCT to achieve ultrawide FOV imaging without any hardware modification.

bioengineering↗

bioRxiv2026

Zebra finch females flexibly communicate with each other and with AI-driven acoustic interaction models

Vocal interactions are fundamental for social functioning across animals, including humans. The diverse rules underlying these exchanges remain largely unknown, and emerging AI technologies offer promising avenues for investigation. We used computational tools to collect and analyze >1,000 hours of vocal interactions between female zebra finches and discovered that their interactions were characterized by correlated call production and structure, rapid acoustic modulation, and response selectivity. To test these interaction rules, we developed a generative audio large language model (ZF-AIM Acoustic Interaction Model) that engaged in real-time vocal exchanges with birds. When birds interacted with ZF-AIM, their vocal production and flexibility recapitulated key naturalistic features, which did not happen with non-interactive playbacks. Targeted ablations of ZF-AIM revealed that call timing and structure differentially contribute to natural vocal interactions. Using these AI-animal interactions, we demonstrate how AI can be leveraged to reveal fundamental rules underlying animal communication.

animal behavior and cognition↗

bioRxiv2026

Hydrogel-imposed boundary conditions guide single-lumen neuroepithelial morphogenesis

Three-dimensional (3D) stem cell-based cultures have emerged as promising in vitro model systems for studying human neurodevelopment. Current neural organoid protocols lack well-defined extracellular matrix (ECM) signaling and are limited by the formation of irregular tissue morphologies with multiple organizing centers, in contrast to the single neuroepithelial structure that emerges during embryonic development. This variability limits inter-organoid reproducibility and constrains their utility for modeling early developmental processes. To overcome these limitations, we leverage a materials-based approach to impose dynamic boundary conditions that extrinsically guide the self-organization of human induced pluripotent stem cells (iPSCs). Specifically, we develop a family of hyaluronic acid-elastin-like protein (HELP) hydrogels crosslinked with dynamic covalent bonds that recapitulate key biochemical and biophysical properties of the developing human neural ECM. Within these HELP hydrogels, iPSCs robustly self-organize from a single cell into complex neuroepithelial tissues with a single lumen. By tuning the boundary conditions imposed by the hydrogel, we identify matrix stress relaxation rate and tensional homeostasis as key regulators of single-lumen rosette formation and maintenance. With this hydrogel-enabled system, we identify phenotypic abnormalities in an early neurodevelopmental model of 22q11.2 deletion syndrome. Ultimately, our tunable engineered hydrogel supports the initiation of single-cell derived 3D neuroepithelial tissues, enables investigation into how matrix-imposed boundary conditions guide developmental morphogenesis, and establishes a reproducible platform for disease modeling.

bioengineering↗

bioRxiv2026

Systemic and Local Delivery of siRNA to the CNS and Periphery via Anti-IGF1R Antibody Conjugation

siRNA delivery platforms capable of accessing both central and peripheral tissues are critically needed to expand the therapeutic potential of oligonucleotides. To address this, we developed a novel siRNA-antibody conjugate by attaching an Hprt-targeting siRNA to an engineered antibody shuttle. This shuttle targets the insulin-like growth factor 1 receptor (IGF1R) using a fused antibody fragment (Clone F) and utilizes an antibody backbone with no tissue-relevant binding in this study. The resulting conjugate, designated Clone F-Hprt, demonstrated robust in vivo knockdown across multiple tissues. Clone F-Hprt demonstrated enhanced penetration into central nervous system (CNS) tissues compared to unconjugated siRNA following intracerebroventricular (ICV) and intravenous (IV) administration. In peripheral tissues, Clone F-Hprt achieved widespread knockdown in muscle, heart, and lung, consistent with IGF1R expression. The conjugate was well tolerated across all routes, including with repeated dosing. Although several receptor-mediated approaches for CNS delivery are progressing to the clinic (e.g., targeting the transferrin receptor), clinical validation remains to be demonstrated. Our findings highlight IGF1R as an alternative receptor capable of supporting delivery across both central and peripheral tissues, offering a complementary strategy for expanding the therapeutic landscape of oligonucleotide delivery.

neuroscience↗

bioRxiv2026

AmpliPhy improves gene trees by adding homologs without affecting alignments

In phylogenomics, gene tree reconstruction depends on multiple sequence alignment (MSA) and tree inference, and ongoing work continues to improve inference quality. Denser taxon sampling has been associated with improved gene tree inference, suggesting that adding homologs could be a practical route to higher accuracy as sequence databases continue to expand. However, adding sequences can influence multiple steps of typical inference pipelines, and little is known on its specific effect on the multiple sequence alignment, tree reconstruction, and rooting steps. We performed a large-scale empirical and simulated benchmarks to quantify how homolog enrichment affects alignment and phylogenetic inference. Using an enrichment-impoverishment design and a measure of tree accuracy based on taxonomic congruence, we found that enrichment consistently improves tree inference quality, while effects on alignment quality are marginal. We show that this improvement is associated with, but not restricted to accurate root placement on enriched trees when sensitive homolog search is accompanied. Notably, much of the benefit can be retained with relatively compact alignments produced by sequence addition. Building on these observations, we provide a tool, AmpliPhy, which efficiently improves phylogenetic reconstruction of protein families through homolog enrichment. The AmpliPhy open-source pipeline software is available at https://github.com/DessimozLab/ampliphy.

evolutionary biology↗

bioRxiv2026

Proteomic Profiling of Human Omental and Subcutaneous Adipose Tissue in Individuals with a Broad Range of BMI.

Obesity is a major public health challenge affecting an ever-increasing proportion of the global population. It is associated with numerous comorbidities. Progressive expansion and remodeling of adipose tissue may lead to depot specific changes in adipose tissue biology and energy partitioning. Such changes likely precede the development of obesity-related complications. To facilitate a deeper understanding of adipose tissue biology, a comprehensive and quantitative proteomic dataset at the peptide and protein level is presented. Data-independent acquisition LC-MS/MS data were acquired from matched subcutaneous and omental adipose tissues from metabolically healthy individuals with no comorbidities and covering a wide range of body mass indexes. Adipose tissue samples were collected during elective surgeries and immediately processed for histology or frozen until proteomic analysis. Internal and external quality control systems ensured high quality data. All data presented are available via ProteomeXchange. This dataset will allow new insights into biological changes that evolve with increasing adiposity captured before the onset of comorbidities. Matched sampling across fat depots provides an opportunity to uncover depot-specific physiological signatures.

systems biology↗

bioRxiv2025

Fluid-Structure Interaction Dynamics of Cervical Lymphatic Vessel Pumping and Valvular Function

A substantial portion of cerebrospinal fluid (CSF) drains through cervical lymphatic vessels (CLVs), a pathway mediated by basal and dorsal meningeal lymphatics. Impaired drainage along this route has been implicated in aging, Alzheimers disease, and traumatic brain injury. Despite considerable experimental investigation of CLV structure and function, computational modeling of this pathway remains limited. Here, we present a fully coupled two-dimensional fluid-structure interaction (FSI) model of a murine CLV constructed using the Lattice Boltzmann method for fluid dynamics and the immersed boundary method for the vessel geometry. Distinct from previous lymphatic vessel models, this framework is parameterized using data from recent in vivo imaging studies of CLVs. Using this model, we characterize the transient FSI dynamics within a single lymphangion, the pumping performance across a chain of three lymphangions with varying contraction phase delays, and the role of circular sinus geometry in regulating CSF transport under both favorable and adverse pressure gradients. Our results provide the first high-fidelity simulation of CSF drainage through CLVs, bridging a gap between experimental observations and mechanistic understanding. This work offers new insights into CLV pumping behavior and valve function, which helps inform the design of future experiments and therapeutic strategies aimed at enhancing CSF clearance.

physiology↗