Biology subjects

Kim, M.

Publications and source records attributed to Kim, M..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

High-throughput microbiome profiling and co-occurrence with antibiotic resistance genes in Lucilia sericata

Blow flies such as Lucilia sericata (Diptera: Calliphoridae) serve important ecological functions as decomposers. However, due to their close association with decaying organic matter they also play potential roles as reservoirs for pathogenic bacteria and antimicrobial resistance genes (ARGs). In this study, we characterized the bacterial communities and resistome profiles of L. sericata specimens collected from six provinces across South Korea using 16S rRNA gene metabarcoding and targeted PCR screening. The microbiome was dominated by Dysgonomonas, Vagococcus, Pseudomonas, Ignatzschineria, and Providencia with geographic variation in community structure. Flies from Chungnam exhibited the lowest microbial diversity, while samples from Jeonnam and Gyeonggi showed greater richness and evenness. Beta diversity analyses confirmed geographic structuring of bacterial communities, with semi-urban, rural locations harboring more diverse taxa. Notably, opportunistic pathogens such as Proteus mirabilis and Providencia were detected, alongside a range of ARGs (blaTEM, ermB, sul1, aac(6')-Ib-cr, cat and mecA) and integron elements (intI and intII), suggesting that L. sericata may act as a reservoir of clinically important microbes and resistance genes. ImportanceThe environment plays a significant role in shaping the microbiome of flies. Due to their motile nature and close association with decomposing matter blow flies of the species Lucilia sericata can harbor diverse bacterial communities, including potential pathogens that threaten human and animal health. Furthermore, due to their synanthropic lifestyle, this species is also exposed to bacteria that host antibiotic resistance genes (ARGs). Here we investigate the role of blowflies as reservoirs of potential pathogens and ARGs using metabarcoding. Our study revealed a diverse microbiome and resistome shaped by location and possible biotic or abiotic factors. These findings provide baseline information for wildlife surveillance and emphasize the importance of including synanthropic flies in strategies aimed at controlling the dissemination of antibiotic resistance.

ecology↗

bioRxiv2025

Systematic characterization of the ovarian landscape across mouse menopause models

Menopause affects not only fertility but also systemic health. Yet mechanisms underlying this coupling are still poorly understood, partly due to the absence of robust, age-relevant preclinical models with comprehensive molecular and phenotypic characterization. To address this, we systematically compared three candidate mouse models of menopause: (1) intact aging, (2) chemical ovarian follicle depletion using 4-vinylcyclohexene diepoxide (VCD) administered at multiple ages, and (3) Foxl2 haploinsufficiency, a genetic model based on a gene linked to human premature ovarian failure. Through histology, serum hormone profiling, single-cell transcriptomics and machine-learning approaches, we identify both shared and model-specific features of follicle loss, endocrine disruption, and transcriptional remodeling. Our comparative framework enables informed selection of context-appropriate preclinical rodent models to study menopause and the broader physiological consequences of ovarian aging. TeaserThis systematic characterization of mouse menopause models lays the groundwork for future preclinical work on the systemic impacts of menopause.

genomics↗

bioRxiv2025

Local optogenetic control of genome editing and tumorigenesis in vivo using wireless implantable optoelectronics

Precise spatial regulation of site-specific DNA recombination (SSR) in vivo remains a challenge due to limited tunability of current platforms. Here, we present an optogenetic approach that overcome these limitations by employing engineered light-regulated recombinase E-LightR-Cre and tunable wireless implantable optoelectronic devices. E-LightR-Cre meets the key criteria for spatial regulation of SSR in vivo, showing no detectable activity in the dark, while demonstrating robust activation upon blue-light illumination. To achieve local E-LightR-Cre activation in murine lungs, we developed wireless, fully-implantable optoelectronic devices enabling focal illumination with no discernible organ damage. By modulating illumination intensity and duration, we can control the size of the activated area. Local expression of oncogenic KRas-G12D in a photoactivated subpopulation of cells in vitro revealed rapid reprogramming of the mutant expressing cells and their non-activated neighbors. Light-guided activation of E-LightR-Cre in mouse lungs resulted in focal expression of a reporter gene and allowed us to induce local formation of oncogenic lesions in vivo.

bioengineering↗

bioRxiv2025

Single-cell metabolic imaging and digital scoring of fat tissue remodeling by label-free metabolic imaging

Adipose tissue plasticity and functional heterogeneity play a central role in maintaining energy homeostasis, and their malfunction leads to metabolic disorders such as obesity, diabetes, and cardiometabolic disease. Rapid, single-cell metabolic imaging of intact fat tissue not only extends our understanding of metabolic dynamics and heterogeneity but also holds great potential as a tool for clinical diagnosis. However, the use of exogenous labels and dyes in conventional optical microscopy results in tissue deformation and requires time-consuming tissue preparation. Here, we demonstrated single-cell imaging of metabolic changes and heterogeneity in freshly excised adipose tissues that can distinguish tissue types without the need for exogenous labels using bond-specific, non-destructive, mid-infrared optoacoustic microscopy (MiROM) that allows preserving the native tissue architecture with minimal sample preparation time. Further leveraging MiROM, we monitored intracellular molecular and morphological changes during postnatal remodeling of adipose tissue when metabolic characteristics of adipocytes undergo a transient drastic change. Additionally, we developed an AI-based quantitative spatial tissue analysis tool (Q-SAT) to predict the spatial distribution of white fat- and brown fat-like features, providing a robust digital scoring method for adipose tissue phenotypic assessment. Collectively, we implemented MiROM as an enabling technology to provide fast, label-free metabolic imaging of unprocessed adipose tissue, opening a new perspective for understanding and characterizing the morpho-functional dynamics of adipose tissue remodeling.

bioengineering↗

bioRxiv2025

Mechanical force-mediated cellular crosstalk maintains the integrity of the lung gas exchange niche

Respiratory motion imposes a constant mechanical strain that has important but poorly defined impact on tissue niches in the lung. We developed a reversible bronchial ligation model to induce and reverse unilateral blockade of lung mechanical motion in vivo and show that this leads to transcriptomic changes in multiple cell lineages that are not normalized upon reinitiation of respiratory motion. Perturbation of mechanosignaling specifically in alveolar epithelial type I (AT1) cells alters the transcriptomic state and fate of their niche neighbors, demonstrating that AT1 cells act as a node that propagates a mechanical cascade throughout the lung alveolus. Mechanically perturbed AT1 cells induce a distinct capillary endothelial cell state that persists after reactivation of respiratory motion, which is mediated by an integrin/TGF-{beta} network within the alveolus that is vulnerable to pharmacological intervention. Importantly, AT1 mechanosignaling and intercellular communication are altered in chronic human lung diseases, highlighting the critical role of an AT1-driven mechanosensing network in lung disease biology. Thus, mechanosensing cells propagate biophysical signals that regulate tissue function and program tissue responses in disease.

cell biology↗

bioRxiv2025

Tuning viscoelasticity and fine structure of living materials via synthetic adhesion logic and rheological perturbations

Engineered living materials (ELMs) at the multicelluar level represent an innovation that promises programmable properties for biomedical, environmental, and consumer applications. However, the rational tuning of the mechanical properties of such ELMs from first principles remains a challenge. Here we use synthetic cell-cell adhesins to systematically characterize how rheological and viscoelastic properties of multicellular materials made from living bacteria can be tuned via adhesin strength, cell size and shape, and adhesion logic. We confirmed that the previous results obtained for non-living materials also apply to bacterial ELMs. Additionally, the incorporation of synthetic adhesins, combined with the adaptability of bacterial cells in modifying various cellular parameters, now enables novel and precise control over material properties. Furthermore, we demonstrate that rheology is a powerful tool for actively shaping the microscopic structure of ELMs, enabling control over cell aggregation and particle rearrangement, a key feature for complex material design. These results deepen our understanding of tuning the viscoelastic properties and fine structure of ELMs for applications like bioprinting and microbial consortia design including natural systems.

synthetic biology↗

bioRxiv2025

Episymbiotic Saccharibacteria suppresses epithelial immunoactivation through Type IV pili and TLR2 dependent endocytosis

Saccharibacteria are episymbionts that require host-bacteria to grow. They are positively associated with inflammatory diseases within the human microbiome, yet their mechanisms for interacting with the human host and contributing to diseases remain unknown. This study investigated interactions between a Saccharibacterium (Nanosynbacter lyticus), its host-bacteria (Schaalia odontolytica), and oral epithelial cells. The host-bacteria induced proinflammatory cytokines in epithelial cells, while Saccharibacteria were immune silent. Remarkably, Saccharibacteria dampened cytokine responses to host-bacteria during coinfection. This effect was driven by Saccharibacteria-induced clustering of TLR2 receptors, a process likely facilitated by type IV, ultimately leading to reduced TLR2-mediated cytokine signalling. High resolution imaging showed that Saccharibacteria were endocytosed by oral epithelial cells, and colocalized with endosome markers, eventually trafficking to lysosomes. Moreover, a subset of the Saccharibacteria survive endocytosis long-term, and retains their capability to reinfect host-bacteria, highlighting a mechanism for persistence in the oral microbiome and a vital role in mammalian immune system modulation.

immunology↗

bioRxiv2025

Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models

How do related proteins with a common fold perform diverse biological functions? Although the average structure may be similar, structural excursions from this average may differ, giving rise to allosteric rewiring that enables differential activity and regulation. However, this idea has been difficult to test in detail. Here we used the qFit algorithm to model "hidden" alternate conformations from electron density maps for an entire protein family, the Protein Tyrosine Phosphatases (PTPs), spanning 26 enzymes and 221 structures. To interrogate these multiconformer models, we developed a new algorithm, Residue Interaction Networks From Alternate conformations In RElated structures (RINFAIRE), that calculates networks of interactions between flexible residues and quantitatively compares them. We show that PTPs share a common allosteric network which rewires dynamically in response to catalytic loop motions or active-site vs. allosteric ligand binding, but also that individual PTPs have unique allosteric signatures. As experimental validation, we show that targeted mutations at residues with varying sequence conservation but high network connectivity modulate enzyme catalysis, including a surprising enhancement of activity. Overall, our work provides new tools for understanding how evolution has recycled modular macromolecular building blocks to diversify biological function. RINFAIRE is available at https://github.com/keedylab/rinfaire.

biophysics↗

bioRxiv2025

AI-Guided Discovery and Optimization of Antimicrobial Peptides Through Species-Aware Language Model

The rise of antibiotic-resistant bacteria drives an urgent need for novel antimicrobial agents. Antimicrobial peptides (AMPs) show promise solutions due to their multiple mechanisms of action and reduced propensity for resistance development. This study introduces LLAMP (Large Language model for AMP activity prediction), a target species-aware AI model that leverages pre-trained language models to predict minimum inhibitory concentration (MIC) values of AMPs. Analysis of attention values allowed us to pinpoint critical amino acid residues (e.g., Trp, Lys, and Phe). Our work demonstrates the potential of AI to expedite the discovery of peptide-based antibiotics to combat antibiotic resistance.

bioinformatics↗

bioRxiv2025

The interaction of XPG with TFIIH through p62 and XPD is required for the completion of nucleotide excision repair

Nucleotide excision repair (NER) is the key pathway for the removal of DNA damage induced by UV irradiation and chemotherapeutic reagents. Protein-protein interactions are crucial for the dynamic and coordinated assembly of the proteins involved at DNA lesion. Here we focus on the role of interactions between the multi-subunit helicase/translocase complex TFIIH and the 3 endonuclease XPG. We show that XPG interacts with the p62 and XPD subunits of TFIIH through its long spacer region located in the middle of its split active site. We show the interactions between three acidic regions of XPG with the pleckstrin homology (PH) domain of p62 are of moderate importance for NER, while interactions with XPD are critical for activity. Combining mutations in the p62 and XPD interaction domains leads to additive defects in NER activity. Unexpectedly, we show that these interactions are not required for the recruitment of XPG, but rather for the formation of a catalytically competent NER complex and for triggering the incision 5 to the lesion by ERCC1-XPF. Our studies provide fundamental insights into how interactions between TFIIH and XPG contribute to the NER pathway and more generally how modular protein-protein interactions control each step along the NER reaction coordinate.

biochemistry↗

bioRxiv2025

TRPM8 protein dynamics correlates with ligand structure and cellular function

Protein dynamics have emerged as a key feature associated with function in various systems. Here, NMR-based studies coupled with computational cheminformatics and cellular function are leveraged to identify a relationship between the human cold and menthol receptor TRPM8 dynamics, chemical structure, and cellular potency. TRPM8 is a validated target for a variety of pain indications but generally has been clinically limited by on-target side effects impacting thermosensing and thermoregulation. This study shows that cheminformatic analysis of a TRPM8 regulating small molecule ligand library correlates with cellular function. Electrophysiology studies further validate the relationship and show a correlation between chemical structure and functional features such as compound potency. Solution NMR studies of the TRPM8 voltage sensing-like domain, which houses the canonical menthol ligand binding site, show that ligand binding conformationally selects NMR-detected TRPM8 dynamics in a manner that quantitatively correlates with chemical structure. The relationship between chemical structure and protein dynamics can be used predictively, where a chemical structure is predictive of dynamics in a latent reduced dimensionality space. Moreover, the robustness of the conformational selection of the dynamic ensemble is evaluated by varying related and divergent chemotypes, signal-to-noise sensitivity, and sample bias. Taken together, this study identifies that protein dynamics can serve as a quantifiable bridge between chemical structure and cellular function, which has implications for drug discovery in difficult systems.

biophysics↗

bioRxiv2025

Resting state periodic and aperiodic brain oscillations from birth to preschool years: Aperiodic maturity predicts developmental course

The non-invasive assessment of resting-state (RS) neural activity via electrophysiology provides information on brain function and brain health. Our understanding of RS neural activity in older children and adults is limited by our poor understanding of the maturation of RS activity (oscillatory and non- oscillatory) from infancy to preschool ages. The present study used MEG with source imaging and an adapted Dark Room eyes-open task to assess oscillatory and non-oscillatory RS activity. 107 typically developing children 2 to 68 months were enrolled. For the Dark-Room eyes-open task, each child alternated between viewing an Inscapes video without audio for 20s and then resting with their eyes open for 30s in total darkness. This was repeated for 6 cycles. Whole-brain RS activity maps were computed using Minimum Norm Estimates, with RS power spectra divided into estimates of periodic measures (dominant frequency and power) and aperiodic measures (the exponent - slope of the 1/f function; the offset - vertical displacement of the 1/f function). An infant dominant peak was observed more often in the Dark-Room (94% of children) than in the Video-On condition (83% of children). The Dark-Room condition elicited a 36% increase in dominant oscillation activity than the Video-On condition. The maturation of the parietal-occipital periodic dominant frequency increased non-linearly as a function of age. The maturation of aperiodic measures decreased nonlinearly as a function of age, with aperiodic measures as well as their maturation rate differing across the brain. Finally, more mature aperiodic values predicted better adaptive behaviors and daily living skills. Present findings demonstrate that (1) the use of an appropriate Dark-Room eyes-open task provides measures of young child RS periodic activity with excellent SNR, (2) an understanding of the development of infant RS activity is best achieved via obtaining measures in brain source space in order to detect regional differences in aperiodic activity, and (3) a more mature aperiodic value predicts higher developmental behavior scores.

neuroscience↗

bioRxiv2025

High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform

We present a multiomics platform comprising Teton, a detection assay system, and AVITI24, a dual-flowcell instrument that performs both cellular imaging and sequencing readout. Teton integrates a compartmentalized flowcell for cell culture with methods to measure morphology, RNA, and protein at subcellular resolution. The platform quantifies morphological features through cell painting of 6 cellular components, RNA expression of up to 350 transcripts via sequencing of oligonucleotides hybridized to mRNA, and protein expression of up to 200 targets using antibody-linked oligonucleotide sequencing. The flow cell accommodates >1 million cells in a 10 cm squared open-well format or can be subdivided into 12 or 48 wells to support experiments with multiple conditions or time points. We describe and validate the detection methods of the platform and showcase its capabilities by co-culturing three cancer cell lines and elucidating the cellular pathways triggered by various drug treatments as a function of time. Using multiple time points enables us to capture the dynamics of cellular processes including receptor activation and signaling cascades. The results demonstrate how different cancer cells evade TNF-induced apoptosis by activating compensatory signaling programs that maintain survival despite pro-apoptotic cues. Our model system replicates previously published results and highlights the versatility of the platform in enabling rapid, high-throughput analysis of complex cellular responses in varied biological contexts.

genomics↗

bioRxiv2025

H2O2-induced astrocytic collagen triggers neuronal death via fucosylation-dependent glial barrier formation upon ischemic stroke

The cascade of molecular and cellular events leading to neuronal death after a focal ischemic stroke remains enigmatic. Although astrocytes form glial barriers that may protect surrounding tissue, how barriers develop and contribute to neuronal death is unclear. Here, we show that H2O2 induces astrocytic type I collagen (COL1)-production via miR-29-mediated post-transcriptional and fucosylation-dependent post-translational regulations, leading to integrin activation and neuronal death. In photothrombosis (PT)-induced cortical stroke model, PT triggered H2O2-surge, astrogliosis, glial barrier formation, COL1 expression, fibrotic scarring, altered N-glycosylation, neuronal loss, and neurological deficits. Remarkably, these effects were reversed by astrocyte-specific COL1 or FUT8 gene-silencing or treatment with KDS12025, an H2O2-decomposing peroxidase enhancer. KDS12025s neuroprotective effects were also recapitulated in non-human primate stroke model. These findings delineate a previously unrecognized astrocyte-driven mechanism in which oxidative stress induces COL1 production, promoting neuronal death, and position H2O2 and astrocytic COL1 and FUT8 as promising therapeutic targets for ischemic stroke.

neuroscience↗

bioRxiv2025

Heterologous immunization modulates B-cell epitope competition between helper peptides and the MPER segment in MPER/liposome vaccines

Subdominant B-cell immune responses to conserved epitopes are major obstacles in eliciting broadly neutralizing antibodies (bnAbs) against HIV-1 through natural infection or vaccination. Although the sequence conserved membrane proximal external domain (MPER) of HIV-1 gp41 is partially occluded on the virion surface, epitope-focused immunogens could mitigate access limitations. Here, we found that a MPER/liposome vaccine delivered with single CD4 T cell helper epitope results in a post-priming response hierarchy, eliciting low affinity MPER-specific B cells. Heterologous boosting, however, promotes MPER-specific B cell clonal expansion and enhances plasma antibody functionality. This improvement is associated with increased B cell affinity for MPER and reduced competition from B cells targeting the helper epitope. While helper peptide co-delivery increases affinity of serum antibodies, the outcome of subsequent MPER antibody responses is shaped by the priming antigen. Our results offer insights into heterologous immunization strategies to potentiate subdominant B cell responses against frequently mutating viruses. Significance StatementA key challenge in vaccination against mutable viruses like HIV-1 is the immune systems focus on highly variable regions. The conserved MPER segment of gp41 elicits weak antibody responses due to poor B cell accessibility. This study evaluated a liposome-based MPER vaccine strategy. Initial priming generated low-affinity MPER-specific memory B cells, influenced by strong B cell affinity for a dominant T cell helper peptide. However, heterologous boosting overcomes subdominant MPER responses by increasing B cell affinity for booster immunogens while also reducing competition from other helper peptides. Co-delivery of helper peptides enhanced antibody affinity, though the priming antigen was critical in shaping responses. These findings suggest heterologous immunization is a promising strategy to enhance subdominant B cell responses.

immunology↗

bioRxiv2025

Ontology-aware DNA methylation classification with a curated atlas ofhuman tissues and cell types

AO_SCPLOWBSTRACTC_SCPLOWDNA methylation (DNAm) is a core gene regulatory mechanism that captures cellular responses to short- and long-term stimuli such as environmental exposures, aging, and cellular differentiation. Although DNAm has proven valuable as a baseline biomarker for aging by enabling robust characterization of disease-associated methylation shifts associated with age, its potential to reveal analogous shifts in the context of tissue remains underex-plored. A major obstacle has been the absence of comprehensive, curated reference atlases spanning diverse normal human tissues, limiting most existing work to disease-subtype differentiation or localized tissue comparisons. To bridge this gap, we assemble the largest and most diverse atlas of exclusively healthy human tissue and cell samples profiled by 450K arrays, comprising of 16,959 samples across 86 tissues and cell types. Leveraging this resource, we introduce an ontology-aware classification framework that identifies robust CpG features associated with tissue and cell identity while integrating known anatomical and functional relationships (e.g., prefrontal cortex in the brain, leukocytes in blood). Our novel application of Minipatch learning distills a set of 190 CpG sites that can accurately support multi-label classification. We further validate our approach through an ontology-based label transfer task, demonstrating the effectiveness of ontology-informed learning to accurately predict relevant labels for 31 tissues and cell types not seen during training. These findings underscore the potential of our framework to enhance our understanding of healthy methylation landscapes and facilitate future applications in disease detection and personalized medicine.

bioinformatics↗

bioRxiv2025

Characterization of Human Anterior Neural Organoids as a Model for Investigating Cohen Syndrome

Neural organoids display three-dimensional (3D) structures that resemble in vivo neural architectures. Previously, we developed a novel two-dimensional (2D) neural induction-based protocol for culturing spinal cord organoids, enabling size control and recapitulating neural tube morphogenesis. In this study, we evaluated the application of this concept to induce the anterior regions of the brain and generate human anterior neural organoids (hANOs). By inducing neuroepithelial (NE) cells in 2D and re-aggregating them led to tube-forming morphogenesis similar to that posterior spinal cord induction. The transcriptome profiles of these hANOs resembled the frontal cortex of 20 weeks post-conception (PCW) human embryos. Using this hANOs protocol, we investigated microcephaly phenotypes associated with Cohen syndrome (CS), caused by biallelic loss-of-function variants in VPS13B gene. Deleting VPS13B in human pluripotent stem cells resulted in Golgi dispersion and growth retardation onset in mutant hANOs, akin to CS patients with postnatal microcephaly. This delay is partly linked to reduced neuronal growth. Additionally, mature CS organoids showed enhanced hyper-excitability associated with an excitatory/inhibitory imbalance. In conclusion, this protocol is suitable for studying microcephaly phenotypes from human genetic mutations due to its simplicity and scalability.

neuroscience↗

bioRxiv2025

Structural insight into binding of novel PET tracer MODAG-005 to lipidic ????-Synuclein fibrils

Accumulation of -synuclein (Syn) aggregates in the human brain is the major hallmark of synucleinopathies such as Parkinsons Disease, Multiple System Atrophy, and Dementia with Lewy bodies. Positron Emission Tomography (PET) plays a vital role in diagnosing these diseases and monitoring their progression by enabling the non-invasive and sensitive detection of Syn aggregates in the brain. However, developing PET tracers with specific target binding, as well as identifying the binding site and complex structure present significant challenges. Here, we investigated the interaction between lipidic Syn aggregates and MODAG-005, a new Syn PET tracer candidate, using nuclear magnetic resonance spectroscopy, cryogenic electron microscopy and molecular dynamics (MD) simulations. Two binding sites of MODAG-005 were found, one on the surface and one in a tubular cavity of the fibril, of which the occupancies were found to depend on the preparation protocols. The cavity binding site is thermodynamically more stable than the external binding site and is the only site occupied when MODAG-005 is applied with liposome as carriers to the aggregates. This is corroborated by MD simulations in which stable interactions between MODAG-005 and glycine containing backbone motifs of the tubular cavity of the aggregates are observed.

biochemistry↗