Biology subjects

Kim, S.-H.

Publications and source records attributed to Kim, S.-H..

At least 19 recordsLinked to original sources

bioRxiv2026

Nanoscale identification of organic pigments in biogenic calcite by atom probe tomography

Spatially-resolved mass spectrometry could contribute to the understanding of biological processes. Atom probe tomography (APT) is a technique which could, in principle, fill an analytical gap for nanoscale mass spectrometry. Yet, because of a limited understanding of the process of fragmentation of biomolecules, biological or biochemical interpretation of the obtained data has so far not been successful. Here, we report on analyses of synthetic and biogenic pigmented calcite minerals. The purple coloration of Sphaerechinus granularis sea urchin spines is due to the occlusion of polyhydroxylated naphthoquinone (PHNQ) molecules, mainly spinochrome A, within the calcite phase. Peaks relating to these pigments as well as to other intra-crystalline macromolecules were identified by APT analysis of the purple spine region with comparison to measurements of synthetic calcite single crystals, calcite crystals doped with PHNQ, and the uncoloured (white) region of sea urchin spines. To facilitate the molecular identification of peaks appearing solely in purple-coloured spines, which are possible fragments from PHNQ, we introduce novel APT data filtering techniques based on spatial and temporal correlations in the detection of ions of targeted mass-to-charge state ratios. This allows us to discuss the fragmentation of organic molecules under field conditions and improve the identification of peaks in the mass spectrum, while also determining nanoscale spatial distribution of fragments related to specifically targeted biomolecules in 3D and elucidate the relationship these organic pigment molecules have to the calcite lattice and inorganic elements such as magnesium. The study aims to improve identification of complex molecular structures by APT, including organic molecules, with the potential ability to provide structural information at a near-atomic scale for a range of materials.

biophysics↗

bioRxiv2026

Primary tumor transcriptomic signature is associated with locoregional dissemination in canine mammary carcinoma

Canine mammary carcinoma (CMC) exhibits heterogeneous metastatic behavior, while accurate assessment of locoregional dissemination may be limited by incomplete sampling, occult metastasis, and variable sentinel lymph node anatomy. We investigated whether primary-tumor transcriptomic programs are associated with locoregional dissemination. The training cohort comprised 113 CMC RNA sequencing samples classified by peritumoral lymphatic vessel invasion, and the independent evaluation cohort comprised 27 microarray samples classified by histopathologically confirmed lymph node (LN) metastasis. Expression profiles were mapped to human ortholog gene symbols, and single-sample gene set enrichment analysis (ssGSEA) was performed using Molecular Signatures Database (MSigDB) gene sets. Seven candidate gene sets selected through univariable screening and literature-guided curation were entered into least absolute shrinkage and selection operator (LASSO) logistic regression, yielding a four-gene-set transcriptomic risk score (RS). The RS showed an apparent receiver operating characteristic area under the curve (ROC-AUC) of 0.949 (95% confidence interval, 0.906-0.993) and precision-recall area under the curve (PR-AUC) of 0.725 in the training cohort; bootstrap internal validation yielded an optimism-corrected ROC-AUC of 0.920. In the evaluation cohort, the ROC-AUC was 0.890 (95% confidence interval, 0.766-1.000) and PR-AUC was 0.869. Discrimination was attenuated but retained in histologically restricted sensitivity analyses, and higher RS remained associated with locoregional dissemination after clinicopathologic adjustment. These findings support gene-set-level transcriptomic scoring as a potential complementary approach for characterizing dissemination-associated primary-tumor states in CMC.

cancer biology↗

bioRxiv2026

Temperature dependence of pollen germination in Douglas-fir (Pseudotsuga menziesii): A machine learning-based detection of pollen viability from microscopic images

Background and Aims: Pollen germination and tube growth are critical stages of plant reproduction that are highly sensitive to temperature but remain labor-intensive to quantify. This study aimed to develop a deep learning-based approach for pollen phenotyping and to characterize the temperature dependence of pollen germination and elongation in Douglas-fir (Pseudotsuga menziesii). Methods: A convolutional neural network (CNN) was trained to segment pollen grains and classify germination status from microscopic images. Germination percentage and pollen length were quantified across a range of incubation temperatures from 5 to 40{degrees}C. Gamma functions were fitted to temperature response curves to estimate the optimal temperatures for pollen germination and elongation among Douglas-fir populations collected across an elevational gradient. Key Results: The CNN achieved high segmentation accuracy (intersection over union = 0.846), accurately distinguishing pollen grains from the background but showing moderate accuracy in separating germinated from ungerminated pollen during early elongation. Both pollen germination and elongation exhibited bell-shaped temperature response curves with distinct thermal optima. Pollen elongation consistently reached its optimum at higher temperatures than pollen germination. Estimated optimal temperatures fell within a narrow range, approximately 19 to 23{degrees}C. No significant relationship was detected between elevation and thermal optima, although some higher-elevation populations exhibited lower optimal temperatures. Comparisons with previous analyses of three western North American conifers showed that each species occupied a distinct reproductive thermal niche corresponding to the spring temperatures of its native habitat. Conclusions: Deep learning provides an efficient approach for high-throughput quantification of pollen germination and elongation from microscopic images. The narrow thermal range for reproductive performance suggests that Douglas-fir pollen is sensitive to temperature variation and that warming climates may alter reproductive success. These findings improve our understanding of the thermal sensitivity of conifer reproduction and provide a scalable framework for assessing impacts of climate warming on forest regeneration.

ecology↗

bioRxiv2026

Interpretable spatial ecological dynamics reveal ecological retention escape and amplification in pediatric leukemia

Spatial transcriptomics enables tumor ecosystems to be examined within their native tissue architecture, yet many computational approaches remain primarily descriptive and provide limited insight into how spatial organization may constrain or facilitate disease persistence. Here, we develop a therapy-aware spatial ecological framework that integrates ecological-context discovery, ecological opportunity landscapes, Ornstein-Uhlenbeck (OU)-like retention, Levy-like escape, and branching-like amplification to characterize pediatric leukemia tissues. Using normal bone marrow reference programs and pediatric leukemia spatial transcriptomic sections, we identify five recurrent candidate ecological contexts with distinct malignant, immune, stromal, vascular, inflammatory, and stress-associated features. These contexts form spatially heterogeneous ecological opportunity landscapes across bone marrow and extramedullary samples. OU-like summaries quantify context-specific attractor position and ecological retention, whereas Levy-like analyses identify rare cross-context displacements consistent with discontinuous ecological remodeling. Branching-like amplification integrates ecological abundance, latent displacement, opportunity, escape, and escaped-state fraction into an interpretable index of ecological expansion. An independent treatment-associated cohort shows that a primitive-state retention proxy, escape, and amplification generate coherent ecological profiles qualitatively consistent with residual persistence and relapse-associated expansion. Because the available spatial datasets are cross-sectional, these quantities are interpreted as operational summaries of tissue organization rather than direct estimates of temporal evolutionary processes. Together, the framework moves spatial transcriptomic analysis beyond static tissue mapping by providing an interpretable representation of ecological constraint, rare displacement, amplification, and therapy-associated persistence in pediatric leukemia.

cancer biology↗

bioRxiv2026

Deep Learning-Guided Holotomography Reveals Early Structural Remodelling During Pluripotency Exit

Real-time assessment of human pluripotent stem cell (hPSC) quality is critical for reproducibility and safety in regenerative medicine, yet current methods are invasive, labor-intensive, or highly operator-dependent. We present DeepHOPE (Deep-learning-guided Holotomography for Pluripotency Evaluation), a non-invasive, automatizable, and statistics-driven platform that integrates three-dimensional (3D) refractive index imaging with deep learning to assess pluripotency. DeepHOPE performs robustly across diverse contexts, including germ-layer differentiation, retinoic acid-induced differentiation, and mid-reprogramming cultures, enabling streamlined cell production workflows and improving the efficiency of midbrain dopaminergic neuron differentiation through informed colony selection. Mechanistically, DeepHOPE detects minute colony-scale topological changes that precede molecular loss of pluripotency. These early changes are associated with rapid F-actin remodeling, including apical-to-basal redistribution during early differentiation. Consistent with a functional role for cytoskeletal regulation in state transitions, sustained reduction of actomyosin tension decreases pluripotency, identifying cytoskeletal dynamics as an upstream determinant of early pluripotency exit. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/720508v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1d73508org.highwire.dtl.DTLVardef@1dab29aorg.highwire.dtl.DTLVardef@1039f76org.highwire.dtl.DTLVardef@da29a1_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2026

3-Minute Hematoxylin and Oil Red O (H-ORO) Staining Protocol for Frozen Sections of Zebrafish

Optimized histological techniques are crucial for visualizing cellular morphology across zebrafish tissues. Here, we report a rapid and reliable hematoxylin and Oil Red O (H-ORO) staining protocol for frozen sections that can be completed in less than three minutes. Mayers hematoxylin is used for nuclear staining, followed by Oil Red O (ORO) to visualize lipid-rich structures such as the endomysium surrounding myofibers, white matter of the brain, and myelin layers of major axonal tracts. Importantly, our optimized H-ORO protocol preserves tissue integrity and minimizes artifacts such as myofiber shrinkage commonly observed with ethanol-based hematoxylin and eosin (H&E) staining in both frozen and paraffin sections.

pathology↗

bioRxiv2026

Rapid Assessment of Immune Effector Cell-mediated Cytotoxicity using mRNA Lipid Nanoparticles

Cellular immunotherapy has revolutionized cancer treatment by enabling more targeted and personalized disease management. As the field progresses, there is an increasing need for high-throughput in vitro assays to efficiently assess the cytotoxicity of therapeutic cells. Conventional cytotoxicity assays pose various limitations in the workflow and scalability. Here, we present an mRNA lipid nanoparticle (mRNA-LNP) approach to efficiently and robustly deliver reporter genes to target cells for assessing immune effector cell-mediated cytotoxicity. This approach enables the rapid, homogenous reporter expression without compromising the viability of target cells. The cytotoxicity results obtained using mRNA-LNP-transfected cells are highly consistent and comparable to those obtained using cell lines with stable reporter gene expression. Finally, we highlight the mRNA-LNP approachs compatibility across a diverse range of tumor models, including primary tumor-derived models, enabling rapid and high-throughput assessment of the potency of various cytotoxic therapeutic cells.

immunology↗

bioRxiv2026

Reactive Astrocytes Drive Extracellular Acidification to Mediate α-Synuclein Neurodegeneration

Astrocytes are increasingly recognized as key players in neurodegeneration1-3, yet the molecular mechanisms by which they drive disease remain elusive. Here, we uncover a fundamental pathway in which reactive astrocytes fuel neurodegeneration in -synucleinopathies--including Dementia with Lewy bodies and Parkinsons disease dementia--by acidifying the brains extracellular environment. We demonstrate that both human patient tissue and a gut-to-brain -synuclein mouse model exhibit accumulation of reactive astrocytes and extracellular acidosis. Mechanistically, we show that astrocytic lysosomal exocytosis releases acidic contents, driving a drop in pH that activates neuronal acid-sensing ion channel 1a (ASIC1a), resulting in neuronal loss and behavioral decline. Blocking this pathway--either by inhibiting astrocytic lysosomal exocytosis or genetically or pharmacologically targeting neuronal ASIC1a--mitigates pathology and rescues neurodegenerative phenotypes in vivo. These findings provide a conceptual advance by establishing a mechanistic link between glial inflammation, acid-base homeostasis, and neuronal vulnerability, and suggest that targeting astrocyte-driven acidification or ASIC1a signaling could offer new avenues for disease modification in -synucleinopathies.

neuroscience↗

bioRxiv2025

Hybrid Ornstein-Uhlenbeck-Branching Modeling of Pediatric Leukemia Evolution: A Computational Extension and Cohort-Level Application

Pediatric cancers evolve under developmental constraints that limit mutational diversity yet preserve adaptive potential. A computational extension of the Hybrid Ornstein-Uhlenbeck (OU)-Branching framework was developed to model clonal diversification and phenotypic stabilization in pediatric leukemia. The OU component captures mean-reverting dynamics representing developmental homeostasis, while the branching component introduces stochastic lineage bifurcation and extinction. Using de-identified clinical metadata from Ahlgren et al. (Nature Communications, 2025; 16:8964), the model simulates patient-specific evolutionary trajectories across relapse categories and disease subtypes (B-ALL, T-ALL, MPAL, AML). Simulations reproduce observed clinical trends--rapid relapse and limited diversification in early or refractory KMT2A-r ALL, and slower, therapy-resistant relapses in AML. Group- and patient-level analyses demonstrate how the balance between stabilizing selection ({theta}) and diversification rate ({lambda}) determines clonal persistence and phenotypic drift. This computational implementation provides a quantitative framework for linking developmental constraint, clonal diversity, and therapeutic response in pediatric malignancies and establishes a tractable platform for model-driven hypothesis testing and translational oncology. Statement of Relationship to Prior WorkThis preprint represents a computational and cohort-level extension of the hybrid OU-Branching framework introduced in the authors manuscript currently under review at Frontiers in Oncology ("A hybrid Ornstein-Uhlenbeck-branching framework unifies microbial and pediatric tumor evolution," Manuscript ID 1727973). The Frontiers paper focuses on experimental validation and cross-domain analogies between microbial long-term evolution experiments (LTEE) and pediatric tumor evolution, emphasizing biological interpretation. In contrast, this preprint focuses on clinical modeling, patient specific simulations, and computational methods applied to pediatric KMT2A-rearranged leukemia. No data, text, or figures are duplicated from the in-review article. All code and simulations presented here are novel and will be released upon publication.

cancer biology↗

bioRxiv2025

Unraveling diel regulation of cuticle biosynthesis

The plant cuticle is vital for growth and adaptation to environmental stresses. Although cuticle biosynthesis is dynamically regulated by environmental cues, the molecular mechanisms integrating these external signals with intracellular responses remain largely unknown. Here, we discovered that cuticle biosynthesis is precisely orchestrated by two distinct regulatory modules acting in synchrony with the diel cycle. Daylight is perceived by phytochrome B (phyB), which suppresses cuticular wax biosynthesis by degradation of PIF4, a phytochrome-interacting bHLH factor that activates wax biosynthetic genes. This suppression is alleviated when phyB itself is degraded by the E3 ubiquitin ligase LRB, leading to diurnal activation of PIF4. In contrast, loss-of-function and transcriptional assays of CFLAP1 demonstrated its direct negative role in cutin biosynthesis. At night, the E3 ubiquitin ligase COP1 mediates proteasomal degradation of CFLAP1, thereby promoting cutin accumulation via activation of BDG1. Together, these results reveal that two regulatory modules, LRB-phyB-PIF4 and COP1-CFLAP1 coordinate the diel regulation of cuticle formation, ensuring timely assembly of the protective barrier.

plant biology↗

bioRxiv2025

Organelle-Aware Representation Learning Enables Label-Free Detection of Mitochondrial Dysfunction in Live Human Neurons

Mitochondrial dysfunction is a convergent hallmark of neurodegenerative diseases and represents a promising biomarker for early diagnosis and therapy. However, current in vitro assays rely on fluorescence or electron microscopy, which are invasive, low-throughput, and incompatible with longitudinal analysis. Here, we present a noninvasive framework by integrating label-free optical diffraction tomography (ODT) with organelle-aware representation learning to detect subtle mitochondrial dysfunction in live human induced pluripotent stem cell (hiPSC)-derived neurons. Through virtual staining of the nuclei, lysosomes, and mitochondria, we establish two complementary and interpretable classification pipelines: a deep learning model with organelle-aware encoder and a logistic regression model on morphometric descriptors. Both models achieve approximately 85% accuracy: the deep model provides end-to-end prediction with minimal feature engineering, whereas the logistic regression model offers a more interpretable, feature-based approach. To our knowledge, this is the first demonstration of ODT-based organelle-resolved virtual staining in live human neurons, establishing a scalable, non-invasive platform for mitochondrial disease modeling, drug discovery, and neurodegeneration research.

neuroscience↗

bioRxiv2025

A single extracellular vesicle-based platform supporting both RBD protein and mRNA vaccination against SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syn-drome coronavirus 2 (SARS-CoV-2) has highlighted the need for novel, effective, and safe vaccine platforms. Extracellular vesicles (EVs) facilitate cell-to-cell communication and can modulate immune responses by delivering antigens. Here, we propose a versatile EV-based vaccine plat-form in which immune-stimulating EVs, engineered using acoustic shock waves (SW), are used to deliver either protein or mRNA antigens. Immunostimulatory EVs derived from LPS-activated THP-1 monocytes (aTEVs) were loaded with SARS-CoV-2 receptor-binding domain (RBD) protein or RBD-encoding mRNA via SW post-loading. Both aTEV-RBD-Pro and aTEV-RBD-mRNA elicited robust RBD-specific humoral and cellular immune responses in mice without the need for external adjuvants. Moreover, lyophilized aTEV-RBD-Pro vaccines retained immunogenicity after storage, supporting their chain-independent stability. These results demonstrate that a single EV-based platform can independently support both protein- and mRNA-based vaccination, highlighting its flexibility for next-generation vaccine development.

immunology↗

bioRxiv2025

Anatomical and functional mapping of vagal nociceptive sensory nerve subsets innervating the mouse lower airways by intersectional genetics

Most vagal sensory afferents innervating the lower airways are activated by noxious stimuli including irritants (e.g. TRPV1 agonist capsaicin) and inflammatory mediators, causing nociceptive cardiorespiratory reflexes (e.g. cough, bronchospasm, changes in respiratory drive and heart rate). Vagal ganglia are comprised of embryologically distinct nodose and jugular neurons, but little is known of their specific contribution to nociceptive reflexes. Using a novel TRPV1Flp mouse in combination with P2X2Cre, Tac1Cre, intersectional reporter mice and AAV we mapped and modulated distinct nociceptive afferents. TRPV1+P2X2+ neurons were found exclusively in the nodose ganglion and were activated by {beta}mATP and capsaicin but rarely expressed Tac1. TRPV1+P2X2+ fibers innervated the lungs (many projected into the alveoli) but not the trachea. Centrally they innervated the nucleus tractus solitarius (nTS). >90% of TRPV1+Tac1+ neurons were found in the jugular ganglion and were activated by capsaicin but not {beta}mATP. TRPV1+Tac1+ fibers innervated the lungs (although none projected into the alveoli) and the trachea submucosa. They terminated solely in the paratrigeminal complex (Pa5). Many TRPV1-Tac1+ neurons were found in both nodose and jugular ganglia that innervated the trachea and large pulmonary airways. These projected to both nTS and Pa5. Using intersectional chemogenetics we selectively stimulated lower airway afferent subsets using intravenous injections of clozapine-N-oxide (CNO). Activation of TRPV1+, TRPV1+P2X2+ or TRPV1+Tac1+ fibers evoked bradycardia and bradypnea. Activation of Tac1+ fibers evoked tachycardia and tachypnea. Activation of vagal TRPV1-Tac1+ neurons only evoked tachycardia. These data show the distinct innervation patterns and reflex function of multiple nociceptive vagal afferent subsets.

physiology↗

bioRxiv2025

The ferroptosis inhibitor NUPR1 coordinates the mitochondrial response to oxidative stress and cell metabolism during COPD pathogenesis in the lung

Chronic obstructive pulmonary disease (COPD) is characterized by chronic injury and oxidative stress leading to progressive lung tissue destruction. Emerging evidence suggests that regulated cell death pathways, particularly ferroptosis, contribute to COPD pathology. We previously identified the stress response protein and known ferroptosis inhibitor nuclear protein 1 (NUPR1) as markedly downregulated in lung tissue from COPD patients. Here, we demonstrate that NUPR1 inhibition exacerbates iron accumulation, enhances lipid peroxidation, impairs mitochondrial function, disrupts cellular metabolism, and increases oxidative stress in lung epithelial cells. Furthermore, Nupr1 knockout mice exhibit mitochondrial abnormalities, increased oxidative damage, and lung tissue changes consistent with COPD pathology. Collectively, our findings establish NUPR1 as a critical regulator of ferroptosis, stress responses, mitochondrial integrity, and metabolic balance in the lung, highlighting its potential contribution to COPD pathogenesis.

cell biology↗

bioRxiv2025

TCR signaling via NFATc1 constrains IL-15-induced NK-like activation of human memory CD8+ T cells

Here we investigated the regulatory mechanisms of TCR-independent bystander activation and NK-like cytotoxicity of human memory CD8+ T cells. We found that TCR signals suppressed characteristic features of IL-15-induced CD8+ T-cell activation, including increased NKG2D expression and upregulation of genes related to NK cytotoxicity and IFN response. Moreover, ionomycin suppressed IL-15-induced bystander activation and NK-like cytotoxicity, indicating that Ca2+-calcineurin signaling is responsible for TCR-mediated suppression of IL-15-induced bystander activation. In detail, NFATc1 suppressed IL-15-induced bystander activation via binding to AP-1 that is necessary for the IL-15-induced upregulation of NK cytotoxicity-related genes. Consistent with these results, calcineurin inhibitors enhanced IL-15-induced NKG2D expression in the presence of TCR signals. Additionally, we defined genes upregulated by IL-15 and downregulated by concurrent TCR signals as an IL-15-induced bystander activation gene set, and found that this gene signature was upregulated in bystander CD8+ T cells from patients with hepatitis A virus infection. This study paves the way for further investigation of bystander CD8+ T-cell activation in various pathological conditions, and its regulation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/632884v2_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1e6c320org.highwire.dtl.DTLVardef@114a23eorg.highwire.dtl.DTLVardef@1a7b9edorg.highwire.dtl.DTLVardef@9faccc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITCR signaling downregulates IL-15-induced transcriptomic features related to NK-like bystander activation of human memory CD8+ T cells via the Ca2+-calcineurin pathway. C_LIO_LINFATc1 suppresses IL-15-induced bystander activation via binding to AP-1, which is responsible for IL-15-induced NK-like cytotoxic activity. C_LIO_LICalcineurin inhibitors cannot suppress IL-15-induced bystander CD8+ T-cell activation, and paradoxically increase IL-15-induced NKG2D expression in the presence of TCR signals. C_LIO_LIGenes upregulated by IL-15 and downregulated by concurrent TCR signals define the gene set of bystander CD8+ T-cell activation, which was validated in disease contexts. C_LI

immunology↗

bioRxiv2025

Crosslinker-free in situ hydrogel induces self-aggregation of human dental pulp stem cells with enhanced antibacterial activity

Recently, injectable hydrogels have garnered significant attention in tissue engineering due to their controlled flowability, strong plasticity, adaptability, and good biocompatibility. However, research on readily injectable in situ-forming hydrogels capable of forming functional three-dimensional (3D) tissue condensations remains limited. This study explores the development and evaluation of a carboxymethyl chitosan (CMCTS) / oxidized hyaluronic acid (oHA) hydrogel incorporated with silver sulfadiazine (AgSD) for tissue engineering applications with inherent antibacterial activity. Through physicochemical analysis, the optimal formulation of CMCTS/oHA hydrogels was established. The hydrogel demonstrated excellent injectability, enabling minimally invasive in situ delivery. In vitro cytotoxicity assays identified 0.1% AgSD as the optimal concentration, supporting cell proliferation while exhibiting antimicrobial efficacy against S. mutans and E. faecalis. In vivo studies revealed complete hydrogel degradation and good biocompatibility, with no adverse tissue reactions. The hydrogels ability to form 3D cell aggregates and support tissue regeneration underscores its potential for future 3D tissue engineering applications. Consequently, the injectable CMCTS/oHA/AgSD hydrogel developed in this study holds significant potential for application in a wide range of bioengineering fields, including antibacterial substance delivery systems and 3D tissue engineering, indicating potential for future clinical application.

bioengineering↗

bioRxiv2024

Teicoplanin attenuates RNA virus infection in vitro

Teicoplanin (TP) is a glycopeptide antibiotic used for Gram-positive bacterial infections, and it has been reported to inhibit SARS-CoV-2 and Ebola virus entry through cathepsin inhibition. Given that TP can inhibit viruses belonging to different virus families, we aimed to expand the potential targets of TP to determine whether TP can be developed as a broad-spectrum antiviral agent. Considering the original indication of TP, we first determined the effects of TP against viruses that cause respiratory tract infections and found that TP inhibits enveloped and non-enveloped RNA viruses, namely: human and avian influenza viruses; representative coronaviruses including porcine epidemic diarrhea virus (PEDV), human coronavirus OC43 (HCoV-OC43), and SARS-CoV-2; measles virus; human respiratory syncytial virus A2; and enterovirus 71 (EV-71). Representative flaviviruses, Zika virus (ZIKV) and dengue virus serotype 2 (DENV2), were also susceptible to inhibition by TP. In contrast, TP did not attenuate infection of human adenovirus 5, a non-enveloped DNA virus. Addition of TP at the endocytosis stage but not at the attachment/binding stage of PEDV infection reduced PEDV production in vitro, indicating cathepsin inhibition. Meanwhile, addition of TP during either the attachment/binding or the endocytosis stage of ZIKV infection reduced ZIKV particle production in host cells, and in silico modeling suggested that TP has potential binding pockets in the envelope proteins of ZIKV and DENV2. These results show that TP can be developed as a broad-spectrum antiviral especially against RNA viruses, with potentially different targets in the replication cycle of various viruses.

microbiology↗

bioRxiv2024

Salicaceae endophyte inoculation alters stomatal patterning and improves the intrinsic water-use efficiency of Populus trichocarpa after a water-deficit.

Microorganisms may enhance plant resilience to water stress by influencing their hosts physiology and anatomy at the leaf-level. Bacterial and yeast endophytes, isolated from wild poplar and willow, can improve the intrinsic water-use efficiency (iWUE) of cultivated poplar (Populus) under water-deficits by lowering stomatal conductance (gsw). However, the relevance of stomatal anatomy underlying this reduction remains unclear. We hypothesized endophyte inoculation could change host stomatal anatomy, and this would relate to decreases in gsw. We subjected Salicaceae endophyte-inoculated and uninoculated Populus trichocarpa to well-watered and water-deficit treatments in greenhouse studies. We examined the changes of individual stomatal traits and related the composition of these parameters, termed stomatal patterning, to leaf gas-exchange under light saturation. After a water-deficit, inoculation improved iWUE at light saturation from preserving carbon assimilation (Anet) and lowering gsw, but these changes were independent of soil-moisture status. Drops in gsw corresponded to underlying shifts in stomatal patterning. Inoculated plants had smaller, more compact stomata and greater anatomical maximum stomatal conductance (gsmax) relative to the control. Salicaceae endophytes may alter stomatal density and size, lowering gsw and increasing iWUE. Future efforts may quantify endophyte colonization of the host to draw direct relationships between microbes and stomatal traits. HIGHLIGHTPoplars inoculated with specific bacteria had leaves containing many, tiny pores relative to the trees without the microbes; these plants with the small, dense pores related to greater intrinsic water-use efficiency.

plant biology↗