Biology subjects

Yu, C.

Publications and source records attributed to Yu, C..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

Mechanistic Studies of Small Molecule Ligands Selective to RNA Single G Bulges

Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated Molecular Dynamics (GaMD) simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity-relationship (SAR) studies and transverse relaxation measurements by NMR spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Strikingly, small structure perturbations on these key contributors, such as the addition of a methyl group that disrupts the planarity of the ligand resulted in > 100-fold reduction in the binding affinity. Our work deepened the understanding of RNA-small molecule interactions and integrated a new generalizable platform for the rational design of selective small-molecule RNA binders.

biochemistry↗

bioRxiv2024

Noradrenergic and Pavlovian underpinnings of compulsive versus adaptive coping strategies

BackgroundLoss of control over coping strategies can result in the development of impulsive/compulsive spectrum disorders (ICSDs) such as obsessive-compulsive disorder or trichotillomania. Rats, like humans, show individual differences in their tendency to engage in and maintain control over coping behaviours. While most rats exposed to a schedule-induced polydipsia (SIP) procedure develop controlled, moderate, polydipsic coping, some vulnerable individuals engage in excessive, compulsive drinking, or hyperdipsia. The development of hyperdipsia depends in part on noradrenergic mechanisms, as it is prevented by the noradrenaline reuptake inhibitor, atomoxetine in highly impulsive vulnerable rats. However, whether noradrenergic mechanisms also underlie the expression of well-established hyperdipsia, or if other traits, such as the ICSD-relevant sign-tracking, confer vulnerability to its development, are unknown. MethodsIn two longitudinal studies in male Sprague-Dawley rats, we investigated whether well-established hyperdipsia is influenced by atomoxetine and whether its development is predicted by sign-tracking. ResultsSign-tracking was associated with faster acquisition of SIP and the development of high or compulsive levels of SIP. Chronic atomoxetine both exacerbated hyperdipsia and increased the mRNA levels of the markers of cellular activity and plasticity c-fos and zif268, across the dorsal striatum, as revealed by qPCR assays. Atomoxetine also altered the transcriptomic landscape of the nucleus accumbens shell and the pattern of cFos and zif268 expression in the amygdalo-striatal system. ConclusionsThese results provide new insight into the biobehavioural basis of compulsive behaviours, revealing a differential noradrenergic control of the development and expression of compulsive coping, the latter involving recruitment of distinct striatal processes.

animal behavior and cognition↗

bioRxiv2024

Multimodal integration of single cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations

Accurately deciphering tumor cellular heterogeneity is crucial for developing effective treatments. While single-cell epigenomics assays offer powerful insights into studying tumor heterogeneity beyond the transcriptional level, their application remains a significant challenge. To address this, we introduce Multimodal-based Analysis of scATAC-Seq data (MAAS), a method designed to identify functional tumor cell subpopulations and reconstruct their lineages from single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq). MAAS uniquely integrates multimodal information, encompassing chromatin accessibility, copy number variations (CNVs), and single-nucleotide variants, through self-expressive multimodal matrix factorization. MAAS outperforms existing methods in accuracy and robustness on both simulated and real datasets. When applied to multiple glioma scATAC-seq datasets, MAAS uncovered a previously hidden tumor cell subpopulation resistant to temozolomide treatment. Furthermore, MAAS effectively detected clinically relevant subpopulations with low CNVs, such as those found in pediatric ependymoma and B-cell lymphoma. Additionally, we developed a novel MAAS-derived clinical signature that provides superior prognostic prediction than traditional clinicopathologic features across multiple cancer types. In summary, MAAS significantly advances the identification of clinically relevant tumor cell subpopulations, thereby accelerating the discovery of potential therapeutic targets.

bioinformatics↗

bioRxiv2024

Isolation and Characterization of a Roseophage Representing a Novel Genus in the N4-like Rhodovirinae Subfamily Distributed in Estuarine Waters

BackgroundRoseobacteraceae, often referred to as the marine roseobacter clade (MRC), are pivotal constituents of bacterial communities in coastal and pelagic marine environments. During the past two decades, 75 roseophages that infect various Roseobacteraceae lineages have been isolated. The N4-like Rhodovirinae subfamily, which encompasses 15 members, represents the largest clade among these roseophages. ResultsIn this study, we isolated a novel roseophage, vB_DshP-R7L, that infects Dinoroseobacter shibae DFL12 from Xiamen Bay in the East China Sea. Conserved genes of Schitoviridae have been identified in the genome of vB_DshP-R7L, and following phylogenetic analysis suggest that the newly isolated phage is a member of the Rhodovirinae subfamily and is indicative of a newly proposed genus, Xianganvirus. The genome of vB_DshP-R7L harbors six auxiliary metabolic genes (AMGs), most of which potentially enhance DNA de novo synthesis. Additionally, a gene encoding ribosomal protein was identified. Comparative genomic analysis of AMG content among Rhodovirinae indicates a distinct evolutionary history characterized by independent ancient horizontal gene transfer events. Read-mapping analysis reveals the prevalence of vB_DshP-R7L and other Rhodovirinae roseophages in estuarine waters. ConclusionsOur work illustrates the genomic features of a novel roseophage clade among N4-like Rhodovirinae. The AMG content of vB_DshP-R7L are under severe purification selection, which revealed their possible ecological importance. We also demonstrated that vB_DshP-R7L and other Rhodovirinae roseophages are restrictively distributed in estuaries. Our isolation and characterization of this novel phage expand the understanding of the phylogeny, gene transfer history and biogeography of N4-like Rhodovirinae infecting marine Roseobacteraceae.

microbiology↗

bioRxiv2024

Discovering Temporally Compositional Neural Manifolds with Switching Infinite GPFA

Gaussian Process Factor Analysis (GPFA) is a powerful latent variable model for extracting low-dimensional manifolds underlying population neural activities. However, one limitation of standard GPFA models is that the number of latent factors needs to be pre-specified or selected through heuristic-based processes, and that all factors contribute at all times. We propose the infinite GPFA model, a fully Bayesian non-parametric extension of the classical GPFA by incorporating an Indian Buffet Process (IBP) prior over the factor loading process, such that it is possible to infer a potentially infinite set of latent factors, and the identity of those factors that contribute to neural firings in a compositional manner at each time point. Learning and inference in the infinite GPFA model is performed through variational expectation-maximisation, and we additionally propose scalable extensions based on sparse variational Gaussian Process methods. We empirically demonstrate that the infinite GPFA model correctly infers dynamically changing activations of latent factors on a synthetic dataset. By fitting the infinite GPFA model to population activities of hippocampal place cells during spatial tasks with alternating random foraging and spatial memory phases, we identify novel non-trivial and behaviourally meaningful dynamics in the neural encoding process.

neuroscience↗

bioRxiv2024

Change in brain molecular landscapes following electrical stimulation of the nucleus accumbens

Deep brain stimulation (DBS) targeting the nucleus accumbens (NAc) is a promising therapeutic intervention for treatment-resistant neuropsychiatric disorders such as depression, anxiety, and addiction. However, the molecular mechanisms underlying the clinical efficacy of NAc DBS remain largely unknown. One approach to address this question is by performing spatial gene expression analysis on cells located in different regions of the same circuit following NAc DBS. In this study, we utilized high-resolution spatial transcriptomics (Stereo-seq) to investigate gene expression changes induced by NAc DBS in the mouse brain. Mice were randomly allocated to received continuous electrical stimulation (0.1 mA, 130 Hz) or sham treatment (electrode implanted, no electrical stimulation given) for one week, and subsequent Stereo-seq analysis identified differentially expressed genes (DEGs) across various brain regions. Our findings reveal widespread alterations in synaptic function and neuronal connectivity, particularly in glutamate receptor-expressing neurons in the NAc, which play a key role in the reward circuitry. Functional enrichment analysis highlighted changes in transporter activity and glutamate receptor binding in brain regions such as the anterior cingulate cortex and lateral septal nucleus. Single-cell resolution mapping further identified key molecular players, including Nlgn1, Snca, PDE10a, and Syt1, which are critical for synaptic plasticity and neurotransmitter release, and have been implicated in various psychiatric disorders. These findings shed light on the molecular underpinnings of NAc DBS and provide insights into its therapeutic potential in modulating neural circuits associated with neuropsychiatric disorders.

molecular biology↗

bioRxiv2024

Dynamical Modulation of Hippocampal Replay Sequences through Firing Rate Adaptation

During periods of immobility and sleep, the hippocampus generates diverse self-sustaining sequences of "replay" activity, exhibiting stationary, diffusive, and super-diffusive dynamical patterns. However, the neural mechanisms underlying this diversity in hippocampal sequential dynamics remain largely unknown. Here, we propose such a mechanism demonstrating that modulation of firing rate adaptation in a continuous attractor model of place cells causes the emergence of different types of replay. Our model makes several key predictions. First, more diffusive replay sequences positively correlate with longer theta sequences across animals (both reflecting stronger adaptation). Second, replay diffusivity varies within an animal across behavioural states that affect adaptation (such as wake and sleep). Third, increases in neural excitability, incorporated with firing rate adaptation, reduce the step size of decoded movements within individual replay sequences. We provide new experimental evidence for all three predictions. These insights suggested that the diverse replay dynamics observed in the hippocampus can be reconciled through a simple yet effective neural mechanism, shedding light on its role in hippocampal-dependent cognitive functions and its relationship to other aspects of hippocampal electrophysiology.

neuroscience↗

bioRxiv2024

Liprin-α/RIM complex regulates the dynamic assembly of presynaptic active zones via liquid-liquid phase separation

Presynaptic scaffold proteins, including liprin-, RIM, and ELKS, are pivotal to the assembly of the active zone and regulating the coupling of calcium signals and neurotransmitter release, yet the underlying mechanism remains poorly understood. Here, we determined the crystal structure of the liprin-2/RIM1 complex, revealing a multifaceted intermolecular interaction that drives the liprin-/RIM assembly. Neurodevelopmental disease-associated mutations block the formation of the complex. Disrupting this interaction in neurons impairs synaptic transmission and reduces the readily releasable pool of synaptic vesicles. Super-resolution imaging analysis supports a role for liprin- in recruiting RIM1 to the active zone, presumably by promoting the liquid-liquid phase separation (LLPS) of RIM1. Strikingly, the liprin-/RIM interaction modulates the competitive distribution of ELKS1 and voltage-gated calcium channels (VGCCs) in RIM1 condensates. Disrupting the liprin-/RIM interaction significantly decreased VGCC accumulation in the condensed phase and rendered release more sensitive to the slow calcium buffer EGTA, suggesting an increased physical distance between VGCC and vesicular calcium sensors. Together, our findings provide a plausible mechanism of the liprin-/RIM complex in regulating the coupling of calcium channels and primed synaptic vesicles via LLPS for efficient synaptic transmission and uncover the pathological implication of liprin- mutations in neurodevelopmental disorders.

neuroscience↗

bioRxiv2024

NEMF-mediated CAT-tailing defines distinct branches of translocation-associated quality control

Ribosome stalling during co-translational translocation at the endoplasmic reticulum (ER) causes translocon clogging and impairs ER protein biogenesis. Mammalian cells resolve translocon clogging vial a poorly characterized translocation-associated quality control (TAQC) process. Here, we combine genome-wide CRISPR screen with live cell imaging to dissect the molecular linchpin of TAQC. We show that substrates translated from mRNAs bearing a ribosome stalling poly(A) sequence are degraded by lysosomes and the proteasome, while substrates encoded by non-stop mRNAs are degraded by an unconventional ER-associated degradation (ERAD) mechanism involving ER-to-Golgi trafficking and KDEL-dependent substrate retrieval. The triaging diversity appears to result from the heterogeneity of NEMF-mediated CATylation, because a systematic characterization of representative CAT-tail mimetics establishes an AT-rich tail as a "degron" for ERAD, whereas an AG-rich tail can direct a secretory protein to the lysosome. Our study reveals an unexpected protein sorting function for CAT-tailing that safeguards ER protein biogenesis.

cell biology↗

bioRxiv2024

Decoding multicellular niche formation in the tumour microenvironment from nonspatial single-cell expression data

Accurate inference of granular cell states that co-occur within the tumour microenvironment (TME) is central to defining pro- and anti-tumour environments. Here, we describe how ecosystems of cell populations can be robustly inferred from nonspatial single-cell RNA-seq (scRNA-seq) atlases. Leveraging a unique discovery-validation setup across eight scRNA-seq datasets profiling pancreatic ductal adenocarcinoma (PDAC), we show highly consistent co-occurrence of fine-grained cell states across patients and characterize the positive predictive value of such analyses. Building on this, we develop a novel probabilistic model to quantify multi-cellular ecosystems directly from such atlas-scale scRNA-seq datasets. By mapping these ecosystems to spatial transcriptomics data, we demonstrate that such ecosystems represent bona fide spatial variation within individual tumours despite being learned from nonspatial data. Importantly, through mapping these ecosystems across two large clinical cohorts, we show they are more predictive of therapy response than any individual cell state and are associated with specific tumour somatic mutations. Together, this work lays the foundation for inferring reproducible multicellular ecosystems directly from large nonspatial scRNA-seq atlases.

bioinformatics↗

bioRxiv2024

Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks

Cross-linking mass spectrometry (XL-MS) is a powerful technology for mapping protein-protein interactions (PPIs) at the systems-level. By covalently connecting pairs of proximal residues, cross-linking reagents provide distance restraints to infer protein conformations and interaction interfaces. While binary cross-links have been remarkably informative, multimeric cross-links can offer enhanced spatial resolution to facilitate the characterization of dynamic and heterogeneous protein complexes. However, the identification of multimeric cross-links remains extremely challenging due to fragmentation complexity and the vast expansion of database search space. Here, we present a novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which can target three proximal lysine residues simultaneously. Owing to its unique structure and MS-cleavability, TSTO enables fast and unambiguous identification of cross-linked peptides using LC-MSn analysis. Importantly, we have demonstrated that the TSTO-based XL-MS platform is effective for mapping PPIs of protein complexes and cellular networks. The trimeric interactions captured by TSTO have uncovered new structural details that cannot be easily revealed by existing reagents, allowing in-depth description of PPIs to facilitate structural modeling. This development not only advances XL-MS technologies for global PPI profiling from living cells, but also offers a new direction for creating multifunctional MS-cleavable cross-linkers to further push structural systems biology forward in the future.

biochemistry↗

bioRxiv2024

Laminin 111 triggers cell quiescence and long-term survival by inducing IQGAP1-mediated cytosolic scaffolding of ERK and BAD inactivation

In an adult human body, only a minority ([~]1%) of cells are dividing; all others are either quiescent, senescent or terminally differentiated. Cellular quiescence, also called G0, is a reversible non-proliferative state in which cells, such as adult stem cells, exist until stimuli trigger their re-entry into the cell cycle. Quiescent cells are known to reside within microenvironment niches of specific extracellular matrix (ECM) composition, but the molecular mechanisms that control their entry and maintenance into G0 and their long-term survival are poorly understood. Here, using a reproducible and homogenous in vitro model of quiescence, ex vivo tissue histology, phosphoproteomics, and molecular cell biological assays, we revealed that Laminin 111 was sufficient to trigger i) reversible cell cycle exit into G0; ii) sustained and elevated MAPK/ERK signaling; and iii) long-term survival. We found that ERK was activated through the Rap1-BRAF-MEK arm underneath Laminin-binding Integrin 3{beta}1. Activated pERK was scaffolded into the cytoplasm by IQGAP1, thereby blocking its translocation into the nucleus and the activation of proliferative transcription factors. Instead, cytoplasmic pERK inhibited pro-apoptotic protein BAD, which mediated the survival of quiescent cells even in absence of mitogen stimuli. Importantly, we confirmed that pERK was elevated and retained in the cytoplasm of Lgr5+ stem cells when they were located within Laminin 1-positive niches in porcine intestine. These findings uncovered a molecular mechanism that may explain how quiescent cell pools, such as dormant adult stem cells, can survive many years despite low mitogen stimuli and be resistant to apoptotic challenges, including chemotherapy. HIGHLIGHTSO_LILaminin 111 is sufficient to induce cellular quiescence (G0) and long-term survival. C_LIO_LILaminin 111 triggers the sustained and elevated activation of ERK during G0. C_LIO_LIERK is activated not by growth factor receptors but through the Rap1-BRAF-MEK arm underneath Laminin-binding Integrin 3{beta}1. C_LIO_LIActive, phosphorylated ERK (pERK) is scaffolded by IQGAP1, which prevents it from translocating into the nucleus and activating proliferative transcription factors. C_LIO_LIInstead, cytoplasmic pERK mediates the phosphorylation, and thus inhibition, of BAD, thereby raising the threshold at which G0 cells enter apoptosis. C_LI

cell biology↗

bioRxiv2024

Inclusive, Exclusive and Hierarchical Atlas of NFATc1+/PDGFR-alpha+ Cells in Dental and Periodontal Mesenchyme

Platelet-derived growth factor receptor alpha (PDGFR-) activity is crucial in the process of dental and periodontal mesenchyme regeneration facilitated by autologous platelet concentrates (APCs), such as platelet-rich fibrin (PRF), platelet-rich plasma (PRP) and concentrated growth factors (CGF), as well as by recombinant PDGF drugs. However, it is largely unclear about the physiological patterns and cellular fate determinations of PDGFR-+ cells in the homeostasis maintaining of adult dental and periodontal mesenchyme. We previously identified NFATc1 expressing PDGFR-+ cells as a subtype of skeletal stem cells (SSCs) in limb bone, but their roles in dental and periodontal remain unexplored. To this end, in the present study we investigated the spatiotemporal atlas of NFATc1+ and PDGFR-+ cells residing in dental and periodontal mesenchyme, their capacity for progeny cell generation, and their inclusive, exclusive and hierarchical relations in homeostasis. We utilized CRISPR/Cas9-mediated gene editing to generate two dual recombination systems, which were Cre/loxP-Dre/Rox combined intersectional and exclusive reporters respectively, to concurrently demonstrate the inclusive, exclusive, and hierarchical distributions of NFATc1+ and PDGFR-+ cells and their lineage commitment. By employing the state-of-the-art transgenic lineage tracing techniques in cooperating with tissue clearing-based advanced imaging and three-dimensional slices reconstruction, we systematically mapped the distribution atlas of NFATc1+ and PDGFR-+ cells in dental and periodontal mesenchyme and tracked their in vivo fate trajectories. Our findings extend current understanding of NFATc1+ and PDGFR-+ cells in dental and periodontal mesenchyme homeostasis, and furthermore enhance our comprehension of their sustained therapeutic impact for future clinical investigations.

developmental biology↗

bioRxiv2024

PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue

Spatial RNA imaging has not been widely adopted because conventional fluorescence microscopy is limited to only a few channels, and the cyclic reactions needed to increase multiplexing in techniques such as sequential fluorescence in-situ hybridization (FISH) require sophisticated instrumentation. Here, we introduce Profiling of RNA In-situ through Single-round iMaging (PRISM), a method that expands coding capacity through color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validate PRISMs versatility across various tissues by generating a 3D atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor-normal transition landscape of human hepatocellular carcinoma (HCC), and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts (CAFs) in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.

bioengineering↗

bioRxiv2024

A host enzyme reduces non-alcoholic fatty liver disease by inactivating intestinal lipopolysaccharide

The incidence of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) has been increasing world-wide. Since gut-derived bacterial lipopolysaccharides (LPS) can travel via the portal vein to the liver and play an important role in producing hepatic pathology, it seemed possible that (1) LPS stimulates hepatic cells to accumulate lipid, and (2) inactivating LPS can be preventive. Acyloxyacyl hydrolase (AOAH), the eukaryotic lipase that inactivates LPS and oxidized phospholipids, is produced in the intestine, liver, and other organs. We fed mice either normal chow or a high-fat diet for 28 weeks and found that Aoah-/- mice accumulated more hepatic lipid than did Aoah+/+ mice. In young mice, before increased hepatic fat accumulation was observed, Aoah-/-mouse livers increased their abundance of Sterol Regulatory Element-Binding Protein 1 (SREBP1) and the expression of its target genes that promote fatty acid synthesis. Aoah-/- mice also increased hepatic expression of CD36 and Fabp3, which mediate fatty acid uptake, and decreased expression of fatty acid oxidation-related genes Acot2 and Ppar-. Our results provide evidence that increasing AOAH abundance in the gut, bloodstream and/or liver may be an effective strategy for preventing or treating MASLD.

immunology↗

bioRxiv2024

A vacuolar invertase gene SlVI modulates sugar metabolism and postharvest fruit quality and resistance in tomato

Sugars act as signaling molecules to modulate various growth processes and enhance plant tolerance to various abiotic and biotic stresses. Moreover, sugars contribute to the post-harvest flavor in fleshy fruit crops. To date, the regulation of sugar metabolism and its effect in plant growth, fruit ripening, postharvest quality and resistance remains not fully understood. In this study, we investigated the role of tomato gene encoding a vacuolar invertase, hydrolyzing sucrose to glucose and fructose. SlVI is specifically expressed during the tomato fruit ripening process. We found that overexpression of SlVI resulted in increased leaf size and early flowering, while knockout of SlVI led to increased fruit sucrose content, enhanced fruit firmness, elevated resistance of postharvest fruit to Botrytis cinerea. Moreover, the content of naringenin and total soluble solids was significantly increased in SlVI knockout fruit at postharvest stage. Transcriptome analysis showed a negative feedback regulation triggered by sucrose accumulation in SlVI knockout fruit resulting in a downregulation of BAM3 and AMY2, which are critical for starch degradation. Moreover, genes associated with cell wall, cutin, wax, and flavonoid biosynthesis and pathogen resistance were upregulated in SlVI knockout fruit. Conversely, the expression levels of genes involved in cell wall degradation were decreased in knockout fruit. These results are consistent with the enhanced postharvest quality and resistance. Our findings not only provide new insights into the relationship between tomato fruit sucrose content and postharvest fruit quality, but also suggest new strategies to enhance fruit quality and extend postharvest shelf life.

plant biology↗

bioRxiv2024

Double training reveals an interval-invariant subsecond temporal structure in the brain

Subsecond temporal perception is critical for understanding time-varying events. Many studies suggest that subsecond timing is an intrinsic property of neural dynamics, distributed across sensory modalities and brain areas. Furthermore, we hypothesize the existence of a more abstract and conceptual representation of subsecond time, which may guide the temporal processing of distributed mechanisms. However, one major challenge to this hypothesis is that learning in temporal interval discrimination (TID) consistently fails to transfer from trained intervals to untrained intervals. To address this issue, here we examined whether this interval specificity can be removed with double training, a procedure we originally created to eliminate various specificities in visual perceptual learning. Specifically, participants practiced the primary TID task, the learning of which per se was specific to the trained interval (e.g., 100 ms). In addition, they also received exposure to a new interval (e.g., 200 ms) through a secondary and functionally independent tone-frequency discrimination (FD) task. This double training successfully enabled complete transfer of TID learning to the new interval, indicating that training improved an interval-invariant component of temporal interval perception, which supports our general proposal of an abstract and conceptual representation of subsecond time in the brain.

neuroscience↗

bioRxiv2024

ROS Mediated the Photodynamic Antibacterial of Vibrio vulnificus by a DNA-Targeted Molecular Rotor Probe

Vibrio vulnificus, a highly pathogenic Gram-negative bacterium, is capable of inducing sepsis, necrotizing fasciitis, and skin and soft tissue infections through contact with wounds. Currently, the majority of V. vulnificus strains have developed resistance to multiple drugs, highlighting the critical necessity for the development of novel therapeutics capable of effectively targeting and eradicating this bacterium. In recent years, material molecules have emerged as promising antimicrobial agents. This study introduces a novel molecular fluorescent probe, BDTP, which demonstrates a wide-ranging antimicrobial effect against both Gram-negative and Gram-positive bacteria while exhibiting minimal toxicity to normal mammalian cells. Of particular significance is BDTPs ability to rapidly detect V. vulnificus, bind to bacterial DNA, and exhibit fluorescence monitoring behavior. Furthermore, BDTP displays enhanced photodynamic antibacterial activity when exposed to white light irradiation. Under a low dose of white light (15mW cm-2), the killing efficiency of V. vulnificus irradiated with 4uM for 10 minutes was more than 99.8%. Moreover, it could significantly inhibit and eliminate the biofilm formed by V. vulnificus. It can induce the production of reactive oxygen species (ROS) in V. vulnificus cells, leading to bacterial cell damage. More importantly, BDTP significantly promoted the healing of infected wounds in an animal model of V. vulnificus infection. Therefore, BDTP shows great promise as a potent antibacterial agent against V. vulnificus infection.

microbiology↗