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Li, Y.

Publications and source records attributed to Li, Y..

At least 469 records · Page 26Linked to original sources
bioRxiv2026

Effect of C6-HSL and chlorogenic acid on spoilage characteristics of Serratia liquefaciens in mutton

Quorum sensing (QS) is a bacterial cell-cell communication system that coordinates group behaviors via self-produced signaling molecules. Serratia liquefaciens, a common mutton spoilage bacterium, precisely regulates its spoilage capacity through the AHL-mediated QS system. The results demonstrated that 20 mol/mL C6-HSL concentration-dependently enhanced AHL activity 1.26-fold, increased biofilm formation by 51.55%, and elevated protease activity and siderophore production by 37% and 26.78%, respectively. In contrast, 80 g/mL chlorogenic acid significantly inhibited AHL activity (by 26.19%), biofilm formation (by 42.54%), protease activity (by 28.92%), and motility (by 38.34%). In stored mutton, chlorogenic acid treatment reduced total plate counts by 6.1% and pH by 5.26%. Transcriptomic analysis revealed that C6-HSL treatment altered metabolic pathways such as flagellar assembly, ABC transporters, two-component systems, and secondary metabolite synthesis, in which spoilage-related genes (slyB, fimA, fliJ, iucD, cheW) were significantly up-regulated. In contrast, chlorogenic acid treatment affected pathways including amino acid metabolism, sulfur metabolism, and carbohydrate metabolism, with spoilage-related genes (fimA, tuf, ibpA, clpS, metQ) significantly down-regulated. These findings demonstrate that AHL activity plays a key role in regulating the spoilage capacity of Serratia liquefaciens, and suggest chlorogenic acid as a potential QS inhibitor with promising application in mutton preservation. ImportanceSerratia liquefaciensis a common spoilage bacterium in refrigerated foods and proliferates extensively in meat, making it one of the primary spoilage organisms. The significance of our research lies in investigating how changes in the activity of the signaling molecule AHL affect both spoilage capacity and mutton quality. Additionally, transcriptomic analysis was employed to elucidate the regulatory mechanisms by which altered AHL activity influences the spoilage potential of S. liquefaciens. The results demonstrated that variations in AHL activity significantly impacted key spoilage-related traits of S. liquefaciens, including biofilm formation, protease activity, and motility, while also contributing to improved meat quality during storage. Furthermore, the study revealed that AHL activity regulates metabolic pathways associated with spoilage as well as the expression of spoilage-related genes. These findings provide a theoretical basis for developing preservation strategies for mutton.

microbiology↗
bioRxiv2026

BiOmics: A Foundational Agent for Grounded and Autonomous Multi-omics Interpretation

While AI has automated bioinformatic workflows, biological interpretation remains fragmented and often disconnected from mechanistic insights. Existing AI is bifurcated between statistical "black-box" models that lack logical grounding and simple agents restricted to shallow knowledge retrieval. To bridge this divide, we introduce BiOmics, a foundational agent that synthesizes multi-omics data with adaptive knowledge for biological interpretation. BiOmics introduces a novel dual-track architecture comprising a harmonized explicit reasoning space for grounded logic and a unified latent embedding space for high-dimensional association mapping. This architecture enables a transformative "Retrieving-Reasoning-Predicting" paradigm for purposeful, cross-scale inference traversing the biological hierarchy, from molecular variants to disease phenotypes. Empirical evaluations demonstrate that BiOmics surpasses state-of-the-art AI agents and specialized algorithms, markedly augmenting the granularity and depth of biological insights. Specifically, BiOmics exhibits unique superiority in uncovering indirect pathogenic variants, achieving reference-free cell annotation, and prioritizing drug repurposing candidates tailored to specific datasets. BiOmics further enriches the interpretive landscape of biological entities, leveraging its reasoning-grounded knowledge graph to uncover deep functional contexts. Ultimately, BiOmics provides a versatile engineering foundation to transition AI for Science from descriptive "data fitting" to autonomous, knowledge-driven interpretation.

bioinformatics↗
bioRxiv2026

PCRD-seq: Proximity Crosslinking-induced RNA Depletion for Low-Input Subcellular Transcriptome Profiling

Chromatin-associated RNAs play critical roles in regulating chromatin organization and transcription, underscoring the importance of their study. Proximity labeling has emerged as a promising and versatile technique for profiling chromatin-associated RNAs with high spatiotemporal resolution. While being a powerful technique, traditional proximity labeling methods depend on complex, high-input enrichment protocols, which significantly limit their wide practical application. Here, we developed a straightforward, enrichment-free chromatin-associated RNA profiling strategy: Proximity Crosslinking-induced RNA Depletion sequencing (PCRD-seq). This approach leverages the proximity crosslinking between chromatin and its surrounding RNAs induced by singlet oxygen generated by HoeDBF, a photosensitizer targeting chromatin region. The proximity crosslinking hinders the release of chromatin-associated RNAs during routine TRIzol extraction, consequently leading to a specific depletion of these RNAs. This method was successfully applied to investigate the role of U1 snRNA in RNA chromatin retention and the differences in chromatin-associated transcriptomes between two ovarian cancer cell lines with opposite metastatic capability. Moreover, our PCRD-seq exhibits potential in profiling nuclear lamina-associated RNAs, which paves the way for its application to profile RNAs associated with other chromatin subdomains. The minimal cell input and simple workflow endow PCRD-seq as a transformative tool for wide applications.

cell biology↗
bioRxiv2026

Long-term Musculoskeletal and Marrow Sparing with Proton FLASH in Juvenile Mice: Implications for Pediatric Osteosarcoma

PurposeOsteosarcoma is the most common primary bone malignancy in children and adolescents. Radiotherapy is limited by intrinsic radioresistance and the risk of severe long-term musculoskeletal toxicities. FLASH radiotherapy, delivered at ultra-high dose rates (>40 Gy/s), has demonstrated normal tissue sparing in preclinical models, but its effects on the developing skeleton and marrow remain poorly defined. This study evaluated the chronic normal tissue effects of proton FLASH in juvenile mice, modeling the pediatric context. Methods and MaterialsJuvenile C57BL/6 mice (3-4 weeks old) were randomized to receive 11 Gy FLASH ({approx}200 Gy/s) or conventional proton irradiation (0.2 Gy/s average), or sham treatment to the left hind leg using a synchrotron-based proton beamline. Mice were followed for 10 weeks post-treatment. Bone toxicity was assessed with microCT (bone mineral density, bone volume fractions, trabecular indices) and histology. Bone marrow cellularity was quantified on H&E-stained sections, and muscle fibrosis was assessed using Massons trichrome. ResultsFLASH-treated mice exhibited significant preservation of bone microarchitecture compared with conventional treated mice, with higher bone mineral density and bone volume fractions (p < 0.05). Trabecular numbers were maintained, while structure model index indicates a mechanically favorable trabecular structures in the FLASH group. Bone marrow cellularity was preserved in FLASH mice (5.3% reduction vs. sham) compared with conventional (11.3 % reduction, p < 0.05). Muscle fibrosis was significantly lower in FLASH group (fibrosis positivity 2.6 % vs. 3.0% for FLASH vs. conventional CONV, p < 0.05). No severe immobility or weight loss was observed across groups. ConclusionsProton FLASH significantly reduces long-term bone, marrow, and muscle toxicities in juvenile mice. These findings provide the first demonstration of musculoskeletal sparing in a synchrotron proton FLASH platform and highlight its translational potential for pediatric osteosarcoma.

cancer biology↗
bioRxiv2026

Microhomology-mediated end joining acts directly on replication forks to repair single-ended double strand breaks

Replication stress, intrinsic to oncogenesis, often leads to fork breakage and double-strand break (DSB) formation. Conventionally, break-induced replication (BIR) is considered the primary mechanism for repairing replication-associated single-ended DSBs (seDSBs). Here, we demonstrate that microhomology-mediated end joining (MMEJ) acts directly to repair seDSBs at broken replication forks (fork-MMEJ), preferentially on the leading strands, and functions cooperatively with BIR. We also showed that while fork-MMEJ is promoted by Pol{theta}, it operates independently of MRE11/CtIP-mediated end resection, relies on RPA, and produces asymmetric deletion patterns, which is distinct from canonical MMEJ (cMMEJ) defined at replication-independent double-ended DSBs (deDSBs). ATR, activated as end resection proceeds, serves as a pivotal switch to suppress fork-MMEJ while promoting BIR. Combined inactivation of ATR and Pol{theta} synergistically kills cancer cells under high replication stress with minimal toxicity to normal cells. Together, our study provides fundamental insights into the MMEJ mechanism and offers new strategies for cancer treatment.

molecular biology↗
bioRxiv2026

THIK-1 channel mediates microglial glucose sensing and modulates AgRP neurons

Microglia play essential roles in maintaining energy homeostasis, and their dysfunction contributes to metabolic disease. Although high-fat diet (HFD) exposure induces microglial activation, the underlying mechanisms remain poorly defined. Here, we identified a previously unrecognized role for THIK-1 channel in mediating glucose sensing of microglia in arcuate nucleus of the hypothalamus (ARH), during HFD-induced obesity. Pharmacological inhibition of THIK-1 channel with tetrapentylammonium (TPA) suppresses feeding and attenuates body-weight gain in diet induced obese mice. Mechanistically, inhibition of agouti-related peptide (AgRP) neurons is indispensable for TPA-induced hypophagia. Moreover, THIK-1 inhibition promotes microglial phagocytosis of perineuronal nets (PNNs), leading to reduced AgRP neuronal activity and feeding suppression. Together, these findings establish THIK-1 as a critical glucose sensor in hypothalamic microglia and uncover a microglia-dependent pathway through which overnutrition modulates AgRP neuronal activity via PNN remodeling to regulate energy balance, highlighting THIK-1 as a potential therapeutic target for treatment of diet-induced obesity.

neuroscience↗
bioRxiv2026

Aerobic Exercise Preserves Capillary Oxygen Homeostasis and Neurovascular Function in a Mouse Model of Alzheimer's Disease

Age-related cerebrovascular dysfunction is increasingly recognized as a critical contributor to cognitive decline and Alzheimers disease (AD) progression. Aerobic physical activity (PA) and other modifiable lifestyle interventions can substantially reduce the likelihood of dementia; however, their ability to mitigate cerebrovascular alterations remains poorly defined. PA reportedly improves systemic vascular health and cognitive function in aging humans, but its impact on cerebrovascular function during aging and amyloid {beta} (A{beta}) pathology is unclear. Here, we longitudinally quantified microvascular oxygen tension and stimulus-evoked oxygen dynamics in awake APP/PS1dE9 mice and wild-type littermates using two-photon phosphorescence lifetime microscopy. Routine aerobic PA initiated in early adulthood preserved basal arteriolar, capillary, and venular oxygenation, prevented age-dependent increases in microvascular heterogeneity, and mitigated excessive oxygen extraction in preclinical AD mice. While amyloid pathology impaired stimulus-evoked oxygen responses across vascular compartments, PA selectively enhanced capillary dilation and accelerated hyperemic kinetics without altering vascular density or architecture. Notably, sedentary AD mice developed lower, widely-dispersed distributions in capillary oxygenation, hallmarks of malignant microvascular dysfunction, which were largely absent in physically active animals. These findings demonstrate that routine aerobic PA preserves basal capillary oxygenation and stimulus-evoked hyperemia during aging and A{beta}, supporting a capillary-centric mechanism through which exercise confers neurovascular resilience in preclinical AD.

neuroscience↗
bioRxiv2026

MIF-mediated reprogramming of myeloid lineage within the glioma tumor microenvironment impacts the efficacy of immune stimulatory gene therapy

Gliomas with mutant isocitrate dehydrogenase 1 (mIDH1) represent a distinct subgroup of brain tumors characterized by unique metabolic and immunological profiles compared to wildtype IDH1 (wtIDH1) gliomas. Despite recent progress, the cellular mechanisms underlying tumor progression and immune modulation in these subtypes remain poorly understood. In this study, we employed single-cell RNA sequencing (scRNA-seq) to characterize the cellular heterogeneity of wtIDH1 and mIDH1 gliomas, with a particular focus on myeloid cell populations. Our analyses revealed a marked reduction of monocyte-derived tumor-associated macrophages (Mo-TAMs) and lower expression of macrophage migration inhibitory factor (MIF) in mIDH1 gliomas, which was attributable to epigenetic reprogramming. Mechanistic studies using MIF and CD74 knockout mice demonstrated that the MIF-CD74 axis plays a crucial role in regulating the glioma immune microenvironment, thereby driving tumor growth and progression. Importantly, the combination of immune-stimulatory gene therapy (HSV1-thymidine kinase/Fms-like tyrosine kinase 3 ligand; TK/Flt3L) with MIF inhibition significantly extended survival in models of wtIDH1 glioma. These findings highlight the therapeutic potential of targeting the MIF-CD74 pathway and underscore the importance of integrating immunomodulatory strategies for the treatment of glioma. HighlightsO_LIMutant IDH1 gliomas exhibit fewer Mo-TAMs and increased Mg-TAMs C_LIO_LIMutant IDH1 gliomas have less MIF expression via epigenetic reprogramming. C_LIO_LIMesenchymal wtIDH1 glioma cells are main source of MIF. C_LIO_LIMIF inhibition plus immune stimulatory gene therapy extends survival wtIDH1 glioma. C_LI

cancer biology↗
bioRxiv2026

Automating the Construction of Contextualized Biomedical Knowledge Graphs for Scientific Inference

Biomedical interactions are inherently dynamic, often shifting or even reversing under specific physiological states. However, existing extraction methods simplify these complex mechanisms into context-agnostic binary associations, resulting in semantic loss and contradictory evidence. Here, we present AutoBioKG, an end-to-end framework that constructs context-aware knowledge graphs by leveraging composite triples to encode environmental conditions and entity attributes alongside core relationships. Powered by an open information extraction model trained on BioOpenIE and further refined through self-training with pseudo-labels from unlabeled literature, the framework exhibits broad generalization. Notably, AutoBioKG achieved the highest zero-shot F1 across DDI, ChemProt, and BioRED, outperforming the best-performing baseline on each benchmark by 3.6-17.8 percentage points. Furthermore, AutoBioKG-derived graphs outperformed existing approaches on yes/no, factoid, and list questions in the BioASQ biomedical question-answering evaluation, particularly for queries requiring fine-grained contextual information. Together, these results support AutoBioKG as a scalable framework for transforming unstructured literature into structured, context-aware biomedical knowledge.

bioinformatics↗
bioRxiv2026

Multiomics reveals epigenetic control of fibroblast activity after myocardial infarction and a key role for RUNX transcription factors

BackgroundAfter myocardial infarction (MI), cardiac fibroblasts proliferate and undergo a sequential differentiation process. They first transition into cardiac myofibroblasts, a transient and highly contractile state, and ultimately into matrifibrocytes, a more stable state that partially resembles chondrocytes. These dynamic transitions are essential for infarct healing and scar formation. While insufficient fibroblast activation can compromise infarct integrity, excessive activation promotes pathological fibrosis that impairs cardiac function. Despite its clinical importance, the transcriptional and epigenetic regulation of these transitions remain poorly understood. Elucidating underlying mechanisms is critical for developing strategies to fine-tune fibroblast activity during cardiac repair. MethodsWe performed bulk RNAseq, ATACseq, CUT&Tag, CUT&RUN, EMseq, and Hi-C on cardiac fibroblasts from uninjured and post-MI mouse hearts. In parallel, we conducted single-nucleus multiomic (snRNAseq and snATACseq) profiling across multiple time points after MI. Subsequent integrated analysis explored epigenetic mechanisms regulating cardiac fibroblast gene expression and activity. Using an improved computational strategy, we constructed gene regulatory networks to identify key transcription factors and biological processes regulated by these transcription factors. To assess the role of Runx1 specifically, we used tamoxifen-inducible, fibroblast-specific Runx1 knockout mice to evaluate transcriptional, epigenetic, and functional outcomes with the same genomic tools and additional complementary assays. ResultsCardiac fibroblasts undergo extensive chromatin remodeling after MI, which is highly correlated with changes in transcriptomic profiles. In contrast, the role of DNA methylation is relatively minor. Gene regulatory network analysis identified Runx1 as a central regulator of cardiac fibroblast proliferation and matrifibrocyte differentiation. In vitro and in vivo validation confirmed Runx1 as a key modulator of transcriptional and epigenetic changes in cardiac fibroblasts. Runx1 KO reduced cardiac fibroblast proliferation, disrupted the myofibroblast-to-matrifibrocyte transition, and affected macrophage cytokine expression through altered cardiac fibroblast-macrophage communication. Fibroblast-specific Runx1 knockout mice showed improved post-MI survival and reduced cardiac dilatation, especially in males. Simultaneous Runx2 deletion further enhanced the effects of Runx1 knockout. ConclusionsCardiac fibroblast activation and differentiation after MI are regulated by dynamic epigenetic changes. Runx1 plays a pivotal role in modulating cardiac fibroblast activities, and its deletion improves cardiac repair by mitigating maladaptive fibroblast responses. By illuminating the centrality of Runx1 in post-MI repair, this study identifies an actionable pathway for therapeutically steering fibroblast responses.

genomics↗
bioRxiv2026

Wash-Free Multi-Target Super-Resolution Microscopy with Photocaged DNA Labels

Super-resolution microscopy with DNA-fluorophore labels is primed for multi-target imaging of cell biological samples. However, direct interaction with the sample is required to exchange or add DNA-fluorophore labels in each imaging round, which can impair the accuracy of the imaging data at the nanometer scale. To bypass this requirement, we introduce a wash-free method that employs DNA oligonucleotides equipped with photocaging groups. Irradiation with light removes these photo-modulatable groups and changes the hybridization properties of DNA labels, enabling light-modulated targeting. We demonstrate this concept by imaging various cellular targets with confocal microscopy, single-molecule localization microscopy, and stimulated emission depletion (STED) microscopy.

biophysics↗
bioRxiv2026

Dissociation of Diffusion and Perfusion Responses After Intracerebral Hemorrhage

Background and PurposeIntracerebral hemorrhage (ICH) triggers complex secondary injury processes that extend beyond hematoma formation. While structural and diffusion MRI are widely used to characterize tissue injury, the spatiotemporal evolution of cerebral perfusion after ICH, particularly in small-animal models, remains poorly defined. Here, we performed a longitudinal multiparametric MRI study to delineate the relationship between microstructural injury and cerebral perfusion following experimental ICH. MethodsA collagenase-induced mouse model of ICH was studied longitudinally from baseline to 21 days post-stroke. Hematoma volume, tissue microstructure, and cerebral blood perfusion (CBP) were quantified using T2*-weighted MRI, diffusion-weighted imaging, and pseudo-continuous arterial spin labeling (pCASL) MRI, respectively. Apparent diffusion coefficient (ADC) and CBP were quantified in multiple brain regions from both ipsilateral and contralateral hemispheres and analyzed using linear mixed-effects models. ResultsHematoma volume peaked acutely and gradually attenuated over time. ADC exhibited an early reduction largely confined to the striatum, followed by progressive recovery, consistent with localized cytotoxic edema and subsequent attenuation. In contrast, CBP showed a marked bilateral hypoperfusion during the acute phase, followed by a delayed perfusion increase that was spatially restricted to the ipsilateral striatum. Notably, significant contralateral perfusion alterations were observed despite minimal contralateral diffusion changes, indicating a dissociation between microstructural injury and vascular regulation. ConclusionsMicrostructural and perfusion responses after ICH follow distinct spatiotemporal trajectories. Whereas diffusion abnormalities are largely localized to the hemorrhagic core, perfusion disturbances extend bilaterally beyond the lesion site. These findings challenge the common assumption of contralateral physiological stability after focal hemorrhage and highlight the value of quantitative perfusion MRI for capturing systemic cerebrovascular responses that are not reflected by diffusion or anatomical measures alone.

physiology↗
bioRxiv2026

Development of Integrin α5β1-targeted PET/NIR imaging probes for glioblastoma intraoperative navigation and intracavity targeted radionuclide therapy

Incomplete extent of tumor resection is the major factor of glioblastoma recurrence, leading to its poor prognosis. Developing therapies that enable the minimal tumor cell remnant during surgical resection is a major challenge to combat this aggressive cancer. This study develops a glioblastoma integrin 5{beta}1-selective peptide binder through series strategy screening and labeling it with 68Ga, indocyanine green (ICG), or 177Lu for efficacious multimodal treatment. This strategy combines positron emission tomography (PET) imaging for preoperative diagnosis, intraoperative NIR-II fluorescence-guided surgery for maximal tumor resection, and followed by intracavity targeted radionuclide therapy for elimination of residual tumor cells. We identified GR, with five arginine mutation, exhibiting superior integrin 5{beta}1 binding affinity and brain penetration. [68Ga]GR demonstrated substantial tumor uptake and prolonged retention time in both mouse models and tissues from glioblastoma patients. The guidance of ICG-GR achieved accurately intraoperative tumor imaging and maximal tumor resection in orthotopic mouse glioblastoma models. Notably, combining intracavity administration of [177Lu]GR following ICG-GR guiding resection markedly inhibited tumor growth and reduced possibility of tumor recurrence compared with surgery alone (unguided or ICG-GR-guided) or unguided surgery followed by [177Lu]GR. Therefore, we have reported the integrin 5{beta}1-targeted radionuclide and optical agents for maximal elimination of tumor cells during surgical resection in glioblastoma patients. HIGHLIGHTSO_LIGR is a glioblastoma-specific peptide with both favorable binding affinity superior brain penetration. C_LIO_LIICG-GR is a glioblastoma-targeted NIR probe enabling maximal surgical resection. C_LIO_LIICG-GR-guided surgery with [177Lu]GR-based adjuvant therapy allows robust elimination of tumor cells. C_LI

cancer biology↗
bioRxiv2026

Intramolecular loops control SARS-CoV-2 nucleocapsid protein self-association and nucleic acid binding dependent on phosphorylation

The nucleocapsid protein of SARS-CoV-2 scaffolds genomic RNA into ribonucleoprotein complexes (RNP) for assembly in the virion, but also fulfills critical intracellular functions in replication and the suppression of host defense. It is comprised of a folded nucleic acid binding domain (NTD) and a dimerization domain, connected by a disordered linker containing a serine/arginine-rich (SR) region and a leucine-rich sequence (LRS). The switch between intracellular and assembly functions of N-protein is controlled by phosphorylation of the SR region, but the molecular details are unclear. Here we describe a model in which two mutually exclusive intramolecular loops bind the NTD and dynamically control self-association and nucleic acid binding properties dependent on the SR linker phosphorylation state. The model is supported by biophysical properties and interactions of full-length protein, point mutants, and peptide fragments. We find SR linker phosphorylation compacts the protein and inhibits nucleic acid binding and RNP formation, while enhancing self-association through promotion of transient coiled-coils in the LRS of the linker. These changes shift the nucleocapsid protein to a configuration poised for multi-valent interactions that support intracellular functions.

biophysics↗
bioRxiv2026

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

Bonobos (Pan paniscus), an endangered species, have for decades been genetically understudied, partly due to difficulties in obtaining high-quality samples. The study of their genome is important not only for understanding their evolution, but also for improving conservation efforts, including population management, diversity and inbreeding assessment, and tracking rescued individuals to combat illegal wildlife trafficking. Here, we use chromosome 21 target capture data from 156 non-invasively collected faecal samples from wild bonobos to perform a comprehensive analysis of their population structure. We confirm the existence of three previously suggested subpopulations identified here as Western, Central and Eastern bonobos which are defined by natural barriers of gene flow such as the Lomami River. By estimating levels of inbreeding, diversity and differentiation, we find support for isolation of mainly Western and Eastern populations and add information on the dispersal routes of their ancestors. We infer split times and separation of these populations and apply a genetic framework to geolocalize samples of unknown origin, showing that locations of their potential origin can be estimated with a precision of up to a median of [~]50 km. Our study provides valuable insight into the evolution and population structure of bonobos and reveals how rivers act as strong barriers between populations. It also offers resources for conservation efforts and highlights the need to monitor bonobo populations more closely, in particular isolated ones. ImpactBonobos have been difficult to study genetically due to their remote forest habitat and endangered status. Here we used non-invasive sampling and chromosome 21 target capture sequencing to perform the most detailed analysis to date of their population structure. We find three main subpopulations and genetic differentiation influenced by river barriers, especially with populations found on the Eastern side of the Lomami river. This data will be useful for identifying the geographic origin of confiscated samples and thus aid bonobo conservation efforts.

bioinformatics↗
bioRxiv2026

Severity-dependent proteomic alterations in the rat hippocampus following pilocarpine-induced status epilepticus

Status epilepticus (SE) is a prolonged seizure state that can induce lasting hippocampal damage and promote the development of spontaneous seizures and cognitive deficits. The severity and duration of SE strongly influence these long-term outcomes; however, many experimental studies rely on behavioral assessments such as the Racine scale, which may not capture subclinical or non-convulsive seizure activity. Consequently, the molecular consequences of lower-severity seizures that do not meet conventional criteria for severe SE, but may nonetheless contribute to epileptogenesis, remain poorly understood. To address this gap, we investigated whether behavioral seizure severity in the pilocarpine model correlates with distinct proteomic alterations in the hippocampus. Seizures were induced in adult male rats using pilocarpine, and animals were behaviorally classified into three groups: control, mild SE, and severe SE. Hippocampal tissue was collected from control (n = 3), mild SE (n = 5), and severe SE (n = 6) rats and subjected to mass spectrometry-based proteomic analysis. Proteomic profiles were analyzed using partial least squares discriminant analysis (PLS-DA), and differentially expressed proteins (DEPs) were identified using volcano plots. Functional enrichment analyses were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway databases. Our findings revealed distinct hippocampal proteomic signatures across control, mild SE, and severe SE groups, as revealed by PLS-DA. Severe SE was associated with widespread proteomic alterations, including 129 DEPs linked to synaptic structure, RNA regulation, and metabolic processes. In contrast, mild SE was associated with fewer changes (81 DEPs), primarily involving synaptic organization and endocytosis. A direct comparison of the severe and mild SE groups identified 76 DEPs enriched in pathways related to synaptic plasticity and neurodegeneration. Notably, 23 proteins showed a stepwise expression pattern across groups, suggesting a molecular gradient correlated with seizure severity. Correlation analyses identified and further confirmed glial and inflammatory molecules as candidate molecular markers associated with seizure burden. In conclusion, behavioral seizure severity in the pilocarpine model corresponds to distinct hippocampal proteomic profiles, with severe SE inducing broader and more pronounced molecular alterations than mild SE. Importantly, lower-severity SE is associated with biologically meaningful changes in pathways related to synaptic organization and cellular processing, highlighting mechanistic differences between mild and severe SE that may contribute to epileptogenic progression.

neuroscience↗
bioRxiv2026

Preparation and application of YFV-17D-derived Anterograde Trans-neuronal Viral Vectors for Neuroscience Research

Trans-neuronal viruses that spread between synaptically connected neurons have become invaluable tools in neuroscience, enabling circuit mapping and targeted delivery of genetic material to cells within defined pathways. Although most available trans-neuronal viral tracers propagate retrogradely, an anterograde trans-neuronal virus that spread from presynaptic to postsynaptic neurons would substantially expand experimental capabilities. We previously demonstrated that YFV-17D--a live attenuated yellow fever vaccine used clinically for decades--spreads anterogradely along neuronal circuits. We further developed a suite of recombinant YFV-17D-based vectors for diverse applications, including tracing monosynaptic projectome of defined neuronal cell types, multiplex mapping of parallel pathways, and trans-neuronal genetic manipulation with minimal neurotoxicity. We have now tested and optimized procedures for vector production and application. Based on these optimizations, here, we present a two-part guide for preparing and deploying this viral vector system to map brain connectivity. The first part describes the molecular biology and cell culture workflows required to generate high-quality viral vectors, yielding titers of [~]1 x 10^10 to 5 x 10^11 genomic copies per milliliter within approximately two weeks. The second part outlines optimized animal procedures, including intracranial injections, perioperative care, and experimental considerations tailored to specific aims and vector variants. Depending on the application, efficient trans-neuronal tracing can be achieved within 1-4 weeks following delivery.

neuroscience↗