Biology subjects

Shi, L.

Publications and source records attributed to Shi, L..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Neural Correlates of Trial Outcome Monitoring during Long-term Learning in Primate Posterior Parietal Cortex

Monitoring behavioral outcomes is crucial for optimizing behavior and learning new tasks. However, how the brain monitors outcome information during long-term learning remains largely unknown. Using two-photon calcium imaging in behaving monkeys, we tracked neuronal activity in area 7a of the posterior parietal cortex (PPC), an important associative cortex that has not been typically implicated in associative learning (AL), while the macaque monkeys learned new visual-motor associations over multiple days. We found robust neuronal representation of salient behavioral outcomes (correct vs. incorrect) which closely correlated with the monkeys learning behavior. Furthermore, outcome representation significantly reorganized when monkeys transitioned to learn novel associations, followed by gradual evolution over subsequent learning days, a process constrained by the functional connectivity among neurons within local network. These suggest a substantive role for primate PPC in long-term AL through monitoring trial outcome, and indicate a principle for long-term learning: network connectivity constrains the evolution of neural encodings.

neuroscience↗

bioRxiv2025

Targeting intracranial electrical stimulation to network regions defined within individuals causes network-level effects

Intracranial electrical stimulation (ES) is routinely used therapeutically, diagnostically, and to provide causal evidence in neuroscience studies. However, our understanding of the brain network-level effects of ES remains limited. We applied precision functional mapping (PFM), based on functional magnetic resonance imaging (fMRI), to define large-scale networks within individual epilepsy patients. We show that single-pulse electrical stimulation (SPES) and high-frequency electrical stimulation (HFES) are more likely to evoke within-network responses and elicit network-related behavioral effects, respectively, when applied near to a PFM-defined network region. Network-level effects were more likely when stimulating sites in white matter, in close proximity to the targeted network, and within a region predominantly occupied by the targeted network. Further, network-specific modulation may be achievable by applying lower current intensities at these sites. Our findings support that modulation of specific networks is achievable by targeting ES to a functional anatomic "sweet spot" that can be identified using PFM.

neuroscience↗

bioRxiv2025

Caffeic acid promoted deep vein thrombosis resolution in mice by suppressed macrophage M1 polarization through Keap1/Nrf2 pathwayv

BackgroundDeep vein thrombosis (DVT) carries significant health risks, with macrophages playing a key role in thrombus resolution. Caffeic acid (CA) has been shown to inhibit thrombosis, but its role in DVT resolution remains unclear. PurposeThis study aimed to investigates the effects and mechanisms of CA in accelerating DVT resolution. MethodsA stasis-type DVT model was established in mice via inferior vena cava ligation. The effects of CA were analyzed. Thrombus resolution was assessed using histological staining, gelatin zymography, immunoblotting, and immunofluorescence. Macrophage depletion was conducted with chlorophosphate liposomes, and bone marrow-derived macrophages (BMDMs) were used for polarization studies. RNA sequencing identified potential molecular pathways. Nrf2 gene-deficient mice were used to verify the role of Nrf2 in deep vein thrombus resolution. ResultsCaffeic acid reduced thrombus size, enhanced collagenolysis via increased MMP-2 activity, promoted neovascularization, increased macrophage infiltration, and suppressed M1 polarization and inflammation. CA activated the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway by inhibiting Keap1, leading to enhanced antioxidant responses in both BMDMs and thrombus tissue. Macrophage depletion negated CAs benefits, confirming the central role macrophages. ConclusionCA promoted early thrombus resolution via macrophage recruitment, M1 polarization suppression, and Nrf2 activation, highlighting its potential as a preventive strategy for DVT.

pharmacology and toxicology↗

bioRxiv2025

The Plasma Membrane may Serve as a Drug Depot to Drive the Extreme Potency of Fentanyl

Fentanyl is a leading cause of drug overdose deaths in the United States, yet the mechanisms underlying its extreme in vivo potency remain poorly understood. Recently, new synthetic opioids nitazene derivatives have emerged, among which isotonitazene is 50 times more potent than fentanyl. Here we used state-of-the-art molecular dynamics (MD) simulations and experiments to investigate the membrane-dependent pharmacology of fentanyl, isotonitazene, morphine, and naloxone. Using the weighted-ensemble continuous constant pH MD, we estimated the effective permeability of fentanyl at pH 7.5 to be on the order of 10-7 cm/s, which is about two orders of magnitude faster than the simulation estimate for morphine. In contrast, isotonitazene and naloxone effectively do not partition into the membrane under the same conditions. The simulations captured the protoncoupled permeation processes, challenging as well as refining the long-standing pH-partition hypothesis. Subsequent BRET reporter cell experiments demonstrated that cells exposed to fentanyl, but not morphine, reactivated the receptor after washout and in competition with naloxone. Immobilized affinity membrane chromatography confirmed fentanyls high affinity for phospholipids. Our findings strongly support the hypothesis that fentanyls extreme in vivo potency may be driven by its accumulation within the plasma membrane or intracellularly, enabling it to repartition into the extracellular space to rebind the receptor, or potentially access it via a lipid-mediated route. This highlights the importance of membrane-dependent pharmacology for understanding opioid toxicity and guiding the design of more effective antagonists. Our simulation methodology enables accurate prediction and analysis of membrane permeation of ionizable molecules, providing a valuable tool for ADME optimization in drug development.

biophysics↗

bioRxiv2025

One of these things is not like the others: Theta, beta, & ERP dynamics of mismatch detection

Working memory (WM) enables the detection of mistakes by permitting one to notice when sensory input is mismatched to their internal prediction. Prior studies support the role of frontal midline theta activity, with an overlapping N200 event-related potential (ERP), as a mechanism for comparing incoming sensory stimuli to the internal model. Additionally, posterior low-beta activity has been proposed as a mechanism for processing incoming sensory stimuli in WM. However, it is unknown whether frontal midline theta activity and the N200 support mismatch detection, or whether posterior low-beta activity extends from sensory processing to detecting a mismatch between sensory input and the internal model. Here, we reveal that frontal midline theta supports mismatch detection and explains individual WM performance. Unexpectedly, instead of the N200, results show a positive slow wave ERP overlapping with the frontal midline theta mismatch response. Results additionally indicate a late posterior low-beta response persisting from stimulus presentation into the post-stimulus delay. Our findings establish frontal midline theta as a marker of successful mismatch detection, challenge the domain-general role of the N200 in error detection, and support theories linking posterior low-beta to processing incoming sensory stimuli.

neuroscience↗

bioRxiv2025

Fully Automated and Scalable Pipeline for Macaque Brain Registration

With the rapid development of various whole-brain ex vivo imaging technologies, there is a growing need to develop cross-modal 3D image registration methods to integrate multimodal imaging datasets. While comprehensive cross-modality registration tools such as D-LMBmap and mBrainAligner have been successfully implemented for mouse brains, macaque whole-brain registration presents unique challenges. These include more pronounced non-uniform deformations in larger ex vivo specimens, greater modality-specific contrast differences relative to standard space, and increased inter-individual variability. To address these challenges, we developed Macaca-Star, which incorporates deep learning models and self-individual MRI to tackle cross-modal and ex vivo sample deformation challenges in macaque whole-brain registration. Macaca-Star provides fully automated alignment of fMOST and 2D fluorescent slice images to the NMT MRI standard space, allowing for comprehensive integration of anterograde axonal projections and retrograde-traced neuronal soma profiles.

neuroscience↗

bioRxiv2025

Transient Poly(ADP-Ribose) Triggers FUS Condensation Hysteresis via a Prion-Like Mechanism

Hysteresis--where a system retains memory of a transient stimulus--is common in signaling but can also arise in intracellular organization. DNA repair foci, a type of biomolecular condensate, are initiated by the short-lived noncanonical nucleic acid poly(ADP-ribose) (PAR). PAR recruits proteins with prion-like domains (PrLDs), such as Fused in Sarcoma (FUS), and initiates their condensation, which persists even after PAR degradation. How FUS transitions from PAR-dependent to PAR-independent condensation remains unclear. Here, we show that PAR binding triggers a conformational switch in FUS, enabling sustained condensation. PAR binds to the C-terminal arginine-rich region of FUS, displacing intramolecular contacts, and exposing the N-terminal PrLD. This conformational opening allows PrLD interactions in trans, stabilizing condensates independently of PAR. FUS thus undergoes a regulated, nucleated conformational conversion--reminiscent of classical prions. This mechanism implies a paradigm of nucleic acid-induced conformational memory that may underlie hysteresis in intracellular organization in health and disease. HIGHLIGHTS[bullet] PAR-initiated FUS condensation follows a bi-modular mechanism involving both FUS termini. [bullet]Simulations predict and experiments confirm PAR disrupts FUS intramolecular contacts. [bullet]Upon condensation, FUS adopts a conformation with its N-terminus open for interactions. [bullet]N-terminal interactions maintain FUS condensation when PAR degrades during DNA repair.

molecular biology↗

bioRxiv2025

Deciphering gain-of-function from loss-of-function variants with AlphaMissense: A case study with the mechanosensitive PIEZO1 ion channel protein

Pathogenic missense mutations are commonly found in protein-coding regions of DNA, and often alter protein function. In the past decade, enormous experimental efforts have been undertaken through the development of functional assays, mutagenesis screenings, and computational prediction algorithms to characterize these variants. Indeed, most efforts have been focused towards identifying degrees of loss-of-function (LoF) effects on the three-dimensional structures of proteins, but gain-of-function (GoF) mutations remain poorly understood. Herein, we performed a case study of the PIEZO1 mechanosensitive ion channel protein whose GoF variants (n = 56) are implicated in hereditary xerocytosis (HX) and LoF variants (n = 6) in lymphatic dysplasia (LD), respectively. This study evaluated the abilities of AlphaMissense (AM) to decipher both mutation types, and benchmarked its performance against other algorithmic approaches, including Combined Annotation Dependent Depletion (CADD) v1.7, evolutionary model of variant effect (EVE), and Evolutionary Scale Modeling-1b (ESM-1B). We found that all approaches excelled in identifying LoF variants but were often ambiguous in their predictions for GoF PIEZO1 variants. ESM-1b was a notable exception that demonstrated balance sensitivity to both GoF and LoF variants as it likely identified certain sequential features not utilized in other approaches. Secondly, our findings suggest that GoF variants of HX do not significantly destabilize the PIEZO1 structure and are not generally identified by conventional signatures of damage from these algorithms. GoF variants are not synonymous with direct changes in changes in free energy upon mutations. Furthermore, we validated computational structure predictions of PIEZO1 against resolved cryo-EM structures, and provided biophysical data for variants located on unresolved residues of this ion channel. We formulated a weighted ensemble model that performed similarly to AM and outperformed all other traditional approaches evaluated in this study. Overall, this is the first study to directly evaluate the capabilities of pathogenicity prediction algorithms for deciphering GoF and LoF variants, and underscores the limitations present in current approaches.

biophysics↗

bioRxiv2025

A multimodal imaging approach for imaging the metabolic changes resulting from bronchopulmonary dysplasia

Lung tissue is composed of various functional units, each essential for maintaining the intricate functions of the lung. Disruptions in the molecular and cellular mechanisms in the lung can cause tissue fibrosis, inflammation, and severe breathing difficulties, which are common in conditions such as bronchopulmonary dysplasia (BPD). BPDs molecular changes are not well understood, which hinders effective diagnosis and treatment. Here, we present a new multimodal imaging workflow for detailed molecular and metabolic characterization of tissues at multiple spatial scales. We applied a combined imaging approach using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and ultrafast focused light-based imaging & photonics platform (U-FLIP) that included two-photon fluorescence (TPF), second harmonic generation (SHG), and stimulated Raman scattering (SRS). We also developed a hierarchical multimodal registration network (HiMReg) for the precise co-registration of each modality. This approach revealed previously unknown metabolic changes in distinct functional tissue units affected by BPD, including altered lipid distributions, reduced optical redox states, and specific collagen remodeling in bronchioles. Our findings evidenced alterations in lipid composition and metabolism of BPD-affected alveoli compared to healthy tissue, providing novel insights into disease pathophysiology. Our findings elucidate the intricate spatial and molecular complexity of BPD, building on prior research that did not provide the spatial resolution necessary to capture the nuances of metabolic alterations. This multimodal approach offers exceptional insights into disease exploration and could transform the way we study spatially heterogeneous conditions. By providing detailed maps of the metabolic shifts occurring in distinct tissue microanatomical features, the methods developed here could enable the discovery of new therapeutic avenues, making it highly attractive for the field of biomedical research.

physiology↗

bioRxiv2025

Elucidating the Contribution of OVLT Glutamatergic Neurons to Mineralocorticoid Hypertension in TASK-/- Mice

BackgroundAldosterone overactivity intensifies central sodium sensitivity and sympathetic output, driving salt-sensitive hypertension, but specific mechanisms remain incompletely defined. Herein, we aimed to explore the role of organum vasculosum of the lamina terminalis glutamatergic neurons (OVLTGlut) and their hyperexcitability mechanisms in hyperaldosteronism-associated hypertension. MethodsAdult age matched male TASK-/- mice (primary aldosteronism model) and wild-type controls (TASK+/+) mice were used. Neuronal excitability was assessed via patch-clamp techniques. Arterial blood pressure (BP) monitored via telemetry or carotid catheterization. Chronic drug delivery used minipumps. RNA-seq/qPCR profiled gene expression, and intracerebroventricular hypertonic saline tested sodium sensitivity. ResultsIn TASK-/- mice, heightened OVLTGlut activity increased sympathetic outflow and hypertension, mitigated by OVLTGlut neuron ablation. Optogenetic activation of these neurons or their paraventricular nucleus (PVN) / rostral ventrolateral medulla (RVLM) projections acutely elevated BP, with ablation reducing BP selectively in TASK-/- mice. Aldosterone dependence of OVLTGlut-PVN/RVLM neuron hyperactivity was evident in both TASK-/- mice and TASK+/+ mice with chronic aldosterone infusion. Aldosterone chronic infusion enhanced central sodium pressor effects, that were nullified by OVLTGlut-PVN/RVLM neuron lesioning. RNA-seq indicated that aldosterone-induced ion channel expression spectrum changes, including potassium channels and the epithelial sodium channel, underlie the neuronal hyperexcitability. ConclusionOveractivation of OVLTGlut neurons contributes to hypertension in TASK-/- mice through regulation of OVLTGlut-PVN/RVLM circuits. The hyperexcitability of these neurons, possibly due to aldosterone-induced changes in ion channel expression spectrum, contribute to hypertension by amplifying central sodium sensitivity.

neuroscience↗

bioRxiv2025

Conformational dynamics of the active state of β-arrestin 1

{beta}-arrestins ({beta}arr) regulate the signaling and trafficking of G protein-coupled receptors (GPCRs) in numerous physiological processes and have been implicated in various diseases. Structural and kinetic insights into how ligand-mediated GPCR activation drives {beta}arr coupling and activation remain limited, with the binding mechanism of the phosphorylated GPCR C-terminal tails, such as that of the vasopressin receptor-2 (V2Rpp), and the conformation of the entire {beta}arr tail in the active state still unknown. Here, we simulated both the basal and V2Rpp-bound states of {beta}arr1 with temperature replica-exchange molecular dynamics (TREMD) simulations to probe the activation mechanism of {beta}arr1. Compared to conventional MD, our TREMD simulations, employing an unprecedented 200-replica setup, significantly broadened conformational sampling while preserving the basal state. Our analysis showed that, without the bound Fab30 antibody fragment, the main body of V2Rpp-bound {beta}arr1 tended to transition toward the basal conformation; however, binding of V2Rpp in the N-domain groove allosterically oriented the finger loop to point upward for core engagement with a GPCR. Furthermore, V2Rpp dissociation events suggest that its binding involves a sliding movement along the N-domain groove, during which its phosphorylated residues p3 and p4 transiently occupy the S5 site to facilitate repositioning of p5 into the S5 site, thereby triggering a zippering process of p1 to p3. The dynamic 62-residue {beta}arr1 tail explored a vast conformational space, forming transient secondary structures, and could favorably anchor on the main bodys back side and within the central crest crevice. These findings elucidate key mechanistic steps underlying {beta}arr1 activation.

biophysics↗

bioRxiv2025

Salmonella hijacks a host glucose transporter for intravacuolar proliferation

AbstractsSalmonella is an intracellular pathogen that resides within a vacuole, which protects it from cytosolic host defenses at the expense of limited nutrient access. Glucose serves as a critical carbon source supporting Salmonellas intracellular replication. However, the molecular mechanisms driving glucose enhancement and the pathways by which cytosolic glucose becomes accessible to intravacuolar Salmonella remain poorly understood. Here, we elucidate a sophisticated three-pronged strategy through which Salmonella hijacks GLUT1 to co-opt host glucose metabolism for pathogenic advantage. Firstly, Salmonella infection upregulates the glucose transporter GLUT1 by activating the MAPK signaling cascade, enhancing host glucose uptake, and accelerating glycolytic flux. Secondly, Salmonella redirects GLUT1 to the bacterial vacuolar membrane to establish a glucose-import conduit that facilitates bacterial acquisition of cytosolic glucose. Thirdly, K29-linked ubiquitination modifications on bacterial vacuolar membranes are a previously unrecognized regulatory mechanism that potentiates GLUT1 transporter activity. Inhibition of GLUT1 potentiates Salmonella-triggered innate immune responses and attenuates bacterial virulence in vitro (RAW264.7 macrophages) and in vivo (murine infection model). Collectively, these findings delineate a novel paradigm of metabolic hijacking, wherein Salmonella systematically rewires host glucose metabolic networks to support intracellular proliferation, providing new insights into host-directed antimicrobial interventions.

microbiology↗

bioRxiv2025

Trends Assessment of the Genetic Mutation Induced Protein-Protein Interaction Variation via Protein Large Language Driven Method

Protein-protein interaction (PPI) variations are widely observed in many principal biological processes related to various diseases, while genetic mutation is one of the most common factors resulting in those variations. Unraveling these underlying biomolecular interactions is a key challenge that hinders a profound understanding of disease mechanisms. Although current models can accurately predict quantitative binding affinity, their application in pathogenic research is limited by difficulties in defining trend types, particularly extreme "disrupting" cases, along with poor generalizability beyond single-point mutations (SNP) and insufficient biological interpretability. Here, we present TAPPI, an interpretable large language model-driven deep learning framework, to perform Trends Assessment of Protein-Protein Interaction. It categorizes PPI variations trends into four types: disrupting, decreasing, no effect, and increasing, enabling fine-grained functional assessments and bridging genetic mutation and disease mechanisms. The framework generalizes effectively across both single-point and multi-point mutations and captures complex trend outcomes relevant to diverse disease landscapes. In benchmark evaluations, TAPPI achieved the state-of-the-art prediction performance and demonstrated biological relevance through interpretable results. In external datasets from Autism Spectrum Disorder, Lennox-Gastaut syndrome, and Epileptic Encephalopathies, given the premise that TAPPIs predicted results align with pathogenic patterns, these results reveal how genetic mutations indirectly perturb disease-associated pathways and supporting our perspective of "crucial disrupting" and "bridging mutations-disease". In summary, accurate, interpretable, and pathogenically relevant prediction of PPI variations trend predicted by TAPPI provides a novel approach for mechanistic discovery.

bioinformatics↗

bioRxiv2025

Evaluating the pathogenicity, stability, and stereochemical effects of variants of unknown significance in TREM2 using orthogonal structural analyses

Triggering receptor expressed on myeloid cells 2 (TREM2), an immune receptor expressed on the surface of microglia, has been identified through genome-wide association studies to be one of the risk factors in Alzheimers disease (AD). Several studies have also identified missense variants of TREM2 to be associated with frontotemporal dementia and Nasu-Hakola disease (NHD). To date, 51 novel missense variants of TREM2 have been identified in the literature, with the disease risk profiles of most variants still unknown. Assessing and classifying the pathogenicity of these variants is essential to investigate the disease mechanisms and develop effective treatments. Herein, we classified 32 missense variants involved in TREM2 using structural bioinformatic data with AlphaFold2. Using the protocol described in our previous work (Pillai et al., 2025), we determined the structural, stability, and potential functional effects of these variants. Our evaluations of the mutations were divided into those (i) implicated in NHD, (ii) located on the transmembrane domain, (iii) surface of the IgV-like domain, and (iii) buried in the receptor. Our analysis of variants involved in NHD suggests that, while V126G imposes the greatest effects, the T66M variant exerts significantly less effects on the TREM2 structures compared to the other remaining variants. Variants in the transmembrane domain of TREM2 did not impose significant alterations to the three-dimensional structure. Outside of known variants in the IgV-like domain, we identified 10 variants that imposed significant destabilizing effects to the structure and are of potential interest. Overall, the baseline biochemical data provided from this study may be informative to experimental efforts to better classify rare coding variants of TREM2 that are of unknown biological and clinical significance. HighlightsUsing our previously published protocol, we characterized the structure, stability, and functional effects of 27 unique variants of unknown biological significance in TREM2. Our analysis was divided into variants located on the transmembrane domain, surface of the IgV-like domain, buried in the IgV-like domain, and those leading to Nasu-Hakola disease. Excluding AD- and NHD-causing variants, we identified 10 TREM2 variants that cause significant destabilizing effects to the receptor. The in-silico data provided from this study serve as a baseline, and can guide future experimental efforts involving TREM2 variants. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/656054v1_ufig1.gif" ALT="Figure 1000"> View larger version (35K): org.highwire.dtl.DTLVardef@c426b1org.highwire.dtl.DTLVardef@1c859f1org.highwire.dtl.DTLVardef@88ea70org.highwire.dtl.DTLVardef@d777f4_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease

Allogeneic hematopoietic cell transplantation (alloHCT) is curative for various hematologic diseases but often leads to acute graft-versus-host disease (GVHD), a potentially life-threatening complication. We leverage GVHD as a uniquely tractable disease model to dissect complex T-cell-mediated pathology in 27 alloHCT recipients. We integrate pre-transplant identification of alloreactive T-cells with longitudinal tracking across blood and gut, using mixed lymphocyte reaction-based clonal "fingerprinting", TCR clonotyping, single-cell RNA/TCR sequencing, and spatial transcriptomics. Using DecompTCR, a novel computational tool for longitudinal TCR analysis, we uncover clonal expansion programs linked to GVHD severity and TCR features. Multi-omics profiling of gut biopsies reveals enrichment and clonal expansion of CD8 effector and ZNF683(Hobit) resident memory T-cells, cytolytic remodeling of regulatory and unconventional T-cells, and localization of CD8 effector T-cells near intestinal stem cells in crypt loss regions. This framework defines dynamic immune circuit rewiring and phenotypic plasticity with implications for biomarkers and therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/655962v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@178b77dorg.highwire.dtl.DTLVardef@569226org.highwire.dtl.DTLVardef@1951281org.highwire.dtl.DTLVardef@1f1e046_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPersistent expansion of diverse alloreactive T cell clones is a hallmark of severe GVHD C_LIO_LIDecompTCR reveals dynamic clonal expansion programs linked to GVHD severity and clinical outcome C_LIO_LICD8+ T cell clones exhibit phenotypic plasticity in vivo across intestinal tissue compartments in GVHD C_LIO_LIHigh-resolution spatial profiling shows CD8+ effector T cells localize near intestinal stem cell niches and drive epithelial injury in GVHD C_LI

systems biology↗

bioRxiv2025

RBPSignal: A deep learning approach for predicting RNA-Protein binding signals

RNA-binding proteins play critical roles in post-transcriptional regulation by interacting with RNA to regulate various cellular processes. Inferring the binding signals and sequence patterns of these interactions is essential for elucidating the mechanisms underlying gene expression regulation. In this study, we present RBPSignal, a deep learning-based computational tool designed to predict RBP binding signals on RNAs and identify potential sequence motifs associated with these interactions. RBPSignal leverages the deep learning framework and trains on comprehensive eCLIP datasets, demonstrating an enhanced predictive accuracy. Furthermore, the integration of model interpretability through Integrated Gradients enables the detailed analysis of binding motif syntax. We validate the efficacy of RBPSignal on chromosome data and compare the discovered motifs with existing motif database, showcasing its ability not only to predict binding signals but also to uncover sequence patterns correlated with binding signals. Our findings provide insights into the sequence specificity of RBPs and explore the protein-protein interaction networks. RBPSignal serves as a valuable tool for exploring RBP-RNA interaction landscapes, facilitating further investigations into the regulatory networks underlying gene expression. The web server is freely available at http://www.csbio.sjtu.edu.cn/bioinf/RBPSignal/.

bioinformatics↗

bioRxiv2025

JAK/STAT Signaling Governs Airway Epithelial Homeostasis and Stress Resilience in Drosophila

Airway epithelia must maintain barrier integrity while continuously adapting to changing environmental conditions. This requires key signaling pathways in airway epithelia to operate within a tightly controlled functional range. Here, we show that airway epithelial homeostasis in Drosophila depends on balanced JAK/STAT signaling. Basal pathway activity is constitutively present in differentiated epithelial cells and is necessary for cell survival, epithelial integrity and stress resistance. In accordance with this role as a stress responsive regulator in epithelial biology, environmental stressors, including hypoxia, cigarette smoke, and cold exposure, induce JAK/STAT signaling. In contrast, sustained pathway activation is associated with airway remodeling characterized by epithelial thickening, luminal narrowing, and altered cellular organization. Transcriptomic analysis reveals that sustained activation is associated with a coordinated epithelial stress program integrating immune signaling, proteostasis, and metabolic adaptation. Cross-species comparisons with murine and human datasets suggest that key aspects of this response are conserved. Pharmacological inhibition demonstrates that remodeling depends on continued pathway activity and can be partially reversed in vivo. Together, our findings support a model in which airway epithelial homeostasis depends on maintaining JAK/STAT signaling within a defined functional range. This "Goldilocks" principle provides a conceptual framework for understanding how epithelial stress responses are balanced under physiological and pathological conditions. Graphical abstract

cell biology↗

bioRxiv2025

Multimodal cortical connectome in the default mode network across the adult lifespan

The default mode network (DMN) critically underpins cognitive and affective functions throughout the adult lifespan; however, detailed insights into its complex neuroarchitecture and connectivity patterns across aging remain limited. Leveraging the open-access CamCAN dataset, comprising structural and diffusion magnetic resonance imaging (MRI) alongside magnetoencephalography (MEG) data from 599 adults spanning ages 18 to 88 years, we systematically investigated age-associated changes in multimodal connectomes within the DMN. Our analyses revealed a progressive decline in both structural and functional connectivity among DMN subregions with advancing age. Additionally, MEG-based connectivity assessment demonstrated age-related decreases in high-frequency oscillatory activity (alpha, beta, gamma bands) accompanied by increases in low-frequency oscillations (theta band). Integrating structural data with neurophysiological measures further revealed age-dependent shifts in neurophysiological-structural coupling within the prefrontal cortex, characterized by strengthened coupling at theta frequencies but weakened coupling at higher frequencies. Conversely, coupling within the posterior cingulate cortex consistently declined across all examined frequency bands. Notably, theta-band coupling within the prefrontal cortex significantly correlated with age-related memory performance variations. Collectively, our findings delineate nuanced changes in DMN information transmission dynamics across adulthood, underscoring its promise as a neurobiological biomarker reflective of cognitive aging heterogeneity.

neuroscience↗