Biology subjects

Ye, Q.

Publications and source records attributed to Ye, Q..

At least 19 recordsLinked to original sources

bioRxiv2026

RiboGRAM learns multi-scale non-coding RNA grammar for structural and regulatory inference

Protein-coding sequences are read through the triplet genetic code, whereas the organization of molecular information within non-coding RNA sequences remains elusive. Here, we identify a non-coding RNA grammar defined by multi-scale motif usage and 5'-to-3' positional gradients, and develop RiboGRAM to learn this organization. Across nine organisms, non-coding RNAs showed scale-dependent divergence from coding sequences, with directional U-rich and AU-rich gradients. Integrating multi-scale sequence encoding with contextual modeling, RiboGRAM organized RNA families, revealing motif-associated and pair-like patterns across layers. Without structural supervision, non-coding RNA pretraining improved base-pair recovery over coding or messenger RNA pretraining, with representations supporting alignment-free diffusion-based 3D modeling of short RNAs. In human RNA-protein binding profiles, RiboGRAM identified position-resolved motif organization across protein targets and cell types, with sequence-preference shifts associated with reduced cross-cell transferability. Together, these results establish a learnable grammar of non-coding RNA sequence organization for structural and regulatory inference.

bioinformatics↗

bioRxiv2026

Targeting ALCAT1 Ameliorates Cardiomyopathy in Barth Syndrome

Background: Barth syndrome (BTHS) is an X-linked mitochondrial disorder caused by loss-of-function mutations in TAFAZZIN (TAZ), resulting in defective cardiolipin (CL) remodeling, cardiomyopathy, and premature death. The mechanisms linking TAZ deficiency to impaired mitochondrial quality control remain incompletely understood, and there are no disease-modifying therapies available for BTHS. Here, we investigated the role of Acyl-CoA Lysocardiolipin Acyltransferase-1 (ALCAT1), a stress-inducible phospholipid-remodeling enzyme, in BTHS cardiomyopathy. Methods: Inducible TAZ knockdown (TAZKD) and cardiomyocyte-specific TAZ knockout (TAZcKO) mice were used to determine the effects of genetic ALCAT1 deletion or pharmacological inhibition with Juvenatin, a highly selective small molecule ALCAT1 inhibitor. Cardiac function, exercise capacity, mitochondrial function, lipid remodeling, lysosomal function, and mitophagic flux were assessed. Results: ALCAT1 was markedly upregulated in TAZ-deficient hearts. Genetic ALCAT1 deletion attenuated cardiac dysfunction in TAZKD mice. Juvenatin similarly improved cardiac function in TAZKD mice and reversed established cardiomyopathy in TAZcKO mice. Genetic or pharmacological ALCAT1 inhibition improved mitochondrial ultrastructure and respiration and reduced mitochondrial oxidative stress. These benefits occurred without correcting the characteristic CL abnormalities caused by TAZ deficiency. Instead, ALCAT1 deletion or inhibition corrected pathological phosphatidylinositol remodeling, normalized phosphoinositide signaling, and restored lysosomal function and mitophagic flux, leading to improved mitochondrial quality control in TAZ-deficient cells. Conclusions: ALCAT1 contributes to BTHS cardiomyopathy through a CL-independent pathway involving dysregulated phosphatidylinositol/phosphoinositide signaling, lysosomal dysfunction, and impaired mitophagy. Genetic and pharmacological targeting of ALCAT1 restores mitochondrial and cardiac function despite persistent CL abnormalities, establishing ALCAT1 as a promising disease-modifying therapeutic target for BTHS.

cell biology↗

bioRxiv2026

Uncertainty-Guided Decision-Making in Bumble Bees

The evolutionary origins of cognitive monitoring remain contested. Metacognition, the capacity to monitor one's own cognitive states, has long been linked to complex vertebrate brains, yet whether a miniature brain can evaluate the reliability of its internal representations is unknown. Here we demonstrate that bumble bees engage in uncertainty-guided decision-making. Bees dynamically adjusted opt-out choices according to perceptual difficulty, settling for a smaller guaranteed reward to avoid errors, and actively paid a reward cost to seek information under uncertainty. Without any retraining, bees transferred this 'opt-out-under-uncertainty' rule to novel tactile and working-memory tasks under an all-probe design. This strategy was stable across individuals and accurately captured by a confidence-based decision model. Our findings suggest that a brain of approximately one million neurons can support an abstract domain-general uncertainty-monitoring policy, indicating that the neural substrates for uncertainty-guided decision-making may be far more ancient and widely distributed than previously assumed.

animal behavior and cognition↗

bioRxiv2026

A Single-cell Spatiotemporal Atlas Encoding Age-dependent Evolution of the Ischemic Penumbra

Aging is the predominant risk factor for stroke and a major driver of poor neurological recovery. Although the ischemic penumbra represents a key therapeutic target, its age-dependent molecular landscape remains poorly understood. Here, we generated a spatiotemporal transcriptomic atlas of the post-stroke penumbra in young (3-4 months) and aged (19-20 months) mice at acute (day 3) and chronic (day 14) stages following transient focal cerebral ischemia. Integrating spatial transcriptomics with dissociated single-cell RNA sequencing revealed a persistent transcriptomic penumbra (TP) that remains detectable for at least 14 days after stroke in both age groups, far beyond the window suggested by conventional imaging modalities. Aging profoundly altered TP organization, resulting in dysregulated energy metabolism, impaired neurovascular repair, diminished pro-reparative cell-cell communication, and extensive remodeling of transcriptional regulatory networks. Using this atlas, we further identified regulatory hub genes whose predicted perturbation could simultaneously counteract multiple age-associated pathological pathways. These data define the molecular architecture of the aging post-stroke penumbra and provide a publicly accessible framework for mechanistic discovery and therapeutic target prioritization aimed at improving recovery after stroke.

neuroscience↗

bioRxiv2026

Mapping the brain basis of appraisals and discrete emotions

The Component Process Model of Emotion conceptualizes any emotional episode (e.g., the discrete emotions of sadness, anger, fear, or interest) as being driven by the multiple appraisal components. However, both the specificity of the neural mechanisms underlying appraisal processes and the way these appraisal networks relate to the neural circuits underlying discrete emotions remain unclear. Here we investigated the neural correlates of appraisal processes and compared them with those of discrete emotions. Participants (n = 97) were scanned with functional magnetic resonance imaging (fMRI) while watching short movie clips with varying emotional contents. Intensity for 12 appraisals and 12 basic and epistemic emotions evoked by the movie clips were rated by independent participants (n = 444). The neural responses were modelled with convolved ratings of appraisals and discrete emotions. The results indicated that appraisals and discrete emotions are supported by a shared set of distributed brain regions that extend beyond typically reported emotion-related areas, encompassing perceptual, action-related, and higher-order cognitive systems. Activations were more consistent for and better explained by appraisals versus discrete emotions. Within this network, epistemic emotions elicited less consistent activations than basic emotions, particularly in limbic regions. Our results highlight the functional organization of appraisals and discrete emotions under dynamic and complex conditions and indicate that appraisal theories better explain neural responses than discrete emotion models.

neuroscience↗

bioRxiv2026

A Conserved Flexible N-Terminal Domain Tunes the Calcium Sensitivity of Sorcin by Stabilizing Its Active Conformation

Sorcin is a penta-EF-hand Ca2+-binding protein that acts as a Ca2+ sensor and regulator of Ca2+ homeostasis. Although the structure and Ca2+-dependent activation of Sorcin is well characterized, the function of its flexible N-terminal domain (NTD) remains unclear. We combined sequence analysis, Ca2+-induced aggregation assays, multidimensional NMR spectroscopy, and long-timescale molecular dynamics (MD) simulations to define the NTDs role in Sorcin activation. Sequence comparisons showed that the NTD is conserved across vertebrates despite its intrinsic disorder, indicating functional importance. NTD deletion markedly reduced Ca2+ responsiveness. Relative to full-length Sorcin, the construct with NTD truncation required more than twofold higher Ca2+ concentrations and over tenfold higher protein concentrations to initiate aggregation, while aggregation kinetics slowed by nearly three orders of magnitude. Temperature-dependent measurements yielded an apparent activation energy of 36.7 kJ{middle dot}mol-1, consistent with aggregation driven by Ca2+-induced conformational activation rather than denaturation. NMR chemical shift perturbations localized the effects of NTD removal to the EF-hand Ca2+-binding loops and adjacent D-helix. Apo-state MD simulations revealed transient intra- and intermolecular NTD-SCBD contacts that explain some perturbations and support direct and allosteric regulation. Ca2+-bound simulations further showed that SCBD departs more readily from the crystallographic active conformation than full-length Sorcin, indicating that the NTD stabilizes the active state through dynamic contacts. Together, these findings establish the NTD as a critical regulator that enhances Ca2+ responsiveness by shifting Sorcins conformational equilibrium toward the active state and suggest that flexible N-terminal extensions regulate signaling within the penta-EF-hand protein family.

biophysics↗

bioRxiv2026

A dynamically coupled kinetic model for Arterial Spin Labeling: Enhancing the reliability of ventricular cerebrospinal fluid renewal quantification in vivo

Arterial spin labeling (ASL) provides a valuable non-invasive tool for investigating cerebrospinal fluid (CSF) dynamics. While existing generalized kinetic models provide a useful analytical framework, incorporating explicit fluid mass-conservation constraints may improve the reliability of ventricular CSF quantification. We developed and validated a physics-constrained kinetic model that assumes a constant ventricular volume, under which the volumetric influx and efflux rates are balanced. Under this assumption, the localized CSF renewal rate (f) is modeled as a distinct washout process that acts jointly with intrinsic CSF T1 relaxation R1,CSF, yielding an effective decay rate Reff = R1,CSF + f, providing a more mechanistically interpretable description of the post-arrival signal decay. The model was further tailored to the global inversion physics of the FAIR (Flow-sensitive Alternating Inversion Recovery) sequence and incorporates an explicit zero-clamped pre-arrival boundary condition. When applied to an in vivo preclinical dataset, the proposed model, improved fitting stability and removed the finite-bolus truncation observed in the raw conventional model. Compared with the conventional model, the proposed model showed significantly improved goodness-of-fit (R2 = 0.95 {+/-} 0.05 vs. 0.82 {+/-} 0.06, p < 0.001) and a lower Akaike Information Criterion (AIC = 94.96 {+/-} 5.83 vs. 106.93 {+/-} 2.50, p < 0.001), suggesting it provides a more adequate and efficient representation of CSF dynamics. The proposed model yielded CSF dynamics estimates 14.70% higher than those obtained with the conventional model, with a mean ventricular CSF renewal time of 4.01 {+/-} 0.97 min and a renewal-equivalent volumetric flow rate of 0.97 {+/-} 0.41 {micro}L/min. The resulting estimates might be interpreted as localized, ASL-derived renewal metrics rather than direct measurements of net CSF production.

neuroscience↗

bioRxiv2026

Long-Timescale Molecular Dynamics Reveal a Coordination-Biased Conformational Selection Mechanism for Sorcin Activation

Sorcin is a dimeric penta-EF-hand Ca2+-binding protein that regulates intracellular Ca2+ homeostasis through Ca2+-dependent conformational activation and target recognition, and it has also been implicated in multidrug resistance in cancer. Although crystal structures have defined the apo inactive and Ca2+-bound active states of Sorcin, the transition pathways connecting these states and the conformational ensembles populated under each condition remain poorly understood. Here, we used long-timescale all-atom molecular dynamics simulations on Anton 3, totaling [~]90 s, to define the Ca2+-coupled conformational landscape of dimeric human Sorcin at atomic resolution. Starting from the Ca2+-bound structure, we directly observed the transition from the active to the inactive state following Ca2+ removal, demonstrating that loss of Ca2+ coordination is sufficient to drive inactivation on the microsecond timescale. Simulations initiated from the Ca2+-bound crystal structure with retained ions unexpectedly revealed ultrafast Ca2+ dissociation and rebinding at all EF-hand sites, indicating weak intrinsic Ca2+ affinity and highly dynamic ion exchange. In complementary simulations initiated from the apo structure, Sorcin spontaneously sampled active-like conformations even in the absence of stable Ca2+ binding, supporting a conformational selection mechanism in which Ca2+ shifts the population toward pre-existing active states rather than inducing the transition de novo. Across all conditions, we also observed pronounced and persistent structural asymmetry between the two protomers, revealing that the Sorcin homodimer is dynamically heterogeneous despite its symmetric crystal structures. Together, these results support a coordination-biased conformational selection model for Sorcin activation, in which weak and rapidly exchanging Ca2+ binding stabilizes, rather than induces, the active state. This work provides a dynamic framework for understanding Sorcin function as a fast Ca2+ sensor and offers broader mechanistic insight into activation principles of EF-hand Ca2+-binding proteins.

biophysics↗

bioRxiv2026

TCR-FramePose: a local-frame representation for decomposing global docking and CDR3 loop geometry in TCR-pMHC recognition

T cell receptor recognition of peptide-MHC depends on sequence, interface chemistry, and three-dimensional geometry, but docking geometry is often summarized at the whole-receptor level, leaving CDR3-local pose difficult to compare across structures. We introduce TCR-FramePose, a local-frame descriptor set that represents each TCR-pMHC complex as three bodies -- whole TCR, CDR3, and CDR3{beta} -- measured relative to a pMHC groove frame. For each body, FramePose decomposes the native pose into reach, offset direction on S2, and orientation on SO(3); for tangent-space analyses, these components are mapped to six coordinates per body and 18 coordinates per complex. Applied to 378 curated {beta}TCR-pMHC crystal structures, FramePose recovers known class-associated receptor-placement differences and additionally resolved whole-TCR and CDR3{beta} orientation shifts that were not captured by crossing angle. The same orientation coordinates identified reverse-polarity and off-axis outliers as distinct modes. In cross-validated association analyses, FramePose added nonredundant BSA- and affinity-associated information beyond conventional descriptors, and the modest affinity gain was concentrated in CDR3 orientation blocks which were least recoverable from conventional descriptors. Biological grouping analyses showed that shared receptor pose over peptide-MHC was organized primarily by germline V-region framework. TCRs recognizing the same peptide-MHC target favors shared FramePose geometries rather than strong receptor-specific divergence, whereas CDR3 sequence did not detectably reposition the rigid-body pose after antigen context and germline framework were fixed. MHC allele and peptide length contributed smaller adjustments, localized mainly to CDR3{beta} and groove-normal orientation axes. Finally, interface analyses showed that affinity tracked interface burial, with CDR3{beta} reach linking FramePose geometry to binding through buried surface area. Within engineered panels, mutation-level effects were panel-specific, with CDR3{beta} remodeling localizing to a recurrent interface region but varying in direction across receptors. These properties enable FramePose to serve as a geometric filter for in silico TCR-pMHC models and as a feature layer for structure-guided TCR engineering. Together, TCR-FramePose provides a nonredundant geometric layer for structure-guided TCR-pMHC analysis, linking germline-scaffolded recognition, CDR3-local pose, and interface organization without replacing sequence, contact, or energetic descriptors.

bioinformatics↗

bioRxiv2026

Genetic Rescue of a Lethal Wasting Mutation (Syb1lew/lew) by Neuron-Specific Expression of ECFP-Syb2

Lethal-wasting (lew) is a spontaneous null mutation in the Syb1/Vamp1 gene encoding the vesicular SNARE protein synaptobrevin 1 (SYB1/VAMP1). Homozygous Syb1lew/lew mice exhibit profound impairment in neuromuscular transmission and die around three weeks after birth. Pathogenic variants in human SYB1 are associated with a variety of disorders such as hereditary spastic ataxia and congenital myasthenic syndrome. Although Syb1 expression is highly enriched in neurons, it has also been reported in non-neuronal tissues, raising the possibility that non-neuronal defects contribute to the lethal phenotype. Here, we tested whether neuronal dysfunction is the primary cause of death in Syb1lew/lew mice and whether the closely related isoform synaptobrevin 2 (Syb2/VAMP2) can substitute for Syb1functin in vivo. We show that neuron-specific expression of ECFP-Syb2 in Syb1lew/lew mice fully rescues lethality in Syb1lew/lewmice, restoring normal growth and motor function. Electrophysiological analyses demonstrate complete recovery of neuromuscular synaptic transmission, including spontaneous and evoked release as well as short-term plasticity. These findings establish that neuronal expression of ECFP-Syb2 is sufficient to prevent the lethal phenotype associated with Syb1 deficiency and demonstrate that Syb2 can functionally replace Syb1 at motor nerve terminals in vivo. Significance StatementNeuron-specific expression of Syb2 fully rescues survival, motor function, and neuromuscular transmission in Syb1lew/lew mice. These findings establish presynaptic Syb1 dysfunction as the primary cause of the lethal phenotype and demonstrate that Syb2 can fully substitute for Syb1 in vivo.

neuroscience↗

bioRxiv2026

Loss of ACTA1 leads to delayed γ-AChR / ε-AChR switch in skeletal muscle in mice

Skeletal muscle actin forms the core structural component of thin filaments, which interact with thick filaments to generate contractile force. In addition to force production, the character of muscle contraction activity itself is thought to provide mechanical cues that influence synaptic development and maturation. In mouse skeletal muscle there is an early post-natal switch from embryonic forms of actin to the adult isoform, ACTA1, which increases both filament stability and force production. Newborn mice deficient for ACTA1 (Acta1-/-), although initially able to breath, move and suckle, develop profound muscle weakness and die during the early neonatal period, despite a compensatory, increase in expression of embryonic actins. We took advantage of this to better understand the response of the neuromuscular junction (NMJ) to a disruption in contractility and activity-dependent signaling during development. Morphological analyses of the diaphragm in Acta1-/- mice revealed that the patterning and formation of the NMJ proceed normally through postnatal day 5 (P5), the day at which pups begin to die. Short-term synaptic plasticity, assessed as the endplate potential (EPP) response to paired-pulse stimulation, was also unchanged, indicating normal presynaptic release of neurotransmitters. In contrast, electrophysiological recordings demonstrated significantly prolonged rise and decay kinetics of miniature and evoked endplate potentials, indicating altered postsynaptic receptor properties. Consistent with these functional changes, quantitative real-time PCR showed a reduced ratio of {varepsilon}- to {gamma}-acetylcholine receptor (AChR) subunit mRNA, reflecting a delay in the developmental switch from embryonic {gamma}-containing to adult {varepsilon}-containing AChRs. Together, these findings indicate that -skeletal actin is dispensable for early NMJ morphogenesis but is required for timely postsynaptic receptor maturation, demonstrating a critical role for muscle contractile activity in coordinating synaptic development at the NMJ. HighlightsO_LISkeletal muscle -actin (ACTA1) is the principal structural component of thin filaments and a key determinant of contractile activity. C_LIO_LIUsing Acta1-/- mice, we show that NMJ patterning and early morphogenesis occur normally despite severe impairment in muscle contractility. C_LIO_LIElectrophysiological analysis of the NMJ shows that presynaptic function remains intact, as evidenced by normal paired-pulse responses. In contrast, postsynaptic maturation is disrupted, with prolonged endplate potential kinetics indicating altered AChR function. C_LIO_LIThis defect is associated with a delayed {gamma}- to {varepsilon}-AChR subunit switch, a key step in postnatal NMJ maturation. These findings identify ACTA1-dependent contractile activity plays a critical role in timely postsynaptic receptor maturation. C_LI

neuroscience↗

bioRxiv2026

Ribophorin-1 Governs Spike Abundance of Highly Pathogenic Coronaviruses by ER-associated degradation

The spike protein of highly pathogenic coronaviruses is indispensable for viral entry, pathogenesis, and immune evasion. However, specific host factors governing spike protein degradation and abundance on progeny virions remain largely uncharacterized. Here, we identify Ribophorin-1 (RPN1), a non-catalytic subunit of the oligosaccharyltransferase (OST) complex, as an ER-localized host restriction factor that selectively depletes spike to inhibit coronavirus infection. Conditional knockout of Rpn1 in mouse lung markedly exacerbates SARS-CoV-2 pathogenesis, increasing viral load, immune cell infiltration, and syncytium formation. In cells, RPN1 knockdown enhances susceptibility to diverse variants, whereas its overexpression attenuates infection. Nano-flow cytometry, cryo-EM and LSCM show that RPN1 reduces spike abundance on progeny virions, resulting in reduction in subsequent syncytium formation across SARS-CoV, SARS-CoV-2, and MERS-CoV. Mechanistically, RPN1 promotes VCP/p97-dependent retrotranslocation and AMFR-mediated ubiquitination of spike protein. Heterologous expression of RPN1s functional domain (residues 180-307) confers significant protection against SARS-CoV-2 both in vitro and in vivo. Collectively, our findings define an RPN1-initiated ERAD pathway that selectively targets coronavirus spike for proteasomal destruction, and provide proof-of-concept evidence that targeting this RPN1-dependent pathway represents a promising broad-spectrum antiviral strategy.

microbiology↗

bioRxiv2026

Nmur1 and Cckar fail to support functional genetic access in adult dopamine neurons and challenge GPCR atlas assignments

Apuschkin et al. (2024) proposed a GPCR-based transcriptomic atlas for midbrain dopamine (DA) neuron subpopulations, including candidates such as Nmur1, Cckar, and Ffar4. To guide genetic targeting, these markers must reflect functional expression in adult DA neurons. Using in situ hybridization, Cre-dependent reporter lines, and both intracranial and systemic viral approaches, we find no evidence of adult Nmur1-mediated recombination in DA neurons, while Cckar-driven recombination is consistent with developmental expression only. Notably, Ffar4 expression overlaps extensively with Ntsr1 midbrain populations, indicating that it does not define a distinct DA neuron class. Furthermore, analysis of independent spatial transcriptomic datasets together with our MERFISH data shows that many proposed GPCR markers are not detectably expressed in adult DA neurons. These findings demonstrate that transcriptomic enrichment does not always yield reliable adult markers and highlight the need for functional validation prior to use in circuit targeting.

neuroscience↗

bioRxiv2026

Direct evidence from kinetic D2O-MRI modeling that the choroid plexus is not the major source of cerebrospinal fluid

The role of the choroid plexus (CP) as the primary source of cerebrospinal fluid (CSF) remains controversial. Here, we used dynamic indirect D2O magnetic resonance imaging (MRI) at 9.4T to investigate whole-brain CSF dynamics in rats. Spin-echo echo-planar imaging (SE-EPI) was performed during intravenous D2O infusion with a temporal resolution of 10.69 s and an in-plane resolution of 150 x 150 {micro}m. An echo time of 150.0 ms was employed to effectively suppress signals from brain parenchyma, blood, and interstitial fluid, resulting in preferential visualization of CSF. The ambient and supracerebellar cisterns (AC+SC) exhibited the greatest signal attenuation, reaching 47.32 {+/-} 15.70% of baseline, whereas the lateral ventricles (LV1, LV2) showed smaller reductions (68.73 {+/-} 18.72%-72.64 {+/-} 15.07% of baseline). CSF production rates were quantified using a one-compartment perfusion model. Estimated secretion rates were 0.11 and 0.13 {micro}L/min in the lateral ventricles and 1.30 {micro}L/min in the AC+SC region, indicating a 5.42-fold higher CSF production outside the ventricles. These findings provide direct in vivo evidence that the lateral ventricles are not the primary site of CSF production. The proposed D2O-based dynamic SE-EPI approach is safe, non-invasive, cost-effective, and suitable for widespread application.

neuroscience↗

bioRxiv2025

Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization

We generated a multi-region, subcellular-resolution spatial transcriptomic atlas of the human basal ganglia by integrating MERFISH+ and Stereo-seq across four neurotypical donors. These datasets profiled [~]7 million cells spanning the caudate, putamen, nucleus accumbens, and globus pallidus, resolving 60 transcriptionally distinct cell types. We show region-selective, molecular and spatial diversification of medium-spiny-neuron cell types and multiple non-neuronal populations with distinct molecular identities and spatial localizations. Subcellular RNA localization captures somatic size and projection-inferred signatures that reflect direct and indirect pathway topology. Cellular community analyses reveal the enrichment of sub-clusters of astrocytes and oligodendrocytes at striosome-matrix borders, while primate-expanded interneurons are confined to matrix territories. Cross-species mapping uncovers orthologous striosome-matrix organization and conserved dorsolateral-ventromedial gene expression gradients. This atlas provides a foundational molecular and spatial framework for studying human basal ganglia architecture, offering a multi-centimeter scale resource that links cell types, spatial architecture, and subcellular transcript topography across multiple nuclei. HighlightsO_LIOur multi-centimeter scale spatial taxonomy identifies the precise locations of 60 neuronal and glial cell types of human basal ganglia. C_LIO_LIMERFISH+ and Stereo-seq platforms map consistent spatial modules that align with classical neuroanatomical nuclei. C_LIO_LID1D2 hybrid MSNs and primate-expanded interneurons show regional and domain specific organization C_LIO_LISubcellular RNA localization reports soma morphology and projection-inferred signatures. C_LI

neuroscience↗

bioRxiv2025

Viral protease-Initiated Pyroptosis Activator mRNA therapy as a Universal Antiviral Strategy

Although therapeutic drugs targeting gasdermin (GSDM)-mediated pyroptosis have made remarkable progress in treating various diseases, their potential for antiviral therapy remains largely unexplored. Inspired by the autoinhibitory mechanism of GSDM proteins and the clinical success of mRNA vaccines, herein we propose a concept of viral protease-initiated pyroptosis (VIP) mRNA therapy as a universal antiviral strategy. Using Hepatitis A virus (HAV) as a model, we rationally engineered an HAV-specific VIP activator (VIPA) by replacing the native gasdermin D (GSDMD) cleavage motif with that of HAV 3C protease. Expression of this VIPA selectively triggered pyroptosis in HAV-infected cells, thereby terminating viral replication. Remarkably, in vivo delivery of VIPA mRNA via lipid nanoparticles (LNPs) significantly suppressed viral replication and shedding, alleviated liver injury, and elicited a pyroptosis-driven antiviral immune response in uninfected cells. Similarly, VIPA against Zika virus (ZIKV) also exhibited potent antiviral efficacy in both cell culture and mouse models. Furthermore, a generative artificial intelligence (AI) platform was deployed to design de novo cleavage motifs for the SARS-CoV-2 main protease NSP5, together with experimental screening, yielding optimized VIPAs with enhanced antiviral potency. Our work establishes the concept of VIPA mRNA therapy as a versatile platform for the treatment of diverse viral infections via "kill-and-alert" mechanism.

microbiology↗

bioRxiv2025

Autistic traits modulate neural responses to social signals during natural vision

Impairments in social perception, a hallmark of autism spectrum disorder (ASD), are also evident at subclinical levels in the general population. However, it remains unclear how such variation in autistic traits modulate neural processing of different types of social information. Here, we investigated whether autistic traits in neurotypical individuals are associated with neural responses to a broad array of social perceptual features during viewing naturalistic stimuli using functional magnetic resonance imaging (fMRI). We also tested the generalizability of these effects across two experiments. Ninety-seven participants completed the Autism Spectrum Quotient (AQ) and watched a set of 96 movie clips and a full movie during an fMRI scan. Intensity of 126 social features in the movie stimuli was continuously annotated by independent observers, and 44 most reliably rated features were used to model neural responses. We examined how consistently the responses to each social feature were dependent on the participants AQ scores. Replicable AQ-dependent neural responses to social features were found in both datasets. The temporal cortex and especially the superior temporal gyrus (STG), served as a central "hub" where autistic traits consistently modulated responses to social features across datasets. Different AQ subscales also revealed distinct association patterns in other brain regions. These findings indicate that autism-related traits broadly influence neural processing of naturalistic social signals, providing insight into how characteristics of autistic symptoms relate to socioemotional processing.

neuroscience↗

bioRxiv2025

Siglec-F Protects Against Elastase-induced Lung Inflammation and Emphysema in Mice

Respiratory surfaces are exposed daily to billions of inhaled particles that could cause injury to alveolar tissues where gas exchange occurs. Accordingly, robust defense is essential but must involve minimal physiologic disruption. Airspace macrophages (AMs) protect lung surfaces while also maintaining tissue integrity through non-inflammatory homeostatic responses in health. However, in chronic obstructive pulmonary disease (COPD), AMs contribute to emphysematous alveolar destruction through mechanisms that are poorly understood. We hypothesized that damaging effects of AMs in emphysema result from loss of mechanisms that normally restrain homeostatic AMs. We found that Siglec-F, a common marker of AMs, exerts suppressive effects on tissue resident AMs (RAMs), thereby supporting alveolar integrity in mouse lungs during health and in a model of elastase-induced alveolar destruction. Siglec-F-deficient mice exhibited decreased alveolar numbers at baseline, and they had worsened alveolar damage after elastase challenge that was unexpectedly RAM-mediated. Transcriptomic profiling revealed dysregulation of key pathways involved in tissue remodeling and repair, including extracellular matrix degradation, TGF-{beta} signaling, and phagocytosis. These findings uncover previously unrecognized roles for RAMs and Siglec-F in preserving alveolar integrity. Our findings implicate RAMs and Siglecs as potential therapeutic targets for preserving alveolar integrity in health and for limiting alveolar damage in COPD.

immunology↗