Biology subjects

Liu, Z.

Publications and source records attributed to Liu, Z..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

Sex-Specific Vulnerability to Radiofrequency Electromagnetic Radiation-Induced Reproductive and Neurological Impairment in Mice

Electromagnetic radiation (EMR) constitutes a pervasive environmental stressor, yet the sex-specific vulnerabilities to its biological effects remain inadequately characterized. This study investigated the differential impacts of 3.2 GHz pulsed EMR on reproductive and neurological functions in male and female mice following a four-week exposure regimen. We identified a pronounced sexual dimorphism in systemic and organ-specific responses. Male mice exhibited a primary vulnerability in the reproductive axis, manifesting as severe spermatogenic impairment, including depletion of the spermatogonial stem cell pool, disruption of sperm chromatin remodeling, and consequent declines in sperm quality and quantity. In contrast, exposed females showed preserved ovarian function but displayed marked neurobehavioral deficits, including increased anxiety- and depressive-like behaviors, and cognitive impairment, which were correlated with neurodegeneration in the hippocampus and prefrontal cortex. Proteomic analyses revealed distinct sex-specific biomarker profiles, with serum levels of Mdk, histone H1 variants (H1-1, H1-4, H1-5), Hp1bp3, Ncf2, and Rhoc strongly associated with male testicular dysfunction, while decreased levels of the synaptic motor protein KIF13A in serum and brain tissue were linked to female neurological impairment. Our findings delineate clear sex-divergent pathological pathways that target male spermatogenesis and female neurocognitive function and propose novel circulating protein biomarkers. This work provides a critical foundation for sex-aware risk assessment and the development of targeted preventive strategies against EMR-associated health risks.

pathology↗

bioRxiv2026

Positive Affect Modulates Early Valuation and Conflict Processing in Social Decision-Making

Social decision-making relies on dynamic affect-cognition interactions across distributed brain networks, yet how incidental positive affect modulates these mechanisms at a millisecond timescale remains unclear. This study investigated the impact of music-induced positive emotion on the neural dynamics of decision-making in the Ultimatum Game. Fifty-six participants were assigned to either a happy music group or an active control (rain sound) group. Fifty-six participants were assigned to either a happy music group or an active control (rain sound) group, while electroencephalography was recorded to capture rapid neural dynamics. Behaviorally, happy music accelerated reaction times (RTs) and decoupled the ERP-RT correlations observed in the control condition. Neurally, positive affect amplified event-related potential amplitudes during early conflict detection (220-280 ms) and late valuation (520-560 ms) stages. Multivariate pattern analysis further revealed that happy music enhanced the neural separability and temporal stability of decision states (accept vs. reject). Moreover, using support vector regression based on functional network features, we found that decision acceptance rates were predicted with significantly higher accuracy in the happy music group (R = 0.60) compared to controls (R = 0.41). Crucially, feature weight analysis indicated a topological shift in decision strategy: while the control group relied on frontal-central edges (implicating executive control), the happy music group was characterized by central-temporal connections (suggesting integrative processing). Collectively, these findings provide novel evidence that incidental emotion intervenes at the millisecond timescale to bias social choices, offering a dynamic network-based account of the affect-cognition interaction.

neuroscience↗

bioRxiv2026

Multi-omic landscape of Mn(II) oxidation in Achromobacter pulmonis ss21: From multicopper oxidase to metabolic support electron transfer

Microbially mediated Mn() oxidation plays a critical role in regulating the global Mn() cycle and represents an environmentally friendly strategy for remediation Mn() contaminated waters. This study presents the first demonstration that Achromobacter pulmonis ss21, a bacterium isolated from Baiyangdian Lake, exhibits the excellent capacity to oxidze Mn(). The Mn() oxidation efficiency of ss21 reached 98.82% and 97.05% for 200 and 400 mg/L Mn(), respectively. Transcriptome analysis revealed that direct Mn() oxidation was catalyzed by genes encoding copper resistance system multicopper oxidase (HV701_RS04390), LLM-type flavin oxidoreductase (HV701_RS19365) and quinone oxidoreductase (HV701_RS24690), which regulate extracellular electron transfer for continuous Mn() oxidation. In addition, thioredoxin (HV701_RS19360) and glutathione peroxidase (HV701_RS19445) genes maintained intracellular redox homeostasis, ensuring stable and efficient direct Mn() oxidation under high Mn() stress. Moreover, genes (iscU, hscA, fliS, HV701_RS03300, and HV701_RS06395) associated with metabolic support, motility, and transcriptional regulation supported indirect Mn() oxidation. Metabolomics analysis revealed the upregulation of L-Tyrosine, L-Isoleucine, glutamic acid, Gln-His-His, Flavin Adenine Dinucleotide (FAD), xanthine related to ss21 Mn() oxidation, which corresponded to the direct Mn() oxidation genes. This study provides a comprehensive understanding of the molecular mechanisms of biological Mn() oxidation by Achromobacter sp. and highlights its potential application in the bioremediation of Mn contaminated aquatic environments under high metal stress conditions. IMPORTANCEMicrobially mediated Mn() oxidation is a fundamental process in global biogeochemical cycles and offers a sustainable pathway for remediating heavy metal-polluted waters. Achromobacter pulmonis ss21 showed excellent performance in Mn() oxidation. The highly efficient removal of Mn() was achieved through oxidoreductase catalysis, regulation of extracellular electron transfer, maintenance of redox homeostasis, and ensurance of stable and efficient Mn() oxidation under high Mn() stress. Moreover, the Mn() oxidation was supported by metabolites, which prevented irreversible protein damage from oxidative stress induced by high Mn() concentration, alleviating oxidative stress, and stimulating the production of ROS. These findings expand the known diversity of Mn() oxidizing bacteria and offer valuable information for the molecular mechanisms of biological Mn() oxidation.

microbiology↗

bioRxiv2026

Synora: vector-based boundary detection for spatial omics

Tumor-stroma boundaries are critical microenvironmental niches where malignant and non-malignant cells exchange signals that shape invasion, immune modulation and therapeutic response. Spatial omics platforms now resolve these interfaces at single-cell scale, but computational boundary detection remains challenging because heterogeneous neighborhoods can arise either from true compartment interfaces or from unstructured immune infiltration. Here we present Synora, a modality-agnostic computational framework that identifies tumor boundaries using only cell coordinates and binary tumor/non-tumor annotations, making it readily applicable across a broad range of spatial omics modalities. Synora introduces orientedness, a novel metric that quantifies directional neighborhood asymmetry and distinguishes true boundary cells, where neighbors are spatially segregated by type, from infiltrated regions where cell types intermingle randomly. By integrating orientedness with traditional diversity measures into a unified BoundaryScore, Synora achieves robust boundary identification across synthetic datasets with ground-truth boundaries, maintaining performance under realistic perturbations including 50% missing cells and 25% infiltration. Application to 15 Visium HD spatial transcriptomic datasets across multiple cancer types reveals consistent boundary-enriched gene signatures and cell-type spatial gradients. Validation on a CODEX multiplexed protein dataset demonstrates that Synoras precise boundary identification enables discovery of clinically relevant cellular neighborhoods and disease-associated spatial patterns missed by frequency-based approaches. Synora enables boundary-aware spatial analyses by making tissue interfaces quantifiable from minimal inputs, helping to standardize interface detection and comparison across spatial omics platforms and biological contexts.

bioinformatics↗

bioRxiv2026

A Grass-Specific Structural Feature of Myosin VIII Regulates Protoxylem Development and Hydraulic Conductance in Sorghum

Sorghum (Sorghum bicolor), a C grass adapted to hot semi-arid environments, depends on reinforced xylem vessels to maintain hydraulic conductance under high evaporative demand. During protoxylem differentiation, coordinated microtubule and actin dynamics guide secondary cell wall (SCW) deposition; however, whether actin-based motors directly regulate vascular architecture and hydraulic performance has remained unknown. Here, we identify HEAT-SENSITIVE 1 (HS1), a previously uncharacterized myosin VIII, as a central regulator of protoxylem integrity and water transport in sorghum. The hs1 mutant exhibited severe leaf scorching under field conditions. The hs1 mutant displayed severe leaf scorching under field conditions, accompanied by pronounced protoxylem defects under controlled environments, including vessel collapse, reduced lumen area, and attenuated lignified SCWs. These structural abnormalities compromised longitudinal hydraulic conductance, diminished whole-plant water use, and rendered expanding leaves unable to meet transpirational demand, resulting in transient water deficit and thermal injury. HS1 encoded a grass-specific myosin VIII with a grass-specific N-terminal extension exhibiting high intrinsic disorder and lineage-specific substitutions in the motor domain. Molecular and single-cell transcriptome analyses positioned HS1 within differentiating protoxylem cells of developing leaves, revealing pronounced temporal and cell-type specificity. Furthermore bulk transcriptome profiling and quantitative lignin measurements indicated that HS1 promoted lignin-associated SCW biosynthesis during protoxylem differentiation, functionally linking actin-based motor activity to wall reinforcement. HS1 encodes a grass-specific myosin VIII distinguished by an extended intrinsically disordered N-terminal region and lineage-specific substitutions within the motor domain, suggesting evolutionary specialization. Consistant with core developmental role, reduced nucleotide diversity at the HS1 locus across diverse sorghum accessions further supported strong evolutionary constraint. Together, these findings established HS1 as the first actin-based motor protein shown to control xylem architecture and hydraulic function in plants.

plant biology↗

bioRxiv2026

Liver Disease Reveals KIF12 as a Critical Regulator of Mitochondria, Lysosome and Cilia Localization

Pathogenic variants in kinesin family member 12 (KIF12) cause pediatric liver disease, yet the cellular mechanisms underlying this phenotype remain unknown. Here we show that KIF12 expression in the healthy human liver is primarily detected in biliary epithelial cells, as revealed by single cell RNA-sequencing data. To investigate its role in biliary pathology, we introduced a homozygous KIF12 p.Arg219* mutation into induced pluripotent stem cells (iPSCs), which were differentiated into 2D cholangiocyte-like cells (iCCs) and 3D biliary organoids. Pioneering single-molecule fluorescence microscopy in live iCCs, we observed wildtype KIF12 co-localizing with microtubules, consistent with its predicted role as a microtubule-associated motor protein. Our data reveals that KIF12 dysfunction causes abnormal perinuclear clustering of mitochondria and lysosomes, and mislocalization of primary cilia in cholangiocytes. Restoration of wildtype KIF12 expression in mutant KIF12 iCCs rescued organelle positioning and normalized GGT activity. This study uncovers a novel link between KIF12 dysfunction and organelle dynamics in human cholangiocytes, extending our understanding of kinesin roles beyond their established functions in neuronal systems. Our findings provide new insights into the pathogenesis of KIF12-related cholestatic liver disease and lay the groundwork for developing targeted genetic therapies.

genetics↗

bioRxiv2026

Propagule and Juvenile-derived Foraminiferal eDNA across intertidal habitats and its implications for accurate sea-level reconstruction

Foraminiferal environmental DNA (eDNA) assemblages have recently emerged as a robust and complementary proxy for relative sea level (RSL) reconstruction. However, unlike traditional morphological methods, eDNA assemblages are influenced by diverse DNA sources, including propagules and juveniles, whose effects on RSL reconstruction remain poorly understood. To assess how foraminiferal eDNA from different life stages vary in taxa composition and impact RSL reconstruction, we analyzed foraminiferal eDNA from bulk, 500-63 m and <63 m size fraction sediments from mangrove and mudflat environments in subtropical Hong Kong. The eDNA assemblages in size-fractioned sediments displayed distinct patterns from those in bulk sediment eDNA across different environments. The propagule and juvenile-derived eDNA <63 m fraction exhibited a similar community structure to bulk eDNA in mudflat environments but diverged in mangrove environments, indicating a greater contribution of propagule and juvenile eDNA to the total eDNA pool in the mudflat environment. We applied Bayesian transfer function modeling to estimate the elevation of samples using different size fractions. eDNA assemblages from the <63 m fraction systematically underpredicted elevation in mangrove environments, while elevations inferred from the 500-63 m fraction and bulk sediment eDNA were accurate. Conversely, all eDNA assemblages in the mudflat-mangrove transitional zone led to the overprediction of RSL. These findings confirm the reliability of bulk sediment eDNA for RSL reconstruction in mangrove environments, while highlighting the need for caution when reconstructing RSL in transitional zones.

ecology↗

bioRxiv2026

The Intrinsic Manifold of Spontaneous Activity Constrains Cortical Responses to Naturalistic Stimuli

The cerebral cortex constrains its spontaneous activity to a low-dimensional manifold learnable from resting state functional magnetic resonance imaging (fMRI) data. However, it remains unclear whether this intrinsic manifold also captures cortical responses to complex, naturalistic stimuli. To test this, we pretrained a deep variational autoencoder model on 3-Tesla resting-state fMRI data to learn the latent structure of spontaneous activity, and then applied this model without finetuning to 7-Tesla fMRI data acquired during movie-watching. Despite the different field strengths, the model generalized robustly from resting to movie-watching states. The latent representation of stimulus-evoked responses was confined to a subspace that occupied about 13% of the latent space spanned by spontaneous activity, demonstrating that task-related neural responses do not require a distinct representational space. By representing cortical dynamics as an evolving latent trajectory, we found striking differences across individuals or between brain states. During movie watching, the velocity of the latent trajectory provided a reliable marker of cortical engagement, and its temporal structure was highly reliable and sensitive to naturalistic events. These findings suggest that the intrinsic manifold of spontaneous activity forms a full reservoir of cortical states that the brain can differentially engage when interacting with the external environment.

neuroscience↗

bioRxiv2026

Distinct Biological and Biomechanical Features in TMJ and Knee Cartilages

The temporomandibular joint (TMJ) and the knee joint are two of the most frequently used joints in the body, with the mandibular condylar cartilage (MCC) and the articular cartilage (AC) covering the joint bone surfaces, respectively. Compromised MCC functions lead to various temporomandibular disorders (TMD), including TMJ osteoarthritis (TMJ OA); however, the mechanisms governing MCC homeostasis and its biomechanical properties are still poorly understood. In this study, we comprehensively compared the biological and biomechanical features of the MCC and AC in mice. Histological analysis on P1, P21, 3-month, and 10-month mice revealed the most drastic structural differences between MCC and AC at occlusion establishment (P21), with MCC found to be more susceptible to age-associated cartilage degeneration. Immunostaining revealed differentially distributed cartilage extracellular matrix components in MCC and AC, including collagen type I, II, and X, and highly enriched expression of several key transcriptional factors at the posterior region of the MCC, including sex determining region Y-box 9 (SOX9), runt-related transcription factor 2 (RUNX2), and scleraxis (SCX). The posterior MCC also houses a group of long-lasting, slow-proliferative cells, as evidenced by the BrdU/EdU incorporation assay, suggesting the presence of a potential stem/progenitor cell niche at the posterior TMJ. Unbiased nanoindentation analysis revealed distinct biomechanical features between these joint cartilages. MCC exhibits a significantly lower elastic modulus (EIT) than AC, with the highest EIT observed at the anterior TMJ, which is oppositely associated with the fibrous layer thickness, but positively correlated with the ratio of the collagen type X-positive matrix in the cartilaginous layer. Altogether, this study provides a basic understanding of the biological and biomechanical features of the cartilaginous tissues in two important joints, which may facilitate our understanding of the physiology in the TMJ and knee joint, and support the applications of mouse models to study TMJ dysfunctions.

developmental biology↗

bioRxiv2026

Phyllosphere and rhizosphere microbiomes empower Nicotiana tobacum complex traits dissection and prediction

Understanding how plant-associated microbiomes interact with host genome variation to influence agronomic traits is essential for advancing microbiomeassisted crop improvement. In this study, we characterized the phyllosphere and rhizosphere microbiomes of 164 diverse Nicotiana tabacum accessions using 16S rRNA sequencing and integrated these data with host genomic variation and 22 agronomic traits. The two microbiomes exhibited distinct taxonomic structures, diversity patterns, and predicted metabolic functions. Microbiome genomewide association studies identified extensive host genetic control over microbial abundance, including 49 shared genomic loci that explained nearly half of the heritable variation in both microbiomes. Microbiomewide association studies revealed biologically meaningful associations between specific ASVs and agronomic traits. However, network analysis demonstrated that microbial subcommunities, rather than individual taxa, contributed substantially to phenotypic variation. Then, colocalization analysis further identified genetic variants jointly influencing microbial abundance and metabolite traits, highlighting potential host-microbe-trait causal links. Incorporating microbiome data into genomic selection models, we successfully improved prediction accuracy for several traits, especially plant architecture and flowering. Together, this work provides a comprehensive populationlevel framework linking host genetics, microbiome composition, and agronomic traits in tobacco, offering new insights for microbiomeinformed breeding strategies.

plant biology↗

bioRxiv2026

CLM-X: A multimodal single-cell foundation model with flexible multi-way Transformer for unified scRNA-seq and scATAC-seq analysis

AO_SCPLOWBSTRACTC_SCPLOWAdvances in single-cell multimodal profiling have enabled a more systematic analysis of cellular biology, yet the rapid accumulation of large-scale, heterogeneous datasets poses substantial challenges for integrative analysis. Recently, Transformer-based cell language models (CLMs) are becoming powerful foundational tools for learning transferable cell representations from unimodal single-cell datasets. However, a unified and flexible multimodal foundation model for joint modeling of scRNA-seq and scATAC-seq datasets remains underexplored. Here, we present CLM-X, a multimodal single-cell foundation model built on multiway Transformer architecture. CLM-X employs a harmonized tokenization design together with a stage-wise masked reconstruction pretraining strategy, enabling unified modeling of RNA-only, ATAC-only, and paired RNA-ATAC input within a single Transformer-based framework. We pretrain CLM-X on million-scale unimodal and multimodal datasets, and systematically evaluate its transferability on five downstream tasks including batch correction, modality integration, cross-modal translation, cell type annotation, and perturbation prediction. Across comprehensive benchmarks on 10 datasets, CLM-X consistently outperforms existing multimodal methods and unimodal foundation models, with particularly clear advantages in RNA-ATAC cross-modal translation and genetic-perturbation-response prediction. Overall, CLM-X establishes a unified and flexible multimodal foundation model for integrative analysis of scRNA-seq and scATAC-seq datasets, advancing a more robust, comprehensive, and biological interpretable single-cell analysis beyond current multimodal fusion approaches and unimodal foundation models.

genomics↗

bioRxiv2026

Learning sculpts orthogonal task manifolds for continual skill learning in recurrent networks

Humans and animals can learn and seamlessly perform a vast repertoire of behaviors. However, how neural populations incorporate new skills without disrupting previously learned ones remains poorly understood. This challenge is known as catastrophic forgetting in artificial neural networks and is especially severe in recurrent networks, where computation relies on stable internal dynamics. While current machine learning approaches often rely on explicit weight-protection strategies, such approaches do not directly address this challenge. Here we show that orthogonal task manifolds can emerge in recurrent neural networks from a local predictive, error-driven learning rule. Our model preserves task-specific latent dynamics that remain resilient to interference from subsequent learning. Using low-rank connectivity ablations, we causally isolate these latent dynamics, selectively impairing individual tasks while leaving others intact. We further show that the proposed principle generalizes beyond low-dimensional to high-dimensional naturalistic movie replay, suggesting a scalable mechanism for continual learning. Our results identify a solution to catastrophic forgetting by preserving previously learned dynamics in recurrent connectivity, thereby providing a mechanistic bridge between artificial recurrent networks and biological neural circuits.

neuroscience↗

bioRxiv2026

Physically Grounded Generative Modeling of All-Atom Biomolecular Dynamics

Predicting the kinetic pathways of biomolecular systems at all-atom resolution is crucial for understanding protein function and drug efficacy, yet this task is hindered by the immense computational cost of conventional molecular dynamics (MD) simulations. While deep learning has revolutionized static structure prediction and equilibrium ensemble sampling, simulating the kinetics of conformational transitions remains a critical challenge. We introduce BioKinema, a physically grounded generative model that predicts continuous-time, all-atom biomolecular trajectories at a fraction of the cost of traditional simulations. In particular, BioKinema utilizes a spatial-temporal diffusion architecture motivated by the exponential decay of correlations characteristic of Langevin dynamics, and is explicitly trained to generate trajectories with the correct kinetics and thermodynamics. It employs a hierarchical forecasting-and-interpolation strategy to overcome the error accumulation that often plagues long-horizon generation. Through extensive validation, we demonstrate that BioKinema generates physically stable and dynamically accurate trajectories suitable for rigorous downstream analysis. For protein systems, it reproduces the equilibrium thermodynamics of the conformational ensemble and the underlying kinetics. For protein-ligand complexes, it successfully elucidates mechanisms such as ligand-driven conformational changes and allosteric interactions. Furthermore, BioKinema leverages enhanced sampling data to predict rare kinetic events, emerging as a powerful tool for estimating ligand unbinding pathways. Collectively, these results establish BioKinema as a computationally efficient complement to MD simulations that bridges the gap between static structure and dynamic function, enabling high-throughput exploration of the kinetic landscape for structural biology and drug discovery.

bioinformatics↗

bioRxiv2026

Deletion of NLRP3 gene blocks traumatic brain injury induced abnormal immune response in 3xTg AD mice

Traumatic brain injury (TBI) is a significant risk factor for the development of Alzheimers disease (AD) and related dementia. In both TBI and AD, inflammation plays a pivotal role. It is known that NLRP3 inflammasome plays an important role in pathogenesis of AD while TBI triggers activation of NLRP3 inflammasome in the brain. To evaluate the importance of NLRP3 inflammasome in mediating TBI-induced immune response in the context of predisposition of AD, we have examined the immune profiles in the brain using a novel transgenic AD mouse line with the NLRP3 gene deleted. Briefly, a group of 4 months old male and female 3xTg and 3xTg/NLRP3-/- mice received a moderate lateral fluid percussive injury or sham. Immune cell phenotypes and cytokine gene expression were assessed at 3- and 7-days post injury (dpi). We found that NLRP3 gene deletion counteracted injury-induced alteration of immune response in AD mice with a significant sex-related difference. Specifically, TBI induced a significant brain infiltration of neutrophils, macrophages and {gamma}{delta} T-cells in 3xTg mice in both sexes at 3dpi, and NLRP3 gene deletion blocked this injury effect only in males not in females. NLRP3 gene deletion also blocked injury-enhanced IL-1{beta}, TNF- gene expression in male AD mice, but not in female mice. In conclusion, our study has confirmed that TBI significantly alters the immune response in 3xTg-AD mice and NLRP3 inflammasome is important in mediating these TBI-induced changes with significant sex-related differences.

immunology↗

bioRxiv2026

Nonanticoagulated Heparin Derivatives Mediate Goblet Cell Differentiation to Restore the Mucosal Barrier for Ulcerative Colitis Therapy

Epithelial mucus barrier dysfunction is a pathological hallmark of ulcerative colitis (UC), yet current clinical therapeutic strategies primarily suppress inflammation, lacking reliable approaches for restoration of the mucosal layer. Here, through a systematic screen of our established library of deanticoagulated heparins, we identified NALHP, a non-anticoagulant low-molecular-weight heparin derivative, and its representative fraction S6 as orally active epithelial repair-promoting glycans. NALHP/S6 restored crypt architecture, mucus production and epithelial barrier integrity in experimental colitis. In UC patient-derived colonic organoids, NALHP/S6 reduced aberrant stem/proliferative programs while promoting secretory, absorptive and junctional maturation. Single-cell transcriptomics and temporal validation identified a transient repair-secretory transitional state (RSTS) positioned between classical Wnt-associated stemness and mature barrier-forming epithelial states. Transcriptomic analysis revealed coordinated attenuation of Wnt and Notch signaling, whereas pharmacological reactivation of these pathways opposed NALHP/S6-induced epithelial state progression. These findings define mucosal repair as a regulated epithelial-state transition and identify NALHP/S6 as glycan-based modulators capable of restoring this progression in UC epithelium.

pathology↗

bioRxiv2026

Lipid monounsaturation confers cold tolerance and improves tissue viability during hypothermic storage

The rapid loss of tissue viability during hypothermic storage frequently results in organ failure and high discard rates in transplantation. In contrast, ectothermic animals can tolerate prolonged exposure to low temperatures in their natural environments. Elucidating the mechanisms underlying this cold tolerance may therefore inform improved strategies for tissue preservation. Here, we investigate proteomic and metabolomic responses to cold exposure in the livers of two frog species from distinct habitats: the cold-sensitive African clawed frog (Xenopus laevis) and the cold-tolerant Northeastern Asian brown frog (Rana dybowskii). Cold exposure induced lipid mobilization in X. laevis, whereas it promoted phospholipid mono-unsaturation in R. dybowskii. Notably, treatment with monounsaturated fatty acids (MUFAs) or overexpression of stearoyl-CoA desaturase (SCD) reduced cell death during cold storage. Moreover, MUFA infusion significantly improved cell viability in mouse liver tissue under hypothermic conditions. Together, these findings suggest that lipid mono-unsaturation, an adaptive feature of cold-tolerant frogs, can be leveraged to enhance tissue preservation during cold storage.

biochemistry↗

bioRxiv2026

Interoception Network in the Rat Brain

The brain is never truly at rest. Even in the absence of external stimuli, the central nervous system continuously monitors and regulates visceral organs. However, it remains unclear to what extent this interoceptive signaling shapes the brains resting state networks. Here, we tested the hypothesis that resting state functional connectivity is actively sustained by visceral inputs. Using functional magnetic resonance imaging in 34 anesthetized rats, we identified a cohesive "interoception network" characterized by dense, reciprocal functional connectivity among the dorsal vagal complex, thalamus, hypothalamus, amygdala, insula, and cingulate cortex. The topology of this network was not static but dynamically coupled to the physiological state. Functional integration was robust in the digestive (fed) phase but significantly attenuated in the inter-digestive (fasted) phase. The network relied on the integrity of the vagus nerve. When vagal signaling was eliminated by bilateral cervical vagotomy, the network effectively disintegrated. These findings demonstrate that resting state functional connectivity is not an intrinsic property of the isolated brain but an embodied phenomenon that relies on continuous neural signaling between the brain and viscera.

neuroscience↗

bioRxiv2026

Protenix-v1: Toward High-Accuracy Open-Source Biomolecular Structure Prediction

We introduce Protenix-v1 (PX-v1), the first fully open-source structure prediction model to attain superior performance to AlphaFold3 while strictly adhering to the same training data cutoff, model size, and inference budget. Beyond standard evaluations, we highlight the effectiveness of inference-time scaling behavior of Protenix-v1, demonstrating that increasing the sampling budget yields consistent improvements in prediction quality--a behavior previously observed in AlphaFold3 and largely absent from prior open-source models. In addition to improved accuracy, Protenix-v1 incorporates key capabilities including protein template integration and RNA MSA support. Furthermore, to better support real-world applications such as drug discovery, we additionally release Protenix-v1-20250630, a variant trained on a larger dataset (cutoff: June 30, 2025), delivering further improved prediction accuracy. Finally, we identify limitations in existing benchmarking practices and provide updated evaluation tools and year-stratified benchmarks to support more reliable and transparent assessment. Collectively, these contributions provide a robust foundation for the Protenix series and the broader field.

bioinformatics↗