Biology subjects

Liu, L.

Publications and source records attributed to Liu, L..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

Thermal boundaries and underlying systems biology mechanisms in two waterbloom cyanobacteria

Climate change and recent heatwaves have elevated temperature to the level of nutrients in driving CHABs. In this new dimension of CHABs ecology, it is important to understand the thermal boundaries of each blooming species. One well-known example is the temporal and thermal partitioning between filamentous, nitrogen-fixing taxa such as Dolichospermum spp. and Pseudanabaena spp., which dominate in spring, and colonial/coccoid Microcystis aeruginosa, which predominates in summer and autumn. Here we show that Dolichospermum sp. and M. aeruginosa display converse temperature-growth relations, Dolichospermum sp. grows better at low temperatures (13-15{degrees}C) and M. aeruginosa grows better at high temperatures (29-31{degrees}C), with similar growth rates between 18 and 25{degrees}C. This thermal separation is sustained by systems-level changes, in terms of the macromolecule contents--proteins, ATP, carbohydrates, and lipids--and transcriptome and metabolic fluxes to critical unsaturated fatty acids, which were experimentally verified by supplementing these FAs. The gene regulatory and systems biology mechanisms are explored. Through homologous and evolutionary analyses, a conserved Hik34-Rre1-RpoD cascade underlying differential temperature-responsive gene regulation. Enzyme-constrained metabolic models reproduced genus-specific lipid shifts and uncovered contrasting flux reorganizations under thermal stress. Together, these results establish the metabolic and regulatory foundations that shape the distinct thermal niches of bloom-forming cyanobacteria, providing mechanistic insight into how climate warming may restructure their seasonal dominance.

systems biology↗

bioRxiv2025

NSUN2-dependent 5-methylcytosine Modification Regulates Influenza A virus Gene Expression and Genomic Packaging

Emerging evidence indicates that methyltransferase NSUN2 catalyzes 5-methylcytosine (m5C) modifications on various viral RNAs and plays important roles in viral biology. However, the regulatory roles of NSUN2 in influenza A virus (IAV) replication have not been elucidated. Here, we revealed that NSUN2 negatively regulated the viral RNA transcription and protein production by knocking out and over-expressing NSUN2. By m5C MeRIP-seq and RNA-BisSeq, NSUN2-dependent m5C sites were identified on both the plus and minus viral RNA strands. In NSUN2-KO cells, the m5C modification on vRNAs was reduced, resulting in the production of a large number of deficient interfering particles (DIPs) which had lower vRNA content, imbalanced genome fragments, abnormal morphology and reduced pathogenicity. Mutation of m5C sites at the 5 and 3 ends of PB2 vRNA interfered with the selective packaging of the 8 vRNA segments into virus particles, resulting in the formation of a variety of abnormally packaged virus particles. PB2-vRNA mutants also had reduced replication ability and pathogenicity in mice. Overall, these data demonstrate that the m5C residues catalyzed by NSUN2 are required on vRNAs for the proper assembly of infectious viral particles, suggesting the depletion of m5C modification as a potential strategy that can be utilized to attenuate IAV strains. Significance StatementInfluenza A virus (IAV) infections pose a significant threat to global public health by causing substantial morbidity and mortality. The segmented nature of the IAV genome requires precise regulation of the genomic assembly to produce infectious progeny virus particles. In this study, we demonstrate that m5C modification is crucial for the proper assembly of infectious viral particles. The lowered level of m5C modifications on vRNAs leads to the generation of defective interfering particles with reduced replication capacity and pathogenicity. Our data shed new light on the selective packaging mechanism of IAV segmented genome and highlight a potential new strategy for attenuating IAV strains by targeting the m5C modification machinery.

microbiology↗

bioRxiv2025

Discovery of pseudobaptigenin synthase, completing the (-)-maackiain biosynthetic pathway

Pterocarpans are structurally complex defence compounds produced by legumes (Fabaceae). They are commonly associated with antimicrobial activity and thought to be synthesized de novo or accumulated in response to microbial pathogens. (-)-Maackiain is a lineage-specific pterocarpan detected in some legumes, including red clover (Trifolium pratense). The biosynthesis of (-)-maackiain involves a distinctive methylenedioxy bridge formation step, predicted to be catalyzed by a cytochrome P450. Specifically, this elusive P450 catalyzes the conversion of calycosin to pseudobaptigenin. We integrated metabolomic and transcriptomic datasets of red clover roots treated with the fungi, Fusarium oxysporum and Phoma medicaginis, to identify candidate P450 genes. Over 40 molecular features were characterized as (iso)flavonoid structures, including the highly abundant O-methylated isoflavones (formononetin and biochanin A), as well as their derivatives. Long infection with P. medicaginis resulted in significant increases in (-)-maackiain, trifolirhizin and other pterocarpans. Concurrently, fungal infections led to upregulation of core and specialized metabolism-related transcripts, including those encoding phenylpropanoid and (iso)flavonoid biosynthetic enzymes. Using weighted gene co-expression network analysis (WGCNA), variance-stabilized expression patterns, and enzyme-class phylogeny, we were able to curate five candidate cytochrome P450s for pseudobaptigenin synthase (PbS) activity, assayed in engineered yeast (Saccharomyces cerevisiae). One candidate P450 was capable of methylenedioxy bridge formation, converting calycosin to pseudobaptigenin and pratensein to 5-hydroxypseudobaptigenin. Therefore, it was renamed T. pratense pseudobaptigenin synthase (TpPbS/CYP76F319). The discovery of TpPbS facilitates the reconstruction of the complete (-)-maackiain biosynthetic pathway and the production of this pterocarpan chemistry at scale for health and agricultural applications. Significance statementO_LIThe discovery of pseudobaptigenin synthase in red clover (CYP76F319), a P450 that catalyzes the formation of a methylenedioxy bridge to convert calycosin to pseudobaptigenin and pratensein to 5-hydroxypseudobaptigenin. C_LIO_LIThe identification of enriched (iso)flavonoids and associated transcriptomic changes in red clover roots in response to two fungi with distinct infection lifestyles (hemibiotrophy and necrotrophy). C_LI

plant biology↗

bioRxiv2025

Neural mechanisms of handedness for precision drawing: hand-dependent engagement of cortical networks for bimanual control and tool use

Neural mechanisms underlying handedness remain poorly understood. We used functional magnetic resonance imaging (fMRI) to study performance of a visually guided drawing task with each hand. We hypothesized that the left superior parietal lobule supports drawing with either hand, and individuals with chronic peripheral nerve injury (PNI) to the dominant hand use the same mechanism as healthy adults. Thirty-three right-handed adults (23 healthy, 10 patients) underwent fMRI while performing a precision drawing task, alternating between the right hand (RH) and left hand (LH). BOLD magnitude and functional connectivity (FC) modulation via generalized psychophysiological interaction were analyzed in 12 a priori regions of interest, followed by additional exploratory areas identified via whole brain magnitude analysis. During LH drawing (compared to RH drawing), contralateral primary motor cortex showed lower BOLD magnitude but greater FC with two networks: First, a left motor-premotor network with increased FC and equal-or-greater magnitude during LH drawing. Second, a right parietal network characterized by increased FC during LH drawing but increased magnitude during RH drawing. Exploratory whole-brain analyses supported and extended these motor and parietal networks, and additionally suggested that RH drawing may involve greater magnitude and FC within a bilateral parieto-premotor network centered on right paracingulate cortex. Patient group (PNI vs. control) did not interact with these effects. These results describe the first proposed mechanisms for LH precision drawing, both of which depend on differential engagement of bimanual control networks: a left hemisphere motor-premotor network for precision motor control, which engages intrahemispherically (directly) during RH drawing and interhemispherically (indirectly) during LH drawing; and a right hemisphere parietal network with greater distributed coordination during LH drawing. These mechanisms did not differ between PNI patients and healthy adults, highlighting these mechanisms potential as neuromodulatory targets to enhance LH performance after RH impairment.

neuroscience↗

bioRxiv2025

MitoEM 2.0 - A Benchmark for Challenging 3D MitochondriaInstance Segmentation from EM Images

We present MitoEM 2.0, a curated data resource for training and evaluating three-dimensional (3D) mitochondria instance segmentation in volume electron microscopy. The collection assembles multiscale vEM datasets (FIB-SEM, SBF-SEM, ssSEM) spanning diverse tissues and species, with expert-verified instance labels emphasizing biologically difficult scenarios, including dense mitochondrial packing, hyperfused networks, and thin filamentous connections with ambiguous boundaries. All releases include native-resolution volumes and standardized processed versions, per-volume metadata (voxel size, modality, tissue, splits), and official train/validation/test partitions to enable reproducible benchmarking. Annotations follow a consistent protocol with quality checks and instance reindexing. Data are provided in NIfTI with nnU-Net-compatible layout, alongside machine-readable split files and checksums. Baseline scripts support common training pipelines and size-stratified evaluation. By consolidating challenging volumes and harmonized labels, MitoEM 2.0 facilitates robust model development and fair comparison across methods while supporting reuse in bioimage analysis, algorithm benchmarking, and teaching.

neuroscience↗

bioRxiv2025

Scalable spike sorting across thousands of neurons by modeling neural dynamics with NeuroSort

Neural circuit research requires resolving the functional coding mechanisms at the single-neuron scale. However, neural signals captured from extracellular recordings are inherently complex, shaped both by electrode properties and the spatially distributed neural population activity across recording sites. These factors introduce strong signal mixing and waveform variation, making it diffcult for existing spike sorting methods to reliably isolate individual neurons from large-scale recodings. To address this, we develop NeuroSort, which fuses spatiotemporal information through a contrastive learning strategy to adaptively model neural dynamics. NeuroSort is a GPU-enabled, highly efficient spike sorting framework, enabling the isolating of up to thousands of neurons. We validated NeuroSort on in vivo extracellular recordings, including Utah array data from rhesus macaques performing motor tasks and Neuropixels 1.0 probe data from a rat during rest. Moreover, in a recording collected by the 1,024-channel Neuroscroll probe, NeuroSort sorted the largest number of well-isolated neurons from different brain areas while achieving a 2-8 times speedup over other methods. Taken together, NeuroSort generalizes across recording conditions, providing an interpretable and scalable paradigm for whole-brain dynamic analysis.

neuroscience↗

bioRxiv2025

The Cortical Temporal Axis: MEG-Based Cross-Frequency Gradients with Biological Anchors

Neural oscillations have long been used to characterize the temporal dynamics of individual brain regions, yet a parsimonious, system-level representation that integrates multi-rhythmic activity has been lacking. Using source-localized resting-state magnetoencephalography (MEG) data, we computed regional power spectra and assessed spectral similarity, then applied diffusion map embedding to construct cross-frequency neurophysiological gradients that place whole-brain oscillations within a unified, low-dimensional coordinate system. We found the first three gradients accounted for over 40% of the variance, remained stable across individuals, and aligned with established functional, structural, and geometric cortical axes. Computational modeling showed that these gradients reflect local excitation-inhibition balance, while multimodal analyses revealed strong associations with neurotransmitter receptor distributions, cytoarchitecture, and cell-type-specific gene expression. Lifespan analyses further demonstrated systematic gradient reorganization, with distinct cognitive mappings onto functions such as language, memory, and multisensory integration. Clinically, Parkinsons disease patients displayed disrupted gradients, particularly in regions linked to language and social cognition. Finally, these gradient patterns exhibited high test-retest reliability. These findings establish MEG-derived neurophysiological gradients as robust, low-dimensional representations of cortical organization, offering a biologically grounded framework for studying brain aging and disease.

neuroscience↗

bioRxiv2025

Longitudinal multimodal characterization of radiation dermatitis in the C57BL/6J mouse model

Radiation dermatitis (RD) is a frequent and therapy-limiting toxicity of cancer radiotherapy, yet its mechanistic basis remains poorly understood. To address the need for quantitative, mechanistic insight, we developed a longitudinal C57BL/6J mouse model integrating clinical grading, non-invasive biophysical ("mesoscopic") measurements, histopathology, and bulk transcriptomics. This controlled design enabled pseudo-longitudinal analysis of inflammation, barrier dysfunction, and fibrosis across four weeks after a single 25 Gy exposure. Transcriptomic profiling revealed early activation of phagosome formation, MHC I antigen presentation, and neutrophil degranulation preceding visible skin injury, followed by enrichment of IL-1, IL-10, and IL-13 signaling at peak disease. Mesoscopic erythema, fibrosis, and transepidermal water loss each displayed distinct temporal and molecular signatures, with limited overlap among gene sets. Histologic scoring confirmed early epidermal and inflammatory responses, linked to extracellular matrix remodeling and vascular development. The observed pathways align with prior studies implicating IL-17 and a senescence-associated IL-6/CCR6 axis, extending these findings into a quantitative, time-resolved framework. This multimodal resource bridges molecular, morphological, and functional scales, providing a platform for mechanistic and therapeutic studies of RD.

genomics↗

bioRxiv2025

Microcompartments in Hodarchaeales: a bioenergetic engine that could have fuelled eukaryogenesis

Eukaryotic intracellular compartmentalization is a key innovation in the evolution of complex cellular life. While microcompartments enable metabolic specialization in many bacteria, to our knowledge, no analogous systems have been identified in Archaea. Here, we report the discovery of archaeal microcompartments (AMCs) in Hodarchaeales, an order within the phylum Promethearchaeati (Asgard archaea) that includes the closest known archaeal relatives of eukaryotes. Phylogenetic and structural analyses indicate that these catabolic AMCs, which are specialized for sugar-phosphate metabolism, were acquired by horizontal gene transfer from deep-rooted bacteria of the phylum Myxococcota. The shell pentamers of AMCs are fused to lysine/arginine-rich intrinsically disordered regions that capture cytosolic DNA, facilitating nutrient scavenging. Reaction-diffusion modelling predicts that enzyme colocalization and substrate channelling within AMCs can increase the NADH flux approximately 100-fold. Thus, the AMCs substantially boost energy production in the cell and might have primed the archaeal host for eukaryogenesis.

microbiology↗

bioRxiv2025

Host EV derived lipids promote malaria parasite development via mosquito fatty acid oxidation

Malaria parasites must transition between mammals and mosquitoes, but how they adapt to such distinct environments is unclear. We show that blood from infected mammals buffers this environmental shift by packaging parasite-induced signals into extracellular vesicles (EVs). EVs internalized by mosquito midgut increases expression of VLCAD and raises levels of a 22-carbon fatty acid, driving fatty acid breakdown and acetyl-CoA production. The parasite exploits this metabolic shift to synthesize its own lipids during oocyst growth. Stable isotope tracing confirmed that13C4-labelled behenic acid is degraded and incorporated into parasite fatty acids. Lipidomic profiling further revealed that ceramides enriched in the EVs are key mediators. These findings identify a mechanism by which host bood-derived EVs reprogram mosquito lipid metabolism to promote parasite transmission.

microbiology↗

bioRxiv2025

Blood originates in hypoblasts during embryonic development

Blood is essential for oxygen supply throughout life. The emergence of blood in the human embryo remains poorly understood. Our study leverages multiple stem cell embryo models and advanced lineage barcoding to unveil that hypoblast, originally regarded as forming the yolk sac wall, is heterogeneous and contributes to CDX2+ extraembryonic mesoderm, followed by hemoglobin+ cells as the first blood cells. CDX2 marks the hypoblast-to-hemoglobin+ cell trajectory that functionally sustains oxygen levels in embryo models. These hemoglobin+ cells molecularly and functionally resemble phagocytes. We show that the erythro-core regulatory network is poised in hypoblasts, and its boost endows erythropoiesis to both hypoblasts and phagocytes. Hypoblasts are the origin of the first blood in humans and non-human primates, providing a conceptual framework that earlier blood generation than expected fills the gap in the establishment of circulation. Further, the hypoblast is a place where primates may repurpose the phagocyte program to carry oxygen throughout embryos. HighlightsO_LIBarcode-traced hypoblast fate in human embryo models; C_LIO_LIThe first blood comes from the hypoblast that contributes to hemoglobin+ phagocyte-like cells; C_LIO_LICDX2 marks hypoblast blood that sustains oxygen supply in embryos before heart formation; C_LIO_LIErythro-core regulatory network endows erythropoiesis to human hypoblasts and phagocytes. C_LI

developmental biology↗

bioRxiv2025

Universal super-resolution for subcellular fluorescence imaging

Super-resolution fluorescence microscopy has emerged as an essential instrument for investigating subcellular structures and monitoring intracellular physiology. Despite rapid advances driven by deep learning, most existing approaches are modality specific and exhibit limited generalizability, restricting their practical applicability. Here we introduce universal super-resolution (UniSR), a framework that operates across microscopes and subcellular structures without optical modifications or prior sample knowledge. UniSR is initially pre-trained on simulated image pairs to establish mappings from low-to high-resolution features and subsequently fine-tuned with only one experimental image pair, reducing data demand and acquisition time. Across wide-field and point-scanning modalities, UniSR enhances resolution to match structured illumination, single-molecule localization, or stimulated emission depletion microscopy. Applied to diverse biological samples, it reveals nanoscale structures, dynamic processes, and organelle interactions with high spatiotemporal fidelity. UniSR provides a practical and broadly generalizable tool for super-resolution imaging in live-cell research.

bioinformatics↗

bioRxiv2025

IS110 transposon utilizes two mechanistically distinct RNA-guided transposition pathways

The recently discovered IS110 elements employ RNA-guided transposases that use bridge-RNA to coordinate donor and target DNA recognition and integration via donor- and target-binding loops, offering promise for precise, DSB-free genome editing. However, their transposition mechanism remains unclear, with prior inconsistent observations. Using a IS110 element from Caloranaerobacter azorensis, we show that IS110 transposons utilize two independent transposition pathways. The first depends on bridge-RNA and excises the element via copy-out to form a circular intermediate, revisiting the earlier cut-out model. Integration occurs predominantly through top-strand insertion, suggesting an alternative to the earlier Holliday junction-mediated dual-strand mechanism. The second involves cooperation between a truncated target-binding loop RNA and bridge-RNA, enabling direct top-strand transfer to a new target via two sequential reactions, bypassing circular intermediates. Both pathways preserve the original transposon copy. These findings redefine the mechanistic understanding of IS110 transposition and reconcile prior discrepancies, offering insight into programmable, RNA-guided genome modification.

molecular biology↗

bioRxiv2025

Ribosome remodeling drives translation adaptation during viral infection and cellular stress

The ribosome is the highly conserved molecular machine that decodes mRNAs during protein synthesis. While traditionally thought to consist of a uniform set of proteins, here we discover that ribosome composition is reprogrammed to adapt to intrinsic and external cellular perturbations. During infection by non-segmented negative-sense viruses, viral entry into cells recruits the large ribosomal subunit protein rpL40 to a noncanonical site on the small subunit of 80S ribosomes near the mRNA entry site. These specialized ribosomes preferentially bind viral mRNAs to drive enhanced viral protein synthesis that is critical for replication under host pressures. Unexpectedly, we find that viruses have co-opted this translation pathway from a previously unrecognized endogenous ribosome remodeling program in which metabolic stress alters ribosome structure to promote mRNA translation required for cell survival. Thus, ribosome remodeling is a conserved mechanism enabling dynamic protein synthesis across pathogen and cellular adaptation.

molecular biology↗

bioRxiv2025

Adjacent Rare-Earth Separation via a Protein Atomic Ruler

The separation of rare-earth elements (REEs) poses a formidable challenge due to their nearly identical ionic radii and chemical properties. Here, we present a transformative strategy for REE separation using a multimetal ion-stacking metalloprotein framework (MIF) that functions as an atomic ruler, effectively amplifying subtle differences in REE ionic radii. This approach achieves exceptional selectivity, enabling the separation of all 13 adjacent REE pairs with ultrahigh purity (up to 99.999%). Remarkably, the MIF retains its lanthanide-binding capacity over 410 consecutive absorption-desorption cycles, demonstrating outstanding stability. Structural insights reveal that the MIFs densely packed REE coordination environment magnifies minute radius variations--a key mechanism underlying its unparalleled separation efficiency. Our MIF-based strategy offers a sustainable, scalable solution to rare-earth separation in industrial applications.

biophysics↗

bioRxiv2025

Ethylene receptors are functionally conserved in calcium permeability across the green lineage

The gaseous hormone ethylene plays a key role in regulating plant growth and stress responses. Although Ca{superscript 2} has long been implicated in ethylene signaling, the identity of molecules controlling Ca{superscript 2} permeability involved has remained elusive. Here we show that Arabidopsis ethylene receptors ETR1 and ERS1 are Ca2+ permeable, and that ETR1 mediates ethylene-induced cytosolic Ca2+ increase and regulates hypocotyl elongation. Homologs of ETR1 from eight land plant and algal species also exhibit Ca{superscript 2} permeability, suggesting an evolutionarily conserved function. We further demonstrate ethylene enhances the Ca2+ permeability of ETR1 and its homologue from the charophyte Klebsormidium flaccidum. These findings uncover a previously unrecognized but conserved role of ethylene receptors in Ca{superscript 2} permeability regulation in the green lineage, with broad implications for Ca{superscript 2} signaling in plant development and environmental adaptation.

plant biology↗

bioRxiv2025

Rice Ethylene Receptors Function as Ca2+-Permeable Ion Channels to Orchestrate Calcium-Dependent Antagonism of Ethylene Responses in Roots

The gaseous phytohormone ethylene governs essential plant processes spanning development, productivity, and stress resistance. As an essential nutrient and second messenger, calcium (Ca2+) is widely implicated in diverse plant physiological activities; however, its role in the ethylene signal transduction pathway remains elusive. Here, we identified a calcium-dependent antagonism of ethylene response (CAER) specifically modulates root elongation in the model cereal rice (Oryza sativa). Interestingly, we demonstrate that the ethylene receptors OsERS1 and OsERS2 both function as Ca2+-permeable channels, with OsERS1 further acting as a non-selective cation channel capable of permeating both monovalent and divalent cations. Mutagenesis analysis reveals that OsERS1 channel activity relies on homomeric assembly sites (C4/C6) rather than its ethylene-binding site (C65), indicating a clear decoupling of the molecular modules governing receptor signaling and ion channel function. The loss-of-function mutant Osers1/2 does not exhibit the CAER phenotype of the wild type (WT), confirm that this calcium-dependent regulatory mechanism is dependent on both OsERS1 and OsERS2. These findings uncover an unexpected ion-channel function of ethylene receptors, redefining their molecular identity beyond canonical signaling proteins and establishing the novel "hormone receptor-type ion channel (HRIC)" paradigm--one that fundamentally expands our understanding of how plant hormones transduce signals at the membrane.

developmental biology↗

bioRxiv2025

A systematic comparison of cooperation and coordination across behavioural, psychological, and neural scales

Cooperation and coordination are the two fundamental mechanisms for enhancing social welfare. However, the intrinsic differences between the dynamics of cooperation and coordination remain elusive, particularly from an interpretable perspective that bridges behavioural, psychological, and neural scales. Here, we compare and analyze cooperation and coordination within a unified framework by assigning participants to an adjustable public goods game for iterated real-time interactions. By integrating model-free behavioural patterns and psychological intentions, we show that individuals are driven by increased flexibility and are more susceptible to peer influence in decision-making under cooperation. While under coordination, it is easier to reach the group consensus, inspiring individuals to stick more closely to their existing behavioural patterns and the default social norms. Furthermore, although peer punishment can enhance reciprocal contributions in all scenarios, the detailed impact and the resultant adverse phenomena (anti-social punishment) in cooperation and coordination are different. Notably, behavioural motive differences are also reflected in the neural responses recorded via fNIRS, in which coordination is associated with activation of the rTPJ and more consistent inter-brain synchronization in the dmPFC, while there is a negative correlation between dmPFC-rTPJ connectivity and contributions under cooperation. In addition, rTPJ during the punishment phase is significantly activated compared with the investment phase. Our study systematically reveals the fundamental differences between cooperation and coordination at the multi-scale levels, which not only deepens the understanding of reciprocal behaviour in social groups, but also provides a foundation for designing targeted incentive mechanisms.

animal behavior and cognition↗