Biology subjects

Tian, L.

Publications and source records attributed to Tian, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Neural Innervation Invigorates Yolk Sac Biological Functions beyond Nutrient Reservoir during Zebrafish Embryo Development

The zebrafish yolk sac (YS) is traditionally viewed as a nutrient reservoir. By reconstructing the complete progression of embryonic neural development via live-cell imaging, we previously observed that axonal projections extending from brain cranial neurons come to cover the yolk sac surface, hinting at its uncharacterized functional roles beyond nutrient storage. Using transgenic lines and long-term live imaging, we characterized a dynamic neuro-vascular-metabolic interface on the YS surface. We observed that peripheral neural networks expand radially and mature through hierarchical integration, sharing the same structural and dynamical features as those in the brain and spinal cord. Unexpectedly, YS surface cells harbor transient calcium flashes, reflecting primitive intercellular communication in response to neural innervation. Furthermore, we characterized activity-dependent neuronal pruning and stress-induced lipid droplet crystallization as indicators of developmental refinement and homeostatic collapse, respectively. Finally, we identified directional blood flow occurring before the formation of endothelial tubes, indicating a pre-vascular transport mechanism. These findings demonstrate that neural innervation enables the YS to serve as a coordinated developmental hub, facilitating complex crosstalk between neural, vascular, and metabolic systems during early vertebrate embryogenesis. Significance StatementTraditional paradigms view the embryonic yolk sac simply as a nutrient reservoir. Using advanced live-cell imaging in zebrafish, we uncover that the yolk sac can be innervated by brain-expanded axonal networks during development, invigorating its biological functions, including neural signal, vascular flow, and metabolic activity. Rather than maintaining local neuronal bodies, these long-distance nerve extensions map out an early topological scaffold that may guide future internal organ innervation during yolk resorption. Furthermore, we capture pre-vascular blood transport and stress-induced metabolic shifts on the yolk sac surface. These findings redefine the yolk sac as a neural-controlled functional hub before organs form.

neuroscience↗

bioRxiv2026

Green genetically encoded IP3 biosensor for hierarchical analysis of its signaling network

Inositol 1,4,5-trisphosphate (IP3) is a key second messenger that regulates diverse physiological processes. Visualization of IP3 dynamics in living cells is therefore important for understanding its signaling processes. In this study, we developed genetically encoded green fluorescent IP3 biosensors named Green iPenguins with distinct half-maximal effective concentrations (EC50) for IP3, enabling detection of IP3 signals over a range of concentrations. The biosensors displayed more than a 4-fold increase in fluorescence intensity upon IP3 and showed high specificity for IP3 over structurally related molecules. When expressed in HEK293T cells, the biosensors enabled visualization of IP3 dynamics involved in different signaling pathways. They were also compatible with dual-color imaging, allowing simultaneous monitoring of IP3 together with cAMP or Ca2+ signals. In addition, the hierarchical relationship between IP3 and Ca2+ signaling was visualized, providing insight into the temporal relationship between these two second messengers. The biosensors are expected to facilitate future studies of physiological processes involving IP3 signaling networks.

bioengineering↗

bioRxiv2026

A graph-based pangenome reveals the genetic basis of climate-resilient and horticultural traits in pear

Climate change poses an increasing threat to the cultivation of deciduous fruit trees, placing greater demands on modern pear breeding. Using pear germplasm adapted to diverse environments, we assembled 11 chromosome-level genomes. In combination with 13 publicly accessible pear genomes, we analyzed presence-absence variations (PAVs) and constructed a graph-based pangenome for pear. By performing a PAV-eQTL analysis of the fruit of 123 pear accessions, we identified PAVs significantly associated with expression levels of genes that may be involved in regulating agronomic traits. Population analysis of 268 pear accessions revealed two stop-gained variants in DAM1 of independent origin, which may function in advancing the blooming date and reducing the chilling requirement. We detected complex PAVs at the NOR1 locus, including two copy-number variations and one deletion. These PAVs contributed to the rapid diversification of the NOR1 locus and the fruit development period through regulating ARF5 and other ripening-related genes. We revealed the selection history of the NOR1 locus and developed novel pear individuals that accumulated alleles for low chilling requirement, early blooming date, and short fruit development period. The results provide valuable resources for pear genomics research and offer a guideline for breeding modern pears with climate resilience.

plant biology↗

bioRxiv2026

Magnetogenetic control of endogenous calcium signaling via ROS-sensitive ion channels reveals astrocytic regulation of neural circuit activity

Astrocytes exhibit complex calcium signaling proposed to detect, integrate, and modulate neuronal activity; however, their causal contribution to neural circuit function remains unresolved. This is partly due to the lack of tools that recapitulate physiological astrocyte calcium signaling. Here, we show that experimental magnetic control of endogenous calcium signaling in astrocytes is sufficient to modulate neural circuit dynamics. Using pmFeRIC, a magnetogenetic tool for remote, noninvasive, and on-demand activation of endogenous calcium pathways, we demonstrate that selective activation of astrocyte calcium signaling drives neuronal activity. pmFeRIC uses magnetic fields and endogenous ferritin to generate localized reactive oxygen species (ROS) at the plasma membrane, activating native ROS-sensitive ion channels, inducing calcium influx. In hippocampal circuits in vitro, magnetic activation of endogenous astrocytic calcium signaling produced robust, state-dependent changes in neuronal circuit activity, in part by increasing presynaptic release probability, postsynaptic burst firing, and glutamatergic transmission. These effects were mediated by transient receptor potential channels, amplified by intracellular calcium stores, and abolished when astrocyte calcium signaling was disrupted, establishing a causal role in neural circuit dynamics. In vivo, pmFeRIC activates endogenous calcium signaling in astrocytes with kinetics comparable to locomotion-induced activity, enabling control of astrocyte calcium dynamics that resemble physiological behavioral responses. Together, these findings establish that endogenous astrocytic calcium signaling is sufficient to modulate neural circuit function and introduce a broadly applicable platform for cell-specific, wireless, on-demand control of endogenous calcium signaling through magnetic activation of ROS-sensitive ion channels.

neuroscience↗

bioRxiv2026

CD248 activates TGF-β receptor I to promote vascular remodeling in pulmonary arterial hypertension

I.BackgroundPulmonary arterial hypertension (PAH) is a debilitating cardiopulmonary disease characterized by progressive remodeling of the pulmonary vasculature. Pathologic transforming growth factor-{beta} (TGF-{beta}) signaling is an essential driver of vascular remodeling in PAH. While global inhibitors of TGF-{beta} exist, their clinical application is limited by systemic adverse effects. Therefore, a critically unmet need in PAH is to identify pulmonary vascular-specific regulators of the TGF-{beta} axis, which would selectively enhance clinical efficacy while minimizing adverse effects. As the clinical care of PAH largely promotes vasodilation, and only one FDA-approved agent targets vascular remodeling, this study aimed to identify selective, therapeutically targetable regulators of the TGF-{beta} axis in the PAH pulmonary vasculature. MethodsCD248 was identified via liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics in human lungs. CD248 levels were assessed across human, rat, and mouse lung tissues using western blotting, RTqPCR, and/or immunofluorescence techniques. CD248-null (CD248-/-) mice were used to study the contribution of CD248 to hypoxia-sugen (H/S)-induced PAH. The mechanistic role of CD248 in PAH vascular remodeling and TGF-{beta} signaling was assessed by genetic (siRNA knockdown; overexpression) and pharmacologic (Ontuxizumab) manipulation of primary human pulmonary vascular cells. ResultsLC-MS/MS proteomics coupled with pathway enrichment analysis of human lung tissue identified CD248 as a putative mediator of vascular remodeling that is elevated in PAH lungs. CD248 was elevated in PAH pulmonary artery smooth muscle cells (PASMCs) across human, rat, and mouse lung tissue. CD248-/- mice were protected from H/S-induced elevations in right ventricular (RV) systolic pressure (RVSP), RV hypertrophy, and pulmonary artery muscularization. CD248 knock-down reduced cell proliferation and migration of primary PAH PASMCs. CD248 was essential for phospho-activation of TGF-{beta} receptor I (T{beta}RI) at S165 and canonical phosphorylation of SMAD3 at S423/425. CD248 loss blunted TGF-{beta}-induced gene expression (FN1, Col11, -SMA) and activated expression of the vasoprotective matrix metalloprotease, MMP-8. Mechanistically, CD248 interacted with and enhanced de novo phosphorylation and stability of T{beta}RI, blocking its ubiquitin-mediated proteasomal degradation. Ontuxizumab promoted T{beta}RI instability and attenuated the production of FN1, Col11, and -SMA in primary PAH PASMCs. ConclusionsThis work identifies CD248 as a previously unrecognized co-activator of T{beta}RI in PAH. As CD248 is largely quiescent in most adult tissues yet pathologically upregulated in the PAH pulmonary vasculature, this study supports the potential of anti-CD248 therapy as a novel pulmonary vascular-specific alternative to systemic TGF-{beta} inhibition.

molecular biology↗

bioRxiv2026

RVQ-Alpha: Bridging Single-Cell Transcriptomics and Large Language Models via Discrete Tokenization and Verifiable Reinforcement Learning

Single-cell RNA sequencing yields continuous expression profiles, whereas large language models operate over discrete autoregressive sequences, leaving no shared computational interface for language-model reasoning over cell states. Existing approaches either keep cellular information outside the LLM vocabulary, consume context per listed gene, or learn reconstruction codes without gene-level grounding. We introduce RVQ-Alpha, which systematically adapts four stages of LLM training (tokenization, supervised fine-tuning, reinforcement learning, and distillation) to single-cell analysis. Multi-codebook Residual Vector Quantization (RVQ) lexicalizes each profile into a compact, hierarchical cellular alphabet in the models native token stream, while a paired decoder reconstructs the corresponding expression profile. Evidence-First supervision grounds these symbols in named genes and expression-linked evidence; Fact-Aware RLVR then penalizes contradictory claims to support auditable reasoning. Task-specific RLVR yields strong experts, but a single Mixed policy underperforms them across all four task families. To recover specialist competence in a unified model, we adopt Multi-Teacher On-Policy Distillation (MOPD), which consolidates these experts into one All-in-One checkpoint without retaining a separate policy for each task. On the CAPSTONE benchmark, a four-task suite with explicit biological shifts and deterministic ontology-aware graders, the unified checkpoint improves over Mixed on all 12 metrics and remains within 0.005 of the task-routed specialist reference on every primary metric. Overall, RVQ-Alpha provides a unified pipeline for grounded, auditable multi-task single-cell analysis.

bioinformatics↗

bioRxiv2026

Genotypic and environmental effects on seed coat patterning and nutritional composition in common bean (Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) is the leading grain legume consumed directly by humans and a primary source of nutrients in many communities. This study utilized common bean genotypes with diverse seed coat phenotypes to investigate genotypic and environmental effects on pigmented seed coat area and seed macronutrient (protein, starch, fat, ash, moisture), anti-nutrient (phytate), and mineral nutrient (iron, zinc, calcium, phosphorus, magnesium, potassium, sodium) profiles. Recombinant inbred lines (RILs) that comprise six phenotypic classes for seed coat patterning and nine commercial cultivars were field-evaluated for multiple years across inland, coastal, and intermountain environments in California. A custom near-infrared spectroscopy calibration improved macronutrient prediction accuracy relative to a pre-existing calibration. Environmental effects on macronutrients were pronounced; the 2022 coastal growing environment was the most distinct, characterized by significantly higher starch and moisture content and significantly lower protein content in the RILs relative to any other environments. Across growing years in the RILs, greater consistency was observed at the inland site, where only protein was significantly different; all macronutrient traits significantly differed within the intermountain site. Certain commercial cultivars largely maintained their relative rank for protein content across environments, indicating consistency of genotypic performance, and Black Nightfall ranked among the highest for iron, zinc, phosphorus, and magnesium. Percent pigmented seed coat area was significantly negatively correlated with both calcium and magnesium concentrations. These results underscore the importance of genotype-by-environment field trials for seed coat patterning, seed nutritional composition, and their interplay, to support breeding of common bean among other grain legumes. HighlightsO_LICustom near-infrared spectroscopy (NIRS) calibration improved prediction accuracies C_LIO_LIEnvironmental effects significantly influenced common bean macronutrient composition C_LIO_LICertain cultivars ranked consistently for macronutrient traits across environments C_LIO_LISeed coat pattern was significantly associated with mineral nutrient concentrations C_LI

plant biology↗

bioRxiv2026

Impaired mitochondrial stress signaling mediates bone loss in male mice in the absence of BNIP3.

Osteoblasts generate bone by secreting collagen and mineralizing it in response to various signaling cues. We have previously shown that the majority of ATP generated by differentiated osteoblasts in response to glucose is through glycolysis in contrast to undifferentiated cells that are more dependent on oxidative phosphorylation. To confirm our previous findings, metabolomics was performed for unlabeled polar metabolites, revealing elevated glycolytic metabolites at the later stages of differentiation. Krebs cycle (TCA cycle) metabolites were also changed confirming metabolic rerouting with differentiation. We hypothesized that an increase in mitophagy shifts ATP generation towards glycolysis resulting in the observed bioenergetic and metabolic changes. Utilizing calvarial osteoblasts isolated from a mitophagy reporter mouse model (MitoQC), an increase in mitophagy and the mitophagy receptor, Bnip3, was observed with osteoblast differentiation. KD of Bnip3 in osteoblasts inhibited differentiation and mineralization arising from impaired mitochondrial function. In vivo, male Bnip3 null mice exhibited a significant decrease in osteoblast numbers resulting in lower bone mass. Mechanistically we identified decreased fusion and increased fission factors, impaired stress signaling and increased proapoptotic factors in the absence of Bnip3. These data demonstrate for the first time that BNIP3 expression and mitophagy during osteoblast differentiation are necessary for relieving mitochondrial stress to maintain optimal bone mass.

cell biology↗

bioRxiv2026

On the accuracy of image registration in portable low-field 3D brain MRI

Portable low-field MRI offers an affordable and mobile alternative to conventional high-field scanners, enabling imaging in point-of-care and resource-limited settings. However, its lower signal-to-noise ratio, reduced resolution, and acquisition artifacts raise concerns about the accuracy of standard image registration methods. Reliable registration is critical for a wide range of emerging applications, including frequent brain monitoring, assessment of neurodegenerative disease progression, and evaluation of treatment effects such as those of Alzheimers therapeutics. In this work, we systematically evaluated state-of-the-art registration approaches on simulated low-field scans (obtained by downsampling high-field images) and on real low-field brain MRI data. We compared three representative approaches: classical optimization (NiftyReg), learning-based registration (SynthMorph), and synthesis-based registration (SynthSR+NiftyReg). Using downsampled high-field scans, all methods performed well, achieving high Dice scores and smooth deformation fields, indicating that reduced resolution alone does not hinder registration. In contrast, real low-field data exhibited lower accuracy, primarily due to geometric distortion and other acquisition-specific artifacts. Among the tested approaches, the synthesis-based pipeline achieved the most robust performance across subjects and modalities. Overall, existing algorithms can accommodate resolution limitations, however, future methods could further enhance coregistration by explicitly addressing the distortions present in low-field MRI scans.

neuroscience↗

bioRxiv2026

An agentic framework turns patient-sourced records into a multimodal map of ALS heterogeneity

ALS progression is multidimensional, yet fragmented records and scalar outcomes obscure how patients move through disease states and how those states relate to molecular variation. MEDSTREM converts patient-held medical-record images into standardised longitudinal data, enabling bottom-up cohort construction. Using MEDSTREM-structured records from more than 8,000 AskHelpU participants together with PRO-ACT and Answer ALS, we developed DynaALS, the ALS Disease Dynamics Atlas. DynaALS represents ALS as a dynamic patient-state manifold that captures distinct directions of deterioration and patient movement between them over time. DynaALS retrieved population-referenced future states and decoded them into multidimensional clinical profiles without requiring patient-specific longitudinal histories. Motor-neuron RNA and chromatin profiles linked DynaALS states to developmental and regulatory programs, while neuromuscular-organoid single-cell multi-omics converged on a neural-developmental Netrin-DCC signalling axis across interacting cell types. By coupling MEDSTREM-enabled data construction to dynamic state modelling, DynaALS establishes a transferable patient-state engine for predictive and biologically interpretable disease models.

bioinformatics↗

bioRxiv2026

Physics-Informed Neural Network for Mapping Vascular and Tissue Dynamics Using Laser Speckle Contrast Imaging

SignificanceQuantitatively mapping both cerebral blood flow and tissue dynamics from laser speckle contrast imaging (LSCI) is powerful for studying cerebral blood flow and neurovascular coupling, particularly in the context of stroke. Conventional multi-exposure fitting is slow and difficult to scale. Efficient, physically grounded methods are needed to extract both vascular and tissue dynamic biomarkers from LSCI data. AimTo develop and validate a physics-informed neural network (PINN) that quantitatively estimates fast (vascular) and slow (tissue-related) speckle decorrelation parameters directly from LSCI measurements without requiring ground-truth labels. ApproachWe developed a physics-informed neural network (PINN) to estimate fast (vascular) and slow (tissue-related) speckle decorrelation parameters directly from multi-exposure LSCI data without requiring ground-truth labels. The analytical LSCI model is embedded in the network loss function, enforcing consistency with speckle physics during training. The model operates in a self-supervised manner and performs pixel-wise inference across full-field images. The framework was evaluated using in vivo mouse stroke LSCI datasets. ResultsThe PINN accurately recovered fast decorrelation rates associated with cerebral blood flow and slower dynamics linked to tissue and cellular motion. The parameter maps closely match those from traditional nonlinear fitting, but at orders-of-magnitude higher speed, reducing analysis to under one second per image. It also generalizes to unseen subjects and remains robust under noise. ConclusionsOur approach establishes physics-informed learning as a practical framework for near real-time extraction of vascular and cellular biomarkers from LSCI, enabling longitudinal monitoring of stroke progression and potentially facilitating clinical translation.

bioengineering↗

bioRxiv2026

AADAT-Driven Metabolic Control of Malate and CoQ10 Shapes Immune Evasion in Triple-Negative Breast Cancer

Compared to other subtypes of breast cancer, triple-negative breast cancers (TNBC) have fewer treatment options and exhibit a worse prognosis. Through integrated transcriptomic, metabolomic, immunohistochemical, spatial, and clinical analyses, we identify the mitochondrial enzyme, -aminoadipate aminotransferase (AADAT) as a previously unrecognized metabolic immune checkpoint in TNBC. AADAT mRNA and protein were significantly upregulated in human TNBC, and high AADAT expression was associated with reduced intra-tumoral CD8 T-cell density and inferior survival. Genetic silencing of AADAT in orthotopic murine TNBC models curtailed primary tumor growth and distant metastasis in a CD8 T-cell-dependent manner, enhanced effector T-cell activation, and sensitized tumors to dual PD-1/CTLA-4 blockade. Mechanistically, unbiased metabolomics showed increased malate levels after AADAT knockdown. Additionally, 4-hydroxyphenylpyruvate, an essential precursor for coenzyme Q10(CoQ10) biosynthesis, decreased following AADAT knockdown, suggesting an impaired mitochondrial electron transport chain. CoQ10 supplementation restored metabolic balance and reversed malate accumulation caused by AADAT knockdown, indicating that AADAT helps maintain CoQ10-supported redox homeostasis, thereby preventing malate buildup and export. Notably, malate addition directly boosted CD8 T-cell oxidative metabolism, increased the NAD/NADH ratio and reactive oxygen species, and augmented TNF- and IFN-{gamma} production. In vivo, malate supplementation in drinking water phenocopied AADAT knockdown, restored the response to paclitaxel plus anti-PD-1 therapy in multiple independent syngeneic TNBC models with de novo or acquired resistance to immunotherapy, reduced tumor burden, and prolonged survival. In patient cohorts, higher spatially clustered intra-tumoral malate is associated with co-localization of functional CD8 T cells, decreased exhausted T-cell neighborhoods, and superior post-chemotherapy outcomes. These data position AADAT as a central metabolic orchestrator of immune escape in TNBC and nominate oral malate as a readily translatable adjuvant to reverse chemo-immunotherapy resistance in TNBC. Statement of SignificanceAADAT defines a metabolic-immune axis driving immune evasion and therapy resistance in triple-negative breast cancer. Blocking AADAT or administering oral malate reactivates CD8 T-cell immunity and sensitizes chemo-immunotherapy-resistant tumors to these agents. These findings uncover a readily translatable metabolic vulnerability with potential to improve outcomes for patients with aggressive breast cancer subtypes.

cancer biology↗

bioRxiv2026

Modeling predicts a biochemical feedback mechanism underlying astrocyte calcium refractory periods

Astrocytes exhibit intracellular calcium fluctuations in response to neuronal activity. Repeated receptor stimulation can induce a transient suppression of calcium signaling--a refractory period--yet the underlying mechanisms and timescales of this phenomenon during behavior remain poorly understood. Here, we present a biophysically grounded computational model of astrocytic calcium signaling that incorporates a novel feedback mechanism mediated by conventional protein kinase C (cPKC) and predicts the refractory phenomenon. Unlike previous models developed in vitro, our model is directly validated using in vivo two-photon calcium imaging data from behaving mice. It closely recapitulates astrocytic calcium dynamics across both time and frequency domains, including the emergence of refractory periods and their negative correlation with inter-stimulus intervals. Simulations further predict the timing of recovery from refractory states, consistent with experimental observations. This work provides a mechanistic explanation for astrocytic refractory behavior and establishes a framework for integrating computational modeling with in vivo functional imaging.

neuroscience↗

bioRxiv2026

Mining single-cell transcriptomic data reveals distinct T-cell population in pediatric B-ALL and AML at diagnosis

Immunotherapy represents a promising strategy to improve outcomes in pediatric leukemia; however, its efficacy remains considerably lower in acute myeloid leukemia (AML) compared with B-cell acute lymphoblastic leukemia (B-ALL). To characterize T-cell subsets in AML and B-ALL at diagnosis, we took advantage of existing data sets and performed an integrated single-cell RNA sequencing (scRNA-seq) analysis of T cells present in the bone marrow of pediatric patients with B-ALL (n=89) and AML (n=26), and healthy donors (n=9). In total, 47,610 T cells were analyzed, revealing 17 transcriptionally distinct subsets. Comparative analysis identified T-cell subsets distinguishing B-ALL from AML, such as proliferative, naive CD4, and progenitor exhausted, and naive or resting CD4 regulatory T cells. We identified a rare T-cell subset expressing hemoglobin genes, which was enriched in B-ALL and characterized by upregulation of heme metabolism and chronic hypoxia-associated pathways, and its abundance was associated with better outcomes. Collectively, our findings delineate the transcriptional and functional heterogeneity of T cells in pediatric B-ALL and AML and provide insights that may inform future T-cell-based immunotherapeutic strategies.

immunology↗

bioRxiv2025

PARP10 condensation inhibits viral infection via targeting NAD+ homeostasis

ADP-ribosylation is a critical post-translational modification mediated by diphtheria toxin-like ADP-ribosyltransferases (ARTDs). The human ARTD family comprises 17 members that catalyze either poly- or mono-ADP-ribosylation. However, the functions and regulatory mechanisms of many ARTD proteins remain poorly understood. Here, we uncover an antiviral role for PARP10 through its ability to form biomolecular condensates. Viral infection triggers PARP10 condensation, a process driven by multivalent homotypic interactions among the structured domains. We show that mono-ADP-ribosylation of PARP10 suppresses its condensation, serving as a negative feedback mechanism that regulates condensate dynamics and protein stability. PARP10 condensates exhibit enhanced enzymatic activity, leading to decreased NAD+ levels and disruption of NAD+ homeostasis, ultimately inhibiting viral replication. Our findings establish PARP10 condensation as a novel mechanism for ARTD enzyme compartmentalization, with significant implications for innate immunity and host defense.

cell biology↗

bioRxiv2025

Alphaviral nonstructural protein-host RBP co-condensation as a mechanism to sustain virus replication

It has long been recognized that the intracellular replication of alphaviruses critically relies on several key host RBPs, including G3BP1/2 and FXR1/FXR2/FMR1, but how these RBPs modulate alphaviral replication and whether it would be possible to target these RBPs for antiviral treatment are less explored. Here, using SFV as a model, we report that SFV nsP3 exploits G3BP for its condensation and transforms antiviral stress granules into proviral nsP3-G3BP co-condensates. The gel-like co-condensates of nsP3 and G3BP enrich and protect viral genomic RNAs from host RNase degradation and serve as viral translational hubs to promote viral replication. The mode of nsP3-RBP co-condensation is prevalent across alphaviruses, and disruption of nsP3 condensates is an efficient antiviral approach. Thus, these findings uncover a general anti-alphavirus strategy based on the conserved reliance of nsP3-RBP co-condensation.

cell biology↗

bioRxiv2025

Neurogenesis Leads Early Development in Zebrafish

Vertebrate early neurogenesis is a highly conserved process fundamental to brain function and the emergence of intelligence. However, the cellular dynamics bridging gastrulation and organogenesis remain elusive due to observational challenges. We developed a live-cell imaging platform for transgenic zebrafish that provides, for the first time, a continuous reconstruction of early neurogenesis across subcellular to organismal scales. Our analysis reveals that neurogenesis is a precisely orchestrated process. Neuronal cell bodies initially coalesce into discrete, linearly arranged clusters extending from the brain along the spinal cord. From these hubs, axons radiate outward to innervate the central nervous system and peripheral tissues, including the yolk sac surface. A primary pioneer neuron projects from the brain, coursing ventrally in parallel to the body axis. Secondary neurons then interconnect, forming a pervasive network that is subsequently refined through selective axonal apoptosis. The emergence of frequent Ca{superscript 2}{square} flashes only after structural maturation indicates that functionality is contingent upon an established scaffold. We also observe concurrent material transport and a slow, directional flow of Ca{superscript 2}{square} along axons, suggesting complementary signaling modalities. Furthermore, neurogenesis exhibits precise spatiotemporal coupling with histogenesis, particularly with the developing lateral line and vasculature. Our work, with refined spatial and time resolution, defines the kinetic pathway of early neurogenesis and underscores the critical interplay of subsystems in embryogenesis, offering fundamental insights for neural health and bio-inspired intelligence.

neuroscience↗

bioRxiv2025

Breaking the ''one nucleus, one whole genome'' rule: Neurospora crassa separates its haploid chromosomes into different nuclei

The nucleus is a defining feature of eukaryotic cells, compartmentalizing the genome to enable precise regulation of diverse cellular processes. The long-standing paradigm in textbooks states that each nucleus carries at least a complete haploid genome --the "one nucleus, one whole genome" rule. A striking exception was recently uncovered: in two sclerotia-forming plant pathogenic fungi in the Sclerotiniaceae family, Sclerotinia sclerotiorum and Botrytis cinerea, haploid chromosomes are irregularly distributed across multiple nuclei. However, whether such phenomenon occurs in other eukaryotes, particularly in non-pathogenic fungi, is unclear. Through a literature survey, we identified many fungi that can potentially also separate their haploid chromosomes across different nuclei. Interestingly, Neurospora crassa, a foundational fungal genetics model, came out as a candidate. Its conidia, typically containing two or three nuclei, were believed to harbor a complete haploid genome within each nucleus. However, using approaches including chromosome counting, flow cytometry, and fluorescence in situ hybridization, we found that haploid chromosomes in N. crassa can be unevenly distributed among multiple nuclei. These findings challenge longstanding assumptions in fungal genetics and provide new directions for investigating genome organization. Our results indicate that the organisms violating the "one nucleus, one whole genome" rule are beyond sclerotia-forming pathogenic fungi. Since over 90% of fungi have not even been described, we propose that many more of them may likewise partition their genomes non-uniformly across nuclei, a process that could facilitate their adaptation and evolution.

microbiology↗