Biology subjects

Xi, W.

Publications and source records attributed to Xi, W..

At least 19 recordsLinked to original sources

bioRxiv2026

Brain state shapes the polarity of pulsed infrared neural stimulation responses in individual cortical neurons

Pulsed infrared neural stimulation (INS, 1875nm the peak of energy absorption by water) is a non-viral method developed to activate single submillimeter sites in the brain. When used in ultrahigh-field fMRI, it reveals functionally specific brain-wide columnar networks comprising synaptically activated nodes. INS is non-damaging and effective for use in the human cortex and is useful for neural and behavioral neuromodulation in primates. To investigate how physiological state influences its cellular effects, we performed in vivo two-photon calcium imaging with GCaMP6s in mice and tracked identified cortical neurons in awake vs anesthetized states. Across the tested radiant exposures, INS-evoked responses differed markedly between states: under anesthesia, stimulation produced predominantly positive-going calcium responses, whereas during wakefulness the same identified neurons exhibited negative-going responses. Pharmacological manipulation of this baseline level by GABAergic signaling shifted response polarity in opposite directions: picrotoxin under anesthesia produced awake-like negative responses, whereas muscimol during wakefulness produced anesthetized-like positive responses. Trial-by-trial analyses further showed that the relationship between pre-stimulus baseline level and INS-evoked response depended on physiological state. Because INS relies on transient tissue heating, we also developed an in situ EGFP-based calibration approach to estimate temperature-related fluorescence changes. These fluoro-thermal contributions were modest at lower radiant exposures and became increasingly important at higher exposures, particularly near the fiber pathway. The low-intensity results are consistent with, but do not establish, a state-dependent feed-forward inhibitory framework. Together, these findings show that the neuronal response to focal INS is shaped by ongoing brain state and provide a practical framework for separating state-dependent calcium responses from temperature-related fluorescence effects, making INS a potentially versatile tool for neuroscience and clinical applications.

neuroscience↗

bioRxiv2026

Curvature-guided chiral collective organization of myoblast tissues

Surface curvature is a fundamental geometric cue in tissue morphogenesis, yet its role in guiding collective cell organization has remained elusive. Here, we show that curvature acts as a geometric control parameter that shapes supracellular alignment and chirality while modulating myogenic differentiation in myoblast tissues. Cells cultured on curved substrates self-organize into robust helical assemblies whose handedness is set, and can be reversed, by the sign of curvature: convex fibers produce right-handed helices, whereas concave channels invert the chirality. We identify a previously hidden clockwise bias in single-cell motion associated with the helical actin cytoskeleton. A minimal continuum theory coupling an effective chiral drive to curvature quantitatively captures the emergence and reversal of tissue-scale chiral alignment. On substrates with spatially varying curvature, local curvature gradients organize patterned multicellular architectures while preserving a global handedness. Curvature is also associated with myogenic state, with higher curvature linked to reduced or delayed differentiation. Together, these findings reveal how complex geometries shape the alignment, symmetry, and cellular state of living tissues.

biophysics↗

bioRxiv2026

T2T Genome and Population Resequencing Reveal OfCCD4 Alleles Orchestrate Petal Color and Scent in Osmanthus fragrans

Osmanthus fragrans is prized for its floral color and fragrance, both key targets for genetic improvement. However, the lack of a complete genome assembly and comprehensive population structure hinders gene dissection and marker development for breeding. To investigate the genetic basis of color-scent interaction, a telomere-to-telomere (T2T) genome assembly is generated, and whole-genome resequencing of 100 cultivars is performed. Integrative population and metabolomic analyses reveal a trade-off: orange-red ( Aurantiacus) cultivars accumulate high /{beta}-carotene but low aromatic apocarotenoids (/{beta}-ionone), while yellow-white cultivars show the opposite pattern. Divergence mapping identifies OfCCD4 as the major underlying locus. Three alleles are characterized--functional (A), partially functional (aDel), and a frameshift null (aStop)--with aStop strictly co-segregating with the Aurantiacus phenotype. Transient and stable transformations confirm that A and aDel cleave /{beta}-carotene into /{beta}-ionone, while aStop abolishes this activity. A co-dominant PCR marker is developed based on allele-specific polymorphisms. OfCCD4 is thus established as the key regulator of the color-scent trade-off in osmanthus. The identified alleles and molecular marker enable rapid, low-cost genotyping at the seedling stage--offering particular value for marker-assisted selection in ornamental breeding, where extended juvenility makes phenotypic selection highly time- and resource-intensive.

plant biology↗

bioRxiv2025

The complex microscopic dynamics of cells in high-density epithelial tissues

Epithelial tissues line the surfaces of vital organs and are often densely packed in a disordered, mechanically arrested state, referred to as jammed or glassy state. While collective migration at low-density regimes has been extensively studied, the microscopic dynamics within such jammed epithelia remains poorly understood. Here, we reveal that contrary to expectations from thermal systems with glassy dynamics, jammed epithelial monolayers do not exhibit cage effects that reflect the temporary spatial trapping of the particles. Instead, cells display sub-diffusive creep and Fickian yet non-Gaussian dynamics, accompanied by compressed exponential relaxation, features that reveal stress-driven fluidity. We show that cell divisions and extrusions transiently do enhance local motion, they are insufficient to fluidize the tissue globally. Fast-moving cells form collective, anisotropic clusters, and these dynamic heterogeneities correlate with local structural entropy and low-frequency vibrational modes. These findings challenge the conventional view that jammed tissues are static and inert structures, uncovering a hidden fluidity that can be expected to play a critical role in morphogenesis, wound healing, and early tumor progression.

biophysics↗

bioRxiv2024

OfWRKY33 binds to the key linalool synthase gene OfTPS7 to promote linalool synthesis in Osmanthus fragrans flowers

Volatile aroma compounds make significant contributions to human perception of flowers. Osmanthus fragrans is a famous aroma plant and linalool along with its oxides are proved to be the dominant aroma active compounds. Although some terpene synthases (TPSs) have been characterized, a comprehensive study of the hub metabolic gene and its transcriptional regulation remain to be revealed. Here, we selected a specific cultivar Boyeyingui (BBYG) with the highest content of linalool among 20 wide-cultivated cultivars for genome and transcriptome sequencings. Among the 25 new putative OfTPSs, only OfTPS6, OfTPS7 could exclusively produce linalool in planta. Biochemical analysis demonstrated that OfTPS6, OfTPS7 were able to catalyze geranyl diphosphate (GPP) into linalool and a small proportion of other monoterpenes in vitro. Spatial and temporal correlation analysis further confirmed the transcript level of OfTPS7 was closely associated with linalool content in diverse cultivars and different tissues, suggesting OfTPS7 was the essential linalool synthase gene. Combined with yeast one-hybrid screen and weighted correlation network analysis (WGCNA), a nucleus-localized transcriptional factor OfWRKY33 was considered as a potential modulator. Y1H, dual-luciferase assay and electrophoretic mobility shift assay (EMSA) demonstrated that OfWRKY33 directly bound to the W-box of OfTPS7 promoter to stimulate its transcription. OfWRKY33 could coordinately induce the expressions of OfTPS7, 1-deoxy-d-xylulose 1 (OfDXS1), thereby promoting the linalool formation. The results first revealed the hub linalool synthase gene OfTPS7 and a novel TF participating in the complex transcriptional regulation of linalool biosynthesis in O. fragrans flowers.

biochemistry↗

bioRxiv2024

Integrated Transcriptome and Metabolome Analyses Reveal the Mechanism Regulating Bulbil Initiation and Development in Cystopteris chinensis

Cystopteris chinensis is an endangered fern endemic to China, which only has a small wild population due to its poor reproductive ability. However, we recently found that it can produce bulbils on its pinnule to generate new plants but the molecular mechanism underlying this unique phenomenon remained unknown. In this study, we have identified four distinct stages in the initiation and development of bulbils based on morphological and anatomical observation. We performed transcriptome and metabolome analyses on the collected samples at each stage. Through KEGG enrichment analysis, it was found that the phytohormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways play a significant role in regulating bulbil initiation and development. Specifically, the involvement of three phytohormones and sugar substances was identified in the process of bulbil initiation. Our study provides the first detailed observation of the bulbils in C. chinensis and explains their initiation and development at the molecular level. However, more in-depth studies are needed to discover the functions of key genes controlling the formation of bulbils to conserve the endangered C. chinensis population.

plant biology↗

bioRxiv2024

A multicellular actin star network underpins epithelial organization and connectivity

Epithelial tissues serve as physical barriers against various external pressures yet remarkably maintain structural stability. Various cellular apparatus including bicellular junction and actomyosin network contribute to the epithelial integrity, packing and remodelling. Although their role in morphogenetic and mechanical processes have been extensively studied during embryogenesis and disease development, their synergistic effects in maintaining tissue organization and connection remain poorly understood. In this study, we discovered a tissue-scale actomyosin network connected through bicellular junctions and manifested in the villi of adult murine intestinal tissue. Later we reproduced such supracellular structure in the differentiated compartment of ex vivo intestinal epithelium model. The self-organized actomyosin networks comprised individual actin nodes in each hexagonal cell at the epithelial base with six radial actin branches, presenting an actin star unit. The repeated units were connected through the bicellular junctions, forming a large, multicellular array covering the differentiated domains. Functionally, actin stars contribute to epithelial morphological stability by maintaining cell hexagonality and packing, thereby preserving the solid-like order of the epithelium. Laser ablation experiments validate a modified vertex theoretical model that connects the emergence of such solid-like order to the onset of tension along the actin star branches. Actin stars also acted as locks at the basal side minimizing protrusive activity in the epithelial layer, hindering cell migration and disorganization of the epithelial tissue. Altogether, the supracellular actin star network constitutes a basal biomechanical apparatus coordinating epithelial tissue stability and organization.

cell biology↗

bioRxiv2024

RevGraphVAMP: A protein molecular simulation analysis model combining graph convolutional neural networks and physical constraints

Molecular simulation (MD) is an important research area in the field of life sciences, focusing on understanding the mechanisms of biomolecular interactions at atomic scales. Protein simulation, as a critical subfield of life science, has frequently adopted MD for implementation, where the trajectory data play an important role in drug discovery. With the advancement of high-performance computing and deep learning technology, machine-prediction of protein properties from enormous trajectory data becomes popular and critical, which puts challenges on how to extract useful data features from the complicated simulation data and reasonably reduce the dimensionality. At the same time, in order to better study the Protein system, it is necessary to provide a meaningful explanation of biological mechanism for dimensionality reduction. In order to address this issue, a new unsupervised model RevGraphVAMP is proposed to intelligently analyze the simulation trajectory. RevGraphVAMP is based on the Markov variation method (VAMP) and innovatively integrates graph convolutional neural networks and physical constraint optimization to improve the learning performance of the model. Besides, the attention mechanism is introduced to calculate the importance of protein molecules, leading to interpretation of molecular mechanism. Compared with other VAMPNets models, the new model presented in this paper has achieved the highest VAMP scores and better state transition prediction accuracy in two public datasets. Additionally, it has higher dimensionality reduction discrimination ability for different substates and provides interpretable results for protein structural characterization.

bioinformatics↗

bioRxiv2024

Two-photon imaging of excitatory and inhibitory neural response to infrared neural stimulation

SignificancePulsed infrared neural stimulation (INS, 1875 nm) is an emerging neurostimulation technology that delivers focal pulsed heat to activate functionally specific mesoscale networks and holds promise for clinical application. However, little is known about its effect on excitatory and inhibitory cell types in cerebral cortex. AimEstimates of summed population neuronal response timecourses provide a potential basis for neural and hemodynamic signals described in other studies. ApproachUsing two-photon calcium imaging in mouse somatosensory cortex, we have examined the effect of INS pulse train application on hSyn neurons and mDlx neurons tagged with GCaMP6s. ResultsWe find that, in anesthetized mice, each INS pulse train reliably induces robust response in hSyn neurons exhibiting positive going responses. Surprisingly, mDlx neurons exhibit negative going responses. Quantification using the index of correlation illustrates responses are reproducible, intensity-dependent, and distance-dependent. Also, a contralateral activation is observed when INS application. ConclusionsIn sum, the population of neurons stimulated by INS includes both hSyn and mDlx neurons; within a range of stimulation intensities, this leads to overall excitation in the stimulated population, leading to the previously observed activations at distant post-synaptic sites.

neuroscience↗

bioRxiv2024

Dynamic Lateralization in Contralateral-Projecting Corticospinal Neurons During Motor Learning

Understanding the adaptability of the motor cortex in response to bilateral motor tasks is crucial for advancing our knowledge of neural plasticity and motor learning. Here we aim to investigate the dynamic lateralization of contralateral-projecting corticospinal neurons (cpCSNs) during such tasks. Utilizing in vivo two-photon calcium imaging, we observe cpCSNs in mice performing a bilateral lever-press task. Our findings reveal a heterogeneous population dynamics in cpCSNs: a marked decrease in activity during ipsilateral motor learning, in contrast to maintained activity during contralateral motor learning. Notably, individual cpCSNs show dynamic shifts in their engagement with ipsilateral and contralateral movements, displaying an evolving pattern of activation over successive days. This suggests a flexible and learning-related reconfiguration in the cpCSN network, parallel to motor learning stages. Our findings suggest a complex reorganization in cpCSN activities, underscoring the dynamic nature of cortical lateralization in motor learning and offering insights for neuromotor rehabilitation.

neuroscience↗

bioRxiv2023

An encyclopedia of enhancer-gene regulatory interactions in the human genome

Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease1-6. Here we create and evaluate a resource of >13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and large-scale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 element-gene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancer-promoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.

genomics↗

bioRxiv2023

T2T-YAO: a Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese

Since its initial release in 2001, the human reference genome has been continuously improved in both continuity and accuracy, and the recently-released telomere-to-telomere version--T2T-CHM13--reaches its top quality after 20 years of effort. However, T2T-CHM13 does not represent an authentic diploid human genome, but rather one derived from a simplified, nearly homozygous genome of a hydatidiform mole cell line. To address this limitation and provide an alternative pertinent to the Chinese population, the largest ethnic group in the world, we have assembled a complete diploid human genome of a male Han Chinese, T2T-YAO, which includes telomere-to-telomere assemblies for all the 22+X+M and 22+Y chromosomes in his two haploids inherited separately from his parents. Both haplotypes contain no artificial sequences or model nucleotides and possess a high quality comparable to CHM13, with fewer than one error per [~]14 Mb. Derived from the individual who lives in the aboriginal region of Han Chinese, T2T-YAO shows clear ancestry and potential genetic continuity from the ancient ancestors of the Han population. Each haplotype of T2T-YAO possesses [~]340 Mb exclusive sequences and [~]3100 unique genes as compared to CHM13, and their genome sequences show greater genetic distance to CHM13 than to each other in terms of nucleotide polymorphism and structural variations. The construction of T2T-YAO would serve as a high-quality diploid reference that enables precise delineation of genomic variations in a haplotype-sensitive manner, which could advance our understandings in human evolution, hereditability of diseases and phenotypes, especially within the context of the unique variations of the Chinese population.

genetics↗

bioRxiv2023

A minimal physical model for curvotaxis driven by curved protein complexes at the cell's leading edge

Cells often migrate on curved surfaces inside the body, such as curved tissues, blood vessels or highly curved protrusions of other cells. Recent in-vitro experiments provide clear evidence that motile cells are affected by the curvature of the substrate on which they migrate, preferring certain curvatures to others, termed "curvotaxis". The origin and underlying mechanism that gives rise to this curvature sensitivity are not well understood. Here, we employ a "minimal cell" model which is composed of a vesicle that contains curved membrane protein complexes, that exert protrusive forces on the membrane (representing the pressure due to actin polymerization). This minimal-cell model gives rise to spontaneous emergence of a motile phenotype, driven by a lamellipodia-like leading edge. By systematically screening the behaviour of this model on different types of curved substrates (sinusoidal, cylinder and tube), we show that minimal ingredients and energy terms capture the experimental data. The model recovers the observed migration on the sinusoidal substrate, where cells move along the grooves (minima), while avoiding motion along the ridges. In addition, the model predicts the tendency of cells to migrate circumferentially on convex substrates and axially on concave ones. Both of these predictions are verified experimentally, on several cell types. Altogether, our results identify the minimization of membrane-substrate adhesion energy and binding energy between the membrane protein complexes as key players of curvotaxis in cell migration.

biophysics↗

bioRxiv2023

Effect of cell membrane tension on the lifetime and size of mature clathrin-coated pits and their spatial distribution

Clathrin-mediated endocytosis is the most characterized pathway for cells to internalize diverse receptor-bound cargo, such as proteins, nanoparticles, and viruses. However, the effect of membrane tension on clathrin-coated pit (CCP) maturation remains inadequately characterized. This study aimed to determine the effect of membrane tension on CCP maturation both spatially and temporarily, which remains a controversial and elusive issue. We obtained the sizes and spatial distributions of CCPs by the structured illumination microscopy of fixed cells and observed CCP lifetimes in live cells by total internal reflection fluorescence microscopy. The processes of CCP maturation and abortion were reproduced numerically through Monte Carlo simulation. The results showed that the growth time of CCP was more reasonably proportional to its volume rather than its surface area. We further investigated the spatial distribution of the membrane tension and size of CCPs, finding a significant positive correlation between the membrane tension and the size of mature CCPs spatially. This indicates that the CCPs tend to enrich in the highest-tension region, especially the mature ones. These results agreed with our numerical prediction that the CCP structure grew larger to overcome a higher energy barrier caused by higher background cell membrane tension. Our findings enhance the understanding of CCP maturation dynamics and underscore the importance of membrane tension in regulating CCP development.

biophysics↗

bioRxiv2023

Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions

Comprehensive enhancer discovery is challenging because most enhancers, especially those affected in complex diseases, have weak effects on gene expression. Our network modeling revealed that nonlinear enhancer-gene regulation during cell state transitions can be leveraged to improve the sensitivity of enhancer discovery. Utilizing hESC definitive endoderm differentiation as a dynamic transition system, we conducted a mid-transition CRISPRi-based enhancer screen. The screen discovered a comprehensive set of enhancers (4 to 9 per locus) for each of the core endoderm lineage-specifying transcription factors, and many enhancers had strong effects mid-transition but weak effects post-transition. Through integrating enhancer activity measurements and three-dimensional enhancer-promoter interaction information, we were able to develop a CTCF loop-constrained Interaction Activity (CIA) model that can better predict functional enhancers compared to models that rely on Hi-C-based enhancer-promoter contact frequency. Our study provides generalizable strategies for sensitive and more comprehensive enhancer discovery in both normal and pathological cell state transitions.

genetics↗

bioRxiv2022

Structural basis for substrate recruitment by AMBRA1 E3 ligase receptor

AMBRA1 is a tumor suppressor protein that functions as a substrate receptor of the ubiquitin conjugation system as part of autophagy and cell-cycle regulatory network. The highly intrinsic disorder of AMBRA1 has so far precluded its structural determination. To solve this problem, we analyzed the domain organization and dynamics of AMBRA1 using hydrogen deuterium exchange mass spectrometry (HDX-MS). High deuterium uptake indicates that AMBRA1 is a dynamic and largely unstructured protein, and can be stabilized upon interaction with DDB1, the adaptor of the Cullin4A/B E3 ligase complex. Here we present the cryo-EM structure of AMBRA1 in complex with DDB1 at 3 [A] resolution. The structure shows that parts of N- and C-terminal structural regions in AMBRA1 fold together into the highly dynamic WD40 domain, and reveals how DDB1 engages with AMBRA1 to create a binding scaffold for substrate recruitment. AMBRA1 uses its N-terminal helix-loop-helix and WD40 domain to bind the double-propeller fold of DDB1, whereas different regions target the specific cellular substrates for ubiquitination. We also demonstrate that DDB1 binding-defective AMBRA1 mutants prevent ubiquitination of the substrate Cyclin D1 in vitro and decreased number of autophagosomes in the cells. Together, these results provide structural insights into AMBRA1-ubiquitin ligase complex and suggests a mechanism by which the AMBRA1 acts as a hub involved in various physiological processes.

biochemistry↗

bioRxiv2022

Precision 1070 nm Ultrafast Laser-induced Photothrombosis (PLP) of Depth-targeted Vessels in vivo

The cerebrovasculature plays an essential role in neurovascular and homeostatic functions in health and disease conditions. Many efforts have been made for developing vascular thrombosis methods to study vascular dysfunction in vivo, while technical challenges remain, such as accuracy and depth-selectivity to target single vessel in the cerebral cortex. Herein, we first demonstrates the evaluation and quantification of the feasibility and effects of Rose Bengal (RB)-induced photothrombosis with 720-1070 nm ultrafast lasers in raster scan. A flexible and reproducible approach is then proposed to employ a 1070 nm ultrafast laser with spiral scan for producing RB-induced occlusion, which is described as precision ultrafast laser-induced photothrombosis (PLP). Combine with two-photon microscopy imaging, this PLP displays highly precise and fast occlusion induction of various vessel types, sizes, and depths, which enhances the precision and power of the photothrombosis protocol. Overall, the PLP method provides a real-time, practical, precise, and depth-selected single-vessel photothrombosis technology in cerebral cortex with commercially available optical equipment, which is crucial for exploring brain vascular function with high spatial temporal resolution in brain.

neuroscience↗

bioRxiv2021

Ultra-deep through-skull mouse brain imaging via the union of skull optical clearing and three-photon microscopy

Optical microscopy has enabled in vivo monitoring of brain structures and functions with high spatial resolution. However, the strong optical scattering in turbid brain tissue and skull impedes the observation of microvasculature and neuronal structures at a large depth. Herein, we proposed a strategy to overcome the influence induced by the high scattering effect of both skull and brain tissue via the combination of skull optical clearing (SOC) technique and thee-photon fluorescence microscopy (3PM). The Visible-NIR-II compatible Skull Optical Clearing Agents (VNSOCA) we applied reduced the skull scattering and water absorption in long wavelength by refractive index matching and H2O replacement to D2O respectively. 3PM with the excitation in the 1300-nm window reached 1.5 mm cerebrovascular imaging depth in cranial window. Combining the two advanced technologies together, we achieved so far the largest cerebrovascular imaging depth of 1.0 mm and neuronal imaging depth of >700 m through intact mouse skull. Dual-channel through-skull imaging of both brain vessels and neurons was also successfully realized, giving an opportunity of non-invasively monitoring the deep brain structures and functions at single-cell level simultaneously.

neuroscience↗