Biology subjects

Xi, H.

Publications and source records attributed to Xi, H..

9 recordsLinked to original sources

bioRxiv2026

Mechanistic insights into chromatin modulation by the orphan remodeler ATRX

Alpha-thalassemia/mental retardation syndrome X-linked protein (ATRX) is an ATP-dependent chromatin remodeler that performs diverse functions, including spacing nucleosomes, facilitating the deposition of histone variant H3.3, and preventing replication stress. The mechanism by which ATRX modulates chromatin is unknown. Here, our cryo-EM structure revealed that ATRX recognizes and modulates the nucleosome through its C-terminal regions by embracing and unwrapping [~]18 base-pair nucleosomal DNA near the entry/exit sites in the presence of ADP*BeF3. Strikingly, the DNA minor groove between SHL6 and SHL7 is profoundly deformed by a "pin-like" structure in ATRX, which uniquely intercalates the aromatic side chain of a phenylalanine into the base stackings. Biochemical assays revealed the crucial role of this phenylalanine in sliding the nucleosome without affecting the ATPase activity. Such a "pin-like" structure mimics a "foot-step" on the DNA ladder, which differentiates ATRX from other remodelers. To translocate the DNA on the nucleosome, two more features, including a disordered insertion that contacts the histone surface and a positively charged loop bridging the cross-gyre interactions, serve as essential anchors for the nucleosome modulation by ATRX. Together, we propose a "climbing" model for how ATRX mobilizes the DNA upon ATP hydrolysis.

biochemistry↗

bioRxiv2025

From Single Molecular Detail to Subcellular Dynamics: Real-Time Kinetics Study of dPA Uptake with Raman-based Spectroscopy

Real-time observation of cellular transformations at the subcellular level provides insight into the dynamic biochemical processes underlying cell function and disease. However, many challenges remain in developing methods to analyze metabolic transformations in cells quantitatively. Our study applies Raman spectroscopy (RS) and stimulated Raman scattering (SRS) to link single-molecule resolution with cellular-scale lipid turnover tracking. Using HL-60 cells as a model, we monitor the uptake kinetics of deuterated palmitic acid (dPA), a marker of de novo lipogenesis, from the first minutes to hours. SRS enables microscopic, high-temporal-resolution visualization of dPA incorporation across entire cell volumes, capturing both its distribution and uptake rate. Complementary RS measurements identify distinct metabolic phases: rapid incorporation into pre-existing lipid droplets (LDs) followed by the emergence of new, partially unsaturated LDs associated with cytochrome-linked metabolism. Statistical and spectral analyses reveal cell-to-cell heterogeneity, emphasizing the complexity of lipid metabolism at both the cellular and subcellular levels. By integrating SRS and RS data into time-dependent kinetic profiles, we establish a unified submicron-to-cellular model of fatty acid metabolism. This multi-resolution spectroscopic approach demonstrates how real-time, label-based tracking can uncover dynamic metabolic heterogeneity, advancing understanding of the fatty acid uptake and metabolism in the microscale.

cell biology↗

bioRxiv2025

Two routes from the Fertile Crescent led to the introduction of common vetch into Europe.

Vicia sativa (common vetch, n=6) is an annual leguminous plant with high drought tolerance and high grain protein content. Historically and still today, vetches are important for nitrogen fixation to maintain cereal yields and feeding grazing livestock. In this study, we re-sequenced the genomes of 279 common vetch accessions from a wide geographic range covering western Eurasia and North Africa to construct a comprehensive nucleotide variation map. Population structure analyses indicate that the Middle Eastern region was the centre of origin of common vetch, which then entered Europe in two distinct waves. One wave propagated by humans through Turkey into the Carpathian Basin before spreading throughout Europe via "Danubian" and "Mediterranean" routes. Demographic inferences revealed a significant bottleneck for all common vetch groups initiated during the Last Glacial Maximum, followed by an expansion that coincides with the onset of the warm Holocene epoch and the Neolithic Revolution. Interestingly, we identified selective sweeps for the flowering time regulators VsSOC1 and VsFTb2 in northern latitude populations suggesting that both genes are important regulators of latitudinal adaptation. Overall, we provide valuable genomic resources for conservation and breeding programs to optimize food production in the face of population growth and reduced agricultural resources.

plant biology↗

bioRxiv2025

Insights from modern & historical genomes of Neorhizobium vitis, a new pathogen causing neoplastic growths on grapevine.

Grapevine crown gall is a globally significant disease typically attributed to Agrobacterium species carrying tumour-inducing (Ti) plasmids. In this study, we identify Neorhizobium vitis as a previously unrecognised crown gall-associated pathogen. Four modern isolates from symptomatic grapevines in South Australia and four historical strains collected in New South Wales in 1989 induced weak but consistent neoplastic growths on sunflower hypocotyls and carrot discs. Long-read genome sequencing revealed that all strains lack canonical Ti plasmids and the oncogenes iaaM and ipt, which are essential for classical auxin- and cytokinin-mediated tumorigenesis. Phylogenomic analyses reassigned all strains to the Neorhizobium clade, correcting the original classification of historical isolates as Agrobacterium vitis. The persistence of tumorigenic activity despite the absence of known virulence genes suggests the involvement of alternative, yet uncharacterized pathogenic mechanisms. These findings revise the non-pathogenic status of Neorhizobium, establish N. vitis as a novel tumorigenic lineage, and underscore the value of re-evaluating legacy isolates with modern genomic tools.

plant biology↗

bioRxiv2025

CRISPR-based shuttle cloning of 1,397 human genes into UAS vectors

The construction of genome-wide DNA libraries from publicly available resources is essential for leveraging functional genomics to investigate complex biological systems. However, all existing high-throughput cloning methods for transferring DNA fragments between vectors require PCR amplification of the DNA fragments, rendering the construction of genome-wide DNA libraries labor-intensive and time-consuming. By introducing a concept of CRISPRshuttle cassette, we herein present a method named CRISPR-based shuttle cloning (CRISPRshuttle cloning). This method enables the high-throughput transfer of numerous DNA fragments from original plasmids with identical backbones to a different vector background without the need for PCR amplification of the DNA fragments. The procedure comprises two-step test tube reactions followed by bacterial transformation. Using CRISPRshuttle we successfully generated a library of GAL4/UAS-based UAS-ORF plasmids covering 1,397 human genes conserved in Drosophila. This library may serve as a valuable resource for gain-of-function screening in cultured cells and for the creation of a transgenic UAS-ORF library in Drosophila.

molecular biology↗

bioRxiv2022

Adrenal sympathetic nerve mediated the anti-inflammatory effect of electroacupuncture at ST25 acupoint on a rat model of sepsis

Acupuncture plays a vital anti-inflammatory action on sepsis through activating autonomic nerve anti-inflammatory pathways, such as sympathoadrenal medullary pathway, but the mechanism remains unclear. This study aims to explore the optimum parameter of electroacupuncture (EA) stimulation in regulating sympathoadrenal medullary pathway and evaluate EAs anti-inflammatory effect on sepsis. To explore the optimum parameter of EA at homosegmental acupoint on adrenal sympathetic activity, the left adrenal sympathetic nerve firing rate evoked by different intensities of single shock electrical stimulation (ES) at ST25 in healthy male Sprague-Dawley (SD) rats were evaluated by in vivo electrophysiological recording, and the levels of norepinephrine (NE) and its metabolites were also examined using mass spectrometry. To verify the role of EA at ST25 in sepsis, the rat was given intraperitoneal injection lipopolysaccharide to induce sepsis model, and survival rate, clinical score, and the level of interleukin (IL)-6, IL-1{beta}, and IL-10 were evaluated after EA application. We observed that 3 mA is the optimal intensity on activating adrenal sympathetic nerve, which significantly elevated the level of NE in the peripheral blood. For LPS-treated rats, EA at the ST25 apparently increased the survival rate and improved the clinical score compared to the control group. Furthermore, 3 mA EA at ST25 significantly decreased pro-inflammatory cytokines IL-6 and IL-1{beta} and upregulated anti-inflammatory cytokine IL-10 compared to the Lipopolysaccharide (LPS)-treated group. Overall, these data suggest that 3 mA is the optimal EA intensity at ST25 to activate the sympathoadrenal medullary pathway and exert an anti-inflammatory effect on sepsis. HighlightsO_LI3 mA single shock ES at ST25 drove adrenal sympathetic nerve reflexs. C_LIO_LI3 mA EA at ST25 upregulated NE concentration in peripheral blood. C_LIO_LIEA at ST25 improved the survival rate in a rat of LPS-induced sepsis model. C_LIO_LIEA at the ST25 upregulated anti-inflammatory IL10 and downregulated pro-inflammatory IL1{beta} and IL-6 in LPS-treated rats. C_LI

neuroscience↗

bioRxiv2021

Chromosome-level assembly of the common vetch reference genome (Vicia sativa)

BackgroundVicia sativa L. (Common Vetch, n = 6) is an annual, herbaceous, climbing legume that is distributed in tropical, sub-tropical and temperate climates. Originating in the Fertile Crescent of the Middle East, V. sativa is now widespread and grows in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V. sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we here present a chromosome-level reference genome sequence for V. sativa. ResultsWe applied a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis to construct a chromosome-level genome of V. sativa. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.9 gigabases (Gb) with a median contig length of 684 kb. Benchmarking Universal Single-Copy Orthologs (BUSCO) of the assembly demonstrated a very high completeness of 98 % of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 58,415 protein-coding genes. ConclusionsThe high-quality chromosome-level genome assembly of V. sativa will provide novel insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.

genomics↗

bioRxiv2020

PFRED: A computational platform for siRNA and antisense oligonucleotides design.

PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred/pfred-gui/releases as a java Jar file. The source code and the links for downloading the precompiled version can be found at https://github.com/pfred.

bioinformatics↗

bioRxiv2018

The Population Genetic Variation Analysis of Bitter Gourd Wilt Caused by Fusarium oxysporum f. sp. momordicae in China by Inter Simple Sequence Repeats (ISSR) Molecular Marker

The bitter gourd fusarium wilt caused by Fusarium oxysporum f.sp. momordicae (FOM) was a devastating disease in China and leading to great economic losses every year. A total of 152 isolates, which have the typical Fusarium oxysporum characteristics with abundant microconidia and macroconidia on the white or ruby colonies, were obtained from diseased plant tissues with typical fusarium wilt symptoms. The BLASTn analysis of rDNA-ITS showed 99% identity with F.oxysporum species. Among the tested isolates, three isolates infected tower gourd, and five isolates were pathogenic to bottle gourd. However, they were all pathogenic to bitter gourd. Based on the molecular and morphologic results, the isolates were identified as FOM. For genetic variation analysis, forty ISSR primers were screened and eleven primers were used in PCR amplification. Totally, 121 loci were detected, of which 52 loci were polymorphic at rate of 42.98%. The POPGENE analysis showed that Neis gene diversity index (H) and Shannons information index (I) were 0.0902 and 0.1478, respectively, which indicated that the genetic diversity for the tested 152 isolates was relatively low. It also means that each geographical population was a relatively independent unit. While the value of coefficient of gene differentiation (Gst=0.4929 > 0.15) pointed to the genetic differentiation was mainly among populations. The strength of gene flow (Nm=0.5143<1.0) was weaker, indicating that gene exchanges were blocked to some degree. The dendrogram based on ISSR markers showed that the eight geographical populations were clustered into four groups at the threshold of genetic similar coefficient 0.96. Fujian, Jiangxi and Guangdong populations were clustered into Group I. Group II contained Hunan and Guangxi populations. Group III only had Hainan population. Group IV consisted Shandong and Henan populations. The geographical populations closer to each other grouped together, suggesting a correlationship between geographical origin and genetic differentiation. Two hybridization events were observed between Hainan and Hunan populations and between Guangdong and Guangxi by Structure analysis. Our findings enrich the knowledge on genetic variation characteristics of the FOM populations with helpful of development of effective disease management programs and disease resistance breeding.

microbiology↗