Biology subjects

Lv, B.

Publications and source records attributed to Lv, B..

14 recordsLinked to original sources

bioRxiv2026

Evolutionary Origins and Synthetic Reconstruction of Gingerols

How new enzymatic activities become integrated with existing metabolic networks to generate lineage-restricted plant chemistry remains a central question in metabolic evolution, exemplified by gingerol biosynthesis in Zingiberaceae, whose complete enzymatic basis has remained elusive. Here, we resolve this problem by elucidating the evolutionary origins and the full biosynthetic pathway of gingerol through single-cell transcriptomics, functional screening, structural biology, comparative genomics and pathway reconstruction. A coordinated metabolic program operates in ginger oil cells, thereby guiding the identification of diketide-CoA synthases, gingerol synthases (GS) and gingerol reductases that together constitute the complete pathway. GS remodels the conserved type III polyketide synthase scaffold to organize a fatty acyl-CoA and a phenylpropanoid-derived intermediate for gingerol formation. Furthermore, GS arose through duplication and limited active-site remodeling of a curcumin synthase-like enzyme, accompanied by coordinated recruitment of precursor-supply and reduction pathways. Translating these principles into yeast achieves the first de novo microbial production of 6-gingerol from glucose at 12.4 mg/L. These findings reveal the evolutionary logic by which plants recruit and coordinate novel enzymatic activities to establish lineage-restricted metabolic program, providing a framework for understanding and engineering specialized metabolism across the plant kingdom.

synthetic biology↗

bioRxiv2026

SOLAR Mediates Lysosomal Membrane Repair and Redox Defense

Lysosomal damage is increasingly recognized as a hallmark of aging. Understanding lysosomal quality control may open new therapeutic strategies to enhance lysosomal resilience. Here, we identify SOLAR (SQSTM1/p62 Oligomer-mediated Lysosomal Antioxidant Defense And Membrane Repair), a lysosomal quality control pathway that links CASM (conjugation of ATG8 to single membranes) to p62-driven membrane repair and redox signaling. In this pathway, CASM, but not macroautophagy, recruited p62 to damaged lysosomes. Efficient lysosomal recruitment of p62 required its ATG8-binding and self-oligomerizing domains, enabling p62 assemblies to promote membrane repair. p62 mutations associated with neurodegeneration interfered with p62 recruitment and compromised lysosomal repair. Besides membrane repair, the SOLAR pathway also activated the p62-KEAP1-NRF2 redox signaling axis, driving transcriptional upregulation of antioxidative genes and cholesterol biosynthesis. By integrating membrane repair and redox defense, SOLAR establishes a coordinated lysosomal quality control pathway with implications for aging and degenerative disease.

cell biology↗

bioRxiv2025

PtdIns(3,5)P2 Is an Endogenous Ligand of STING in Innate Immune Signaling

Cytosolic DNA exposure triggers innate immune responses through cyclic GMP-AMP (cGAMP) synthase (cGAS)1-3. Upon binding to DNA, cGAS is activated to produce cGAMP, which functions as a second messenger that binds to stimulator of interferon genes (STING), an endoplasmic reticulum (ER)-localized signaling adaptor3-5. STING then traffics from the ER to the Golgi, leading to activation of the kinases TBK1 and IKK and subsequent induction of interferons and other cytokines6-10. Here we show that phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P2] is an endogenous ligand of STING that functions together with cGAMP to induce STING activation. Proteomics analysis identified a constitutive interaction between STING and PIKfyve, an enzyme that produces PtdIns(3,5)P2 in mammalian cells. Deletion of PIKfyve blocked STING trafficking from the ER and TBK1 activation. In vitro reconstitution revealed a strong and selective effect of PtdIns(3,5)P2 on STING activation. Purified STING bound directly to PtdIns(3,5)P2 in a fluorescence resonance energy transfer (FRET) assay. Consistently, PtdIns(3,5)P2 promoted cGAMP-induced STING oligomerization by binding to a groove between STING dimers as revealed by cryo-EM (Li et al., co-submitted). Similar to PIKfyve depletion, mutation of the PtdIns(3,5)P2-binding residues in STING blocked its trafficking and downstream signaling. These results reveal PtdIns(3,5)P2 as a lipid ligand of STING with essential roles in innate immunity.

biochemistry↗

bioRxiv2025

Diet-Seg: Dynamic Hardness-Aware Learning for Enhanced Brain Tumor Segmentation

Accurate brain tumor segmentation in magnetic resonance imaging (MRI) remains a critical challenge due to complex tumor heterogeneity, fuzzy boundaries, and significant inter-patient variability. In this study, we propose Diet-Seg (Difficulty-Informed Edge-enhanced Tiny Segmentation), a novel segmentation framework that integrates entropy-based pixel-wise hardness estimation into the training process via a dynamic learning rate modulation strategy. Specifically, we employ a pretrained 3D U-Net information model to quantify voxel-level prediction uncertainty, which is then used to guide the optimization of the main segmentation model. Diet-Seg is further enhanced by an RWKV-based U-Net backbone to capture global spatial dependencies and an EdgeNet module to preserve tumor boundaries through edge-aware fusion. Extensive experiments on the BraTS2018-2021 datasets demonstrate that Diet-Seg consistently outperforms state-of-the-art baselines across all tumor subregions. Notably, Diet-Seg achieves superior generalization when trained on one dataset and validated across multiple years. Moreover, the hardness maps offer interpretable insights into segmentation difficulty, potentially enabling human-AI collaboration in clinical practice. These results highlight the promise of entropy-aware training as a general strategy for robust and efficient medical image segmentation. The work is implemented in the open-source project available on GitHub (https://github.com/ManuelTurner/Diet-Seg)

bioinformatics↗

bioRxiv2025

Discover the Maze-like Pathway for Glabridin Biosynthesis

Tailoring enzymes diversify plant metabolite scaffolds through complex, context-dependent modifications, generating maze-like biosynthetic networks that complicate metabolic pathway reconstruction. Here, we systematically deconstructed and reconstructed the biosynthetic network of glabridin, a valuable skin-whitening isoflavone from Glycyrrhiza. By integrating metabolic pathway mining with genome and 183 transcriptomes, we identified four functional routes among sixteen theoretical possibilities and uncovered a previously uncharacterized, ladder-like multi-route tailoring network. Reconstruction of such architecture in yeast revealed metabolic redundancy and interconnectivity confer unexpected robustness, enabling higher production efficiencies compared to a single-route design. Further modular engineering enabled the de novo biosynthesis of glabridin in yeast. Our work establishes a framework for reconstructing metabolic mazes and demonstrates that multi-route architectures can be harnessed to enhance the robustness and productivity of cell factories.

synthetic biology↗

bioRxiv2024

Stearoyl coenzyme A desaturase 1 (SCD1) regulates foot-and-mouth disease virus replication by modulating host cell lipid metabolism and 2C-mediated replication complex formation

The life cycle of foot-and-mouth disease virus (FMDV) is tightly regulated by host cell lipid metabolism. In a previous study, we successfully established a BHK-21 cell model (BHK-Op) for persistent FMDV infection by single-cell clone selection and isolated a virus-negative cell line (BHK-VEC cells) from high-passage BHK-Op cells. BHK-VEC cells could be not infected with FMDV. By conforming the transcriptome data of BHK-VEC cells and BHK-21 cells, we identified that the stearoyl coenzyme A desaturase 1 (SCD1), a key enzyme for the fatty acid metabolism, regulates FMDV replication. SCD1 overexpression or exogenous addition of oleic acid (OA), a product of SCD1 enzyme activity, promoted or upregulated FMDV replication in BHK-21 cells or SCD1 knockdown cells, respectively. Interestingly, overexpression of SCD1 or exogenous addition of OA restored the FMDV infection and replication in BHK-VEC cells. Exogenous addition of OA also promoted FMDV replication in BHK-Op. SCD1 recruited the nonstructural FMDV protein 2C to the detergent-resistant membrane located in the perinuclear nucleus to form replication complex. Inhibition of SCD1 enzyme activity resulted in significantly decreased number of FMDV replication complexes with also abnormal morphology. Importantly, inhibition of SCD1 enzyme activity effectively suppressed replication of other positive-sense RNA viruses, such as REO176, PV1 and EV71. Our results demonstrated that, as a key host regulator of RNA virus replication, SCD1 is a potential target for developing novel drugs against positive-sense RNA virus infection.

microbiology↗

bioRxiv2024

Silicone Wire Embolization-induced Acute Retinal Artery Ischemia and Reperfusion Model in Mouse: Gene Expression Provide Insight into Pathological Processes

Acute retinal ischemia and ischemia-reperfusion injury are the primary causes of retinal neural cell death and vision loss in retinal artery occlusion (RAO). The absence of an accurate mouse model for simulating the retinal ischemic process has hindered progress in developing neuroprotective agents for RAO. We developed a unilateral pterygopalatine ophthalmic artery occlusion (UPOAO) mouse model using silicone wire embolization combined with carotid artery ligation. The survival of retinal ganglion cells and visual function were evaluated to determine the duration of ischemia. Immunofluorescence staining, optical coherence tomography, and haematoxylin and eosin staining were utilized to assess changes in major neural cell classes and retinal structure degeneration at two reperfusion durations. Transcriptomics was employed to investigate alterations in the pathological process of UPOAO following ischemia and reperfusion, highlighting transcriptomic differences between UPOAO and other retinal ischemia-reperfusion models. The UPOAO model successfully replicated the acute interruption of retinal blood supply observed in RAO. 60-minutes of Ischemia led to significant loss of major retinal neural cells and visual function impairment. Notable thinning of the inner retinal layer, especially the ganglion cell layer, was evident post-UPOAO. Temporal transcriptome analysis revealed various pathophysiological processes related to immune cell migration, oxidative stress, and immune inflammation during the non-reperfusion and reperfusion periods. A pronounced increase in microglia within the retina and peripheral leukocytes accessing the retina was observed during reperfusion periods. Comparison of differentially expressed genes (DEGs) between the UPOAO and high intraocular pressure models revealed specific enrichments in lipid and steroid metabolism-related genes in the UPOAO model. The UPOAO model emerges as a novel tool for screening pathogenic genes and promoting further therapeutic research in RAO.

neuroscience↗

bioRxiv2022

Regulation of Hedgehog Signaling Through Arih2-Mediated Smoothened Ubiquitination and Endoplasmic Reticulum-Associated Degradation

During Hedgehog signaling, the ciliary levels of Ptch1 and Smo are regulated by pathway activity. At the basal state, Ptch1 localizes to cilia and prevents the ciliary accumulation and activation of Smo. Upon stimulation with Hedgehog ligand, Ptch1 exits cilia and relieves the inhibition of Smo. Uninhibited Smo concentrates in cilia, becomes activated, and activates the downstream steps of the pathway. Loss of the ubiquitin E3 ligase Arih2 elevates the cellular level of Smo, causes Smo to inappropriately localize to cilia at the at the basal state, and elevates basal expression of Hedgehog responsive genes. Mice express two isoforms of Arih2 with different N-termini, but neither isoform localizes to cilia. Instead, Arih2 is found in the nucleus and Arih2{beta} is found on the cytoplasmic face of the endoplasmic reticulum. Re-expression of endoplasmic reticulum-localized Arih2{beta}, but not nuclear-localized Arih2 returns the cellular Smo levels back to normal and rescues the ciliary Smo accumulation phenotype. When Arih2{beta} is missing, protein aggregates accumulate in the endoplasmic reticulum and the unfolded protein response is activated. Inhibitor studies suggest that Arih2{beta} functions to mark excess or misfolded Smo for degradation by endoplasmic reticulum-associated degradation. When Arih2{beta} is defective, excess Smo, possibly misfolded, is delivered to the cell surface and cilium where it interferes with pathway regulation. These findings add another level of complexity to the Hedgehog pathway.

cell biology↗

bioRxiv2022

Lyophilized mRNA-lipid nanoparticles vaccine with long-term stability and high antigenicity against SARS-CoV-2

Advanced mRNA vaccines play vital roles against SARS-CoV-2. However, due to their poor stability, most current mRNA delivery platforms need to be stored at -20{degrees}C or -70{degrees}C, which severely limits their distribution. Herein, we present lyophilized SARS-CoV-2 mRNA-lipid nanoparticle vaccines, which can be stored at room temperature with long-term thermostability. In the in vivo Delta virus challenge experiment, lyophilized Delta variant mRNA vaccine successfully protected mice from infection and cleared the virus. Lyophilized omicron mRNA vaccine enabled to elicit both potent humoral and cellular immunity. In booster immunization experiments in mice and old monkeys, lyophilized omicron mRNA vaccine could effectively increase the titers of neutralizing antibodies against wild-type coronavirus and omicron variants. In humans, lyophilized omicron mRNA vaccine as a booster shot could also engender excellent immunity and had less severe adverse events. This lyophilization platform overcomes the instability of mRNA vaccines without affecting their bioactivity, and significantly improved their accessibility, particularly in remote regions.

immunology↗

bioRxiv2021

A bacterial Argonaute with efficient DNA and RNA cleavage activity guided by small DNA and RNA

Argonaute proteins are widespread in prokaryotes and eukaryotes. Most prokaryotic Argonaute proteins (pAgos) use 5P-gDNA to target complementary DNA. However, more and more studies on the properties of pAgos make their functions more diversified. Previously reported pAgos only possess several forms of high activity in all eight cleavage patterns, which limits their practical applications. Here, we described a unique pAgo from Marinitoga hydrogenitolerans (MhAgo) with eight cleavage activities. MhAgo can utilize all four types of guides (5OH-gDNA, 5P-gDNA, 5OH-gRNA, and 5P-gRNA) for ssDNA and RNA cleavage. Further studies demonstrated that MhAgo had high activities with 16-21 nt guides and no obvious preferences for the 5-end nucleotides of 5OH-guides. Unexpectedly, MhAgo had different preferences for the 5-end nucleotides of 5P-guides depending on the types of targets. Although the specificity of MhAgo was related to the types of guides, single mismatches in the central and 3-supplementary regions of guides greatly reduced the cleavage efficiency. Additionally, the electrophoretic mobility shift assay (EMSA) demonstrated MhAgo had the weakest affinity for 5P-gRNA:tRNA duplex, which was consistent with its cleavage efficiency. In conclusion, MhAgo is highly active under a wide range of conditions and can be used for programmable endonucleolytic cleavage of both ssDNA and RNA substrates. The abundant biochemical characteristics of MhAgo broaden our understanding of pAgos and expand the potential application in nucleic acids manipulations.

molecular biology↗

bioRxiv2019

Ubiquitin Links Smoothened to Intraflagellar Transport to Regulate Hedgehog Signaling

In the absence of hedgehog ligand, patched-1 (Ptch1) localizes to cilia and prevents ciliary accumulation and activation of smoothened (Smo). Upon ligand binding, Ptch1 is removed from cilia, Smo is derepressed and accumulates in cilia where it activates signaling. The mechanisms regulating these dynamic movements are not well understood but defects in intraflagellar transport components including Ift27 and the BBSome cause Smo to accumulate in cilia without pathway activation. We find that in the absence of ligand-induced pathway activation, Smo is ubiquitinated and removed from cilia, and this process is dependent on Ift27 and BBSome components. Activation of hedgehog signaling decreases Smo ubiquitination, and ciliary removal, resulting in its accumulation. Blocking ubiquitination of Smo by an E1 ligase inhibitor or by mutating two lysine residues in intracellular loop three cause Smo to aberrantly accumulate in cilia without pathway activation. These data provide a mechanism to control Smos ciliary level during hedgehog signaling by regulating the ubiquitination state of the receptor. SummaryHedgehog signaling involves the dynamic movement of receptors and effectors in and out of cilia. We find that the dynamics of Smo is regulated by ubiquitination, which regulates its interaction with the intraflagellar transport system to control ciliary levels of this receptor.

cell biology↗

bioRxiv2019

Neuroprotective effects of crocin I and II in an ischemia-reperfusion injury model

BackgroundCrocin I and II are derived from the medicinal plant Crocus sativus L. (Saffron), and their neuroprotective effects have been attracting more and more attention. However, their protective effect against cerebral apoplexy induced by hypoxia has not been reported. In this study, we aimed to clarify the roles of crocin I and II in protecting against ischemic injury.\n\nMaterials/MethodsWe generated a rat cerebral ischemia-reperfusion injury model using a reversible cerebral artery occlusion suture method and found changes in amino acid neurotransmitters in the frontal cortex after drug administration. We also identified changes in mRNA expression of Bcl2, Bax, Casp3, P38, and NFkb1 in the frontal cortex and changes in antioxidant indices in the brain.\n\nResultsCrocin I and II both had protective effects on ischemic/anoxic injury in vivo by downregulating the expression of Casp3 and Nfkb1 mRNA and the steady-state levels of excitatory amino acids/inhibitory amino acids during ischemia and reperfusion and by improving the total antioxidant capacity and total superoxide dismutase activities during ischemia. We also found that crocin I and II had synergistic effects when used together.\n\nConclusionsThese findings displayed that crocin I and II could protect animal model against ischemic and anoxic injury and provided new evidence for both molecules potential medicinal value.

neuroscience↗

bioRxiv2019

Single-Cell RNA Sequencing Reveals Regulatory Mechanism for Trophoblast Cell-Fate Divergence in Human Peri-Implantation Embryo

Multipotent trophoblasts undergo dynamic morphological movement and cellular differentiation after embryonic implantation to generate placenta. However, the mechanism controlling trophoblast development and differentiation during peri-implantation development remains elusive. In this study, we modeled human embryo peri-implantation development from blastocyst to early post-implantation stages by using an in vitro coculture system, and profiled the transcriptome of individual trophoblast cells from these embryos. We revealed the genetic networks regulating peri-implantation trophoblast development. While determining when trophoblast differentiation happens, our bioinformatic analysis identified T-box transcription factor 3 (TBX3) as a key regulator for the differentiation of cytotrophoblast into syncytiotrophoblast. The function of TBX3 in trophoblast differentiation is then validated by a loss-of-function experiment. In conclusion, our results provided a valuable resource to study the regulation of trophoblasts development and differentiation during human peri-implantation development.

cell biology↗

bioRxiv2018

The rice G protein γ subunit qPE9-1 positively regulates grain-filling process by interacting with abscisic acid and auxin

The rice genome contains a single G (RGA1) and G{beta} (RGB1) and five G{gamma} subunits. Recent genetic studies have shown that DEP1/qPE9-1, an atypical putative G{gamma} protein, is responsible for dense and erect panicles, but the biochemical and molecular mechanisms underlying control of grain size are not well understood. Here, we report that plants carrying qPE9-1 have more endosperm cells per grain than plants contain the qpe9-1 allele. The qPE9-1 line has a higher rate and longer period of starch accumulation than the qpe9-1 line. Additionally, the expression of several key genes encoding enzymes catalyzing sucrose metabolism and starch biosynthesis is higher in the qPE9-1 line than in the qpe9-1 line, especially from the mid to late grain-filling stage. Grains of the qPE9-1 line also have higher contents of two phytohormones, ABA and IAA. Exogenous application of ABA or IAA enhanced starch accumulation and the expression of genes encoding grain-filling-related enzymes in the grains of qPE9-1, whereas only IAA produced these effects in qpe9-1. Based on these results, we conclude that qPE9-1 promotes endosperm cell proliferation and positively regulates starch accumulation largely through ABA and IAA, which enhance the expression of genes encoding starch biosynthesis during the late grain-filling stage.

plant biology↗