Biology subjects

Ding, A.

Publications and source records attributed to Ding, A..

17 recordsLinked to original sources

bioRxiv2026

Listeriolysin O recruits UBA1 to ubiquitinate NLRP3 and suppress inflammasome defence

The NLRP3 inflammasome is a central cytosolic defence pathway against infection, yet intracellular pathogens must restrain this response to preserve their replicative niche. Here we identify a ubiquitin-dependent immune-evasion mechanism in which L. monocytogenes uses listeriolysin O (LLO) to destabilise NLRP3. The N-terminal PEST-like sequence of LLO acted as an adaptor that recruited the host ubiquitin-activating enzyme UBA1 and promoted K48-linked polyubiquitination of NLRP3. This modification drove proteasomal NLRP3 degradation and limited caspase-1 activation, gasdermin D cleavage, IL-1{beta}/IL-18 release, and macrophage pyroptosis. Deleting the PEST region preserved basal haemolytic activity but impaired NLRP3 ubiquitination, thereby enhancing inflammasome activation during infection in macrophages and in vivo. Conversely, UBA1 overexpression suppressed NLRP3-mediated inflammatory responses and supported intracellular bacterial survival. UBA1 depletion restored NLRP3 protein levels, reduced bacterial burden and delayed lethal infection, albeit with increased inflammatory tissue injury. These findings define a ubiquitin-hijacking strategy that operates at the E1 step, whereby a bacterial toxin redirects host ubiquitin activation towards an innate immune sensor.

microbiology↗

bioRxiv2026

4D Biomimetic Morphing Hydrogel Scaffold via Biaxial Gradient Programming

Four-dimensional (4D) materials incorporating functional gradient designs offer a powerful platform for engineering dynamic structures capable of programmed shape transformations in response to environmental stimuli. However, most gradient-based 4D systems rely on uniaxial gradients, which typically generate simple, symmetric deformations with uniform curvature, limiting their ability to recreate biomimetic architectures that require spatially coordinated morphogenesis. Here, we report a biaxial gradient-engineered 4D hydrogel system capable of programmable, non-uniform shape morphing within a single construct. A one-step photocrosslinking strategy integrates vertical light attenuation and horizontal grayscale photomask patterning to establish orthogonal crosslinking gradients along two directions, producing spatially heterogeneous swelling stresses that drive controlled multi-directional deformation. The resulting hydrogels exhibit tunable swelling and mechanical properties, enabling precise regulation of curvature distribution and shape transformation. This biaxial gradient platform generates diverse biomimetic architectures, including swan-neck, fiddlehead fern, sea star, and Euonymus europaeus-like structures. Importantly, the system supports cell-laden biofabrication, where human mesenchymal stem cell-encapsulated constructs maintain high viability and undergo chondrogenic differentiation while preserving programmed morphologies. This work establishes biaxial gradient-programmed 4D hydrogels as a robust strategy for integrating morphogenesis with tissue formation, advancing biomimetic biofabrication and morphogenetic tissue engineering.

bioengineering↗

bioRxiv2026

Self-Actuating 4D Cell-Strand Bioprinting

Engineering biomimetic tissues with dynamically evolving 3D architectures represents an important direction for next-generation tissue engineering, as it enables recapitulation of the continuous morphogenesis of native tissues during development and regeneration. Here, a self-actuating 4D cell-strand bioprinting platform is developed to engineer complex tissue architectures through autonomous cell contractile force (CCF)-driven morphing without requiring external stimuli. The platform integrates a mechanically compliant and self-softening base hydrogel with embedded high-density cell strands printed using a fast-degrading carrier bioink. During culture, the carrier bioink rapidly degrades while the encapsulated cells proliferate and establish connected cellular networks, generating localized contraction that drives programmable shape transformation. Through spatial patterning of embedded cell strands, constructs with diverse morphologies, including V-shaped, helical, folded, and tubular architectures, are generated via controllable self-actuated morphogenesis. The platform further enables engineering of cartilage-like and bone-like tissues with well-defined curvature configurations and mechanically robust tissue matrices. In addition, programmable multi-tissue engineering is demonstrated through fabrication of a muscle-tendon junction-mimicking construct containing spatially organized fibroblast and myoblast compartments. This self-actuating 4D bioprinting strategy enables highly programmable and directionally controlled morphogenesis using a simple construct design with low cell amount requirements, providing a versatile platform for engineering dynamic tissue architectures.

bioengineering↗

bioRxiv2026

AM-DMF-SCP-pro: An Ultrafast and Streamlined Nanolitre-Scale Lab-on-a-Chip Platform for Single-Cell Proteomics and Tumor Microenvironment Profiling

Single-cell proteomics (SCP) remains constrained by slow sample preparation and background interference in low-input, multistep workflows, limiting its broader practical use in complex biological samples. Here we report AM-DMF-SCP-pro, a streamlined active-matrix digital microfluidic workflow that enables rapid on-chip lysis and digestion in 6 nL droplets within a closed nanolitre-confined microenvironment. AM-DMF-SCP-pro reduces total sample-preparation time to as little as 30 min, including a 15 min digestion step, while maintaining quantitative reproducibility and digestion performance. Systematic optimization of mass spectrometry acquisition and nanolitre-scale digestion conditions enables deeper, more sensitive and lower-background proteome profiling from ultra-low peptide inputs. In murine tumor samples, AM-DMF-SCP-pro reliably resolves immune and tumor compartments, identifies treatment-associated tumor cell states and enables quantitative analysis of neutrophil-associated proteomic signatures. These results establish AM-DMF-SCP-pro as a practical workflow for rapid, low-background single-cell proteome profiling in complex biological samples.

systems biology↗

bioRxiv2025

A 4D Bio-Kirigami Strategy for Engineering Complex Tissue Curvatures

AbstractFour-dimensional (4D) systems offer a promising approach for generating sophisticated dynamic structures that mimic native tissue architectures. Among those, Kirigami strategies enable precise, localized control over morphing behaviors, yet their application in 4D tissue engineering remains unexplored. Here, we present a bio-Kirigami system that facilitates the creation of dynamic, transformable structures through spatially patterned hydrogels with distinct deformation modes dictated by encoded swelling differentials. The system consists of two biomaterial components: (1) a photocrosslinked hydrogel framework with controlled degradation and swelling behavior that drives the shape transformation and (2) a rigid support hydrogel frame. By leveraging photolithographic patterning, complex structures with continuously evolving configurations were achieved through preprogrammed deformations. Bio- Kirigami hydrogels encapsulating stem cells developed into tissue-like constructs with sophisticated configurations when cultured in tissue-specific environment. Notably, the engineered tissue constructs kept their shape integrity after excision from the outer support, demonstrating a robust platform for achieving intricate tissue curvatures.

bioengineering↗

bioRxiv2025

Three-dimensional tissue platform co-laid with native collagen fibers and cells for phenotypic screening of stem cell interactions

Phenotypic screening of cell-cell and cell-matrix interactions is critical yet challenging for drug discovery and disease modeling. In this study, a scalable 3D tissue platform was developed by co-laying extracted natural insoluble collagen fibers, mesenchymal stem cells, endothelial cells, and neural progenitor cells for phenotypic screening. Cell growth and interactions were enhanced in the co-laid platform, evident through increased cell proliferation, viability, and vascularization. Dense vascular networks rapidly formed through cell-cell and cell-matrix interactions without adding a traditionally needed growth factor set. Both in vitro and implantation studies confirmed that these blood vessels were of human origin. To evaluate the phenotypic screening of cell-cell and cell-matrix interactions, we propose a phenotype screening prototype for stem cell interactions that utilized multivariate analysis encompassing both cell-cell and cell-matrix interactions and demonstrated its effectiveness to screen vasculature formation and autism spectrum disorder (ASD) models. Using the prototype, we confirmed that collagen crosslinking, ROCK, WNT, and YAP pathways impact vasculogenesis. In addition, ASD donor-derived neural progenitor cells can be distinguished from non-ASD control donor-derived neural progenitor cells.

bioengineering↗

bioRxiv2025

Cell Contractile Force-Mediated Morphodynamical Tissue Engineering via 4D Printed Degradable Hydrogel Scaffolds

Tissue morphogenesis is a critical aspect tissue development. Recent advances in four-dimensional (4D) cell scaffolds have shown promise for modeling morphogenic processes. While current 4D systems often rely on external stimuli, they tend to overlook the role of intrinsic cell-generated forces, such as cell contractile forces (CCFs), in driving tissue morphogenesis. The paradox between the inherent weakness of CCFs and the robustness of tissue scaffolds presents a significant challenge in achieving effective shape transformations. In this study, we introduce an easily printable, freestanding, cell-laden hydrogel platform designed to harness CCFs for 4D shape morphing. These hydrogels initially provide mechanical support to maintain structural integrity, followed by rapid degradation that amplifies CCFs through enhanced cell-cell interactions and increased local cell density, thereby inducing tissue morphogenesis. This platform enables the formation of scaffold-free constructs with programmed shape transformations. By modulating the initial printed geometries, complex and large tissue constructs can be generated via controlled global shape transformations. Furthermore, the platform supports 4D tissue engineering by facilitating tissue differentiation coupled with dynamic shape evolution. This CCF-4D system represents a significant advancement in biomimetic tissue engineering, offering new avenues for creating dynamic tissue models that closely replicate native morphogenesis.

bioengineering↗

bioRxiv2025

Reprogrammable 4D Tissue Engineering Hydrogel Scaffold via Reversible Ion Printing

Shape changeable hydrogel scaffolds recapitulating morphological dynamism of native tissues have emerged as an elegant tool for future tissue engineering (TE) applications, due to their capability to create morphodynamical tissues with complex architectures. Hydrogel scaffolds capable of preprogrammable, reprogrammable and/or reversible shape transformations would widely expand the scope of possible temporal shape changes. Current morphable hydrogels are mostly based on multimaterial, multilayered structures, which involve complicated and time-consuming fabrication protocols, and are often limited to single unidirectional deformation. This work reports on the development of a transformable hydrogel system using a fast, simple, and robust fabrication approach for manipulating the shapes of soft tissues at defined maturation states. Simply by using an ion-transfer printing (ITP) technology (i.e., transferring Ca2+ from an ion reservoir with filter paper and subsequent covering on a preformed alginate-derived hydrogel), a tunable Ca2+ crosslinking density gradient across the hydrogel thickness has been incorporated, which enables preprogrammable deformations upon further swelling in cell culture media. Combining with a surface patterning technology, cell-laden constructs (bioconstructs) capable of morphing in multiple directions are deformed into sophisticated configurations. Not only can the deformed bioconstructs recover their original shapes by chemical treatment, but at user-defined times they can also be incorporated with new, different spatially controlled gradient crosslinking via the ITP process, conferring 3D bioconstruct shape reprogrammability. In this manner, unique "3D-to-3D" shape conversions have been realized. Finally, we demonstrated effective shape manipulation in engineered cartilage-like tissue constructs using this strategy. These morphable scaffolds may advance 4D TE by enabling more sophisticated spatiotemporal control over construct shape evolution.

bioengineering↗

bioRxiv2024

Cell Contractile Forces Drive Spatiotemporal Morphing in 4D Bioprinted Living Constructs

Current 4D materials typically rely on external stimuli such as heat or light to accomplish changes in shape, limiting the biocompatibility of these materials. Here, a composite bioink consisting of oxidized and methacrylated alginate (OMA), methacrylated gelatin (GelMA), and gelatin microspheres is developed to accomplish free-standing 4D bioprinting of cell-laden structures driven by an internal stimulus: cell-contractile forces (CCF). 4D changes in shape are directed by forming bilayer constructs consisting of one cell-free and one cell-laden layer. Human mesenchymal stem cells (hMSCs) are encapsulated to demonstrate the ability to simultaneously induce changes in shape and chondrogenic differentiation. Finally, the capability to pattern each layer of the printed constructs is exhibited to obtain complex geometric changes, including bending around two separate, non-parallel axes. Bioprinting of such 4D constructs mediated by CCF empowers the formation of more complex constructs, contributing to a greater degree of in vitro biomimicry of biological 4D phenomena.

bioengineering↗

bioRxiv2024

In situ cell condensation-based cartilage tissue engineering via immediately implantable high-density stem cell core and rapidly degradable shell microgels

Formation of chondromimetic human mesenchymal stem cells (hMSCs) condensations typically required in vitro culture in defined environments. In addition, extended in vitro culture in differentiation media over several weeks is usually necessary prior to implantation, which is costly, time consuming and delays clinical treatment. Here, this study reports on immediately implantable core/shell microgels with a high-density hMSC-laden core and rapidly degradable hydrogel shell. The hMSCs in the core formed cell condensates within 12 hours and the oxidized and methacrylated alginate (OMA) hydrogel shells were completely degraded within 3 days, enabling spontaneous and precipitous fusion of adjacent condensed aggregates. By delivering transforming growth factor-{beta}1 (TGF-{beta}1) within the core, the fused condensates were chondrogenically differentiated and formed cartilage microtissues. Importantly, these hMSC-laden core/shell microgels, fabricated without any in vitro culture, were subcutaneously implanted into mice and shown to form cartilage tissue via cellular condensations in the core after 3 weeks. This innovative approach to form cell condensations in situ without in vitro culture that can fuse together with each other and with host tissue and be matured into new tissue with incorporated bioactive signals, allows for immediate implantation and may be a platform strategy for cartilage regeneration and other tissue engineering applications.

bioengineering↗

bioRxiv2023

Exploring information exchange between Thesium chinense and its host Prunella vulgaris through joint transcriptomic and metabolomic analysis

Background: Thesium chinense known as "plant antibiotic" is a facultative root hemi-parasitic herb while Prunella vulgaris can serve as its host. However, the molecular mechanisms underlying the communication between T. chinense and its host remained largely unexplored. The aim of this study was to provide a comprehensive view of transferred metabolites and mobile mRNAs between T. chinense and P. vulgaris. Results: The wide-target metabolomic and transcriptomic analysis identified 5 transferred metabolites and 668 mobile genes between T. chinense and P. vulgaris, as well as haustoria formation related 56 metabolites and 189 genes. Furthermore, we inferred a regulatory network that might be involved in haustoria formation, and 18 genes promoting haustoria formation and 1 gene inhibiting it were identified as a consequence. There were 4 metabolites (ethylsalicylate, eriodictyol-7-O-glucoside, aromadendrin-7-O-glucoside and pruvuloside B) that are transferred from P. vulgaris to T. chinense, whereas 2-ethylpyrazine was transferred from T. chinense to P. vulgaris. Conclusions: These results suggested that there was an extensive exchange of information with P. vulgaris including transferred metabolites and mobile mRNAs, which might facilitate the haustoria formation and parasition of T. chinense. Author summaryT. chinense known as "plant antibiotic" is a facultative root hemi-parasitic herb while P. vulgaris can serve as its host. Currently, the information exchange between T. chinense and its host remained unknown, and a comprehensive view of transferred metabolites and mobile mRNAs between T. chinense and its host is critical so that appropriate chemical and genetic improvement can be used to facilitate haustoria formation and successful parasitism. Here, we employ the conjoint wide-target metabolomic and transcriptomic analysis to explore the information exchange between T. chinense and P. vulgaris. We identified 5 transferred metabolites and 668 mobile genes between T. chinense and P. vulgaris, as well as haustoria formation related 56 metabolites and 189 genes. Our study provides new insights into the complex interplay between parasite and host during parasitism.

plant biology↗

bioRxiv2022

4D Cell-Condensate Bioprinting

4D bioprinting techniques that facilitate formation of shape-changing scaffold-free cell condensates with prescribed geometries have yet been demonstrated. Here, a simple yet novel 4D bioprinting approach is presented that enables formation of a shape-morphing cell condensate-laden bilayer system comprised of an actuation layer and a cell condensate-supporting microgel (MG) layer. The strategy produces scaffold-free cell condensates which morph over time into predefined complex shapes. With a sequential printing (i.e., MG printing first onto the preformed actuation hydrogel layer and cell-only printing inside the pre-printed MG construct second), cell condensate-laden bilayers with specific geometries are readily fabricated and can be further UV-crosslinked to form strong interlayer adhesion. Since the bilayers have tunable deformability and MG degradation can be tailored, this enables controllable morphological transformations and on-demand liberation of cell condensates. With this system, large cell condensate-laden constructs with various complex shapes were obtained through predefined conformational conversions. As a proof-of-concept study, the formation of the letter "C" and helix-shaped robust cartilage-like tissues differentiated from human mesenchymal stem cells (hMSCs) was demonstrated. This new system brings about a new versatile 4D bioprinting platform idea that is anticipated to broaden and facilitate the applications of cell condensation-based 4D bioprinting.

bioengineering↗

bioRxiv2022

Highly efficient multiplex genome editing in dicot plants using improved CRISPR/Cas systems

CRISPR/Cas9-mediated gene editing provides a powerful tool for dissecting gene function and improving important traits in crops. However, there are still persisting challenges to obtain high homozygous/bi-allelic (ho/bi) mutations in dicot plants. Here, we develop an improved CRISPR/Cas9 system harboring a calreticulin-like gene promoter, which can boost targeted mutations in dicots. Additionally, the pDC45_dsg construct, combining a 35Spro-tRNA_sgRNA-EU unit and PCE8pro-controlled Cas9, can achieve more than 80.0% ho/bi mutations at target sites in allotetraploid tobacco. We construct pDC45_Fast system that can simultaneously fulfill gene editing and shorten the life span of T0 generation tobacco and tomato. This study provides new tools for improving targeted gene mutagenesis in dicots, and makes manipulations of genes in Solanum more feasible.

plant biology↗

bioRxiv2022

SOX17 Is Not Required for the Derivation and Maintenance of Mouse Extraembryonic Endoderm Stem Cell Lines

Extraembryonic endoderm stem (XEN) cell lines can be derived and maintained in vitro and reflect the primitive endoderm cell lineage. SOX17 is thought to be required for the derivation and maintenance of mouse XEN cell lines. Here we have re-evaluated this requirement for SOX17. We derived multiple SOX17-deficient XEN cell lines from preimplantation embryos of a SOX17-Cre knockout strain and chemically converted multiple SOX17-deficient embryonic stem cell lines into XEN cell lines by transient culturing with retinoic acid and Activin A. We confirmed the XEN profile of SOX17-deficient cell lines by immunofluorescence with various markers, by NanoString gene expression analyses, and by their contribution to the extraembryonic endoderm of chimeric embryos produced by injecting these cells into blastocysts. Thus, SOX17 is not required for the derivation and maintenance of XEN cell lines.

developmental biology↗

bioRxiv2021

Generation of functional ciliates cholangiocytes from human pluripotent stem cells

The derivation of mature functional cholangiocytes from human pluripotent stem cells (hPSCs) would provide a model for studying the pathogenesis of cholangiopathies and for developing novel therapies to treat them. Current differentiation protocols are not efficient and give rise to cholangiocytes that are not fully mature, limiting their therapeutic applications. Here, we describe a new strategy to generate functional hPSC-derived cholangiocytes that display many characteristics of mature bile duct cells including high levels of CFTR and the presence of primary cilia capable of sensing flow. With this level of maturation, these cholangiocytes are amenable for testing the efficacy of new cystic fibrosis drugs and for studying the role of cilia in cholangiocyte development and function. Transplantation studies showed that the mature cholangiocytes generate ductal structures in the liver of immunocompromised mice providing the first indication that it may be possible to develop cell-based therapies to restore bile duct function in patients with biliary disease.

cell biology↗

bioRxiv2020

Arabidopsis ERF4 and MYB52 Transcription Factors Play Antagonistic Roles in Regulating Homogalacturonan De-methylesterification in Seed Coat Mucilage

The Arabidopsis (Arabidopsis thaliana) seed coat mucilage is a specialized cell wall with pectin as its major component. Pectin is synthesized in the Golgi apparatus with homogalacturonan fully methylesterified, but it must undergo de-methylesterification by pectin methylesterase (PME) after being secreted into the cell wall. This reaction is critical for pectin maturation, but the mechanisms of its transcriptional regulation remain largely unknown. Here, we show that the Arabidopsis ERF4 transcription factor positively regulates pectin de-methylesterification during seed development and directly suppresses the expression of PME INHIBITOR13 (PMEI13), 14, 15 and SUBTILISIN-LIKE SERINE PROTEASE 1.7 (SBT1.7). The erf4 mutant seeds showed repartitioning of mucilage between soluble and adherent layers as a result of decreased PME activity and increased degree of pectin methylesterification. ERF4 physically associates with and antagonizes MYB52 in activating PMEI6, 14 and SBT1.7 and MYB52 also antagonizes ERF4 activity in the regulation of downstream targets. Gene expression studies revealed that ERF4 and MYB52 have opposite effects on pectin de-methylesterification. Genetic analysis indicated that the erf4-2 myb52 double mutant seeds show mucilage phenotype similar to wild-type. Taken together, this study demonstrates that ERF4 and MYB52 antagonize each others activity to maintain the appropriate degree of pectin methylesterification, expanding our understanding of how pectin de-methylesterification is fine-tuned by the ERF4-MYB52 transcriptional complex in the seed mucilage. One-sentence summaryArabidopsis ERF4 and MYB52 transcription factors interact and play antagonistic roles in regulating homogalacturonan de-methylesterification related genes in the seed coat mucilage.

plant biology↗

bioRxiv2019

The Biogeography of coelurosaurian theropods and its impact on their evolutionary history

ABSTRACTThe Coelurosauria are a group of mostly feathered theropods that gave rise to birds, the only dinosaurs that survived the Cretaceous-Paleogene extinction event and are still found today. Between their first appearance in the Middle Jurassic up to the end Cretaceous, coelurosaurs were party to dramatic geographic changes on the Earth’s surface, including the breakup of the supercontinent Pangaea, and the formation of the Atlantic Ocean. These plate tectonic events are thought to have caused vicariance or dispersal of coelurosaurian faunas, influencing their evolution. Unfortunately, few coelurosaurian biogeographic hypotheses are supported by quantitative evidence. Here, we report the first, broadly-sampled quantitative analysis of coelurosaurian biogeography using the likelihood-based package BioGeoBEARS. Mesozoic geographic configurations and changes are reconstructed and employed as constraints in this analysis, including their associated uncertainties. We use a comprehensive time-calibrated coelurosaurian evolutionary tree produced from the Theropod Working Group phylogenetic data matrix. Six biogeographic models in the BioGeoBEARS package with different assumptions about the evolution of spatial distribution are tested against the geographic constraints. Our results statistically favour the DIVALIKE+J and DEC+J models, which allow vicariance and founder events, supporting continental vicariance as an important factor in coelurosaurian evolution. Ancestral range estimation indicates frequent dispersal events via the Apulian Route (connecting Europe and Africa during the Early Cretaceous) and the Bering Land Bridge (connecting North America and Asia during the Late Cretaceous). These quantitative results are consistent with commonly inferred Mesozoic dinosaurian dispersals and continental-fragmentation-induced vicariance events. In addition, we recognise the importance of Europe as a dispersal centre and gateway in the Early Cretaceous, as well as other vicariance events like those triggered by the disappearance of land-bridges.View Full Text

paleontology↗