Biology subjects

Chen, C.

Publications and source records attributed to Chen, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Biosynthetic additive manufacturing through mycelium-bacteria consortia

Lignocellulosic biomass is the most abundant renewable raw material on Earth, yet its structural and carbon-storage potential remains unrealized: microbial decomposition returns stored carbon to the atmosphere before it can be harnessed as a durable material. Distinct microbial processes, such as biosynthesis and biomineralization, offer a natural counterpoint, converting organic carbon into mechanically robust, persistent materials such as polymers and minerals. Here, we establish a biosynthetic additive manufacturing strategy through mycelium-bacteria consortia, by coupling fungal self-assembly with bacterial biomineralization inside fabricated three-dimensional scaffolds derived from lignocellulosic biomass. Trametes versicolor forms a continuous living mycelial network that serves as both a structural template and a transport pathway, guiding the spatial colonization of Sporosarcina pasteurii and enabling volumetric calcium carbonate deposition throughout the scaffold interior, overcoming the surface-limited mineralization of conventional microbial systems. Integration with helicoidal Bouligand architectures translates microscale mineral reinforcement into macroscale performance, increasing compressive Young's modulus by 7-14-fold and ultimate strength by 5-fold relative to unmineralized conventional mycelium-based living composites. The living mycelial network also enables autonomous self-healing and modular self-assembly through hyphal bridging without external adhesives or energy input. This work establishes a scalable route for converting and upcycling transient biomass carbon into durable living structural materials for sustainable construction.

bioengineering↗

bioRxiv2026

Pulmonary colonization of Candida albicans drives breast cancer lung metastasis via candidalysin

The intratumoral mycobiome is emerging as a key modulator of cancer progression, with specific fungal taxa as potential biomarkers. However, whether and how mycobiomes colonizing distant organs contribute to tumor evolution remains largely unexplored. Here, we identify selective enrichment of Candida albicans in breast cancer lung metastases. Mechanistically, the fungal virulence factor candidalysin activates pulmonary mast cells, which release chemotactic mediators that expand immunosuppressive populations and suppress cytotoxic lymphocyte activity, remodeling the lung into a metastasis-permissive microenvironment. Analysis of clinical isolates and isogenic mutants further demonstrates that candidalysin secretion levels dictate metastasis-promoting potential. Informed by these findings, we developed a combination regimen that concurrently eliminates fungal colonization, stabilizes mast cells, and reverses the immunosuppressive microenvironment, thereby significantly curtailing metastatic progression. Collectively, our study establishes pulmonary C. albicans colonization as a driver of breast cancer lung metastasis and provides a mechanistic framework for targeting mycobiome-host interactions in metastatic disease.

cancer biology↗

bioRxiv2026

Mechanical history shapes phenotypic plasticity and fibroblast-autonomous 3D remodeling in iPSC-derived cardiac fibroblasts

Human induced pluripotent stem cell-derived cardiac fibroblasts (iPSC-cFBs) offer a renewable, genetically defined stromal cell source for studying cardiac fibrosis and cardiomyocyte-fibroblast crosstalk during development and disease. Because cardiac fibroblasts are proliferative, expansion of iPSC-cFBs in culture is attractive for applications requiring large cell numbers, including drug screening and tissue engineering. However, phenotypic drift during expansion, particularly premature fibroblast-to-myofibroblast transition (FMT), remains a concern. Here, we investigated how differentiation protocol, mechanical culture history, and serial expansion shape iPSC-cFB phenotype, transforming growth factor beta 1 (TGF-beta1) responsiveness, and fibroblast-autonomous remodeling in three-dimensional (3D) tissues. Initial studies of iPSC-cFBs expanded on conventional tissue-culture polystyrene (TCP) revealed passage-associated increases in projected cell area and alpha-smooth muscle actin (alpha-SMA) expression, two markers associated with FMT. These findings prompted us to examine how the stiffness of poly(dimethylsiloxane) (PDMS) substrates (15 kPa or 2 MPa) used during iPSC-cFB derivation and expansion influences basal phenotype and response to TGF-beta1. Across two independent differentiation protocols, mechanical culture history shaped passage-dependent basal phenotypes and responses to TGF-beta1. Notably, its effects on collective TGF-beta1 responses in three-dimensional cultures differed from those observed after replating cells onto two-dimensional substrates. Together, these findings demonstrate that mechanical culture history modulates iPSC-cFB responsiveness and tissue-remodeling behavior without irreversibly determining fibroblast state. Subsequent passage and microenvironmental conditions can attenuate or re-express these history-dependent phenotypes. This work supports the use of iPSC-cFBs in basic biological discovery and future tissue engineering applications.

bioengineering↗

bioRxiv2026

Tumbly: An Open-Source Home-Cage Device for Time-Restricted Feeding in Mice

Time-restricted feeding (TRF) is a common tool for studying metabolism, circadian rhythms, aging, and neurodegeneration. Here, we describe a new device called Tumbly, an automated device for performing TRF studies in mouse home-cages. Tumbly controls access to rodent diets at user-set times via a programmable servo-driven food hopper. Tumbly is also battery powered and compatible with multiple types of vivarium home-cages, due to a removable faceplate that can be customized to fit different cage dimensions without modification. Finally, Tumbly is open-source and affordable, with all design files available online, allowing researchers to build and customize it. As a validation test, we deployed Tumbly in two labs at separate institutions, one with singly housed mice (n = 6, within-subject) and one with group-housed mice (n = 22, between-group). We measured daily body weight and food intake. In both labs, mice on an 8-hour TRF schedule maintained their body weight and ate similar amounts of food compared to ad libitum feeding. Our quantified error rates were also low, with no device failures over >1000 hours of operation. We conclude that Tumbly provides a reliable, low-cost option for running TRF studies in mice.

neuroscience↗

bioRxiv2026

Early-life core microbiota are associated with postlarval survival of Penaeus vannamei: A meta-analysis

Larviculture is critical to the production of Penaeus vannamei, the world's leading farmed shrimp species, but remains constrained by erratic postlarval survival. Although early-life microbiome establishment is increasingly recognized as essential for larval health and survival, microbiome-based hatchery interventions are hindered by limited understanding of larval core microbiota. Here, we synthesized publicly available and self-generated 16S rRNA gene amplicon datasets of larval and rearing-water microbiota from 13 studies encompassing seven major producing regions worldwide to characterize shrimp larval core microbiota, their assembly processes, and their associations with larval survival. Although larval prokaryotic communities exhibited stronger geographic variation than developmental-stage succession, a conserved set of dominant bacterial families, including Roseobacteraceae, Vibrionaceae, Flavobacteriaceae, Moraxellaceae, and Pseudoalteromonadaceae, consistently prevailed across developmental stages and regions. By integrating occupancy, persistence, and ecological network centrality analyses, we demonstrated that common, temporal, and ecological core microbiota differ substantially in composition, diversity, stage specificity, and ecological roles in network stability. Compared with non-core taxa, core taxa were generally assembled more deterministically, irrespective of core category, suggesting stronger host selection and/or more rapid dispersal during microbiome establishment. Core microbiota also generally showed stronger associations with postlarval survival than total communities or non-core taxa, although contrasting survival associations among core members indicated that core microbiota are not ecologically homogeneous. Our work provides the first systematic categorization and characterization of larval core microbiota throughout the shrimp larviculture cycle, offering new insights into the ecological significance of core microbiota and identifying potential universal targets for microbiome-based intervention in shrimp larviculture.

microbiology↗

bioRxiv2026

On technical biases in imaging spatial transcriptomics

Imaging spatial transcriptomics (iST) has revolutionized our ability to contextualize gene expression within intact tissue architectures at single-cell and subcellular resolution. However, these platforms introduce complex technical biases that span the entire measurement pipeline -- from sample preparation to data acquisition to quantification. Here, we categorize these biases into experimental (e.g., sample preservation and spatial sampling) and computational sources (e.g., z-stack registration and field-of-view stitching). Using public datasets, we demonstrate how different biases can compound and manifest, and propose a unified count modeling framework to formalize these sources of variation. Finally, we call for a more integrated understanding of iST data origins and greater knowledge sharing within and across sectors to support the prospective development of more robust experimental design and reliable downstream analysis.

bioinformatics↗

bioRxiv2026

Distinct genetic requirements underlie LITE-1-dependent photosensation and avoidance of high concentration of diacetyl in C. elegans

The eyeless nematode C. elegans can detect and respond to aversive blue and ultraviolet light using the gustatory receptor homolog LITE-1. In addition to its role in phototransduction, LITE-1 also functions as a chemoreceptor for the odorants diacetyl and 2,3-pentanedione. However, whether these different sensory modalities rely on the same downstream signalling components is unknown. In this study, we provide behavioural evidence that unlike its LITE-1-dependent photosensory function which relies on cGMP signalling components, its chemosensory function remains intact in mutants with disrupted cGMP signalling.

neuroscience↗

bioRxiv2026

Epithelial Self-Organization Patterns the Tadpole Oral Disc

Vertebrate epidermal organs are generally patterned through epithelial-mesenchymal interactions, but whether such interactions are essential for all epidermal organs remains unclear. Here we show that the elaborate oral disc of anuran tadpoles arises by partitioning a continuous oral epithelium into developmentally distinct jaw, tooth-row and papilla modules, in the absence of a mesenchymal organizer. Spatially restricted epithelial programs specify, maintain and differentiate these modules, enabling their semi-independent development. Perturbation of lef1, hoxc13, sox7 and pitx2 selectively disrupts individual modules. The resulting module-specific reductions, expansions and rearrangements mirror oral-disc configurations that have evolves repeatedly across anurans. These findings indicate that differential deployment of shared epithelial programs can generates selectable variation in the tadpole oral disc, allowing transient larval feeding structures to diversify independently of adult ecology and enabling tadpoles to exploit diverse ecological niches. Epidermal self-organization can therefore generate structural complexity, promote functional diversification and enhance evolvability in transient vertebrate organs.

developmental biology↗

bioRxiv2026

Ancestral State Reconstruction under Localized Evolutionary Change: Error Patterns and Their Control by Tree Partitioning

Localized evolutionary changes can distort ancestral state reconstruction (ASR) because conventional continuous-trait methods generally treat branchwise changes as draws from a shared background process. A disproportionately large change confined to a single branch therefore creates localized model misspecification, but how the resulting errors vary among reconstruction paradigms and phylogenetic positions remains poorly understood. Using controlled simulations on idealized and empirical mammalian phylogenies, we characterized the error patterns produced by single-branch large changes (SBLCs) across five Brownian-motion-based ASR implementations. On intact trees, errors were highly structured and method dependent: the recursive local method propagated distortion mainly upstream, whereas global methods produced multidirectional effects involving both SBLC boundary nodes, neighboring lineages, and descendants of the affected branch. We then evaluated patching, a conditional robustness procedure that partitions the phylogeny at a candidate branch, applies the same ASR method independently to the resulting subtrees, and estimates the upstream boundary node state by branch-length-weighted interpolation. Patching reduced errors near and away from the affected branch and lowered tree-wide error across trait-increasing and trait-decreasing SBLCs, a broad range of sensitivity analyses, and configurations with two co-occurring SBLCs, while introducing little additional error when no SBLC was present. Under the reference upsizing SBLC, for instance, it cut the maximum-likelihood reconstruction error at the upstream boundary node from 56.20 to 0.03 (mean true state, 4.98), matching the stable-process benchmark. In cetacean body-length evolution, patching candidate branches identified by a Levy-process model generally shifted conventional estimates toward stable-process estimates and nearby fossil references. Under an Ornstein-Uhlenbeck process with strong post-SBLC mean reversion, however, neither patching nor stable-process reconstruction recovered downstream ancestral states once the phenotypic signature of the SBLC had largely disappeared from descendant tip values, revealing an identifiability limit of terminal-only inference. Localized evolutionary change therefore creates structured, method-dependent reconstruction errors, and tree partitioning provides a complementary diagnostic of the robustness of ancestral inferences to candidate branch-localized changes.

evolutionary biology↗

bioRxiv2026

Biophysical modeling of excitation/inhibition imbalance in Alzheimer's disease

INTRODUCTION: Alzheimer's disease (AD) involves early sensory and perceptual changes that can precede memory decline. We developed a two-layer rate-based neural model of early and higher visual areas with feedforward, feedback, and recurrent connections to examine how excitatory/inhibitory (E/I) balance shapes visual motion perception in AD. METHODS: Using Motion-Induced Position Shift and Altered Motion Repulsion stimuli, we factorially manipulated excitatory (E) and inhibitory (I) subfield power and connectivity to examine their effects on illusion representation across visual layers. RESULTS: Increased E, decreased I, and increased E/I reduced illusion representation, consistent with reduced illusion susceptibility in AD, whereas the converse increased illusion representation, reflecting neurotypical processing. Higher-level layer 2 representations were more resistant to E/I perturbations than lower-level layer 1. Illusion representation was less affected by E/I increases in intra-areal (recurrent) connectivity than in inter-areal (feedforward/feedback) connectivity. DISCUSSION: This mechanistic framework links E/I balance and connectivity to altered visual motion illusion representations in AD and suggests that E/I and connectivity measures may provide probes of early AD neurobiology. The framework may also generalize beyond vision.

neuroscience↗

bioRxiv2026

Two new gastropod holobionts from Atlantic hydrothermal vents showing different levels of endosymbiosis dependence

Chemosynthetic symbioses underpin animal life at deep-sea hydrothermal vents, encompassing substantial variabilities in symbiont identity, metabolic capacity, and host dependence. Here, we characterise symbioses in two peltospirid snails from Mid-Atlantic Ridge vents, Peltospira gargantua and P. smaragdina, using 3D anatomical reconstruction, stable isotope analyses, fluorescence in situ hybridization, transmission electron microscopy, and metagenomics. Both species hosted abundant intracellular Campylobacterota within bacteriocytes of a hypertrophied oesophageal gland. Their dominant symbionts belonged to genus Sulfurimonas, but the two hosts were associated with distinct symbiont lineages. Symbiont genomes encoded carbon fixation through the rTCA cycle, sulfide oxidation, and Group I Ni-Fe hydrogenases, indicating combined thiotrophic and hydrogenotrophic capacities. Hydrogenase copy number varied across vent fields from one to three copies. The P. gargantua symbiont from the hydrogen-enriched Hydra vent field carried two divergent copies, including one with a truncated catalytic region, potentially reflecting local adaptation to vent geochemistry. Anatomical and isotopic comparisons further revealed contrasting host dependence, with P. gargantua having a proportionally larger oesophageal gland and ventricle coupled with a reduced radula, as well as a greater nitrogen-isotope enrichment between symbiotic and non-symbiotic tissues. The smaller oesophageal gland and larger feeding apparatus of P. smaragdina point to it being mixotrophic. Previously, all known peltospirid symbioses have partnered with Gammaproteobacteria, and we expand the known diversity of peltospirid symbioses. Our findings underscore how closely related hosts can exhibit different degrees of dependence on symbiosis, and that mixotrophic symbiosis may be prevalent in small vent species previously thought to be non-symbiotic.

ecology↗

bioRxiv2026

Genome-wide mapping of endogenous topoisomerase cleavage complexes reveals TOP1 at the interface of DNA topological regulation and genome instability

Topoisomerase cleavage complexes (TOPcc) are covalent protein-DNA intermediates formed transiently during topoisomerase catalysis and constitute a major class of DNA-protein crosslinks in human cells, yet their endogenous genomic distributions remain difficult to resolve. Here, we developed protein-DNA adduct immunoprecipitation followed by sequencing (pDAIP-seq), a highly sensitive method for detecting endogenous TOPcc that enables their genome-wide profiling under normal physiological conditions without stabilization by topoisomerase poisons. Using pDAIP-seq, we found that camptothecin treatment, required by existing TOP1cc profiling methods, not only increased TOP1cc abundance but also substantially altered its genomic distribution. Endogenous TOP1cc were globally reduced upon transcriptional suppression and increased upon TOP2A depletion, supporting TOP1cc regulation by the maintenance of genome-wide DNA topological homeostasis. Interestingly, both the regional distribution and nucleotide-scale positioning of TOP1cc, including the positions of TOP1 catalytic cleavage sites, were largely specified by local DNA sequence context. By extending pDAIP-seq to capture transient covalent protein-DNA intermediates involved in DNA repair, including TDP1-, PARP1-, and KU70-DNA adducts, we further identified endogenous TOP1cc as a potential major source of spontaneous DNA breaks in human cells. Finally, pDAIP-seq also enabled genome-wide mapping of TOP2cc, TOP3cc, and SPO11-DNA covalent intermediates in mouse testis undergoing programmed meiotic DNA cleavage. Together, these findings establish pDAIP-seq as a broadly applicable method for the mapping of covalent protein-DNA intermediates and reveal endogenous TOP1cc as a key intermediate between DNA topological regulation and human genome instability.

genomics↗

bioRxiv2026

Topoisomerase-mediated resolution of negative DNA supercoiling sustains human transcription and gene activation

Transcription generates DNA supercoiling that can influence gene expression, but how transcription-associated supercoiling shapes RNA polymerase II (RNAPII) dynamics in human cells remain poorly understood. Here, we show that topoisomerase-mediated resolution of negative DNA supercoiling is required for productive transcription. Acute topoisomerase perturbation causes negative supercoiling to accumulate around transcription start sites (TSS), with greater negative supercoiling accumulation associated with stronger transcription reduction. Elevated negative supercoiling behind the elongating RNAPII, but not positive supercoiling ahead, is associated with reduced RNAPII elongation rates. Using NOTE-seq2 to simultaneously profile newly synthesized and total RNA in single cells, we further demonstrate that acute TOP1 depletion increases gene expression noise by reducing both transcriptional burst size and frequency. Mechanistically, negative supercoiling accumulation at TSS increases RNAPII promoter occupancy and promoter-proximal pausing, providing a potential basis for reduced burst size. Micro-C analysis shows that TOP1 depletion largely preserves chromatin compartments and TADs but weakens short-range chromatin loops, including enhancer-promoter interactions, likely contributing to reduced burst frequency. Finally, during T-cell activation, impaired resolution of negative supercoiling compromises rapid gene upregulation and attenuates the transcriptional activation program. Together, these findings establish topoisomerase-mediated resolution of negative DNA supercoiling as a key mechanism linking DNA topological homeostasis to RNAPII dynamics, chromatin looping, and rapid gene activation.

genomics↗

bioRxiv2026

Immune Reconstitution and Antigenic Exposure History Shape Virus-Specific Humoral Immunity in People with HIV

CD4+ T-cell recovery is widely used to assess immune reconstitution in people with HIV, but its relationship to virus-specific humoral immunity across pathogens remains unclear. We characterized neutralizing activity against SARS-CoV-2, HIV-1, and influenza viruses in ART-treated, virologically suppressed individuals spanning distinct CD4+ T-cell levels. BA.5 was the dominant SARS-CoV-2 neutralization target across CD4 strata, whereas D614G neutralization increased with greater immune reconstitution. This gradient was largely absent for the antigenically divergent NB.1.8.1 and XFG variants. HIV-1 neutralization was inversely associated with CD4+ T-cell count, while influenza showed strain-dependent patterns. Neutralization-to-protection bridging preserved a CD4-associated gradient for D614G but not for highly immune-evasive variants. These findings show that immune reconstitution does not translate uniformly into antiviral humoral function. Instead, antibody profiles reflect host immune status, prior antigenic exposure, and viral antigenic evolution, supporting pathogen-specific functional assessment alongside conventional immune monitoring.

immunology↗

bioRxiv2026

Antibodies targeting a conserved cryptic epitope at the influenza hemagglutinin head-stem interface via distinct binding modes

Influenza A virus continues to pose pandemic threats, as demonstrated by the recent global spread of highly pathogenic H5N1 strains. Consequently, the development and characterization of vaccines targeting zoonotic influenza subtypes have become a major focus of the field. In this study, we characterize two broadly reactive antibodies previously isolated from H5N1 vaccines. Although they have distinct immunoglobulin germline gene usage and binding modes, cryo-EM analysis shows that both antibodies share a highly conserved cryptic epitope at the interface of the hemagglutinin (HA) head and stem domains. The antigenicity of this epitope is influenced by natural amino acid variation at residue 293 of HA subunit 1, and its access is facilitated by acid-induced conformational change of HA. Nevertheless, both antibodies are non-neutralizing and possess only marginal protective efficacy against seasonal and H5N1 viruses in vivo, thus representing suboptimal vaccine responses. Overall, our findings expand the interactions of cross-reactive antibodies with an under-characterized HA epitope and provide insights for next-generation influenza vaccine design.

biochemistry↗

bioRxiv2026

Heterogeneous Graph Contrastive Learning for Drug-Gene-Disease Motif Prediction

Drug repurposing and target discovery offer critical strategies for advancing therapeutic development by uncovering the potential biological pathways and novel associations among drugs, genes, and diseases. However, experimental discovery remains expensive and time-consuming, which limits the scalability of large-scale studies. In addition, existing computational approaches often struggle to effectively integrate heterogeneous biomedical data, capture the complex higher-order topological signatures of biological interactomes, and generalize to unseen entities. Here, we present HANAMI (Heterogeneous grAph coNtrastive leArning for drug-gene-disease Motif predIction), a multi-view deep graph learning framework designed to model complex interactions among drugs, genes, and diseases. HANAMI integrates diverse heterogeneous biomedical knowledge, including chemical structures, genomic sequences, and clinical phenotypes, and leverages relation-aware topology encoding, structure-aware aggregation, and contrastive learning to enable accurate motif prediction with biological context from the network. Systematic evaluation on benchmark datasets shows that HANAMI achieves up to 6% improvements over existing state-of-the-art methods in predicting drug-gene-disease motifs. The framework further demonstrates strong inductive generalization, maintaining an [~]18% performance advantage in zero-shot settings involving previously unseen entities. Beyond predictive performance, HANAMI effectively prioritizes drug-disease relationships investigated in Phase II or III trials while identifying candidate genes that suggest plausible mechanistic links. Together, HANAMI provides a computational framework for interpreting complex biomedical interactions, offering a scalable foundation to accelerate drug repurposing and therapeutic innovation.

bioinformatics↗

bioRxiv2026

An expanded microsporidia species attribute database documents the extensive ecological and phenotypic diversity of these parasites

Microsporidia are a group of parasites that exhibit vast morphological, ecological, and genetic diversity. To catalog this diversity, we previously generated a database of attributes for microsporidia species. Here we expand this database to include species described since 2021, previously missed descriptions, and provisional species defined by clustering GenBank 18S rRNA sequences, resulting in 1,795 species. Using these data, we describe when and where microsporidia have been reported, their hosts and host habitats, the tissues they infect, and their spore morphology. A phylogeny of 18S sequence clusters shows that closely related microsporidia tend to infect closely related hosts, such that sequence identity is predictive of host taxonomy. Clustering also reveals previously unappreciated genetic diversity within some named species, in particular the human pathogen Vittaforma corneae, suggesting that these may comprise multiple species. We have also generated a web portal through which new species information can be submitted, which will facilitate regular updates. This database provides a resource for systematic analysis of microsporidia properties and a reference for taxonomic descriptions.

microbiology↗

bioRxiv2026

The OxyR-Responsive TacAT Module Promotes Oxidative Stress Adaptation and In Vivo Fitness in K. pneumoniae

During infection, Klebsiella pneumoniae must withstand host-derived oxidative stress not only by detoxifying reactive oxygen species (ROS) but also by repairing oxidative damage to cellular physiology. How these detoxification and stress-adaptive responses are coordinated remains unclear. Here, we identify a plasmid-encoded tacAT locus as an OxyR-responsive regulatory module that supports peroxide tolerance and in vivo fitness in K. pneumoniae. Guided by the conservation of the OxyR DNA-binding domain and its consensus binding motif, we surveyed promoter-proximal regions of the K. pneumoniae CRK3022 chromosome and plasmids for candidate OxyR-responsive loci. This analysis identified tacAT, a putative type II toxin-antitoxin (TA) module, as the only plasmid-associated candidate. OxyR directly bound the tacAT promoter and contributed to tacAT induction during hydrogen peroxide (H?O?) stress. The TacAT complex exhibited DNA-binding and transcriptional regulatory activity, promoting the expression of genes linked to protein quality control and membrane/envelope homeostasis, including clpB, htpG, cadC, bhsA, and marA. Deletion of tacAT compromised survival under lethal peroxide challenge and attenuated bacterial dissemination, tissue pathology, and inflammatory responses in a murine bacteremia model. These findings define an OxyR-TacAT regulatory branch that connects peroxide sensing with stress-adaptive gene expression, revealing how a TA-associated module can be integrated into stress-adaptive programs during host-associated oxidative stress.

microbiology↗