Biology subjects

Chen, C.

Publications and source records attributed to Chen, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Surface-stabilized sub-micron condensates for compartmentalizing synthetic cells and enhanced enzyme kinetics

Living cells harbor numerous membraneless organelles (MOs), which are dynamic protein/nucleic acid assemblies responding to specific physicochemical triggers. Liquid-liquid phase separation (LLPS) plays a crucial role in their formation and activity. Inspired by the natural MOs that maintain their individual identities, this work presents a bioengineering strategy to generate LLPS-driven, isochemical MO populations using surfactant-like peptides that stabilize the MO interface. The result is highly stable, monodispersed, sub-{micro}m-sized MO populations, which are not only capable of compartmentalizing synthetic cells but also provide superior environments for enzymatic reactions. This is achieved using pH-responsive elastin-like polypeptides (PREs) as MOs and formulating an amphiphilic PRE-based peptide to stabilize the MO interface. Relative abundance of the surface-active peptide, as well as the rate of pH change, allows direct control over the MO size. Encapsulating these components within synthetic vesicles using a microfluidic platform leads to on-demand multi-compartmentalization via an external pH trigger. Lastly, a functional consequence of the acute size control is shown through a phosphatase reaction, where the highest reaction rate is observed in size-controlled MOs when compared to dilute environments and surfactant-free MOs. The presented strategy provides a new avenue for designing programmable MOs and thus achieve functional compartmentalization within synthetic cells.

bioengineering↗

bioRxiv2026

Haplotype-based insights into the genetic architecture of net blotch resistance in barley

Net blotch, caused by Pyrenophora teres, is a major constraint to barley production worldwide and occurs as two epidemiologically distinct forms: net form net blotch (NFNB) and spot form net blotch (SFNB). Although numerous resistance loci have been reported in recent years, their genetic relationship remains poorly understood, and the effective deployment of resistance is constrained by the complex genetic architecture of net blotch resistance. In this study, we used a haplotype-based mapping approach to dissect the genetic basis of resistance to NFNB and SFNB in a diverse panel of 950 barley accessions from the Australian Grains Genebank (AGG). Disease responses were evaluated across 13 experiments, and a total of 40 quantitative trait loci (QTL) were identified, including 26 associated with NFNB, 29 with SFNB, and 15 common for both diseases. Most loci co-localized with previously reported QTL, while six putative novel haploblocks highlighted untapped genetic diversity within the AGG collection. Correlation analyses across phenotypic, genetic and haploblock levels revealed a partial but incomplete overlap in resistance mechanisms between NFNB and SFNB. Among the 4,497 haploblocks, approximately 60% of them showed positive local genetic correlations between the two diseases, suggesting shared genomic contributions to resistance. Haplotype composition analysis further identified a resistant haplotype group, mainly comprising accessions of Asian origin, that exhibited high levels of resistance to both forms of net blotch. Through in silico haplotype stacking, we demonstrated the cumulative genetic potential achievable by combining favourable haplotypes. When the breeding objective was to improve resistance to both NFNB and SFNB, dual-disease stacking strategies outperformed single-disease approaches, highlighting the value of prioritising haplotypes with positive pleiotropic effects. Overall, this study provides a comprehensive haplotype-level framework for understanding net blotch resistance and delivers practical insights for breeding barley cultivars with durable and broad-spectrum resistance to both NFNB and SFNB.

plant biology↗

bioRxiv2026

From tiny to massive: exploring genome evolution in the model 1 grass genus Brachypodium

Brachypodium is a powerful model system for investigating grass genome evolution, yet genomic resources remain concentrated in the three annual species, whereas perennial species are less sampled. Here, we present chromosome-level assemblies for two perennial species, Brachypodium mexicanum and B. arbuscula, which represent the earliest-diverging lineages of the genus and the earliest-diverging lineage of the core perennial clade, respectively. Synteny-based phylogenomics indicate that B. mexicanum is a meso-allotetraploid composed of two closely related but temporally distinct x=10 subgenomes, here designed as P and U, each carrying subgenome-specific chromosome rearrangements. We further show that the unusually large B. mexicanum genome, in contrast to the reduced genomes of most other Brachypodium species, is primarily due to transposable elements distributed across all chromosomal regions. By contrast, the diploid genome of the earliest-diverging core perennial, B. arbuscula, contains few transposable elements, whereas the most recent diverged diploid perennial B. sylvaticum shows evidence of a secondary TEs proliferation. Comparisons of lineage-specific and functionally enriched orthogroups among B. mexicanum, core perennial species and annual species suggest that ancestral hybridization between annual and perennial lineages may have contributed to the origin of allotetraploid B. mexicanum. These assemblies provide a framework for testing how polyploidy, descending dysploidy, transposable-element turnover, and life-history evolution jointly shaped genome architecture in Brachypodium.

evolutionary biology↗

bioRxiv2026

Drought-tolerant phenotypes associated with patterns of deterministic microbiome assembly across peanut genotypes

Plant-associated microbiomes contribute to plant health and resilience, yet the extent to which host traits shape microbiome assembly remains poorly understood despite increasing interest in leveraging them for crop performance. Here, we investigated whether drought-response phenotypes are associated with reproducible patterns of microbiome assembly across peanut genotypes under field conditions. The cultivars represented three drought-response categories: water-savers with tighter stomatal regulation, water-spenders with deeper root systems, and drought-sensitive genotypes. Bacterial and fungal communities were characterized from bulk soil, rhizosphere, and root endosphere compartments of six non-stressed peanut cultivars. Both host genotype and drought-response phenotype were associated with microbiome composition, with phenotype-associated patterns remaining detectable across multiple genetic backgrounds. Unexpectedly, the strongest phenotype-associated differences occurred in bulk soil communities, suggesting plant-mediated effects extending beyond the immediate root zone. Community differences were driven primarily by shifts in the relative abundance of existing taxa rather than turnover of distinct microbial lineages. Fungal communities responded more strongly to host phenotype than bacterial communities, with water-spender genotypes supporting greater fungal diversity and uniquely enriched taxa in the rhizosphere and endosphere. Neutral community modeling indicated stronger deterministic filtering of fungi than bacteria. Together, these findings demonstrate that drought-response phenotypes shape reproducible microbiome variation before stress exposure. HighlightThis study investigates the potential for host phenotype-associated drivers of microbiome assembly in drought-tolerant peanut cultivars that represented different physiological mechanisms for drought tolerance.

microbiology↗

bioRxiv2026

Astrocytic FMRP regulates the function of spinal parvalbumin-expressing neurons in Fragile X Syndrome

Tactile hypersensitivity is a common symptom of Fragile X Syndrome (FXS) characterized by over-responsiveness to innocuous touch or textures. Yet, the neural circuitry underlying this altered sensory processing remains incompletely understood. Previous studies have focused on cortical and peripheral neuron dysfunction. However, the spinal dorsal horn circuits, which make up the first central site of somatosensory integration, also comprises elements that could contribute to the hypersensitivity to innocuous stimuli, yet its involvement in this pathology has remained incompletely understood. Here, we show that spinal parvalbumin (PV)-expressing interneurons (PVNs), an inhibitory population that gates touch sensory input from activating nociceptive pathways, are dysfunctional in FXS. Using a mouse model of FXS (global Fmr1 knockout; gKO), we showed that dorsal horn PVNs exhibit impaired function characterized by reduced PV expression and inability to sustain tonic firing. To determine whether these deficits arise through cell-intrinsic mechanisms, we selectively deleted Fmr1 in PVNs. This deletion failed to reproduce the molecular and electrophysiological changes observed in the gKO mice. In contrast, astrocyte-specific deletion of Fmr1 recapitulated key features of the gKO mice, including decreased PV expression and firing. To understand the biophysical basis of this firing deficit, we simulated spinal PVNs using conductance-based Hodgkin-Huxley type modelling. Surprisingly, modifying intrinsic membrane conductances alone was insufficient to account for the experimental data. In fact, PVN firing required incorporation of an additional calcium-dependent extrinsic synaptic component consistent with the experimental finding that astrocytic, but not PVN-specific, loss of FMRP reproduced the PVN phenotype in gKO mice. Together, these findings show that these deficits in spinal PVNs arise primarily from loss of FMRP in astrocytes rather than in PVNs themselves. It reveals astrocyte-dependent dysfunction of dorsal horn inhibitory circuits as a previously uncharacterized consequence of FXS.

neuroscience↗

bioRxiv2026

Xeno-Free Peptide-Functionalized Hydrogels Support hiPSC Encapsulation and In Situ Differentiation into Structurally Mature Cardiomyocytes

While defined synthetic substrates can replace Matrigel for human induced pluripotent stem cell (hiPSC) culture and hiPSC-derived cardiomyocyte (hiPSC-CM) production, existing approaches culture cells on two-dimensional surfaces and yield structurally immature cardiomyocytes, limiting their use in disease modeling and regenerative medicine. Here, we developed a xeno-free, fully-defined cyclic RGD (cRGD)-functionalized alginate platform in which we encapsulated hiPSCs to support their expansion and in situ cardiac differentiation. cRGD functionalization was essential for hiPSC survival and pluripotency, with maximal support achieved at a low ligand density (25 {micro}M). In the presence of cRGD, hiPSC encapsulation into softer gels made from lower molecular weight alginates led to enhanced hiPSC expansion and improved cardiogenesis. Strikingly, differentiation in situ with 3D gels led to hiPSC-CM with higher structural maturity, including a markedly increased proportion of Desmin-positive cardiomyocytes. Finally, after enzymatic retrieval from hydrogels, cardiomyocytes derived from softer gels formed tissue-engineered myocardium with superior contractile force compared to tissue fashioned from hiPSC-CM derived from more rigid gels. Together, these results demonstrate the promise of this defined, tunable platform for biomanufacturing of structurally mature cardiomyocytes from hiPSC.

bioengineering↗

bioRxiv2026

ScaleSurfer: multi-scale anatomical segmentation and parcellation of the human brain

Human brain magnetic resonance imaging (MRI) revolutionized our ability to non-invasively probe individual differences in neuroanatomy. These anatomical scans, in turn, also allow us to accurately localize functional MRI (fMRI) activity. However, extracting anatomical labels and structural characteristics, such as cortical surface area or thickness, is a computationally demanding task, taking on the order of hours per brain volume. This is an intrinsically multi-scale problem given that local image structure defines fine boundaries, whereas accurate assignments depend on broader anatomical context. Here, we introduce ScaleSurfer, a three-dimensional convolutional vision transformer model based on multi-scale learning. Convolution blocks capture local anatomical detail and a transformer bottleneck integrates the distributed spatial context. This approach provides rapid, whole-brain morphometric feature estimation, including volume, cortical thickness, surface area, and curvature. Importantly, ScaleSurfer accomplishes this nearly five orders of magnitude faster than current pipelines, taking 150-500 ms instead of 5 hours. We validated ScaleSurfer on multiple datasets, showing stable learning across heterogeneous MRI collections, and demonstrate feasibility by training an interpretable Alzheimers disease classifier that identifies reductions in primarily medial temporal lobe subregions compared to healthy controls. ScaleSurfer positions multi-scale representation learning as a practical route toward faster, anatomically faithful structural MRI processing, whose speed paves the way for nearly real-time anatomical quality control during scanning.

neuroscience↗

bioRxiv2026

Kappa opioid receptors (KORs) in the anterior paraventricular nucleus of the thalamus (aPVT) mediate morphine withdrawal-, anxiety-, fear-, and KOR agonist-induced aversion-like behaviors in mice

PVT is involved in stress responses, fear, anxiety, arousal, aversion and reward. Anterior and posterior PVT (aPVT and pPVT) have different neuronal connections, molecular contents, and functional roles. PVT expressed a high level of KOR. Herein we mapped the projection targets of aPVT KOR(+) neurons and explored the behavioral significance of aPVT KOR. Using KOR-iCre mice and Cre-dependent anterograde tracer, we found that KOR(+) glutamatergic neurons in aPVT primarily projected to NAc, CeA, BNST, PFC, and reticular nucleus of the thalamus (RT). 3-D images showed the pathway emanating from aPVT to the ventral RT, through NAc, and out to the other regions, indicating widespread axonal collateralization. We conditionally knock-downed KOR (KOR cKD) in aPVT by injection of AAV-eGFP-Cre or AAV-eGFP (control) into aPVT of Oprk1lox/lox mice. [3H]U69,593 receptor autoradiography revealed substantial KOR cKD in aPVT. In both male and female mice, the KOR cKD in aPVT significantly reduced anxiety-like behaviors in the elevated plus-maze test, cue-induced freezing after fear conditioning and naloxone-precipitated morphine withdrawal-associated jumps. KOR cKD attenuated U50,488H-induced conditioned place aversion in males only, while having no effect on forced swim immobility or the U50,488H-induced visceral analgesic and antipruritic effects in either sex. Thus, our results reveal for the first time that KOR-mediated inhibition of aPVT neurons may mediate morphine withdrawal, anxiety, and cue-induced fear in both sexes but contribute to KOR agonist-induced aversion only in males. Notably, our findings reveal a previously unrecognized role for aPVT in regulating morphine withdrawal, acting in a manner distinct from pPVT.

neuroscience↗

bioRxiv2026

Genetically Encoded Melanin as a Photostable Scattering Contrast for Whole-Brain Tomography

Large-scale brain imaging has traditionally depended on fluorescent reporters, but challenges like photobleaching and inconsistent signals hinder quantitative analysis in intact tissues. In response, we present MelaCAST (melanin-based scattering CAST imaging), a novel genetically encoded scattering method for whole-brain visualization. Using AAV to deliver tyrosinase allows for cell-type-specific melanin synthesis, providing a stable intracellular scattering contrast across the mouse brain. Combining tissue clearing with scattering tomography, MelaCAST offers non-photobleaching, high-throughput volumetric imaging of genetically targeted cell populations in intact brains. This technique establishes melanin as a genetically encoded scattering reporter and broadens whole-organ imaging capabilities beyond traditional fluorescence methods.

neuroscience↗

bioRxiv2026

Nuclear phylogenomics clarifies the family-level backbone and gene-tree conflict in Zingiberales

Zingiberales includes eight morphologically distinctive families, but its family-level backbone has remained unstable, especially around Musaceae, Heliconiaceae, Lowiaceae, and Strelitziaceae. We analysed 1566 low-copy nuclear genes from 52 samples, representing all eight families and Pontederia crassipes as outgroup. Concatenated maximum likelihood and multispecies coalescent analyses recovered the same backbone: ((Zingiberaceae, Costaceae), (Cannaceae, Marantaceae)) is sister to (Musaceae, (Heliconiaceae, (Lowiaceae, Strelitziaceae))). Penalized-likelihood dating placed the sampled crown group in the Late Cretaceous, with several deep family-level divergences occurring on short internodes. Analysis of 1248 rerooted gene trees showed that conflict is concentrated on these deep branches and in several shallow clades. HyDe tests of empirical and simulated matrices, each including 62,475 triples, did not support widespread ancient hybridization among the major family-level lineages after filtering against the simulated null model. The nuclear data recover a stable Zingiberales backbone, and the long-standing instability of several deep nodes is best explained by rapid early divergence and extensive incomplete lineage sorting.

evolutionary biology↗

bioRxiv2026

An engineered IdeS variant with enhanced activity and performance for IgG degradation

IgG-degrading enzymes have emerged as innovative therapeutic agents for treating conditions driven by pathogenic antibodies. Here, we used structure-guided rational design to engineer IdeSM33, a double mutant (K167R/D226E) of the IgG-specific bacterial protease IdeS from Streptococcus pyogenes, with improved catalytic efficiency. Biolayer interferometry revealed a fourfold increase in binding affinity relative to wild-type IdeS (IdeSWT). This enhancement is likely attributable to mutations that strengthen hydrogen bonding at the enzyme-IgG Fc interface. In vitro, IdeSM33 has higher performance than IdeSWT in cleaving serum IgG. In vivo studies in rabbits demonstrated that IdeSM33 effectively depleted circulating IgG and showed better performance at a dose of 0.005 mg/kg than the IdeSWT. Although doses greater than 0.2 mg/kg demonstrated higher plasma concentrations of IdeS and a larger AUClast, they did not show a significant enhancement in the pharmacodynamics of IgG degradation. Importantly, a single dose of IdeSM33 (0.2 mg/kg) potently degraded binding and neutralizing antibodies against AAV9 within 1-2 days and restored hepatic AAV9 transduction in pre-immunized animals. Together, these findings highlight IdeSM33 as a potent and safe engineered enzyme with therapeutic potential for autoimmune disorders, transplant rejection, and overcoming pre-existing humoral immunity in gene therapy.

bioengineering↗

bioRxiv2026

Synaptic activity controls local exposure of an 'eat-me' signal via ANO3-ITPR1 signaling

Neuronal synapses are eliminated during brain development and disease through pruning by glial cells. Individual synapses are marked for engulfment by eat-me signals, which include externalized phosphatidylserine. In apoptotic cells, phosphatidylserine externalization is driven by caspase-dependent activation of Xkr scramblases1 and inactivation of specific flippases2. Localized caspase activation at neuronal synapses can mediate spatially-restricted synaptic phosphatidylserine exposure leading to synapse pruning by glial cells during development and neurodegeneration3-6. It is unknown which caspase-regulated flippases and scramblases promote synaptic phosphatidylserine exposure and whether there are any caspase-independent mechanisms of phosphatidylserine exposure relevant for synapse elimination. To address this question, we here develop a scalable CRISPR screening approach, COMPASS-seq (compartment-anchored sgRNA screen sequencing), to uncover the genetic underpinnings of subcellular phenotypes. COMPASS-seq is compatible with in vitro and in vivo systems and a wide range of subcellular compartments; we here apply it to the neuronal synapse. We discover that inhibition of the caspase-independent, calcium-activated anoctamin ANO3 (TMEM16C) is sufficient to increase synapse numbers in vivo. ANO3 co-localizes with IP3 receptor 1 (ITPR1), a calcium channel in the endoplasmic reticulum, to form a postsynaptic signaling platform that drives spatially restricted phosphatidylserine exposure at synapses. Activation of the ITPR1 calcium channel activity is sufficient to drive synaptic phosphatidylserine exposure via an ANO3-dependent but caspase-independent mechanism. Our results suggest a mechanism for integrating synaptic activity information to control synaptic pruning. The role of ANO3 in regulating synapses could shed light on the mechanisms underlying its numerous associations with both dementia7 and other neurological diseases8,9.

neuroscience↗

bioRxiv2026

High-throughput whole-brain scattering imaging resolves Amyloid plaques through clearing-assisted contrast modulation

Label-free scattering imaging is widely used in pathology because it enables sensitive tissue assessment without exogenous contrast agents. Yet its limited optical penetration has prevented scattering-based methods from being applied to whole-organ pathology mapping. Here we present clearing-assisted scattering tomography (CAST), a high-throughput, label-free whole-brain mesoscope enabled by selective lipid clearance for scattering enhancement (SELiC). SELiC modulates endogenous refractive-index heterogeneity in cleared tissue, providing whole-brain optical penetration while retaining strong scattering contrast from amyloid plaques and white-matter fibre bundles. CAST enables volumetric imaging of intact mouse brains and brain-wide mapping of amyloid plaque pathology across anatomical regions. This platform establishes a scalable route for label-free, system-level analysis of amyloid pathology and tissue architecture in Alzheimers disease (AD) models.

bioengineering↗

bioRxiv2026

PARROT: Phase-Altering Regulatory Rewiring Over Time

MotivationGene regulatory networks undergo dynamic restructuring during development and disease. Identifying when and how these networks change is crucial for understanding developmental and disease transitions, yet existing change-point detection methods often ignore network structure or lack interpretable community assignments. ResultsWe present PARROT (Phase-Altering Regulatory Rewiring Over Time), a framework for detecting change-points in dynamic networks using Stochastic Block Models. PARROT jointly estimates change-point locations and community structure across four network classes: unipartite and bipartite with either Gaussian or Bernoulli edge models. Simulations demonstrate improved performance and community recovery compared to other methods. Applications to human cardiac differentiation and mouse lung development data successfully recovered known phase boundaries. PARROT identifies both which genes are reassigned across modules and how the connections change between states. AvailabilityPARROT is available as an R package at https://github.com/cchen22/PARROT. Contactchenchen9945@gmail.com Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2026

Temporal dynamics and functional divergence of the chloroplast division apparatus in Oryza sativa

O_LIChloroplast division is governed by a conserved protein machinery, yet empirical characterization of these regulators remains limited in rice, a primary target for C4 engineering. Increased chloroplast occupancy in bundle sheath cells is a hallmark of the C4 pathway and so manipulating division is a potential strategy to achieve this goal. C_LIO_LIThrough developmental transcript profiling and image analysis, we identified a discrete window of active chloroplast proliferation in rice leaves, coinciding with peak expression of conserved plastid division genes. Functional characterization via overexpression revealed regulatory behaviours distinct from those in Arabidopsis thaliana. Overexpression of OsFtsZ1&2 resulted in fewer, enlarged chloroplasts per bundle sheath cell, whereas OsMCD1&OsMinE restricted plastid expansion without altering division rates. Conversely, overexpressing OsPDV1&2 or OsARC6&OsDRP5B increased plastid size without affecting total count. When OsPDV1&2 were co-expressed with transcriptional regulator ZmG2, we observed modest increases in chloroplast size alongside reduced stomatal aperture, increased stomatal density, and higher intrinsic water-use efficiency. C_LIO_LIThe results define the temporal landscape of plastid biogenesis in rice and demonstrate divergence across lineages. Our findings suggest that manipulating the division apparatus is insufficient to drive C4-like chloroplast biogenesis in the rice bundle sheath, highlighting the complexity of plastid-host cell coordination in cereals. C_LI

Plant Biology↗

bioRxiv2026

Aberrations in stromal signaling, muscle contractility and epithelial architecture underlie poor embryo-implantation outcomes after murine ovarian stimulation

Ovarian stimulation is widely used in assisted reproductive technologies, yet its effects on uterine architecture and embryo implantation remain poorly understood. Using a mouse model, we show that ovarian stimulation or superovulation disrupts pre-implantation luminal epithelial folding and induces aberrant smooth muscle structure and contractile function. These structural defects result in embryo trapping within aberrant longitudinal folds, impaired implantation chamber formation, misalignment of the embryo-uterine axis, and subsequent embryo loss. These ovarian stimulation effects were reversible after rest and restoration of normal estrus cycling. Transcriptomic analysis suggests widespread disruption in the stroma and immune compartments of the stimulated uteri. Pathway analysis revealed significant disruption of stromal extracellular matrix and enhanced probability of stroma-immune communication via collagen signaling. Platelet derived growth factor receptor A (PDGFRA) expression was elevated in both the stroma and smooth muscle of the stimulated uteri. Short-term pharmacological inhibition of PDGFRA in the stimulated uteri prior to implantation fully restored epithelial fold transition and implantation chamber formation and partially restored smooth muscle architecture and contractility. Importantly, PDGFRA protein was also elevated in endometrial biopsies from women undergoing ovarian stimulation when compared to natural cycle biopsies. Together, this study establishes muscle contractions and stromal and smooth muscle PDGFRA signaling as novel non-cell autonomous regulators of uterine epithelial architecture critical for embryo implantation.

Developmental Biology↗

bioRxiv2026

Steller: a high-resolution platform for spatial clonal tracing of mammalian brain development

Resolving both lineage history and spatial position at single-cell resolution is essential for understanding how tissue assemble, yet simultaneously interrogation of both dimensions remains technically challenging. Here, we present Steller (Spatio-temporal cell lineage tracker), an integrated experimental and computational framework that overcomes the sensitivity bottleneck limiting lineage barcode detection in high-resolution spatial transcriptomics (ST). By co-depositing capture probes alongside conventional poly(T) oligonucleotides on high-density spatial arrays, Steller achieves targeted enrichment of lineage barcodes at spatial single cell resolution. Applied to clonally labeled embryonic day 12.5 (E12.5) mouse forebrain development harvested at postnatal day 4 (P4), Steller increased the proportion of barcode-detectable cells and recovered higher clonal diversity compared with poly(T) chip. Leveraging this enhanced sensitivity, we resolved distinct spatial clonal architectures across three forebrain regions: horizontal or radial-to-horizontal transitions in hippocampal pyramidal neurons, dorsoventrally restricted yet multi-nuclei spread in thalamus, and fate-restricted spiny projection neuron lineages. Steller establishes a generalizable strategy for lineage-enhanced spatial profiling compatible with existing high-resolution spatial transcriptomics platforms and adaptable to diverse biologic process, providing a framewrok for investigating lineage-dependent tissue organization. HighlightsO_LISteller integrates targeted lineage-barcode enrichment with high-resolution spatial transcriptomics C_LIO_LISteller substantially improves clonal detection sensitivity at single-cell resolution C_LIO_LISteller reveals region-specific spatial clonal architectures across the developing mouse forebrain C_LI

Developmental Biology↗

bioRxiv2026

Physics-driven self-supervised learning for quantitative high-fidelity structured illumination microscopy

Structured illumination microscopy (SIM) enables rapid, long-term super-resolution (SR) imaging of live-cell dynamics. However, although current state-of-the-art (SOTA) SIM reconstruction methods achieve high-fidelity structural SR, they consistently lack reliable intensity quantification, restricting their use in quantitative biology. Here, we develop qHiFi-SIM, a physics-driven self-supervised learning framework for quantitative high-fidelity SR-SIM imaging. By leveraging the wide-field image as a physical intensity reference, our approach enables self-supervised training without reliance on SR data with ground-truth intensity. qHiFi-SIM achieves high structural fidelity (structural similarity, SSIM > 0.95) with a twofold resolution enhancement, while maintaining excellent intensity linearity (coefficient of determination, R{superscript 2} > 0.99). It also exhibits strong transferability across diverse SIM setups and typical samples, and is compatible with SOTA SIM algorithms, enabling direct quantitative correction of their intensity deviations without retraining. We demonstrate the unique advantages of qHiFi-SIM for live-cell quantitative visualization of mitochondrial structure, intensity, and membrane potential dynamics, as well as for high-fidelity SIM-FRET (Forster resonance energy transfer) functional imaging. We anticipate that qHiFi-SIM will serve as a practical tool for SR structural visualization and quantitative functional imaging in live cells.

Cell Biology↗