Biology subjects

Li, X.

Publications and source records attributed to Li, X..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Jasmonate restrains the enhanced growth response of lateral roots induced systemically by a local water deficit

Water availability in drying soils is most often spatially heterogeneous, requiring plants to adjust their root system architecture to sustain water uptake. This acclimation response to water deficit (WD) relies on the integration of local and systemic signals. The later and their mode of action remain poorly understood. Using hydroponic split-root systems in maize and Arabidopsis, we show that, with respect to control well-watered plants, a local WD does not affect shoot biomass but suppresses lateral root (LR) growth in the water-deprived compartment while promoting LR elongation in the well-watered compartment. Spatiotemporal analyses in maize revealed an early and transient (<2h) transcriptomic response of LRs triggered by both local and systemic WD signals. This response involved activation of jasmonate (JA) biosynthesis and signaling components, including MYC2 like regulators and JAZ repressors. It occurred in both the water-deprived and well-watered root halves of split roots, with no evidence of long-distance transport of JA. Furthermore, exogenous methyl jasmonate locally inhibited LR elongation, whereas the Arabidopsis JA insensitive jar1-1 mutant showed an enhanced systemic LR growth response to a local WD. Together, these findings demonstrate that JA acts as an early negative regulator that counterbalances the systemic enhancement of LR growth induced by a local WD, thereby fine-tuning root system architecture and water uptake during local soil drying.

plant biology↗

bioRxiv2026

Notch1 and Notch2 receptors mediate the prosensory functions of the Notch ligand Jagged1 in the mammalian cochlea

Mechanosensory hair cells in the cochlea of the inner ear are essential for sound detection. Previous studies have shown that loss of the Notch ligand Jagged1 (JAG1) disrupts maintenance of prosensory progenitors, from which hair cells and their surrounding supporting cells derive. However, the molecular and cellular mechanisms by which JAG1 regulates prosensory progenitor maintenance are poorly understood, and the Notch receptors that mediate this function in the developing cochlea remain unknown. To address this, we generated Jag1 conditional knockout mice and characterized their prosensory deficits using transcriptomic and phenotypic analyses. We show that JAG1 loss abolishes prosensory expression of CDKN1B (p27Kip1) and reduces expression of essential neurotrophic factors, thereby disrupting the stereotyped pattern of cell-cycle exit and innervation within the prosensory domain. Furthermore, conditional knockout of Notch1 and Notch2 (Notch1/2) receptors in supporting cells phenocopied the Jag1 deletion phenotype, showing both a severe reduction in outer hair cell formation and a disrupted pattern of cell-cycle exit and innervation, thereby confirming their essential roles in mediating the prosensory functions of JAG1.

developmental biology↗

bioRxiv2026

Integrating CSF and EV Proteomes Enhances Biomarker Discovery by Capturing Shared Variation Across Compartments

Cerebrospinal fluid (CSF) contains brain derived proteins that can be leveraged as biomarkers for Alzheimer's disease (AD) and other neurodegenerative diseases. However, converting protein intensities to a disease signal remains a challenge because physiology driven changes to the localization of proteins across CSF subcompartments are obscured when CSF is analyzed alone. Where subcompartment data, such as that from extracellular vesicles (EVs), are also measured, separate but parallel analyses of EVs and CSF can obscure their shared disease signal. Here, we present an integrated matrix factorization approach that combines proteomic signals from matched CSF and phosphatidylserine exposed EVs and nanoparticles (EVps). In a ROS/MAP cohort of 48 participants, integrating CSF and EVps signals improved biological concordance across compartments and increased the number of candidate proteins distinguishing participants with AD from controls. Notably, the joint signal identified as many brain related biomarker candidates as studies using substantially larger cohorts. By demonstrating that integration of CSF and EVps proteomes maximizes information from limited samples, this framework offers a path toward more efficient biomarker discovery across two compartments increasingly leveraged in neurodegenerative disease research.

systems biology↗

bioRxiv2026

Multi-omics fine-mapping uncovers a pleiotropic intestinal enhancer variant linking PMAIP1 regulation to pig growth and fatness

Genetic loci influencing multiple complex traits often remain difficult to interpret because the underlying functional variants, target genes and tissue contexts are unresolved. Here, we investigated the regulatory basis of a shared signal for average daily gain (ADG) and backfat thickness (BF) in Yorkshire pigs. By integrating GWAS in 7,972 pigs, targeted capture sequencing, LD-based fine-mapping, porcine epigenomic annotations, three-dimensional chromatin interaction maps and functional assays, we narrowed the shared SSC1 signal to a 1.59-Mb interval and functionally prioritized rs334769214 (T>G) as the leading candidate variant. The T>G substitution produced marked allele-specific differences in enhancer activity and nuclear-protein binding, while transcription-factor co-transfection assays identified FOXL1-responsive, allele-dependent regulatory activity. Chromatin interaction and CRISPRa analyses supported a regulatory connection between the rs334769214-containing enhancer and PMAIP1, and PMAIP1 overexpression promoted apoptosis in porcine intestinal epithelial cells. In the capture-sequenced subset, the G allele was associated with higher ADG and BF, consistent with a relative loss-of-activation model. Together, these findings delineate a candidate FOXL1-enhancer-PMAIP1 regulatory pathway and demonstrate how multi-omics fine-mapping can advance a shared quantitative-trait locus toward a testable molecular mechanism underlying variation in growth and fatness.

genetics↗

bioRxiv2026

TET loss of function selects for aneuploidies that confer a proliferative advantage

Mutations in the Ten-Eleven Translocation (TET) family of DNA dioxygenases are among the most common epigenetic alterations in clonal hematopoiesis and hematologic malignancies, yet how TET loss of function reshapes genome evolution during cellular expansion remains to be fully understood. Here we show that loss of Tet2/3 in invariant natural killer T (iNKT) cells drives aggressive lymphoid expansion that is consistently associated with recurrent chromosome 17 trisomy, a dominant aneuploid state observed across more than ten independently derived tumors following transplantation into immunocompetent recipient mice. Single-cell whole-genome sequencing of TET-deficient iNKT cells induced to proliferate in culture with antigen and IL-2 stimulation revealed that rare pre-existing cells with chromosome 17 trisomy appeared soon after Tet gene deletion in the thymus, together with cells harboring other copy number alterations, but only the cells with chromosome 17 trisomy were progressively enriched during further expansion. Similarly, inducibly Tet-deficient mouse embryonic stem cells (mESCs) showed selection for aneuploid states that were present prior to Tet gene deletion, including trisomy of chromosome 6. Reanalysis of independent datasets from Dnmt3a-deficient mouse lymphomas identified recurrent chromosome gains, including chromosome 17 trisomy. Our results establish TET and DNMT3A deficiency as drivers of karyotypic evolution, and suggest that disruption of DNA methylation/ demethylation pathways through either TET or DNMT3A deletion promotes chromosomal instability, in part by facilitating the emergence and selection of cryptic aneuploid subclones during clonal expansion.

genetics↗

bioRxiv2026

Early dynamics of a neutrophil interferon program drive immunotherapy resistance and limit durable anti-tumor immunity

Despite the remarkable success of immune checkpoint blockade (ICB), durable clinical benefit remains limited to a subset of patients, highlighting the need for predictive biomarkers and new therapeutic targets. Here, we investigated the early immune dynamics associated with anti-PD1 responsiveness using longitudinal single-cell transcriptomics, spatial transcriptomics, and neutrophil-specific genetic perturbations in preclinical models of triple-negative breast cancer. We identified a conserved neutrophil interferon-stimulated gene (ISG) program that emerges before overt tumor divergence and predicts resistance to anti-PD1 therapy. Successful treatment was associated with an early reduction of IFN-responsive neutrophils in both blood and tumor tissues, whereas persistent neutrophil IFN signaling correlated with therapeutic resistance. Mechanistically, genetic disruption of either type I or type II interferon signaling in neutrophils enhanced anti-PD1 efficacy and promoted durable anti-tumor immune memory. Spatial analyses further revealed an inverse association between IFN-responsive neutrophils and tertiary lymphoid structure-enriched regions during effective therapy. Together, these findings identify IFN-responsive neutrophils as early determinants of immunotherapy outcome and establish dynamic neutrophil interferon programs as candidate blood-based biomarkers and therapeutic targets for cancer immunotherapy.

cancer biology↗

bioRxiv2026

A genome-scale ORF screen for resilience factors that protect the RPE and restore vision in aged mice

Aging is a complex phenomenon, yet therapeutic discovery has largely relied on testing individual hypothesis-driven targets. Here, we performed a genome-scale open reading frame (ORF) screen for oxidative-stress resistance in retinal pigment epithelium (RPE) cells, which are vulnerable to oxidative damage during aging. The screen identified nine protective ORFs including antioxidant factors and an epithelial-to-mesenchymal transition regulator. Notably, we also identified three factors that reduce transcriptomic age including the cardiac transcription factor NKX2-5. NKX2-5 conferred robust oxidative resilience in vitro and in vivo. Domain dissection revealed that its homeodomain is dispensable for resilience, enabling development of NKX2-5{Delta}HD, which retained protective activity without detectable toxicity over 14 months. In middle-aged mice, subretinal NKX2-5{Delta}HD restored visual and electrophysiological function, and its systemic delivery improved grip strength and reduced frailty in late-aged mice. These findings highlight the value of unbiased, genome-scale gain-of-function screening, as resilience factors normally expressed in other contexts can be reengineered as potential therapeutics for age-related decline in other tissues.

genetics↗

bioRxiv2026

A scalable recombinant pipeline for disulphide-stapled peptides

Constrained macrocyclic peptides can engage protein surfaces that resist both small molecules and biologics but producing them at library scale still depends on chemical synthesis and macrocyclisation workflows that are slow, specialised and hard to parallelise. We describe a recombinant pipeline for disulphide-stapled cyclic peptides, compatible with 96 well plates, that lowers this barrier. Peptide-encoding sequences are introduced by extension PCR and in vivo assembly (IVA) cloning at about $2 per variant, expressed as small ubiquitin-like modifier (SUMO) fusions secreted to the oxidising periplasm, where the intramolecular disulphide forms spontaneously, and purified by immobilised metal-affinity chromatography (IMAC) with analytical size-exclusion chromatography (SEC). The route from a list of designs to characterised material takes about one week, much of it unattended. Applied to a 60-design library across nine protein targets, the pipeline gave purified products for all 60 designs, at a median total soluble yield of approximately 135 micrograms per 6 mL culture (range 9 to 261) that varied by target. Ellman's assay across 38 designs showed disulphide-formation failure to be sequence-driven and uncorrelated with yield, detecting a failure mode invisible to chromatography. Surface plasmon resonance confirmed target binding and showed that the recombinant SUMO fusion constructs retained affinities comparable to their corresponding peptide-only forms. Complementary to general-purpose recombinant platforms, the pipeline enables higher-throughput disulphide macrocycle screening and is amenable to partially or fully automated workflows.

biochemistry↗

bioRxiv2026

Cyclic uremia without kidney injury drives cardiovascular disease with rapid onset of immunosenescence and heart failure

End-stage kidney disease (ESKD) is a major driver of cardiovascular disease (CVD) and requires dialysis treatment leading to a unique metabolic phenotype with cyclic transitions between accumulation and clearance of uremic toxins. Although ESKD patients display the highest cardiovascular mortality among CKD patients, the effect of cyclic uremia on cardiovascular disease remains subject to discussion. Existing mouse models rely on induction of kidney injury and do not resolve the interconnected pathophysiological effects of metabolic, hypertensive and endocrine renal failure. They are therefore unable to distinguish uremia-driven effects from well-established drivers of cardiovascular disease such as hypertension. Here, we established a simple, reproducible, and sex-inclusive mouse model of uremia in absence of kidney injury or hypertension leveraging a bistable vesico-peritoneal shunt (VPS). Strikingly, we identify cyclic uremia as an independent driver of ESKD-induced CVD, that induces heart failure with preserved ejection fraction (HFpEF), vascular inflammation and immunosenescence. As such, the VPS represents the first preclinical model that enables investigation of cyclic uremia as a driver of cardiovascular disease.

systems biology↗

bioRxiv2026

Therapeutic Potential of iPSC-Derived TH+FOXA2+ Neuronal Extracellular Vesicles in Parkinson's Disease Revealed by Organoid and Rodent Models

Background: Parkinson's disease (PD) is characterized by the progressive loss of midbrain dopaminergic (DA) neurons and aberrant alpha-synuclein (alpha-syn) aggregation, yet disease-modifying therapies that simultaneously retard neurodegeneration and foster regeneration remain lacking. Methods: In this study, we isolated extracellular vesicles (TH and FOXA2 double-positive cell-derived EVs) from TH and FOXA2 double-positive differentiated neural cells, a distinct midbrain floor-plate-derived neural cell population that co-expresses the floor-plate transcription factor FOXA2 together with TH and should therefore not be equated with conventional mature midbrain dopaminergic neurons, and systematically evaluated their therapeutic potential across three complementary models: A53T transgenic mice, 6-OHDA-lesioned rats, and 6-OHDA-treated human midbrain organoids. Integrative transcriptomic and single-cell sequencing analyses, together with toxicological evaluations in rodents and non-human primates, were performed to investigate the underlying mechanisms and safety profile. These TH and FOXA2 double-positive cells were generated using a fully suspension-based, matrix-free, and chemically defined differentiation system devoid of N2/B27 supplements and fetal bovine serum (FBS). This approach offers a simple, controllable, low-cost, and scalable platform with high batch-to-batch consistency for EV manufacturing. Throughout this study, the term "TH and FOXA2 double-positive cells" refers to this distinct TH and FOXA2 double-positive cell population and should not be interpreted as conventional terminally differentiated dopaminergic neurons. Results: Intranasal administration of TH and FOXA2 double-positive cell-derived EVs in A53T mice and 6-OHDA-lesioned rats significantly ameliorated motor deficits, increased nigral tyrosine hydroxylase (TH)-positive neuron counts, reduced alpha-syn aggregation, and suppressed gliosis. In human midbrain organoids, TH and FOXA2 double-positive cell-derived EVs preserved DA neuronal morphology and reduced GFAP and alpha-syn expression. Notably, when EVs were administered simultaneously with 6-OHDA modeling rather than after modeling was completed, the protective effect was stronger. Multi-omics analysis revealed that TH and FOXA2 double-positive cell-derived EVs reversed pathological signatures of interferon-responsive microglia and oxidative stress-adapted astrocytes, while restoring WNT- and non-canonical WNT-mediated intercellular communications. Safety evaluations showed no discernible organ toxicity. Conclusions: TH and FOXA2 double-positive cell-derived EVs exert neuroprotective effects across multiple PD models by modulating specific glial subpopulations and reinstating development-associated signaling pathways. Together with a fully suspension-based, matrix-free, and N2/B27-free differentiation process that enables low-cost, scalable, and highly reproducible manufacturing, TH and FOXA2 double-positive cell-derived EVs represent a promising therapeutic candidate for Parkinson's disease.

neuroscience↗

bioRxiv2026

Biologically grounded cell profiling across microscopy modalities

Microscopy-based cell profiling has broad applications in biological discovery, disease characterization, and phenotypic drug screening. Modern microscopy continues to push the limits of resolution, speed, depth and throughput, but better imaging does not automatically lead to better biomedical discovery and translation. A key bottleneck is feature representation: existing features are either handcrafted or learned as black-box embeddings and often lack explicit biological meaning. Here we propose biological grounding as a first principle for cell profiling and implement it through MorphAgent, an AI agent framework in which each quantitative feature originates from a biological hypothesis and is anchored to a cellular structure or process. By integrating biological knowledge, multimodal reasoning and automated validation, MorphAgent makes biologically grounded feature design systematic and scalable. We show biological grounding fundamentally changes the properties of cell profiling features. Across three microscopy modalities, MorphAgent produces compact, expressive and transferable features for drug screening, cell state characterization and disease morphology analysis. In wide-field Cell Painting, a common assay for phenotypic drug screening, it improves perturbation-retrieval mean average precision by 48% over CellProfiler and 20% over DeepProfiler while using substantially fewer dimensions. In confocal mitochondrial imaging, biologically grounded features transfer across independently acquired datasets and imaging resolutions, supporting accurate aging-state classification. In structured illumination microscopy (SIM) imaging of Tau-labeled samples, biologically grounded super resolution features reveal nanoscale morphologies inaccessible at conventional resolution, enhancing the discrimination of disease-associated mutations. Moreover, biologically grounded features provide a hierarchical organization of cellular morphology, enabling multilevel alignment with transcriptomics data and facilitating mechanistic understanding. Biologically grounded cell profiling thus brings AI reasoning closer to biological mechanisms, advancing biomedical discovery and translation.

bioinformatics↗

bioRxiv2026

PGG Enhances Olaparib Efficacy via cGAS-STING Signaling and Sensitizes Triple-Negative Breast Cancer to PD- L1 Blockade

Triple-negative breast cancer (TNBC) is a highly aggressive malignancy and options for targeted therapy are limited. Although PARP inhibitors (PARPi) like olaparib (Ola) leverage synthetic lethality, their clinical utility is severely impeded by drug resistance and low frequency of BRCA mutations. In this study, 1,2,3,4,6-penta-O-galloyl-{beta}-D-glucose (PGG), a natural polyphenolic compound, can induce a state of homologous recombination deficiency (HRD) in TNBC cells by inhibiting the PALB2-BRCA2 interaction. PGG potentiated the inhibitory effects of Ola on the in vitro proliferation, clonogenic potential, migration, and invasion of TNBC cells. Mechanistically, the dual therapy triggered severe oxidative stress and mitochondrial collapse, which accelerated the classical apoptosis cascade and promoted the emission of immunogenic cell death (ICD)-associated DAMPs. The accumulated cytosolic double-stranded DNA activated the innate immune cGAS-STING pathway, thereby promoting robust intra-tumoral infiltration of CD8+ T cells. Furthermore, since cGAS-STING hyperactivation drives compensatory PD-L1 upregulation on TNBC cells, incorporating anti-PD-L1 antibody into the combination regimen further reversed the immunosuppressive barrier, achieving near-complete tumor eradication and maximum infiltration of cytotoxic T cells in vivo. Bioinformatics analyses further suggested a potential network of PGG targets associated with extracellular matrix organization, offering a bioinformatics-derived hypothesis for its theoretical involvement in modulating stromal tension and vascular homeostasis. Collectively, this study establishes PGG as a multi-functional therapeutic agent integrating intracellular synthetic lethality and innate immune sensing, while providing a preliminary bioinformatic rationale for prospective microenvironmental investigation. This study also shows PGG as a multi-functional therapeutic agent that integrates intracellular synthetic lethality, innate immune sensing, and microenvironmental remodeling to convert immunologically "cold" TNBC into "hot" tumors.

biochemistry↗

bioRxiv2026

Identification of alcohol use disorder-associated and ethanol-responsive proteins and candidate biomarkers using human cortical organoids

Genome-wide association studies of alcohol use disorder (AUD) have identified >100 loci, yet the functional impact and the downstream molecular mechanisms are not well understood. As functional effectors of genes, proteins provide direct insight into disease mechanisms. However, most proteomic alterations in postmortem human brains of AUD likely reflect a combination of inherited susceptibility (AUD-associated), the consequences of alcohol exposure (ethanol-responsive), other environmental and lifestyle factors, as well as sample preparation. Here, we profiled the proteome of human microglia-containing cortical organoids derived from human induced pluripotent stem cells from individuals with AUD (n=11) and without (n=5), paired with or without intermittent ethanol exposure. To maximize statistical power, donors were selected based on high or low genetic liability for AUD as measured by polygenic scores. Among 8,952 proteins that passed quality control, 1,038 were AUD-associated and 718 were ethanol-responsive. AUD-associated proteins were enriched for neuronal signaling, immune, mitochondrial, and extracellular matrix pathways, whereas ethanol-responsive proteins were enriched for RNA processing, ribosome biogenesis, protein translation, vesicle trafficking, and membrane transport pathways. Twenty ethanol-responsive proteins were replicated in a postmortem human prefrontal cortex proteomic dataset. Using UK Biobank plasma proteomics data, we identified 26 candidate AUD-associated biomarkers and 9 candidate ethanol-responsive biomarkers. We also found that major proteomic variation was significantly correlated with AUD polygenic scores. Together, these findings reveal distinct proteomic signatures of inherited susceptibility to AUD and ethanol exposure, providing new insights into mechanisms underlying AUD and identifying candidate circulating biomarkers for further investigation.

cell biology↗

bioRxiv2026

Xenon improves autism-like behaviors in mice through potentiation of PVT-CeA glutamatergic neurotransmission

Autism spectrum disorder (ASD) is a common neurodevelopmental disease with no currently effective treatments. In this study, Xenon (Xe), a noble gas used clinically as an anesthetic and a neuroprotectant, has been investigated for its potential therapeutic effects in ASD. Two genetic ASD mouse models (Mef2c mutant and Shank3-/- mice) were exposed to a low concentration of xenon (25%) mixed with oxygen (30%) and balanced with nitrogen for a single exposure of 30 min or for 10 min per day for 10 days. These Xe exposure paradigms rescued ASD-like behaviors in both male and female mice. The behavioral improvements persisted for up to 10 days following termination of the 10-day exposure paradigm. Mechanistically, Xe reduced glutamic acid decarboxylase expression in the inhibitory neurons (verified with RNAseq) of the paraventricular thalamic nucleus (PVT) and decreased GABA release during social interaction. Targeted infusion of the GABAA receptor agonist muscimol into the PVT abolished the Xe-mediated behavioral improvements. Reduced GABAergic transmission following Xe exposure increased PVT glutamatergic neuronal activity. Chemogenetic inhibition of these neurons eliminated the therapeutic effects of Xe, whereas chemogenetic activation mimicked the Xe-induced behavioral improvements. Furthermore, opto-inhibition of PVT glutamatergic projections to the central amygdala (CeA) blocked Xe-mediated behavioral improvement. Opto-activation of the PVT-CeA glutamatergic circuit reversed ASD-like behaviors. These findings demonstrate that Xe ameliorates ASD-like phenotypes in mouse models by modulating the PVT Glu-CeA circuit, supporting Xe as a novel potential therapy for ASD.

animal behavior and cognition↗

bioRxiv2026

ARSA: an autonomous research scientist for target nomination in Alzheimer's disease and related dementias

Expanding therapeutic options for Alzheimer's disease and related dementias (ADRD) requires biologically grounded targets, yet nomination demands labor-intensive analysis and multidisciplinary evidence synthesis. To address this challenge, we present ARSA, an autonomous research scientist that transforms natural-language research interests and molecular data into prioritized, evidence-grounded target shortlists. ARSA formulates and audits hypotheses, adapts molecular analyses to observed results, and prioritizes targets using cross-cohort evidence and disease-specific knowledge, preserving the evidence and decisions underlying each nomination. Across three complementary evaluations, we show that ARSA generates hypotheses corresponding to subsequent research and identifies credible candidates within and beyond community nomination records. In structured assessment by 14 experts spanning all four technical cores of the Indiana University School of Medicine-Purdue University TREAT-AD Center, every expert assigned higher mean credibility to ARSA-retained candidates than to rejected comparators. ARSA enables systematic, transparent target exploration, opening opportunities to broaden the therapeutic mechanisms investigated in ADRD.

bioinformatics↗

bioRxiv2026

A Neutrophil Defensin-VDAC1 Axis Drives Steatotic Liver Disease

Neutrophils infiltrate the liver as metabolic dysfunction-associated steatotic liver disease (MASLD) progresses from simple steatosis to steatohepatitis, but whether neutrophil effectors merely mark this transition or cause it is unknown. Here we show that human neutrophil peptides (HNPs), or alpha-defensins, are drivers rather than bystanders of disease. In a clinical cohort of patients with MASLD, the abundance of HNPs localized to diseased tissue correlates with the histological severity of steatosis. In vitro, HNPs enter hepatocytes to induce multimerization of voltage-dependent anion channel 1 (VDAC1) in the mitochondrial outer membrane, causing mitochondrial dysfunction and lipid accumulation. Under lipid overload, but not on a standard diet, HNP1-transgenic mice develop increased adiposity and steatohepatitis, which is reversed by an orally available prodrug that inhibits HNP-induced VDAC1 multimerization. These findings link neutrophil innate immunity to hepatocyte mitochondrial dysfunction, recast host-protective HNPs as pathogenic effectors when hepatocyte mitochondria are lipid-burdened, and establish the HNP-VDAC1 axis as a therapeutic target in MASLD.

immunology↗

bioRxiv2026

Integrated anthocyanin profiling and transcriptome analysis identify candidate genes associated with petal color variation in Cyclamen persicum

Petal coloration is a key ornamental trait in Cyclamen persicum Mill. and is closely associated with anthocyanin composition and relative accumulation, yet the major anthocyanins and candidate molecular factors associated with color variation remain unclear. In this study, anthocyanin profiling and transcriptome analysis were integrated to investigate three Cyclamen materials with distinct petal colors, BXK, FXK, and SHXK. Anthocyanin profiling showed clear separation among the three materials, indicating that petal color divergence was associated with differences in anthocyanin composition and relative abundance. Petunidin-, peonidin-, delphinidin-, malvidin-, and cyanidin-related derivatives exhibited distinct accumulation patterns. Transcriptome analysis revealed marked transcriptional divergence, with phenylpropanoid and flavonoid biosynthesis repeatedly enriched across comparisons, whereas isoflavonoid and flavone and flavonol biosynthesis were enriched in selected comparisons. Mapping differentially expressed genes onto the anthocyanin biosynthetic pathway revealed branch-specific expression patterns of structural genes, including CHS, F3H/F3'H, F3'5'H, DFR, and ANS. Notably, Cluster-26256.0, annotated as a putative anthocyanidin synthase gene, showed a progressive increase in expression from BXK to FXK and SHXK, consistent with increasing petal pigmentation. Several DFR-related transcripts also showed relatively high expression in SHXK. Co-expression analysis linked key anthocyanins, structural genes, and transcription factors, while qRT-PCR generally confirmed RNA-seq trends. These results suggest that late anthocyanin biosynthesis, particularly ANS-related transcriptional variation, may contribute to dark red petal coloration. This study provides a metabolite-transcript framework for Cyclamen petal coloration and identifies ANS-related genes as priority candidates for future functional studies and flower-color breeding.

plant biology↗

bioRxiv2026

AI-Guided Multi-Objective Engineering of Glucoamylase Enables Acidification-Free Starch Saccharification

Glucoamylase is essential for industrial starch saccharification, but the limited thermostability and near-neutral pH tolerance of fungal glucoamylases necessitate cooling and acidification of liquefied starch. Here, we developed an artificial intelligence-guided strategy to simultaneously improve the thermostability, pH tolerance, and catalytic activity of glucoamylase from Penicillium oxalicum (PoGA). Two property-specific machine-learning models, CASPE-T and CASPE-A, identified substitutions associated with thermostability and pH tolerance, respectively. Experimental screening identified beneficial substitutions in 11 of 21 CASPE-T and 12 of 22 CASPE-A candidates. Folding-energy-guided recombination integrated the two traits while maintaining structural compatibility. The optimal variant, PoGA T513E/Q305N, exhibited 2.21-fold higher specific activity than the wild type, with half-life extended from 22.3 to 57.9 min at 60 degrees C and from 16.6 to 64.7 min at pH 8.0. Molecular dynamics simulations attributed these improvements to reinforcement of high-occupancy hydrogen-bonding networks, suppression of conformational fluctuations in the linker and carbohydrate-binding module, enhanced long-range dynamic coordination, and preservation of a compact catalytic architecture. At 60 degrees C and pH 6.5 without acidification, PoGA T513E/Q305N produced 219.9 g/L glucose and achieved 89.1% starch conversion, 31.4% higher than the wild type. This work provides an efficient framework for multi-objective enzyme engineering and sustainable starch biorefining.

synthetic biology↗