Biology subjects

Ma, Z.

Publications and source records attributed to Ma, Z..

At least 19 recordsLinked to original sources

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

Targeting cyclic-AMP/phosphodiesterase signaling to quiet nasal tuft cell calcium responses

Background: Airway tuft cells, also called solitary chemosensory cells, are enriched in nasal polyps and are likely the main epithelial source of interleukin-25 (IL-25) in chronic rhinosinusitis with nasal polyps (CRSwNP). Tuft cells are activated through G protein-coupled receptors (GPCRs) that signal through Ca2+. These receptors may also lower cyclic AMP (cAMP), but whether the cAMP pathway can be used to suppress tuft cell responses is unknown. Methods: Ca2+ and cAMP were measured by live cell imaging in isolated Trpm5-GFP mouse nasal tuft cells, and Ca2+ responses were measured in primary human nasal epithelial air-liquid interface (ALI) cultures from patients with CRSwNP. Defensin and IL-25 release were measured by ELISA and ciliary beat frequency (CBF) by high-speed imaging. Phosphodiesterase (PDE) expression was assessed using publicly available single cell RNA sequencing datasets. Results: Agonists of bitter taste receptors (T2Rs), the succinate receptor SUCNR1, and the A1 adenosine receptor increased Ca2+ in GFP-positive mouse nasal tuft cells. T2R and A1 receptor stimulation also lowered cAMP, and these decreases were blocked by pertussis toxin. Glucose, which activates taste family 1 receptors, increased cAMP. Tuft cells were enriched for Pde2a. PDE2A-selective inhibitors (PF-05180999 and BAY 60-7550) increased cAMP and reduced agonist-evoked Ca2+ responses in mouse tuft cells. In human nasal ALIs, both compounds reduced denatonium-evoked Ca2+ responses, defensin release, and IL-25 release without increasing CBF. Conclusions: GPCRs that activate nasal tuft cells also lower cAMP, and by raising cAMP through PDE2A inhibition, tuft cell Ca2+ signaling and IL-25 release were reduced in vitro.

physiology↗

bioRxiv2026

Systematic mapping of the prokaryotic noncoding sequence space with a genomic language model

Prokaryotic genomes encode a vast repertoire of noncoding elements such as ribozymes, riboswitches, and CRISPR RNAs. The sequence-level diversity of these intergenic elements precludes alignment-based clustering that would enable annotation and discovery of novel noncoding RNA families. Here, we show that a genomic language model fine-tuned on prokaryotic intergenic sequences learns representations of noncoding elements from DNA sequence. We used these embeddings to organize 376 million intergenic regions from 1.3 terabase pairs of prokaryotic genomes and metagenomes into 5.14 million clusters. This approach nominated 20,149 clusters of putative structured RNAs with a candidate protein partner. Periodicity in token entropies revealed internal architecture, recovering CRISPR, TIGR and VIPR arrays together with their cognate effector proteins from sequence alone. Targeted clustering of bridge recombinase-adjacent sequences identified bridge RNA variants with longer guide recognition sequences than any characterized ortholog. Finally, we directed teams of AI agents to mine the database under researcher-defined criteria, uncovering divergent riboswitches, ribozymes, and other structured RNAs with biological hypotheses for their function. We release a publicly available database that transforms the dark matter of prokaryotic genomes into an explorable resource for human-agent molecular discovery.

genomics↗

bioRxiv2026

RiboBridge couples RNA backbone generation to sequence design through a learned interaction topology

Designing ribonucleic acid (RNA) molecules with prescribed structures and functions is central to RNA engineering. Backbone-first approaches generate three-dimensional geometry before assigning a nucleotide sequence, yet leave open how that geometry should be represented for downstream sequence design. Here we introduce RiboBridge, which infers a probabilistic residue-pair state from backbone geometry, recycles binary pair probabilities through a second pass and transfers binary and typed signals as soft attention biases for sequence decoding. On 550 generated backbones, pair-type decoding achieved joint refolding validity of 0.451 versus 0.335 for an architecture-matched topology-free decoder. On a matched 110-backbone intervention cohort, replacing aligned pair states with exact-length donors matched on pair-state statistics reduced joint validity from 0.464 to 0.214, showing backbone alignment matters. Pair-confidence ranking enriched the joint-validity rate from 0.451 overall to 0.596 among the top 248 before external refolding, with the same ranking signal transferring to independently generated RFDpoly and RNA-FrameFlow backbones. On 53 experimentally determined backbones, pair-coupled decoding improved secondary-structure agreement relative to residue-wise argmax. These results support a learned relational interface between sequence-free backbone generation and sequence design.

bioinformatics↗

bioRxiv2026

PPARγ brakes cytosolic DNA-induced macrophage inflammation by super-enhancer metabolic reprogramming

Cytoplasmic DNA sensing triggers intense innate immune responses that require tight regulation. PPAR{gamma} is a master metabolic regulator in macrophages, but its role in cytoplasmic DNA immunity remains unclear. Using poly(dA:dT) to mimic cytoplasmic DNA stimulation, we combined transcriptomics, epigenomics (PPAR{gamma}/H3K27ac ChIP-seq), and functional assays. Poly(dA:dT) induced a cytokine storm with MAPK activation and apoptosis/necrosis. PPAR{gamma} activation by rosiglitazone (RGZ) antagonized this response, reducing cell death and transcriptionally inhibiting MAPK genes (e.g., DUSP4/10). Mechanistically, PPAR{gamma} bound promoters/enhancers via PPRE motifs and distal intergenic regions, remodeling H3K27ac (reduced at inflammatory loci, increased at metabolic genes). RGZ induced de novo super-enhancers coupling PPAR metabolic programs (e.g., CPT2) with immune suppression by targeting TLR4, CEBPB, and PIM3. Thus, PPAR{gamma} acts as a brake in cytoplasmic DNA immunity, integrating metabolic reprogramming and inflammation suppression through a multi-level genomic/epigenetic program. This study highlights PPAR{gamma} as a key immune-metabolic integrator and therapeutic target for diseases driven by excessive cytoplasmic DNA sensing.

immunology↗

bioRxiv2026

In Utero Alcohol Exposure Reprograms Mammary Gland Development and Stem/Progenitor Cell Activity in a Non-Tumorigenic Mouse Model

In utero alcohol exposure (IUE) can alter mammary development and increase mammary tumor susceptibility in experimental models. However, most previous studies have relied on carcinogen-induced or genetically tumor-prone models, leaving it unresolved whether prenatal alcohol exposure produces mammary developmental and molecular changes before the introduction of an oncogenic challenge. Here, we addressed this question using non-tumorigenic C57BL/6 mice. Pregnant dams received a Lieber-DeCarli liquid diet containing 1.7% (v/v) ethanol or an isocaloric control diet from gestational day 11 to 19, and mammary glands from female offspring were examined during puberty (postnatal day 40, PND40) and young adulthood (PND70). At PND40, IUE enhanced mammary ductal morphogenesis, increased terminal end bud numbers, and elevated epithelial proliferation. These developmental alterations persisted at PND70, with increased lateral branching and proliferative activity. IUE also altered mammary epithelial composition, expanding the basal/myoepithelial compartment and the CD24highCD49fhigh mammary repopulating unit/stem cell-enriched population. Mammary epithelial cells from IUE-exposed offspring exhibited increased colony-forming cells (CFCs), mammosphere formation, and 3D Matrigel growth, indicating enhanced stem/progenitor-associated activity. At the molecular level, IUE increased ER; expression and phosphorylation together with Cyclin D1, c-Myc, E2F1, and Bcl-2, and enhanced AKT, ERK, and STAT3 phosphorylation, IL-6 expression, and SOX2 at PND40. Importantly, major components of this signaling phenotype remained altered at PND70, including ER;-associated signaling, AKT/ERK activation, and IL-6/STAT3 signaling, whereas the pubertal increase in SOX2 was not sustained. Together, these findings demonstrate that prenatal alcohol exposure induces profound and persistent histomorphological, cellular, and signaling alterations in the mammary gland in the absence of a carcinogenic challenge or genetically introduced oncogenic driver. These results identify intrinsic developmental reprogramming of normal mammary tissue as a potential basis through which prenatal alcohol exposure may modify subsequent responses to tumor-promoting or other environmental challenges.

developmental biology↗

bioRxiv2026

Transcriptomic Analysis of the Newborn Mammary Gland Identifies Prenatal Ethanol-Induced Remodeling of Insulin Signaling and Enhanced Proliferative Programming

Prenatal alcohol exposure (PAE) can produce persistent alterations in mammary development and increase susceptibility to mammary tumorigenesis, but the early molecular events underlying these effects remain poorly understood. Here, we examined whether PAE alters the molecular program of the mammary gland at birth. Pregnant MMTV-ErbB2 mice received control or ethanol-containing liquid diets during gestation, and mammary tissues were collected from newborn female offspring. RNA sequencing revealed exposure-level-dependent transcriptional reprogramming, with substantially broader alterations following moderate compared with lower ethanol exposure. Pathway analyses identified prominent changes in metabolic and growth-regulatory networks, including insulin signaling, with coordinated alterations in components of the insulin/IGF-IRS-PI3K/AKT pathway. Biochemical analyses further demonstrated exposure-dependent changes in IGFBP expression and IRS1 abundance and phosphorylation, supporting remodeling of insulin/IGF-associated signaling. Transcriptomic analyses also revealed enrichment of RNA metabolic and translational processes and, particularly following moderate exposure, enhanced DNA-replication, cell-cycle, and mitotic programs. These molecular signatures were accompanied by increased proliferative features in newborn mammary tissue. Together, these findings demonstrate that PAE establishes substantial molecular reprogramming of the mammary gland by birth and identify altered insulin/metabolic signaling and proliferative programming as prominent features of this early developmental response.

developmental biology↗

bioRxiv2026

Chronic Alcohol Exposure Induces Persistent DNA Damage Response Signaling and Sensitizes Breast Epithelial Cells to PARP Inhibition

Chronic alcohol consumption is associated with increased breast cancer risk; however, the long-term effects of alcohol exposure on DNA damage response (DDR) signaling and therapeutic vulnerability in breast epithelial cells remain incompletely understood. In the present study, we established a chronic alcohol exposure model using immortalized human breast epithelial MCF-10A cells to investigate persistent alterations in DNA damage signaling and sensitivity to poly (ADP-ribose) polymerase (PARP) inhibition. MCF-10A cells that chronically exposed to 0.2% alcohol for 20 weeks and then withdrew alcohol treatment for 4 weeks still retained elevated {gamma}H2AX levels and sustained activation of ATM/ATR-associated DDR pathways. Chronic alcohol-exposed cells also exhibited increased sensitivity to the PARP inhibitors olaparib and veliparib, as demonstrated by reduced cell viability, decreased clonogenic survival, and enhanced apoptosis. Mechanistically, olaparib induced greater G2/M checkpoint activation and replication-associated DNA damage in chronic alcohol-exposed cells compared with control cells. In addition, chronic alcohol exposure increased PARP expression and enhanced activation of DDR signaling following PARP inhibition. These findings demonstrate that chronic alcohol exposure induces persistent DNA repair stress and sensitizes breast epithelial cells to PARP inhibition. Our study suggests that chronic alcohol-associated genomic stress may create potential vulnerability to PARP inhibition.

cell biology↗

bioRxiv2026

Alcohol Promotes ER+ Breast Cancer Cell Proliferation and Invasion Through the Upregulation of Neuregulin 1-Mediated ER-ErbB3 Crosstalk

Alcohol consumption is an established risk factor for breast cancer, with a particularly strong association with estrogen receptor-positive (ER+) disease. Although the estrogenic activity of alcohol is well recognized, how alcohol-induced ER signaling is coupled to growth factor receptor pathways that promote tumor cell growth and progression remains incompletely understood. Here, we identify neuregulin-1 (NRG1) as a functional mediator, linking alcohol-induced ER activity to ErbB3 receptor tyrosine kinase signaling in ER+ breast cancer cells. Under estrogen-depleted conditions, alcohol induced proliferation, clonogenic growth, and S-phase progression in MCF-7 and T47D cells. Alcohol concurrently increased ER phosphorylation and transcriptional activity, including enhanced ER occupancy at the endogenous TFF1/pS2 regulatory region, and activated ErbB3 and downstream Akt, ERK, and p38 signaling. Notably, alcohol induced NRG1 expression in both cell lines. Pharmacological inhibition of ER signaling with ICI 182,780 (fulvestrant) substantially attenuated NRG1 induction, ErbB3/RTK activation, and alcohol-promoted growth, indicating that NRG1 induction and engagement of RTK signaling are strongly dependent on functional ER signaling. Conversely, shRNA-mediated NRG1 depletion suppressed alcohol-induced proliferation, clonogenic growth, and cell-cycle progression and markedly reduced alcohol-induced migratory and invasive phenotypes. NRG1 depletion also attenuated ErbB3/Akt/ERK signaling while reducing ER activation and ERE-dependent transcription, demonstrating a functional contribution of NRG1 to both arms of the signaling response. Together, these findings support a reciprocal ER-NRG1-ErbB3 signaling circuit in which alcohol-induced ER activity promotes NRG1 expression, while NRG1-dependent ErbB3 signaling reinforces ER activity and tumor-promoting phenotypes. Our study identifies NRG1 as a previously unrecognized molecular link between the estrogenic activity of alcohol and growth factor receptor signaling and provides a mechanistic framework for understanding alcohol-associated promotion of ER+ breast cancer.

cell biology↗

bioRxiv2026

ALDH2 Knockout Induces Dysregulation of Arginine biosynthesis in SKBR-3 Breast Cancer Cells

Background/Objectives: Aldehyde dehydrogenase 2 (ALDH2), a mitochondrial enzyme, mitigates cellular stress by detoxifying reactive aldehydes produced during alcohol exposure and endogenous metabolic processes. ALDH2*2 polymorphism, which results in deficient catalytic activity, is prevalent in East Asian populations and is associated with an increased risk of cancer and other diseases. While the effects of ALDH2 deficiency on cellular stress responses are well documented, the specific metabolic dysregulations arising from this deficiency require further investigation. Methods; An ALDH2 knockout subline of SKBR-3 cells was established using CRISPR/Cas9 strategy. The metabolomic profiles of control (SKBR-3/C) and ALDH2 knockout (SKBR-3/ADKO) cells were evaluated via ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS). Results: ALDH2 knockout in SKBR-3 cells resulted in increased cellular stress, evidenced by elevated levels of 8-OHdG, reactive oxygen species (ROS), and malondialdehyde (MDA). Metabolomic analysis of the paired cell lines assigned a total of 5,033 signals, of which 281 were significantly different (fold change [≥] 2, p-value <0.05) between the two groups. Pathway analysis with MetaboAnalyst identified significant metabolic pathways associated with ALDH2 deficiency, particularly those involving arginine biosynthesis, and arginine and proline metabolism. ALDH2 deficiency reprogramed arginine metabolism toward polyamine pathways while suppressing the urea cycle. Network analysis further revealed alterations in amino acid and lipid metabolism in ALDH2-deficient cells. Conclusions; This study provides a novel insight into the role of ALDH2 in cancer metabolism and may have broader implication for cancer biology.

cell biology↗

bioRxiv2026

TH1834-Mediated TIP60 Inhibition Protects Against Ischemia/Reperfusion Damage in Human iPSC-Derived Cardiomyocytes and Cardioids

Ischemia/reperfusion injury limits functional recovery after myocardial infarction through mitochondrial dysfunction, oxidative stress, energetic failure, impaired calcium handling, and contractile dysfunction. We previously identified the acetyltransferase TIP60/KAT5 as a maladaptive regulator of post-ischemic cardiac injury and showed that pharmacologic TIP60 inhibition with TH1834 mitigates myocardial infarction injury in mice. Here, we tested whether TH1834 promotes recovery in complementary 2D and 3D human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) and cardioid (hiPSC-CO) models. Maturation-enhanced hiPSC-CMs subjected to hypoxia/reoxygenation (H/R) reproduced key features of ischemia/reperfusion injury, including mitochondrial loss, oxidative stress, cell death, impaired calcium handling, and contractile dysfunction. RNA sequencing further showed activation of stress programs and suppression of oxidative-metabolic pathways. At a non-arrhythmogenic dose, TH1834 inhibited TIP60 acetyltransferase activity, improved post-H/R survival and beating recovery, preserved mitochondrial and myofibrillar integrity, reduced reactive oxygen species, restored calcium transient kinetics, normalized sarcoplasmic reticulum calcium reserve, and improved contraction and relaxation. A central effect of TH1834 was enhancement of metabolic flexibility: following H/R, treatment restored mitochondrial respiratory capacity while simultaneously increasing glycolytic capacity and reserve. Because CM calcium cycling and mechanical work are highly dependent on energetic supply, this recovery of complementary oxidative and glycolytic capacity provides an energetic basis for improved calcium homeostasis and contractile recovery. Transcriptomic analysis supported this phenotype, showing preferential counter-regulation of H/R-induced stress programs and attenuation of persistent HIF1A-ARNT-PDK1 hypoxic metabolic signaling. In 3D hiPSC-COs, TH1834 similarly enhanced mitochondrial respiratory reserve and glycolytic capacity while improving calcium dynamics, contractile performance, beating recovery, and survival. Together, these findings identify enhanced metabolic flexibility as a central feature of TH1834-mediated protection against H/R, linking restoration of energetic capacity to preservation of calcium signaling and contractile function, supporting TIP60 as a therapeutic target for ischemic heart disease.

cell biology↗

bioRxiv2026

Dual-Binding Scaffold RRsS1 Bridges Pol IV Transcripts and DNA Templates for Robust Reproductive siRNA Biogenesis

Cytosine DNA methylation established by RNA-directed DNA methylation (RdDM) is critical for transposon silencing and genome integrity in plants. In reproductive tissues, RNA Polymerase IV (Pol IV) is recruited to specific genomic loci by DNA motifs and the transcription factor-GDE1-CLSY3/4 complex to initiate abundant siRNA biogenesis and de novo DNA methylation, but the mechanisms that stabilize the Pol IV transcription complex at these sites remain elusive. Using immunoprecipitation-mass spectrometry of the Pol IV complex, we identify Reproductive RdDM siRNA Scaffold 1 (RRsS1) as a novel Pol IV interactor. RRsS1 colocalizes genome-wide with motif-dependent RdDM factors in floral tissues. Loss of RRsS1 significantly impairs 24-nt siRNA accumulation at a subset of CLSY3/4-dependent loci, particularly those exhibiting high Pol IV enrichment. We show that chromatin association of RRsS1 is stabilized by GDE1 and CLSY3/4. Structural modeling and biochemical assays characterize RRsS1 as a chimeric protein containing HRDC, Nudix, and DRBM modules that bind single-stranded DNA (ssDNA) and double-stranded DNA (dsRNA), respectively. Together, our findings support a model in which RRsS1 acts as a dual-binding scaffold, bridging Pol IV-RDR2 transcripts to their DNA templates within transcription bubbles to ensure robust siRNA production during plant reproduction.

plant biology↗

bioRxiv2026

Risk-Window Palbociclib Exposure Delays ErbB2-Driven Mammary Tumorigenesis and Suppresses Mammary Epithelial Cell Stemness

ErbB2 overexpression occurs in 15-20% of invasive breast cancer (BC) and inactivation of Cyclin D1-CDK4/6 axis reduce mammary stem/progenitor cells in ErbB2-driven tumorigenesis. Here, we explored the preventive role of short-term palbociclib intervention in MMTV-ErbB2 mice. Palbociclib significantly inhibited the proliferation and stemness of ErbB2-overexpressed BC cells in vitro and in vivo. Furthermore, short-term palbociclib exposure during the early premalignant risk window significantly delayed mammary tumor development and reduced tumor multiplicity, accompanied by the suppression of epithelial proliferation and ductal/alveolar morphogenesis in premalignant tissues, as well as prolonged tumor-free survival compared with controls. Importantly, palbociclib reduced the luminal epithelial (CD24high/CD49flow), mammary reconstitution unit-enriched (CD24high/CD49fhigh) subpopulations, and luminal progenitor/TIC-enriched (CD61high/CD49fmid) subpopulations. These changes were accompanied by diminished mammary epithelial cell stemness functions, including colony-forming, mammosphere-forming, and 3D growth activities of mammary epithelial cells. Mechanistically, palbociclib-treated tissues showed inhibition of the Cyclin D1-CDK4/6-RB-E2F axis and coordinated attenuation of ER-, ErbB2- and Wnt/{beta}-catenin-associated signaling. Together, we demonstrate that short-term CDK4/6 inhibition during a premalignant risk window produces a sustained delay in ErbB2-driven mammary tumorigenesis, associated with remodeling of the mammary epithelial hierarchy and suppression of proliferative and stem/progenitor-associated activity, suggesting CDK4/6 inhibition as a strategy for ErbB2-positive BC prevention.

cancer biology↗

bioRxiv2026

Taylor's Law, Smith's Law, and Diversity Power Laws: A Novel Triple Power Law Methodology for Scaling Diversity and Heterogeneity

Taylor's power law (TPL) and Smith's power law (SPL) are two foundational scaling laws describing how variance scales with mean density and plot area, respectively. While TPL captures ecological heterogeneity (variation among interacting organisms), SPL captures environmental heterogeneity (variation in the abiotic template). Diversity scaling, traditionally approached through species-area relationships, has been extended to diversity-area relationships (DAR) using Hill numbers. Here we integrate TPL, SPL, and DPL, including three newly proposed models [diversity-mean, diversity-variance, and diversity-heterogeneity relationships (DHR)], into a unified triple power law methodology for scaling diversity and heterogeneity in microbial ecosystems. Using human gut and vaginal microbiome datasets, we systematically vary two orthogonal factors: scale (unit vs. multi-unit) and accrual (without vs. with sample accrual). Our results show that TPL and SPL are complementary: classic TPL captures cross-sectional heterogeneity at the community scale, while accrual TPL, a new extension based on sample accrual, captures heterogeneity accumulation at the metacommunity scale and appears less scale-dependent. SPL provides a tool for relating environmental heterogeneity to diversity, supporting the reciprocity principle with ecological heterogeneity. Among the four diversity power laws, DHR, using the variance-to-mean ratio as a direct heterogeneity metric, is most aligned with the diversity-heterogeneity nexus. The triple power law methodology reveals that heterogeneity scaling predicts diversity scaling in the majority of models, with the strongest predictive relationships observed for accrual TPL at higher diversity orders. Nevertheless, the commonly assumed scale-invariance proved elusive, occurring in fewer than 20% of the power law models tested. This framework may extend beyond microbiome ecosystem to any complex system where heterogeneity and diversity arise from interacting components, from ecosystems to economies to artificial intelligence.

ecology↗

bioRxiv2026

siProGenA: Generative siRNA Candidate Construction via Position Proposal and Guide Generation

Small interfering RNAs (siRNAs) are short guide RNAs that recruit the RNA-induced silencing complex (RISC) to complementary target sites on messenger RNAs (mRNAs), triggering Ago2-mediated cleavage and gene silencing. siRNA design requires compact candidate sets that cover a target while preserving efficacy, specificity, and practical sequence constraints. Existing pipelines usually enumerate candidate windows, assign a canonical guide to each window, and then rank preconstructed siRNA--mRNA pairs. This has produced strong pairwise efficacy predictors, but leaves a candidate-construction gap: candidate positions and guide sequences are fixed before the model begins to rank them. We address this gap by decomposing siRNA candidate construction into two generative decisions: where to place candidates within an mRNA segment, and what constrained guide variants to consider at a candidate position. We instantiate this framework as siProGenA, using a Discrete Denoising Diffusion Probabilistic Model (D3PM) for mRNA-conditioned position proposal and a Bayesian Flow Network (BFN) for temperature-controlled guide generation. On 62 positive test segments, the diversity-aware final library reaches Hit@1 = 0.790 and Hit@5 = 0.903. In a measured-site controlled Stage~2 evaluation, seed- and cleavage-preserving variants outscore the canonical complement for 89.8% of measured sites, with supporting gains across additional computational scorers, random-mismatch controls, and biophysical diagnostics. Together, the results support a modular proposal--generation view of siRNA candidate construction for prioritizing compact candidate sets.

bioinformatics↗

bioRxiv2026

Five novel ubiquitous totiviruses function as virulence-promoting symbionts in the obligate biotrophic fungus Puccinia triticina

Mycoviruses modulate fungal fitness and pathogenicity, yet their biological roles in obligate biotrophic phytopathogens remain poorly understood. Here, we report the first functional characterization of totiviruses in rust fungi, identifying five novel totiviruses, designated Puccinia triticina totivirus 1 to 5 (PtTV1?PtTV5), from the wheat leaf rust fungus Puccinia triticina (Pt). All five PtTVs possess the canonical genomic architecture of Totiviridae, including two overlapping ORFs and a conserved ?1 ribosomal frameshifting motif. Transcriptional profiling revealed that PtTVs are highly expressed during early Pt infection. PtTV-encoded proteins suppressed BAX-triggered programmed cell death in Nicotiana benthamiana, indicating immune-suppressive activity. Using BSMV-mediated host-induced gene silencing (HIGS), we showed that knockdown of PtTV transcripts significantly impaired fungal hyphal expansion and uredinial formation, concomitant with enhanced host H?O? accumulation. A survey of 90 Pt field isolates from four major wheat-growing regions of China revealed that PtTVs are ubiquitously distributed in natural rust populations. Collectively, these findings demonstrate that totiviruses function as virulence-promoting symbionts in Pt, establishing for the first time a functional link between totiviral infection and enhanced pathogenicity in cereal rust fungi and identifying candidate targets for RNAi-based disease control.

plant biology↗

bioRxiv2026

From distyly to stigma-height dimorphism: phylogenetic insights into the evolutionary breakdown of distyly in Jasminum

Background and AimsDistylous polymorphisms (distyly) are adaptations for plants to improve efficiency of cross-pollination and reduce pollen wastage. Theoretical models suggest that distyly evolves from stylar monomorphism via an intermediate stage of stigma-height dimorphism (SHD), however, this evolutionary scenario is only observed in few distylous lineages. The genus Jasminum have many species exhibit either distyly or SHD, providing an ideal opportunity to test models of the evolution of distyly. Focusing on the evolution of distyly, we investigated floral morphs and evaluated the occurrence of distyly and SHD in Jasminum using phylogenetic reconstruction and morphological analysis. MethodsWe investigated floral morphs and evaluated the occurrence of distyly and stigma-height dimorphism through morphology observation. To perform phylogenetic analysis, we sequenced plastomes of forty species from Jasminum and Chrysojasminum using Illumina next generation sequencing, and then constructed phylogenetic tree using maximum likelihood method and Bayesian inference. Based on the phylogenetic tree, we inferred the ancestral floral type through ancestral reconstruction. Key ResultsOur results suggest that the distyly originated in the common ancestor of Jasminum and Chrysojasminum. SHD occurs in several Jasminum species scattered in different clades of the phylogenetic tree, suggesting multiple independent reversions from distyly back to SHD. However, this transition is not associated with the loss of ancillary polymorphisms, as all the species examined in this study well retain dimorphic traits for other floral organs such as pollens and stigmas. Moreover, most species maintain strict heteromorphic self-incompatibility, while J. officinale has lost or at least partially lost self-incompatibility, suggesting that distyly is not always linked to self-incompatibility. ConclusionsIn Jasminum, breakdown of distyly resulted in evolutionary transitions to stigma-height dimorphism for multiple times, suggesting that distyly is not a stable floral polymorphism under certain selective forces. These findings advance our understanding on the evolution of distyly and plant reproductive systems.

plant biology↗

bioRxiv2026

MS4A8B regulates Orai1-dependent Ca2+ influx to control motile cilia function in human nasal epithelial cells

Motile cilia demonstrate coordinated beating to propel fluids across epithelial tissues, and changes to their beating frequency are largely regulated by intracellular second messengers including Ca2+. In the airway epithelium, ciliary beating is essential to mucociliary clearance. Mucociliary clearance involves trapping inhaled pathogens and irritants in sticky mucus lining the airways for motile cilia to sweep away contaminated mucus, preventing infection and reducing general airway inflammation. Many chronic respiratory diseases, including chronic rhinosinusitis and asthma, are characterized by an acquired ciliary dysfunction. Despite the importance of Ca2+ signaling in cilia physiology, the identity and molecular mechanisms governing localized ciliary Ca2+ transport remain poorly understood. MS4A8B is an uncharacterized cilia-localized transmembrane protein. Other MS4A homologs have been indirectly linked to Ca2+ signaling via uncharacterized mechanisms. Using primary human nasal epithelial cells differentiated at air-liquid interface, we demonstrated that MS4A8B regulates motile cilia function. MS4A8B knockdown impairs ciliary beating and impacts cilia structure. Live-cell imaging combined with genetic analysis revealed that MS4A8B potentiates Orai1-mediated Ca2+ influx. Co-immunoprecipitation and FRET microscopy in ectopic expression systems demonstrated that MS4A8B interacts with Orai1 channels. Orai1 was further identified to reside in motile cilia of primary human nasal epithelial cells, allowing ciliary beat frequency to be stimulated by Orai1 agonists including arachidonic acid. MS4A8B functional coupling with Orai1 acts as an autonomous cilia signaling network. Targeting this compartmentalized signaling pathway offers a novel therapeutic approach to restore or enhance mucociliary clearance in airway diseases.

physiology↗