Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 307 records · Page 17Linked to original sources

bioRxiv2025

Multicolored, Sonosensitizer-optimized Organic Mechanoluminescent Nanoparticles for Functional Sono-optogenetics

Light enables precise visualization and control of cellular processes, but its utility in deep tissues is fundamentally limited by poor optical penetration, particularly in the deep brain. Ultrasound-triggered mechanoluminescence offers a non-invasive strategy for remote light delivery, yet existing organic systems remain monochromatic and low-intensity, largely due to an incomplete understanding of ultrasound-induced emission. Here, we report a multicolor mechanoluminescence platform that couples reactive oxygen species-responsive chemiluminescent donors with fluorescent acceptors via Forster resonance energy transfer, generating tunable emission from blue (459 nm) to red (592 nm). Systematic screening potentially reveals that electronic energy gap-dependent reactive oxygen species generation serves as a predictive design principle for high-performance mechanoluminescent materials. The emitted spectrum and intensity are sufficient to activate ChR2 and ChRmine and inhibit eOPN3, enabling bidirectional, fiber-free neuromodulation under focused ultrasound. By integrating spatially precise ultrasound with programmable photon output, this platform establishes a non-invasive strategy for deep-tissue neural monitoring and provides a foundation for applications in bioimaging, gene editing, and precision therapeutics.

bioengineering↗

bioRxiv2025

Nuclear N-Glycosylation Redefines the Glycoscape and Directs Cell Identity

Glycans modify nucleic acids, proteins and lipids in fundamental biological processes, but have long been considered confined to the secretory pathway and cell surface. Here, we challenge this view with evidence that N-glycosylation, a ubiquitous glycan modification, occurs within cell nuclei across tissues and species, exhibiting cell type-dependent abundance and localization patterns. Using a multi-faceted approach, we show that numerous classical membrane and secreted glycoproteins localize to the nucleus with N-glycan modifications, exemplified by the cell adhesion molecule L1CAM. Mechanistically, we show that the N-glycosylated L1CAM is transported to the nucleus by KPNB1, where it transcriptionally modulates neuronal differentiation. Moreover, this nuclear N-glycosylation event contributes to neurodevelopmental disorders and is pharmacologically reversible. These findings revise the cellular geography of N-glycosylation and expand the known routes of protein trafficking, and highlight nuclear N-glycosylation pathways as potential therapeutic entry points for developmental disorders.

cell biology↗

bioRxiv2025

Engineering chimeric DNA polymerases for DNA movable type storage

DNA-based information storage offers a promising alternative to conventional media due to its high density, long-term stability, and low energy requirements. However, its application remains hindered by synthesis costs, limited sequence length and poor scalability. DNA polymerase is a critical enzymatic tool in the DNA storage systems by enabling high-fidelity data writing and targeted sequence amplification. In this study, we engineered chimeric DNA polymerases by fusing the high-fidelity 9{degrees}N DNA polymerase with double-stranded DNA binding proteins derived from thermophilic archaea. These fusions significantly enhanced processivity, thermal stability, and salt tolerance by stabilizing enzyme-template interactions, mimicking sliding clamps while preserving catalytic efficiency. Leveraging these properties, we demonstrated precise file retrieval from a mixed oligonucleotide pool using orthogonal barcode primers. Compared with wild-type 9{degrees}N, the chimeric polymerases, particularly PLS, exhibited reduced substitution error rates and improved read accuracy. We then applied these enzymes to a DNA movable type storage system, where prefabricated DNA modules were assembled into encoding blocks. Using engineered polymerases, these blocks were recombined to enable flexible data rewriting without de novo DNA synthesis. Moreover, a multi-enzyme assembly strategy enabled the construction of kilobase-scale DNA sequences encoding a classical Chinese poem, achieving complete data recovery. All assembled fragments remained stable in E. coli over 100 generations, exhibiting the potential for in vivo storage. Collectively, our findings demonstrated the role of engineered DNA polymerases for DNA-based information storage. Moreover, this system reduced synthesis demands, supported scalable rewriting, and ensured long-term preservation, offering a practical route to sustainable, high-fidelity DNA data storage.

synthetic biology↗

bioRxiv2025

A coherent feed-forward loop fine-tunes KatG to maintain redox homeostasis in mycobacteria

Bacteria survive and reproduce in fluctuating environments by balancing their basic physiological needs, such as relying on iron-containing enzymes to detoxify reactive oxygen species (ROS) while conserving scarce iron. Understanding the regulatory networks that balance these conflicting needs is key to deciphering bacterial adaptability. Here, we identify a coherent feed-forward loop in mycobacteria that integrates the transcriptional regulator FurA3, the small RNA MrsI, RNA sponge FutR, and the catalase-peroxidase KatG. This circuit fine-tunes antioxidant responses according to iron availability. Under iron limitation, the iron-containing enzyme KatG is dually repressed by FurA3 transcriptionally and by MrsI post-transcriptionally, which conserves iron at the cost of antioxidant capacity. However, when iron deprivation coincides with oxidative stress, the circuit triggers an emergency response: H2O2 inactivates FurA3, relieving transcriptional repression of katG and futR, while induced FutR sequesters MrsI to post-transcriptionally derepress katG expression, enabling rapid KatG synthesis for effective peroxide detoxification. Our findings reveal a tightly regulated network that allows mycobacteria to balance iron homeostasis and oxidative stress defense, providing mechanistic insights into bacterial physiological trade-offs.

microbiology↗

bioRxiv2025

Gasdermin E couples mitochondrial damage to pyroptotic neurodegeneration in Parkinson disease

Parkinsons disease (PD) features progressive loss of nigrostriatal dopamine neurons, but how mitochondrial damage engages programmed cell death pathways remains unresolved. Here, we identify gasdermin E (GSDME), the caspase-3-activated executor of pyroptosis, as a critical mediator of neurodegeneration in toxin-based PD models. In primary neurons and SH-SY5Y cells, the mitochondrial complex I inhibitor MPTP/MPP triggered caspase-3 activation, GSDME cleavage, and lytic membrane rupture. Genetic silencing of Gsdme or its transcriptional regulator SP1 reduced neuronal death. In vivo, Gsdme deficiency preserved substantia nigra pars compacta dopaminergic neurons, improved motor performance, and mitigated anxiety- and depression-like behaviors after MPTP administration. Loss of Gsdme also dampened microglial and astrocytic activation and lowered proinflammatory cytokines in striatum and substantia nigra. Mechanistically, cleaved GSDME localized to mitochondria, disrupted membrane potential, increased reactive oxygen species, and precipitated organelle injury, thereby coupling mitochondrial dysfunction to pyroptotic cell death. These findings identify GSDME-mediated pyroptosis as a mechanistic link between mitochondrial toxicity and neuroinflammation in PD and nominate GSDME as a therapeutic entry point to slow disease progression. SignificanceHow mitochondrial injury kills dopamine neurons in Parkinsons disease is a central unresolved question. We show that the pyroptosis executor GSDME is required for neurodegeneration and neuroinflammation in MPTP models, mechanistically linking caspase-3 activation and mitochondrial damage to lytic cell death. Targeting GSDME may provide a strategy to protect vulnerable neurons in PD. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=191 SRC="FIGDIR/small/694264v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@15364e7org.highwire.dtl.DTLVardef@57b65org.highwire.dtl.DTLVardef@1e85108org.highwire.dtl.DTLVardef@1200d34_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsGSDME drives PD-linked neuronal loss. Silencing GSDME (or its transcriptional factor Sp1) ameliorates MPTP-triggered neuronal cell death. Genetic ablation of Gsdme is protective in the MPTP-induced PD mouse model. Gsdme-/-mice retain nigrostriatal DA neurons, show improved motor and affective behaviors, and exhibit reduced microglial and astrocytic activation and cytokines release upon MPTP treatment. Cleaved GSDME accumulates on mitochondria, collapses {Delta}{Psi}m, raises ROS, and links mitochondrial toxicity to pyroptosis, thus positioning GSDME as a tractable target to slow PD progression.

neuroscience↗

bioRxiv2025

VIP-OT: Dissecting Single-Cell Biochemical State Dynamics under Perturbation via Vibrational Painting and Optimal Transport

Dissecting the heterogeneous response of individual cells towards genetic and chemical perturbations is central to understanding the dynamic functions of cells and multicellular systems. However, characterizing and modeling how individual cells transition between different states remains a major challenge. Vibrational imaging provides high-content, biochemically informative, label-free molecular fingerprints of single cells but it remains at its infancy for dynamic or predictive analysis of cell state transition. Here, we introduce Vibrational Painting-Optimal Transport (VIP-OT), an integrated experimental-computational framework that overcomes this fundamental limitation. VIP-OT couples multiplexed infrared (IR) and Raman imaging with optimal transport to computationally reconstruct single-cell perturbation trajectories from unpaired population snapshots. When applying to over 22,000 single-cell spectra profiles from human breast adenocarcinoma cells under 16 drug treatments, this framework can retrospectively trace drug response heterogeneity back to baseline metabolic states. We leverage the inferred cell pairings to develop a machine learning model that accurately predicts the full post-treatment metabolic state of individual cells from their pre-treatment spectra. Furthermore, by modeling transitions across dose gradients, we introduce the concept of Spectral Velocity to map dynamic response trajectories and resolve drug combination effects into distinct, path-dependent molecular routes. Together, VIP-OT opens a new direction for dissecting heterogeneous perturbation responses at single cell resolution and serves as a foundation for building virtual simulators of cells under perturbations through high-throughput, high-content, and low-cost vibrational imaging, as well as interpretable in silico modeling.

bioengineering↗

bioRxiv2025

Fast Loading and Transformation of Large-Volume Bioimaging Data Consistently Approaching the I/O Peak Speed

High-resolution large-volume biological imaging techniques are now widely used in biological research, but inefficiencies in data processing and visualization persist due to bottlenecks in loading/saving pipelines and limitations of conventional pyramid formats. To address these issues, we have decoupled data loading process into reading from disk and in-memory decompression, while data saving has been separated into in-memory compression and writing to disk. This approach allows us to dedicate more CPU cores to decompression and compression tasks, optimizing resource allocation and maximizing disk I/O throughput. As a result, both loading and saving processes operate near the disks peak data transfer capacity. Further, we integrated a video stream-inspired format into the pyramid structure, allowing direct access to regions of interest (ROIs) without loading extraneous data into RAM, reducing memory overhead. Compared to the latest methods, our approach improves pyramid data transformation efficiency by at least 6x and dramatically accelerates downstream tasks like visualization and deep learning inference. TeaserNovel bioimaging data processing pipeline achieves near-peak I/O throughput via decoupled architecture and video-formatting.

bioinformatics↗

bioRxiv2025

Super-CUT&Tag: A Sensitive, Spatially Resolved Approach for Epigenomic Profiling in Tissue Sections

Spatial profiling of protein-DNA interactions is essential for understanding gene regulatory processes, but current methods suffer from low sensitivity, limited resolution, and complex workflows. Here we introduce Super-CUT&Tag (Solid-phase interface embedded with an Ultra-dense DNA barcode array to Profile Epigenomic landscapes for spatially Resolved CUT&Tag), a robust spatial epigenomic method that directly transfers in situ protein-DNA interactions from tissue sections onto a pre-fabricated spatially barcoded array. Incorporating 3D polyamidoamine (PAMAM) dendrimers markedly improves chromatin capture efficiency, achieving several-fold higher sensitivity compared to current spatial CUT&Tag approaches. Using Super-CUT&Tag, we profile H3K27ac spatial landscape and uncover previously hidden active-chromatin heterogeneity across mouse embryonic tissues and stages. Integration with spatial transcriptomics further reveals spatiotemporal enhancer regulation dynamics of Neurod2 during corticogenesis. By overcoming key bottlenecks in sensitivity, resolution and usability, Super-CUT&Tag establishes a powerful platform for spatial epigenomic profiling in complex tissues.

genetics↗

bioRxiv2025

A global atlas of deep-sea cold seep viruses uncovers extensive genomic novelty, pervasive viral dark matter, and biotechnological potential

Cold seeps are globally distributed deep-sea ecosystems harboring diverse chemosynthetic microbial communities, yet their viral components remain poorly understood. Here, we establish the Global Cold Seep Virome, a comprehensive catalog of 191,937 species-level viral operational taxonomic units (vOTUs) and 2.44 million viral protein clusters reconstructed from 314 metagenomes spanning 18 cold seep sites worldwide. Most vOTUs are distinct from those in existing environmental viromes, suggesting that cold seeps harbor a largely unexplored viral reservoir. Host prediction suggests diverse viral associations with key prokaryotes, including anaerobic methanotrophic archaea. Protein annotation reveals that these viruses encode widespread uncharacterized proteins and viral hallmark proteins with divergent physicochemical properties, potentially contributing to their ecological adaptability. We also identify putative auxiliary metabolic genes, anti-defense genes, and lysins, and experimentally validate representative anti-defense proteins and lysins with strong activities. This resource expands current knowledge of deep-sea viral diversity and provides a foundation for studying virus-host interactions, testing biogeochemical hypotheses, and exploring biotechnological potential in cold seep ecosystems.

microbiology↗

bioRxiv2025

From genomic decay to functional advantage: Trait-based evidence for long-term host residency of a next-generation coral probiotic

A key bottleneck in microbiome engineering is ensuring the long-term host association of introduced microbes. Selecting probiotic candidates based on evolutionary genomic decay signatures of emerging host dependency offers a potential solution. The Ruegeria strain B4 of the population MC10, identified by such signatures, has shown persistent colonization in corals in a companion study. Whether this persistence translates into a measurable host benefit compared to other coral-associated Ruegeria strains, and which mechanisms underlie such benefit, remained unknown. Here we directly compare the probiotic efficacy of MC10-B4 against two sympatric Ruegeria strains isolated from the same coral colony and mucus compartment, controlling for host genotype and microenvironment. MC10-B4 inoculation significantly increased heat stress tolerance in the coral model cnidarian Aiptasia (Exaiptasia diaphana strain H2), outperforming both sympatric control strains. To understand the mechanistic basis of this probiotic efficacy, we characterized the functional profile of MC10 using an integrated multi-omics approach. The genome of MC10 is enriched in genes associated with host-interaction, including siderophore-mediated iron acquisition and exopolysaccharide biosynthesis, which were phenotypically confirmed by detectable iron scavenging and enhanced biofilm formation. Following exposure to coral tissue extract, MC10-B4 underwent a coordinated motility-to-sessility proteomic reprogramming, downregulating flagellar motor components while upregulating flagellin and biofilm regulators. This response was distinct from its sympatric relatives, which instead mounted broad upregulation of nutrient acquisition systems. MC10-B4s functional profile, particularly its sensitivity to oxidative stress, contrasts with the traits typically favored in conventional probiotic screens. Our results move beyond the descriptive identification of a coral probiotic by providing initial mechanistic insight into traits associated with long-term host association and improved thermal performance. These findings validate an evolution-guided approach that prioritizes innate colonization potential over pre-defined laboratory functionalities, informing the rational design of durable probiotics.

microbiology↗

bioRxiv2025

Elucidation and engineering of arabinofuranosyltransferase to enable total de novo biosynthesis of paris saponins in yeast

Paris saponins (PSs) are structurally complex steroidal saponins that, due to their diverse glycosylation patterns, exhibit a range of significant pharmacological activities, including anti-tumor and antibacterial effects. However, incomplete characterization of the key enzymes responsible for glycosylation modifications has hindered their efficient heterologous biosynthesis. In this study, we reprogrammed the sugar donor specificity of a steroidal rhamnosyltransferase (UGT93M3) to enable the transfer of arabinofuranose (Araf). Through structural analysis, we identified key amino acid residues (368H/Q) that play an important role in determining Araf donor specificity. Guided by this insight, we successfully reconstructed the paris saponin I (PSI) biosynthetic pathway in Saccharomyces cerevisiae using engineered enzymes. To address challenges related to donor availability, we introduced UDP-sugar biosynthetic modules (UDP-Rha and UDP-Araf) into yeast. With this integrated platform, we were able to de novo produce a range of paris saponins, including diosgenin-3-O-glucosyl-(1[->]6)-glucoside (DGG), diosgenin-3-O-rhamnosyl(1[->]2) [glucosyl(1[->]6)]glucoside (DRGG) and paris saponin II. This work establishes a novel microbial platform for the sustainable production of paris saponins, particularly PSI, advancing the biosynthesis of steroidal glycosides and providing a potential strategy for the industrial-scale production of bioactive saponins. TeaserIn this study, we report the first complete de novo biosynthesis of four bioactive PSs, PSI, PSII, DGG and DRGG, in Saccharomyces cerevisiae from simple carbon source. Key advances include: (i) A single amino-acid switch (N368H) in the rhamnosyltransferase UGT93M3 endowed high-efficiency transfer of the rare five-membered arabinofuranose, solving a bottleneck in PS I biosynthesis; (ii) Elucidation of the molecular basis for sugar-donor specificity through AlphaFold3 docking and 300-ns molecular-dynamics simulations, revealing a histidine "latch" that stabilizes UDP-Araf in the catalytic pose; (iii) Construction of a 16-gene yeast chassis that integrates plant P450s, optimized glycosyltransferases, and de novo modules for UDP-rhamnose and UDP-arabinofuranose supply, achieving de novo microbial production of PS II, DGG, DRGG and PS I from glucose alone.

synthetic biology↗

bioRxiv2025

A tailored in vivo CRISPR screen identifies BAP1 as a potent tumor suppressor of soft tissue sarcoma

Undifferentiated pleomorphic sarcoma (UPS) is one of the most common soft tissue sarcomas (STS) in adults. Despite decades of research, therapeutic advancements for STS, including UPS, have remained limited. The genetic complexity of UPS, characterized by the absence of recurrent driver oncogene mutations, has hindered the development of effective targeted therapies beyond conventional chemotherapy and immunotherapy. To address this challenge, we conducted a customized in vivo CRISPR/Cas9 screen in mice to systematically identify potential tumor suppressors involved in UPS development. Our screen revealed BRCA1-associated protein 1 (Bap1) as a potent tumor suppressor in STS. Using total RNA sequencing, multiplex immunohistochemistry, and flow cytometry, we found that Bap1-deficient mouse sarcomas exhibit significant immune suppression. Further analysis indicated that polo-like kinase 1 (Plk1) is essential for the survival of Bap1-deficient sarcomas. Treatment with volasertib, a Plk1 inhibitor, markedly inhibited tumor growth in both syngeneic and spontaneous mouse models of Bap1-loss sarcoma. In conclusion, our findings suggest that PLK1 inhibition, or combined with immunotherapy, may represent a promising targeted therapeutic strategy for tumors lacking BAP1.

cancer biology↗

bioRxiv2025

Rapid ecosystem collapse and biofilter formation following seabed methane leakage

Globally, vast amounts of methane are trapped within subseafloor gas hydrates. Recent evidence suggests that climate- and human-induced perturbations can destabilize gas hydrates and trigger methane release, yet the response of deep-sea ecosystems to these changes remains poorly understood. Here we show multi-year in situ monitoring of seabed ecosystem following methane leakage induced by hydrate exploration activities. Within just two years, benthic microbial and eukaryotic diversity in the affected areas declined significantly, while microbial and macrofaunal abundance increased. Integrated geochemical and omics analyses reveal the rapid successional shift of seabed ecosystem to a novel chemosynthetic system. Aerobic methanotrophs (Methyloprofundus) co-established with unexpectedly fast growing anaerobic methanotrophic archaea (ANME-3), accompanied by a rapid recruitment of opportunistic polychaetes that bioirrigated the seabed to >50 cm depths. The active animal-microbe interactions sustained exceptionally high rates of methane oxidation that utilized diverse electron acceptors. We demonstrate that methane hydrate destabilization can trigger rapid collapse of native seabed ecosystem while driving the formation of an effective methane biofilter consuming this potent greenhouse gas much faster than previously estimated. Understanding seabed ecosystem response and feedback is critical for predicting benthic methane cycling under ongoing global change and for developing sustainable strategies for methane hydrate resource management.

ecology↗

bioRxiv2025

Single-cell multi-omic characterization of the soybean root response to cyst nematode infection

Soybean cyst nematodes parasitize soybean roots by inducing the formation of multinucleate syncytia to feed and complete their life cycle. However, the molecular basis of syncytia initiation and development remains limited. Here, we generated an integrated single-nucleus RNA and chromatin accessibility profile of soybean roots from infected and uninfected plants. We profiled 56,448 high-quality nuclei and identified all major root cell types, including distinct subpopulations enriched with syncytial nuclei. Transcriptomic and chromatin accessibility analyses support their procambium cell signature that progresses through distinct stages associated with immune suppression, cell fusion, and endoreduplication. Integrative gene expression and transcription factor motif chromatin accessibility analyses identified CAMTA1, as a potential transcriptional repressor of defense-related genes including receptor-like kinases, whereas MYB, MYB-related, and E2F were identified as potential transcriptional activators that coordinate cell wall remodeling, chromatin modification and DNA replication, respectively, across developmental trajectories. These findings provide mechanistic insights into host reprogramming during nematode parasitism and serve as a foundational resource for engineering nematode-resistant soybean.

plant biology↗

bioRxiv2025

The Human Hippocampus Is Involved in Auditory Short-Term Memory Trace Formation

The human hippocampus has been claimed to play an important role in long-term memory, or episodic memory, but its contribution to short-term memory remains debated. Here, we demonstrate human hippocampal involvement in auditory short-term memory (ASTM) trace formation. We used a classic oddball paradigm and intracranial recordings across various human brain areas. High frequency activities evoked by deviant stimuli in subjects indicate the generation of ASTM trace. Analysis of auditory response latencies across the hippocampus, insula, and temporal, parietal, and frontal lobes revealed the early processing of ASTM trace at a pre-attention stage. Granger causality analysis further showed that ASTM trace processing engages hierarchical cortical areas and clarified their interactions. Bottom-up signals flow from the insula and auditory temporal regions to the frontal lobe early on, followed by top-down information from the frontal lobe to the hippocampus, inferior temporal lobe, and insula at a later pre-attentive stage. Critically, Bayesian model selection of dynamic causal modeling revealed that deviant stimuli selectively enhanced the effectiveness of top-down connections to the hippocampus, thereby facilitating ASTM trace formation. These results provide compelling evidence that the human hippocampus contributes to auditory short-term memory at a pre-attention stage and suggests a challenge to entrenched beliefs in the classification of memory systems.

neuroscience↗

bioRxiv2025

Beyond correlation: Causal discovery of cell program interactions in lung tissue

Cell-cell communication networks govern tissue function in health and disease, yet existing computational tools rely on static ligand-receptor databases or correlation-based analyses that cannot distinguish direct causal relationships from confounded or indirect associations. We introduce Cell-CLIP (Cellular Causal Learning and Inference Pipeline), a modular framework that combines (i) mask-aware patient-level JASMINE activity scoring with low-percentile imputation in raw activity space, (ii) five complementary causal-discovery algorithms -- PC, GES, FCI, DirectLiNGAM, and GRaSP -- each fed an algorithm-matched per-column transform of the same masked JASMINE matrix, (iii) direction-preserving bootstrap aggregation with a weighted two-phase consensus, (iv) Joint Causal Inference (JCI) for principled pooling of patient cohorts via context indicators, and (v) a residual-independence (RESIT) direction audit, all evaluated under a systematic three-by-three-by-three hyperparameter sweep. Applied to a 611-patient multi-phenotype lung atlas spanning normal tissue, COVID-19 pneumonia, and lung cancer, the cross-cohort joint-causal-inference graph constructed by stratifying patients into normal, COVID-19, and tumour contexts before pooling recovers 100% of evaluable curated ground-truth edges (8/8; Wilson 95% CI 0.68-1.00) with 75.0% direction accuracy (6/8; 95% CI 0.41-0.95) and zero forbidden-orientation violations (0/8; 95% CI 0.00-0.32) -- the only configuration in a comprehensive ablation series spanning 7 cohort/pool configurations, 27 hyperparameter settings, and 3 consensus types to simultaneously reach all three optimal Pareto corners. The single-cohort universal cross-phenotype graph (12 cross-phenotype programs over the full 611-patient atlas) similarly achieves 100% evaluable recall (8/8; 95% CI 0.68-1.00) with 62.5% direction accuracy (5/8; 95% CI 0.31-0.86) and zero forbidden violations (0/3; 95% CI 0.00-0.56) under the same systematic hyperparameter sweep with low-percentile imputation, exceeding an earlier zero-imputation baseline configuration of the pipeline on every reported metric (Table 6, Table 8); given small ground-truth denominators (n_eval = 8), these point-estimate improvements lie within the Wilson 95% intervals of the baseline and should be read as direction-of-effect rather than as confirmatory comparisons. We further show that single-cohort causal inference on the disease-extended pooled cohorts (which apply the COVID- and cancer-extended program sets to all 611 patients) recovers strong skeleton recall (35.0%-55.2% evaluable) but suffers a structural direction collapse (down to 14.3% direction accuracy and 60% forbidden rate at union) caused by within-cohort averaging over heterogeneous normal-plus-disease patient populations; the patient-stratified joint-causal-inference pool dissolves this collapse without altering the underlying algorithms. Cell-CLIP provides a hypothesis-generating framework for inferring directed cell-program networks from patient-level scRNA-seq atlases, with all reported relationships requiring experimental validation due to observational data limitations. O_TBL View this table: org.highwire.dtl.DTLVardef@1b18810org.highwire.dtl.DTLVardef@5c027eorg.highwire.dtl.DTLVardef@a7b806org.highwire.dtl.DTLVardef@122adf2org.highwire.dtl.DTLVardef@1ca0a39_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 6C_FLOATNO O_TABLECAPTIONHeadline validation metrics across reporting cohorts, with Wilson 95% confidence intervals on every binomial rate. C_TABLECAPTION C_TBL O_TBL View this table: org.highwire.dtl.DTLVardef@1653cb1org.highwire.dtl.DTLVardef@173c6baorg.highwire.dtl.DTLVardef@1fc115forg.highwire.dtl.DTLVardef@1d87e39org.highwire.dtl.DTLVardef@46d53b_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 8C_FLOATNO O_TABLECAPTIONAblation matrix: evaluable recall at the recall-best configuration. Variants are defined in the Sensitivity analysis section. Cells marked not run were not executed for that combination of cohort x variant; reasons are given in the table caption. C_TABLECAPTION C_TBL

systems biology↗

bioRxiv2025

Plant Face: Machine learning decodes genetic, environmental and developmental imprints in leaf appearance

Leaf appearance is a crucial plant phenotype. However, traditional methods for extracting this information are inefficient, limiting its full utilization. Deep learning based on convolutional neural networks (CNNs) enables us to capture previously inaccessible information from images. In this study, we made the surprising discovery that the leaf appearance of each individual plant is unique. Using deep learning, leaves from one plant could be efficiently distinguished from those of another plant of the same species and cultivar. We term this phenomenon the "Plant Face" and suggest the potential to develop a "plant face recognition system," analogous to human facial recognition. We also applied similar methods to study the relationship between leaflet appearance and their position on compound leaves, leaf bilateral symmetry, and differences in leaves from twining stems with different chirality. These results collectively indicate that plant genetic characteristics, growth conditions, and developmental features can be stored within their appearance. With appropriate decoding, leaf appearance is poised to play an increasingly important role in phenomics. SignificanceThe saying "no two leaves in the world are identical" holds philosophical significance, as such variation encompasses considerable contingency and randomness. Here, we assert that no two trees have identical leaves; meaning that even for plants of the same species and cultivar, the leaf morphology of each individual plant is distinct at the population level, even though single leaves may overlap in appearance. Genetic, environmental, and developmental information is recorded in some manner within the phenotypic appearance of leaves. With advancements in computational technologies like artificial intelligence, this information can now be decoded. HighlightsO_LIThe leaves of each individual plant are statistically unique. C_LIO_LIThe relationship between leaflet appearances in compound leaves hints at their developmental patterns. C_LIO_LILeaves are not necessarily bilaterally symmetric in a statistical sense. C_LIO_LILeaves from stems with different chirality (twining direction) exhibit distinct appearances. C_LI

plant biology↗

bioRxiv2025

Viral transcriptional regulators extensively rewire host pathways through diverse mechanisms

Viral transcriptional regulators (vTRs) reprogram host gene regulatory networks to promote replication, persistence, and immune evasion. Despite the identification of hundreds of vTRs in human viruses, how they rewire host pathways remains unclear. Here, we systematically profiled 95 vTRs from diverse human viruses across multiple functional assays. vTRs perturb immune, cell proliferation/death, and signaling pathways through various mechanisms; some bind DNA directly, others cooperate or antagonize human transcription factors (hTFs), and some remodel chromatin. vTRs can act as activators or repressors and recruit similar but not identical repertoires of proteins as hTFs. These findings reveal vTRs as versatile transcriptional modulators that converge on conserved host "pressure points" while diversifying across pathways to promote viral replication and persistence. Notably, many vTR dysregulate genes within autoimmune, neurological, and cardiovascular risk loci, revealing mechanistic links to disease. Together, we provide a comprehensive resource for understanding and targeting viral control of human transcription.

genomics↗