Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

3'UTR Insertion of a Directed-Evolved RNA Element for Enhanced Translation

Translation efficiency remains a major limitation for RNA therapeutics. Conventional optimization targets the 5 untranslated region (5 UTR), while the 3 UTR is viewed mainly as a stabilizing element. Here, we demonstrate that the 3 UTR can be rationally engineered to actively enhance translation. Using an intracellular directed-evolution platform based on the SINEB2 element, we identified RNA modules P51 and its compact variant P51t3,which markedly increased protein output without affecting mRNA levels. P51t3 consistently boosted expression two- to six-fold across plasmid, in vitro transcribed mRNA, and recombinant AAV systems. Mechanistic studies revealed that P51t3 binds ribosomal protein RPL39, recruiting 60S subunits to the initiation site through the natural closed-loop translation model. By integrating evolutionary selection with 3 UTR design, this work redefines the 3 UTR as an active translational enhancer and provides a broadly applicable regulatory element for next-generation mRNA and gene-delivery therapeutics.

molecular biology↗

bioRxiv2026

Neuromodulation of Foxp2+ hypothalamic neurons induces therapeutic hypothermia

The inability to selectively trigger therapeutic hypothermia independent of environmental cooling has hindered causal analysis of its broader physiological benefits. Here, we employed P57, a natural product that pharmacologically induces therapeutic hypothermia circumventing external cold stress, to identify the neuronal substrates underlying hypothermia-induced antitumor effects. Integrating functional ultrasound imaging, activity-dependent neuronal labeling, and single-nucleus RNA sequencing, we identify a previously unrecognized population of Foxp2 neurons in the medial preoptic area (MPA) that are selectively activated by P57. Inhibition of MPA Foxp2+ neurons abolishes P57-induced hypothermia, whereas the paraventricular hypothalamus (PVH) serves as a critical downstream node. Importantly, targeted activation of MPA Foxp2 neurons is sufficient to induce sustained hypothermia, suppress systemic metabolism, and inhibit tumor growth, providing causal evidence that neuronally driven reductions in core body temperature can exert antitumor effects. Together, these findings establish MPA Foxp2 neurons as a controllable node for therapeutic hypothermia induction and demonstrate that neuromodulation of defined neuronal populations can achieve therapeutic benefit by directly controlling physiological states.

neuroscience↗

bioRxiv2026

The conserved QTQTX motif in the SARS-CoV-2 spike protein is dispensable for cleavage and lung cell entry of the emerging variant BA.3.2

The furin motif in the SARS-CoV-2 spike (S) protein is important for lung cell entry. It is embedded in an extended loop structure and preceded by a highly conserved QTQTX motif that is required for efficient furin cleavage of the SARS-CoV-2 WA-1 S protein. BA.3.2 is an emerging SARS-CoV-2 saltation variant that is spreading globally in April 2026 and encodes for a highly mutated S protein. Here, we analyzed whether the QTQTX motif is also required for spike protein cleavage and lung cell entry of BA.3.2. We report that two patient-derived spike sequences of the BA.3.2 subvariant BA.3.2.2 lack the first QT repeat of the QTQTX motif and show that this motif is largely dispensable for both cleavage and lung cell entry of BA.3.2.2, which we found to depend on TMPRSS2. Our results suggest that the reconfiguration of the BA.3.2 S protein during persistent infection may have significantly altered the determinants of furin cleavage. IMPORTANCEThe furin motif in the SARS-CoV-2 spike (S) protein is unique among sarbecoviruses and constitutes a virulence determinant. A QTQTX motif located immediately upstream of the furin motif is required for furin cleavage of the S protein of the virus that circulated early in the pandemic. Here, we show that the QTQTX motif is largely dispensable for S protein processing and S protein-driven lung cell entry of the emerging saltation variant BA.3.2, which is currently spreading globally. Thus, BA.3.2 evolution within immunocompromised individuals may have relaxed the requirements for furin processing of the spike protein.

microbiology↗

bioRxiv2026

Striatal FOXP2 is essential for stable vocal production in non-human primates

The transcription factor FOXP2 is the most well-known language-related gene in humans, yet its role in primate vocalization remains poorly understood. Here we report that knockdown of FOXP2 in the striatum markedly disrupts vocalization stability in the marmoset monkey, a valuable non-human primate model for studying vocal behavior. FOXP2 exhibited high expression in the marmoset striatum, especially during early development. Using the CRISPR-Cas12 system, we achieved specific in vivo editing of the FOXP2 gene and effective knockdown of FOXP2 protein expression in the marmoset striatum. Two neonatal marmosets received bilateral striatal injections of the gene-editing and control virus, respectively, and were raised together in the same family. In three such marmoset pairs, analysis of vocalizations recorded during 6-15 weeks post-injection revealed that striatal FOXP2 knockdown significantly altered vocal features and increased intra-individual variability in phee syllables--the most common marmoset vocalization, often produced repetitively as multi-syllable phee calls. Notably, in FOXP2-edited marmosets, acoustic alterations were minimal in the first syllable of phee calls but became progressively more pronounced in subsequent syllables, which exhibited a marked upward shift in the frequency spectrum over time with progressively steeper slopes. These temporal dynamics in vocal features reflect a reduction in the stability of continuous vocal production. In line with the known striatal functions in motor control, our findings provide the first evidence of FOXP2 in controlling vocalization in non-human primates, thereby opening new avenues for investigating the neural mechanisms underlying FOXP2 function.

neuroscience↗

bioRxiv2026

Reversible hypervascularization drives cognitive decline and blood-brain barrier damage during aging

Cerebrovascular dysfunction emerges early in neurodegeneration, yet how vascular structure, blood-brain barrier (BBB) failure, and cognition are linked remains undefined. Using VesselPro, a whole-brain pipeline integrating perfusion-resolved 3D imaging with spatial proteomics, we mapped vascular aging across the mouse lifespan. We identify two discrete trajectories: a hypovascular state and a previously unrecognized hyper-vascular, BBB-compromised state, defined relative to a young-adult vascular baseline. The hyper-vascular trajectory, concentrated in the cortex and hippocampus, was associated with marked spatial memory impairment and pervasive BBB leakage. Spatial proteomics revealed a coordinated program involving angiogenic activation, endothelial stress, cytoskeletal remodeling, and inflammatory signaling. Cross-species comparison with human proteomic biomarkers from the UK Biobank showed strong alignment between the mouse hypervascular signature and vascular dementia risk, but minimal concordance with Alzheimers disease, defining a vascular-specific dementia endotype. Transient Tie2 activation with AKB-9778 attenuated this trajectory, improving vessel organization, BBB integrity, and memory performance. Our findings show that endothelial instability is a key mechanistic driver of this heterogeneous vascular aging state. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/720441v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@39494aorg.highwire.dtl.DTLVardef@faa4acorg.highwire.dtl.DTLVardef@1511dd5org.highwire.dtl.DTLVardef@7db29b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIVesselPro: we developed a pipeline for capturing perfused blood vessels in the brain: unexpected bifurcation in vascular aging: traditional hypovascular state and a novel, hypervascular, BBB-compromised state. C_LIO_LIHypervascular pathology: Linked the hypervascular profile in the cortex and hippocampus to spatial memory impairment, pervasive BBB leakage, and angiogenic inflammatory signaling. C_LIO_LIClinical endotype: Cross-species analysis via the UK Biobank confirms this hypervascular signature aligns with vascular dementia risk rather than Alzheimers disease. C_LIO_LIPharmacological stabilization: Demonstrated that Tie2 signaling activation (AKB-9778) improves the vessel organization, BBB integrity, and memory performance. C_LI

neuroscience↗

bioRxiv2026

Foxp4+ Mandibular Skeletal Stem Cells Orchestrate Bone/Tooth Development and Regeneration

The identity of stem/progenitor cells that drive mandible/tooth development and regeneration remains poorly understood. Here, we show that cranial neural crest-derived Foxp4+ mesenchymal cells condense to form Meckels cartilage, and simultaneously promote mandible development and tooth germ formation. In postnatal mandibles, Foxp4+ cells localize in the endosteum, periosteum and dental pulp, which undergo osteogenesis and odontogenesis under steady state, as well as chondrogenesis during fracture repair. Importantly, transplantation of embryonic or adult Foxp4+CD200+CD105- mandibular skeletal stem cells (mdSSCs) generate ectopic bone and tooth. In contrast, genetic ablation of Foxp4+ cells severely impairs mandible/tooth development and delays fracture healing. Mechanistically, we find that primary cilia critically regulate mdSSC maintenance and differentiation into bone and tooth. FOXP4+PDPN+CADM1+ mdSSCs also exist in adult human mandible, which generate ectopic bone and intact tooth upon transplantation into immunodeficient mice. Taken together, we identify Foxp4+ mdSSCs with potential therapeutic applications in regenerating mandibular bone and tooth.

cell biology↗

bioRxiv2026

CellPulse: A Foundation Model of Coordinated Gene Dynamics Simulating Viral Infectious Diseases

Understanding how cells respond to perturbations like viral infections requires models capturing coordinated gene dynamics. However, current gene expression foundation models are predominantly reliant on single-cell data and static gene expression, limiting their applicability in real clinical scenarios. We present CellPulse, a direction-aware foundation model trained on the Virus Stimulated Atlas (VISTA), a newly curated atlas of over 23 million bulk RNA-sequencing differential expression profiles from viral infections. CellPulse models the direction and magnitude of gene expression changes via a structured representation of differential expression and a direction-aware attention mechanism, enabling the learning of coherent regulatory programs. It shows powerful diagnosing capability by accurately classifying 31 distinct virus types across diverse clinical and laboratory samples, solely from host transcriptional signatures. Crucially, without prior knowledge injection, CellPulses interpretability reveals virus-associated host factors that mediate infection. Using a selection of host factors for in silico drug screening yielded numerous compounds with confirmed efficacies in wet-lab assays, while cell-based and animal experiments further verified the causal relationship between host targets and viral infections. Overall, CellPulse represents a generalizable foundation model for deciphering coordinated gene dynamics from bulk transcriptomics, bridging host response modeling with clinical relevance and therapeutic discovery for infectious diseases and beyond.

bioinformatics↗

bioRxiv2026

Identification of AAV Capsids with Enhanced Intravitreal Transduction and Favorable Safety Profile in Non-Human Primates

We report the discovery of novel adeno-associated virus (AAV) capsid variants engineered for superior intravitreal (IVT) gene delivery to the primate retina. Utilizing the REACH platform, we constructed a diverse AAV variant library and employed a multi-stage screening strategy involving in vitro selection on human retinal pigment cells followed by direct in vivo screening in non-human primates (NHPs). Following IVT administration in NHPS of a barcoded variant pool, next-generation sequencing analysis of retinal tissues identified lead candidates (e.g., E52, E54, and E57) that achieved transduction levels in the neural retina and RPE 5-10 fold higher than the benchmark R100. Concurrently, these high-potency variants exhibited an exceptional ocular confinement profile, with minimal to undetectable vector genome distribution in systemic organs. This combination of markedly enhanced retinal transduction and stringent local tropism establishes these engineered capsids as promising next-generation vectors for the treatment of inherited and acquired retinal diseases via a minimally invasive IVT route.

bioengineering↗

bioRxiv2026

A transcriptomic analysis reveals shared and inducer-specific expression patterns of cellular senescence

Cellular senescence is a heterogeneous cell state induced by diverse stressors, including telomere attrition, genotoxic agents, oxidative damage, and inflammation. Despite ongoing efforts to identify conserved senescence biomarkers, it remains unclear whether senescence-inducing stimuli converge at the level of individual genes or broader molecular processes. Here, we profiled transcriptomic changes in human primary lung fibroblasts (IMR-90) driven toward senescence by replicative exhaustion, bleomycin, H2O2, or ionizing radiation under matched, dose- or time-resolved conditions. Across all four senescent inducers, global transcriptomic variation aligned along a shared axis of senescence progression, consistent with established machine learning-based senescence classifiers. However, overlap at the level of individual genes was limited, with most responses being inducer-specific or only partially conserved. In contrast, pathway-level analysis revealed far more consistent enrichment across all conditions, including downregulation of proliferation-associated pathways and activation of stress-related and pro-inflammatory pathways, accompanied by distinct inducer-specific patterns. These results support a hierarchical organization of the senescent transcriptome, in which diverse senescence inducers converge on shared pathway-level features while maintaining gene-level heterogeneity. These results provide a foundational basis for interpreting senescence signatures and may facilitate the development of more robust transcriptome-based markers of cellular senescence in aging and disease.

genomics↗

bioRxiv2026

A novel reporter mouse for astrocyte-derived extracellular vesicles reveals trafficking of cargo to neuronal mitochondria

Extracellular vesicles (EVs) mediate intercellular transfer of lipids, proteins, and nucleic acids between nearly all cell types. We previously showed that astrocyte-derived EVs modulate neuronal mitochondria in vitro, but whether endogenous astrocytic EVs are trafficked to neuronal mitochondria in vivo remained unknown. To address this, we generated an EV reporter mouse, Aldh1l1-Cre; CD9-tGFPfl/fl, in which astrocyte-secreted EVs are labeled with a CD9-turboGFP fusion protein (CD9-tGFP). Astrocyte-specific expression of CD9-tGFP was verified in brain tissue and isolated EVs, comprising 13.2 {+/-} 1.6% of total brain EVs. In primary glial cultures, CD9-tGFP was restricted to astrocytes, localizing to vesicular compartments and cell protrusions (filopodia and cilia), with 89.3 {+/-} 2.2% of astrocyte-derived EVs carrying the label. These EVs were enriched with the sphingolipid ceramide, consistent with its co-distribution with CD9-tGFP in astrocytic cell protrusions. In the cortex, hippocampus, and cerebellum, CD9-tGFP was predominantly detected in astrocytic processes co-labeled with GLAST1 and GFAP, forming contacts with laminin-positive capillaries and parvalbumin-positive neurons. CD9-tGFP-labeled EVs were detected inside capillaries and neurons, and super-resolution STED microscopy revealed partial overlap with neuronal mitochondria. Live-cell spinning disk confocal imaging and AI-assisted proximity analysis confirmed uptake of CD9-tGFP EVs by neuronal cells and trafficking of their cargo to mitochondria in vitro. Biochemical isolation of synaptic and non-synaptic mitochondria confirmed EV-derived cargo on mitochondria in vivo, with 3-fold higher association of CD9-tGFP with synaptic than non-synaptic mitochondria. Together, these findings validate the Aldh1l1-Cre; CD9-tGFPfl/fl reporter mouse as a powerful tool for tracking astrocyte-derived EVs in vivo and provide direct evidence that their cargo is preferentially trafficked to synaptic mitochondria. Graphical AbstractAstrocyte-derived extracellular vesicles target neuronal mitochondria in vivo O_FIG O_LINKSMALLFIG WIDTH=156 HEIGHT=200 SRC="FIGDIR/small/718987v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@174d92aorg.highwire.dtl.DTLVardef@5d8248org.highwire.dtl.DTLVardef@114483borg.highwire.dtl.DTLVardef@924d55_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Acute exposure to cell-free mitochondrial DNA induces pregnancy-specific aortic endothelial dysfunction and organ-selective inflammation in rats

Pregnancy complications such as preeclampsia are associated with circulating cell-free mitochondrial DNA (mtDNA), a damage-associated molecular pattern capable of activating Toll-like receptor 9 (TLR9). We hypothesized that acute mtDNA exposure induces maternal inflammation and endothelial dysfunction during pregnancy via TLR9 activation. Non-pregnant and pregnant rats (gestational days 14-15) were treated intravenously with saline or purified mtDNA and euthanized 4 h after treatment. mtDNA increased cytokine mRNA expression in lung and liver of non-pregnant and pregnant rats, with magnitude varying by pregnancy status and organ. Aortas from pregnant, but not non-pregnant, rats exhibited reduced acetylcholine (ACh)-induced relaxation following mtDNA treatment (Emax, saline: 90.1 {+/-} 3.9 % vs. mtDNA: 62.1 {+/-} 20.7 % KClmax, p<0.05), while uterine artery function was preserved, indicating vascular bed-specific effects. Ex vivo incubation of aortic rings with mtDNA {+/-} white blood cells did not replicate in vivo findings, implicating systemic rather than direct vascular mechanisms. Nuclear DNA did not affect ACh-induced relaxation (p>0.05), confirming that the vascular effects were mtDNA-specific. Pharmacological antagonism of TLR9 with ODN2088 partially attenuated mtDNA-induced maternal endothelial dysfunction. Although overt vascular ROS increases were not detected, aortas from pregnant rats had reduced sod-1 expression (p<0.05) and increased eNOS protein abundance (p<0.05). Acute mtDNA exposure during pregnancy induces maternal organ inflammation and impairs endothelium-dependent vasodilation, with partial TLR9 involvement. In conclusion, aortic transcriptional changes in antioxidant pathways and increased eNOS abundance were also observed, though their functional significance remains to be determined. New & NoteworthyTo our knowledge, this is the first study to demonstrate that acute exposure to circulating mtDNA induces pregnancy-specific maternal endothelial dysfunction and organ-selective inflammatory responses. Our findings reveal pregnancy- and vascular-bed specific responses of the maternal vasculature to mitochondrial danger signals, with partial TLR9 involvement. Aortic transcriptional changes in antioxidant pathways and increased nitric oxide synthase abundance were identified as molecular correlates of this dysfunction.

physiology↗

bioRxiv2026

Multiscale Mechanisms of Human Memory Modulation by Deep Brain Stimulation

The highly variable effects of deep brain stimulation (DBS) on cognition highlight a fundamental gap in our understanding of how external perturbations interface with the brains ongoing, task-engaged state. The current study addressed this challenge by combining intracranial EEG recordings with hippocampal DBS stimulation in human participants during spatial sequence memory task. We found 50 Hz stimulation targeting hippocampal white matter enhanced memory performance, whereas 5 Hz stimulation targeting hippocampal gray matter impaired memory. These opposing behavioral outcomes were both governed by two dissociated mechanisms: a region-specific modulation of theta rhythms in an engagement-dependent fashion, and a global modulation of the fidelity of memory representations across the cortex. Our results suggest targeted stimulation can concurrently fine-tune specialized circuits and govern the brains global state, which not only offers a novel roadmap for understanding how external inputs shape human cognition, but also helps to design precise, state-dependent neuromodulation therapies.

neuroscience↗

bioRxiv2026

Hippocampal and Midbrain Function in Superagers Relates to Memory for Novelty and Expectation Violation

Memory performance typically declines with age, but the underlying neurobiological mechanisms remain unclear. Superagers, people over 80 years of age with episodic memory performance comparable to individuals 30 years younger, appear to resist this decline. Novelty and expectation violations are known to engage the hippocampus-midbrain system to enhance memory formation. Here, we examined whether superagers superior memory performance is supported by preserved hippocampal-midbrain function during novelty and expectation processing. We manipulated item and contextual novelty (i.e., expectation violations) during encoding to test whether superagers show greater mnemonic benefits than their age-matched peers, whether these benefits reflect enhanced hippocampal and midbrain functioning as measured by fMRI, and whether they are associated with preserved dopaminergic integrity measured with neuromelanin-sensitive MRI. Our results show that, although superagers demonstrated overall superior memory performance, both groups exhibited superior recognition of contextually unexpected items. Nevertheless, differences emerged in the processing of expectation during encoding. Superagers exhibited stronger hippocampal responses to expectation violations and habituation to expected events, irrespective of item novelty. Conversely, typical older adults exhibited reduced midbrain response when expected novelty was absent. Neuromelanin accumulation did not account for group differences in midbrain activity or memory performance. Taken together, these findings suggest superagers benefit from adaptive responses to expectation and its violation, which is therefore a candidate mechanism distinguishing exceptional from typical cognitive ageing. SIGNIFICANCE STATEMENTAlthough memory typically declines with age, superagers are individuals aged over 80 who maintain memory performance comparable to people 30 years younger. We examined whether preserved hippocampal-midbrain function during novelty and expectation processing could underlie their superior memory. Superagers exhibited adaptive hippocampal responses to expectation and its violation, with higher activation for unexpected events and habituation to expected events. In contrast, typical older adults showed hippocampal and midbrain responses oriented towards anticipated novel content, despite not showing differences in neuromelanin accumulation. These findings underscore the critical role of hippocampal function in supporting memory preservation in late life and advance our understanding of the neural mechanisms underlying healthy cognitive ageing.

neuroscience↗

bioRxiv2026

Age-associated increases in inter-individual gene expression variability across human tissues

Aging involves progressive physiological decline, yet the underlying transcriptomic patterns remain poorly understood. Although differentially expressed genes (DEGs) have been the primary focus of previous studies, here we investigate differentially variable genes (DVGs) using a novel Gene Stability Score (GSS). In 30 tissue types from nearly 1,000 individuals in the Genotype-Tissue Expression (GTEx) project, age- and sex-related DVGs account for approximately 15% of overall expression variability between samples of the same tissue, with age-related DVGs specifically contributing 7.7%. We further show that DEGs and DVGs affect distinct biological pathways, and that inter-individual instability is significantly correlated with cell-to-cell transcriptional noise. Moreover, gene regulatory network analysis reveals that this variability is not random but is shaped by local network architecture. Finally, we identify robust reference genes, including TBP, PUM1, and TMEM199, for RT-qPCR experiments in studying age-related gene expression changes in humans. Together, our findings suggest that aging involves both coordinated transcriptional programs and increased stochasticity across individuals and cells.

genomics↗

bioRxiv2026

Rapid estimation of photon measurement density functions using a deep convolutional neural network for functional near-infrared spectroscopy

The photon measurement density function (PMDF) plays a fundamental role in both pre-experimental optode arrangement and post-experimental data analysis in functional near-infrared spectroscopy (fNIRS). Conventionally, PMDFs are derived from structural MR images through tissue segmentation and photon propagation modeling (PPM), which are computationally demanding and time-consuming, thereby limiting their practical use. In this study, we propose a novel deep learning-based framework to estimate PMDFs directly from MR images and channel configurations. The proposed method supports flexible source-detector distances and eliminates the need for explicit tissue segmentation and repeated photon simulations. Specifically, a convolutional neural network is trained to predict photon fluence distributions, from which PMDFs are subsequently derived using the adjoint formulation. The trained model is evaluated on channels placed in both trained and unseen scalp regions across commonly used source-detector distances. The results demonstrate that the proposed method achieves PMDF estimations comparable to those obtained from PPM. Overall, this approach significantly reduces computational cost and has the potential to facilitate broader adoption of PMDF-based methods in the fNIRS community.

bioengineering↗

bioRxiv2026

U-Probe: universal agentic probe design for imaging-based spatial-omics

Probe design for fluorescence in situ hybridization (FISH) underpins spatial transcriptomics, three-dimensional genome studies, and clinical diagnostics, yet remains constrained by two challenges: dependence on expert knowledge for parameter selection and quality evaluation, and the inability of existing tools to accommodate the diverse probe architectures introduced by rapidly emerging methods. Here we present U-Probe, a universal and agentic probe design platform. U-Probe employs a declarative configuration system with a directed acyclic graph (DAG)-based assembly engine that supports arbitrary probe structures from established protocols such as MERFISH, seqFISH, and MiP-seq to entirely novel architectures without code modifications. Integrated LLM-based AI agents enable conversational design workflows, allowing users to specify experimental goals in natural language and receive synthesis-ready probe sequences. We validated U-Probe in three scenarios: agent-driven MiP-seq panel design for influenza-infected mouse lung tissue, genome-tiling DNA-FISH for herpesvirus detection, and a novel RCA-based ligation probe for single-nucleotide mutation discrimination. U-Probe is available as an open-source tool with CLI, Web, and agent interfaces.

bioinformatics↗

bioRxiv2026

Fruit trichome density outweighs cuticle thickness as the dominant barrier to postharvest water loss in tomato

Fruit cuticle thickness and biochemical composition have traditionally been regarded as the primary determinants of postharvest water loss in fleshy fruits. However, several reports indicate that some tomato mutants with thinner fruit cuticles or less cutin and waxes do not always show increased transpiration, suggesting that additional surface features influence postharvest water loss. Here, we s how that fruit trichome density is a previously underappreciated determinant of postharvest water loss in tomatoes. Using two independent mutants, cr-slhdziv7 and cr-slhdziv9, which exhibit reduced fruit trichome density, we found that both mutants displayed reduced water loss rates and extended shelf life during postharvest storage despite having thinner cuticles and reduced levels of key cutin monomers. Further molecular analyses, including RNA-seq, yeast one-hybrid (Y1H), and dual-luciferase reporter assays, revealed that these two HD-ZIP IV proteins not only regulate fruit trichome formation but also directly or indirectly modulate the expression of multiple cutin biosynthesis genes. Collectively, our results demonstrate that the benefit of reducing trichome-associated microchannels can outweigh the negative effects of cuticle thinning on postharvest water loss. This study establishes fruit trichome density as an important and previously underestimated target for improving postharvest fruit quality and shelf life. HighlightO_LIFruit trichome density controls tomato postharvest water loss and dominates over cuticle thickness barrier. C_LIO_LILess trichomes reduce microchannels, lowering transpiration despite thin cuticles and extending tomato fruit shelf life. C_LI

plant biology↗

bioRxiv2026

TCMCard: A High-Confidence Digital Infrastructure for Traditional Chinese Medicine Quantified by Multi-Dimensional Evidence Integration

Network pharmacology has become a widely used approach for deciphering multi-component, multi-target mechanisms of traditional Chinese medicine (TCM). Here we introduce TCMCard, a high-confidence digital infrastructure built on a Multi-Dimensional Evidence Integration (MDEI) framework. The framework integrates experimental activity data from authoritative chemical databases, literature-derived evidence, and structure-based similarity inference. Preprocessing steps include chemical structure normalization, species-specific filtering, and target quality scoring. Applied to conventional interaction datasets, this pipeline leads to the removal of over 60% of low-confidence noise. TCMCard supports network pharmacology exploration through an interactive visualization platform, and module analysis identifies functionally relevant communities that offer insights into the synergistic actions of TCM formulas. Overall, TCMCard may help move the field beyond simple data aggregation toward evidence-informed curation and quality-driven analysis. As an interactive and publicly accessible platform, it reveals an organized backbone within complex interaction networks, offering a more reliable basis for understanding multi-component synergy in TCM.

bioinformatics↗