Biology subjects

Wang, F.

Publications and source records attributed to Wang, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Efficient recovery of transgene-free edited tobacco using the transgene self-elimination system via de novo regeneration

Elimination of integrated editing constructs remains a major challenge for generating transgene-free progeny in plant genome editing based on Agrobacterium-mediated regeneration. Here, we adapted the Transgene Killer CRISPR (TKC) concept to tobacco and established the transgene self-elimination system, in which CRISPR/Cas9 is coupled with developmentally regulated BARNASE cassettes. Three pU3TR-derived vectors carrying DLL-, OsRP3- or PHAS-driven Barnase regenerated normally after leaf-disc transformation. The DLL construct pEB138 showed the highest T editing frequency, with 56 of 69 independent T plants (81.16%) carrying mutations at one or both NtDFR target loci. Under a stringent lineage-level screen in which up to 48 T progeny were tested per T line, 36 of 43 pEB138 lineages (83.72%) yielded uniformly marker-negative progeny for the three assayed T-DNA markers, compared with 0 of 7 lineages transformed with the parental pU3TR vector. The platform also supported recovery of dfr mutants with altered flower pigmentation and NtA622-edited lines with reduced nicotine accumulation. Moreover, introduction of DLL-iBarnase into the independent pDC45 editing backbone did not impair shoot regeneration, and representative NtBBL progeny showed markedly reduced nicotine content together with loss of the selectable cassette. These results demonstrate that BARNASE-assisted transgene elimination can be integrated with Agrobacterium-mediated de novo regeneration in a dicot, enabling one-step recovery of transgene-free edited tobacco progeny.

molecular biology↗

bioRxiv2026

Stromal control of sympathetic rewiring in metastatic lymph nodes

Metastatic lymph nodes (LNs) are dynamically remodeled tissues, but this process has been understood mainly in immune and stromal terms. We show that tumor-driven LN remodeling also involves adaptive neural rewiring. In a mouse model of nodal metastasis, sympathetic fibers, but not sensory fibers, progressively expanded during LN remodeling and tracked with metastatic progression. Fibroblastic reticular cells (FRCs) adopted a neuro-supportive program characterized by increased hepatocyte growth factor (HGF) production, while local stromal HGF acted through MET on sympathetic neurons to stimulate neurite outgrowth. Increased substrate stiffness enhanced FRC activation and HGF production, suggesting that mechanical remodeling may reinforce the neuro-supportive stromal state. Inhibition of HGF signaling or ablation of sympathetic innervation reduced LN enlargement and nodal tumor burden. These findings identify neural plasticity as a functional component of the metastatic LN niche and reveal a stromal/mechanical/neural framework that supports metastatic LN progression.

cancer biology↗

bioRxiv2026

TFL1 homolog integrates temperature signals to control timing of developmental transitions in woodland strawberry

In overwintering plants of temperate climates, inflorescence and flower buds commonly form in autumn under cool temperatures, while flowering occurs the following spring. However, how cool temperatures regulate inflorescence and flower development remains poorly understood. We used woodland strawberry (Fragaria vesca L.), a perennial Rosaceae herb, to investigate the effects of cool temperature on reproductive development. We characterized temperature-dependent developmental patterns at macroscopic and microscopic scale and combined time- and stage-specific gene expression analyses. We show that cool temperature accelerates floral transition but subsequently slows inflorescence and flower development, causing increased inflorescence branching, higher floral organ numbers, and berry fasciation. These effects were restricted to the apical inflorescence and flower meristems, whereas higher-order meristems remained unaffected. Expression analyses revealed stage- and temperature-dependent changes in the abundance and spatial distribution of TERMINAL FLOWER1 (FvTFL1) encoding the floral repressor. Loss of functional FvTFL1 abolished temperature-dependent differences in floral transition, inflorescence branching, and floral organ numbers. Our results establish FvTFL1 as a major regulator of temperature-responsive reproductive development. The stage-specific activity of FvTFL1 provides a mechanism through which woodland strawberry integrates temperature signals to balance developmental plasticity of the primary growth axis with the robustness of lateral branches.

plant biology↗

bioRxiv2026

Spontaneous Hemodynamic Oscillations during Sleep Coordinate Directional CSF Flow in the Subarachnoid Space and Ventricles

During sleep, cerebrospinal fluid (CSF) flow is enhanced and thought to facilitate clearance of metabolic waste from the brain. Human imaging has shown that sleep is associated with large waves of bulk CSF flow in the fourth ventricle; however, the CSF flow dynamics around brain tissue are unknown. Here, we investigated how CSF flow is organized across the subarachnoid space, a key site both for fluid exchange across cortical surface and for transport out of the cranium. We used an MRI technology at 7 Tesla that simultaneously measures cortical hemodynamics and slow subarachnoid CSF flow and applied this during sleep. We found that spontaneous infraslow hemodynamic oscillations were coupled to spatially structured, directional CSF flow throughout both ventricular and subarachnoid compartments. Hemodynamic oscillations and fourth-ventricle bulk flow were both associated with brain-wide CSF flow at different phases, indicating that they reflect a single coordinated CSF movement cycle. Compared to cardiac pulsations, a canonical driver of CSF movement, hemodynamic-driven CSF flow showed a distinct directional pattern and was smaller in instantaneous amplitude but produced substantially greater cumulative displacement and thus greater potential for transport within an oscillation period. Together, these findings show that hemodynamic oscillations during sleep are coupled to temporally coordinated and directional CSF flow throughout the ventricles and subarachnoid space, suggesting that sleep-dependent neuronal activity drives fluid movement across the human brain in a distinct spatial pattern.

neuroscience↗

bioRxiv2026

Charting sex divergence in the human brain across the lifespan

Biological sex fundamentally shapes human brain organization, but sex-specific normative neuroanatomical trajectories across the lifespan remain largely uncharted. Here, we constructed independent, sex-specific lifespan brain charts using structural neuroimaging data from 59,915 healthy individuals (29,760 males and 30,155 females) ranging in age from 266 postconception days to 100 years. By examining 296 structural phenotypes across global, cortical, and subcortical measures, these models revealed widespread sex differences in maturational timing, with males reaching peak milestones later than females. These trajectories demonstrate that sex differences evolve dynamically, with phenotype-specific windows of emergence and maximal separation. Compared with conventional sex-pooled references, sex-specific models achieved superior predictive accuracy and reduced misestimation of individual deviations in healthy populations. Across five neuropsychiatric conditions, sex-specific models improved the detection of extreme deviations and revealed both shared and sex-dependent patterns of disorder-related neuroanatomical abnormalities. These sex-specific charts establish tailored normative references for assessing brain development, ageing, and disease.

neuroscience↗

bioRxiv2026

Biologically inspired alignment reveals distributed and directionally asymmetric correspondence between rat and human cortices

Rodent models enable causal interrogation of brain circuits, but translating their systems-level organization to humans requires correspondence beyond one-to-one anatomical homology. Guided by the view that cortical areas are characterized by their relationships within distributed functional networks, we developed BrainMapping, a biologically inspired framework for aligning rat and human cortex using resting-state functional MRI. The framework combined a shared representation with optimal transport to derive probabilistic, bidirectional maps. These alignments revealed distributed, many-to-many correspondences that generalized to held-out subjects and preserved functional connectivity architecture, cortical gradients, and graph topology. Organizational preservation was directionally asymmetric. Human-to-rat mapping preserved organization more uniformly across rat cortical systems, whereas rat-to-human mapping showed stronger preservation in human association-related networks than in primary sensory and motor networks. The maps recovered literature-consistent default-mode and salience-system correspondences and generated testable non-canonical predictions. These findings provide a framework for expressing rat functional organization in human functional-network coordinates.

neuroscience↗

bioRxiv2026

Alignment-Aware Genomic Coordinate Encoding for Long-Range DNA Modeling

Existing genomic foundation models (GFMs) are adept at capturing local, sequential dependencies in DNA. However, their architectures often struggle to efficiently model gene regulation features, such as sparse motifs and distal regulatory elements that operate beyond linear proximity. Moreover, standard positional encodings fail to fully exploit the reference genome coordinate system. Therefore, we present USM-AA, an alignment-aware genomic foundation model that incorporates reference genome coordinates through a non-contiguous positional encoding, Alignment-Aware Rotary Position Embedding, and an alignment embedding module encoding chromosome, strand, and Compact Idiosyncratic Gapped Alignment Report (CIGAR) information. To improve long-range sequence modeling, USM-AA leverages a reverse-complement masked learning strategy. Pretrained on alignment-aware genomic sequences spanning cross-species evolution and human population variation, USM-AA consistently outperforms existing models across multiple downstream tasks, highlighting the importance of alignment-aware representations for genomic sequence modeling.

genomics↗

bioRxiv2026

Temporal organization of shared brain states characterizes heterogeneity in major depressive disorder

Major depressive disorder (MDD) is biologically heterogeneous, but how this variability is expressed in the temporal organization of brain activity remains unclear. Using resting-state functional MRI from 2,225 participants, we applied hidden Markov modeling to identify recurrent brain states and quantify their temporal organization. Five states formed a shared repertoire across individuals with MDD and healthy controls, while MDD-related alterations were distributed across states, functional systems, and temporal properties. Within MDD, unsupervised clustering of state occupancy, persistence, and switching delineated two prototype neurodynamic architectures characterized by preferential deployment of ACS/VSS or MAS/DMS states within a preserved state repertoire and broadly similar transition backbone. The architectures showed different within-group brain-symptom associations and symptom-network patterns. Connectome transcriptome analyses organized architecture-state imaging patterns into three transcriptomic state families shared across architectures, and contrasting group-level deployment patterns were recovered in an independent MDD cohort. These findings suggest that MDD heterogeneity is expressed not only through spatially distributed neural alterations, but also through differences in how a common repertoire of recurrent brain states is organized over time.

bioinformatics↗

bioRxiv2026

From Spelling to Reading: Onset-Rime Representations as a Neural Link

Visual orthographic knowledge may provide a shared foundation for reading and spelling, yet the nature of its underlying representations remains debated. Behavioral measures offer indirect evidence and may be influenced by other metalinguistic processes. It remains unclear whether early readers encode larger orthographic structures, such as onset-rime units, beyond individual letters and letter combinations, and whether neural sensitivity to these structures helps explain the relationship between spelling and reading. To address these questions, we used a a fast periodic visual stimulation (FPVS) paradigm to contrast pseudowords constructed with the typical ordering of onset followed by rime elements (i.e., onset-rime) against matched strings in which the same elements appeared in the reverse order (i.e., rime-onset). Neural sensitivity to onset-rime orthographic structure was associated with both spelling ability and word-reading efficiency and, critically, mediated the relationship between these two literacy skills. These relationships remained significant after controlling for age and removing influential observations, and sensitivity to onset-rime orthographic structure explained additional variance in word-reading efficiency beyond spelling ability and age. Together, these findings provide neurophysiological evidence that sensitivity to onset-rime structure may reflect an intermediate orthographic representation, with neural sensitivity to this structure mediating the relationship between spelling and reading.

scientific communication and education↗

bioRxiv2026

Low-Density Lipoprotein Cholesterol and Cerebral Pericyte Dysfunction in Acute Ischemic Stroke: Clinical and Experimental Evidence

Background: Low-density lipoprotein cholesterol (LDL-C) is an established risk factor for atherosclerotic cerebrovascular disease, but its effects on the cerebral microcirculation are poorly defined. We investigated whether LDL-C is associated with pericyte dysfunction in acute ischemic stroke (AIS) and explored underlying mechanisms. Methods: Serum soluble platelet-derived growth factor receptor-{beta} (sPDGFR{beta}) was measured in two independent AIS cohorts (n=97 and n=86). Cerebral pericyte transcriptional responses to LDL-C were analyzed by single-cell RNA sequencing in Apoe-knockout mice fed control or high-fat diet (n=4 [male/female: 2/2]/group), and cultured human brain pericytes were exposed to purified human LDL cholesterol with or without N-acetyl-L-cysteine. Results: Higher serum sPDGFR{beta} was associated with greater neurological deficit and circulating neurofilament light chain. LDL-C positively correlated with sPDGFR{beta} in both clinical cohorts. High-fat diet induced coordinated suppression of type-I interferon pathways, and a positive shift in reactive oxygen species-related transcriptional programs in mouse pericytes; exploratory sex-by-diet analyses suggested larger transcriptional responses in females. In cultured human pericytes, LDL-C induced oxidative-stress, lipid-handling, and ferroptosis-associated transcriptional programs while suppressing type-I interferon signaling. Cross-species enrichment analysis showed that LDL-C-induced and -repressed signatures in cultured pericytes aligned with the sex-by-diet interaction in Apoe-knockout mice. LDL-C also reduced cell-surface PDGFR{beta} and increased sPDGFR{beta} release in cultured pericytes, which were significantly attenuated by N-acetyl-L-cysteine, whereas LDH activity increased numerically but not significantly. Conclusions: Clinical and experimental findings support an LDL-pericyte axis linking atherogenic lipid stress to cerebral microvascular dysfunction, with possible sex-dependent modulation of oxidative stress and type-I interferon signaling as potential mechanisms.

neuroscience↗

bioRxiv2026

TE-aware state analysis and evolution in dynamic network connectivity

Multi-echo functional magnetic resonance imaging (fMRI) acquires signals with distinct contrast profiles across echo times (TEs). Empirical evidence suggests that different TEs capture distinct signal contributions with varying sensitivity to BOLD and non-BOLD processes from long to short TEs (Stroman, 2002; Krishnamurthy, 2023; Dong, 2024). Previous literature has not yet examined how brain states extracted from temporal dynamic functional connectivity (dFNC) evolve across TEs. Here we present a methodological and empirical study of TE-dependent evolution of dynamic connectivity states, with a phenomenological two-component model for interpretation. Multiple echoes were acquired with an echo planar time-resolved imaging (EPTI) sequence. TE-specific components were extracted via atlas-based group ICA (Neuromark 1.0), and brain connectivity states were generated via windowed dFNC and spatial ICA clustering of windows. Within-subject and group-level states evolved across TEs in network organization and variance. States exhibited TE-dependent variance profiles, with distinct peak echo times; and group-level points of state transition were independently mapped to TE-dependent transitions in variance. We modified a bi-exponential model to simulate and model changes in the dFNC time-course across TEs. The bi-exponential model revealed high consistency with subject states (R2 fit=0.86, res. error=0.55, 86% model convergence rate), suggesting a two-component signal system contributing to dynamic TE-dependent connectivity changes in state. A significant correlation between relative model terms was estimated on a cell-wise basis across states (r(24) = -0.43, p=0.03, 95% CI [-0.70, -0.04]). This suggests that specific bi-exponential signal parameters (i.e., short FNC1,TE=0, long FNC2,TE=0, and long FNC2,decay) were associated with the observed TE-dependent variations in connectivity states across TEs. In sum, our analyses provide downstream implications for TE-aware state analysis dependent on connectivity magnitude (FNCTE=0) and rate of connectivity decay (FNCdecay), in a two-component signal model, with future implications for TE-dependent state biomarkers.

neuroscience↗

bioRxiv2026

Superficial spinal Tac1-lineage neurons are polymodal nociceptive

Tac1-lineage neurons in the spinal dorsal horn have been implicated in coping behavior in response to sustained noxious stimuli, but their developmental origin, cellular heterogeneity, and functional contribution remain incompletely understood. Here, we characterized the molecular identity, developmental trajectory, electrophysiological properties, and sensory responses of spinal Tac1-lineage neurons. In adults, Tac1-lineage neurons comprised a heterogeneous population of excitatory and inhibitory interneurons and excitatory projection neurons distributed across the superficial dorsal horn. In contrast, at embryonic day 16.5, Tac1-lineage neurons in laminae I/IIo were exclusively projection neurons, revealing a marked developmental transition in the composition of the Tac1 lineage. Electrophysiological recordings from spinal cord slices further demonstrated substantial functional heterogeneity, with most Tac1-lineage neurons exhibiting phasic or single-spike firing and smaller populations displaying tonic or reluctant firing. In vivo calcium imaging in anesthetized mice revealed prominent responses to noxious mechanical and thermal stimulation. Interestingly, Tac1-lineage neurons used distinct strategies to encode cold and heat intensity. Together, these findings reveal pronounced developmental and functional heterogeneity within the Tac1 lineage and demonstrate that adult Tac1-lineage neurons are predominately polymodal nociceptive.

neuroscience↗

bioRxiv2026

Implementation and calibration of the Vaganov-Shashkin model in the virtualRings R package

Process-based tree growth models provide a mechanistic framework for investigating how climate conditions regulate tree growth across daily to annual time scales. Yet, their broader application across species and environments is constrained by the limited accessibility in open-source environments and the difficulty of estimating physiological parameters that are rarely measured directly. Here, we present virtualRings, a new R package integrating the Vaganov-Shashkin model (VSM) and the RINGS3 models, and focus on the implementation and calibration of VSM. Using tree-ring width observations from seven Northern Hemisphere sites across various environmental conditions, we compared the traditional bootstrap-based calibration approach with the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). CMA-ES improved agreement between simulated and observed radial tree growth and provided an efficient approach for model parameter estimation. We further evaluated practical CMA-ES settings to balance computational cost and performance and discussed its potential limitations. The virtualRings package provides an open and reproducible platform for tree growth simulation, facilitating the application of important process-based models across species and environments and the investigation of how temperature and moisture constraints regulate daily tree-ring formation across spatial and temporal scales.

plant biology↗

bioRxiv2026

The mitochondrial RNA extrusion-induced innate immunity is regulated by N6-methyladenosine machinery

Mitochondrial RNA (mtRNA) released into the cytosol functions as a damage associated molecular pattern that activates pattern-recognition receptor (PRR)-mediated inflammation, yet its release mechanisms and cytoplasmic fate remain poorly understood. Here we report that chemical Abt-373-treatment and Vesicular stomatitis virus (VSV) infection induce mtRNA extrusion through Bax/Bak and VDAC1 channels, accompanied by mtDNA release. Extruded mtRNA in A549 cells activates multiple cytosolic PRRs, including RIG-I, MDA5, TLR3/7/8, and PKR, each contributing differentially to the innate immune signaling. Analysis of GEO datasets and methylated RNA immunoprecipitation (MeRIP) assays further reveals that mtRNA carries methyladenosine (m6A) modification. m6A machinery proteins are involved in the cytoplasmic retention time of mtRNA and its interaction with RIG-I, thereby modulating mtRNA-induced innate immunity. Thus, our work establishes in vitro models of mtRNA extrusion, and highlights m6A-dependent modulation as a potential therapeutic target for mtRNA-driven inflammation.

immunology↗

bioRxiv2026

VGLL3 Links Pericyte Hypercontractility to Perivascular Fibrosis of the Cerebral Microcirculation, a Novel Vasculopathy Leading to Distinct Long-Term Cerebral Autoregulation Dysfunction After Subarachnoid Hemorrhage

BACKGROUND: Cerebral ischemia following subarachnoid hemorrhage (SAH) has traditionally been considered transient because functional alterations of the cerebral microcirculation are thought to be self-limiting. However, we identified a previously unrecognized vasculopathy, perivascular fibrosis of the cerebral microcirculation (PFCM), characterized by excessive type I collagen deposition after SAH. This study investigated the mechanisms underlying PFCM and its subsequent effects on cerebral hemodynamics. METHODS: In vivo SAH was modeled in mice by autologous blood injection, whereas oxygenated hemoglobin (OxyHb) exposure was used to mimic SAH in vitro. Pericyte-deficient mice (Pdgfr{beta}+/-) and pericyte-specific vestigial-like family member 3 (VGLL3) conditional knockout mice (Vgll3{Delta}PC) were generated. Pericyte contractility was measured by nanoindentation and traction force microscopy. Molecular mechanisms were examined using Western blotting, immunofluorescence, CUT&Tag, RNA-seq, transmission electron microscopy, and molecular docking. PFCM, impaired dilation of the cerebral microcirculation, and cerebral autoregulation were assessed by two-photon imaging, transcranial Doppler with continuous blood pressure monitoring, super-resolution ultrasound imaging, and photoacoustic imaging. RESULTS: After SAH, mice developed long-term cerebral autoregulation dysfunction marked by impaired dilation of the cerebral microcirculation, with the abnormality being most evident within the relatively lower blood pressure range. The marked reduction in PFCM in Pdgfr{beta}+/- mice indicated that pericytes were the principal cellular contributors. Mechanistically, OxyHb-induced cytoskeletal remodeling in vitro increased pericyte contractility and promoted nuclear translocation of SAH-upregulated VGLL3. This was followed by increased genomic occupancy, Col1a1 transcriptional activation, and type I collagen deposition. Pericyte-specific VGLL3 knockout abolished PFCM and, consequently, significantly alleviated long-term cerebral autoregulation dysfunction. CONCLUSIONS: Our findings identify PFCM mediated by pericytic VGLL3 as a novel vasculopathy leading to long-term cerebral autoregulation dysfunction after SAH.

neuroscience↗

bioRxiv2026

Chimeric Induced Cooperativity Opens the Design Space of Eukaryotic Gene Regulation

Predictive engineering of eukaryotic transcription is limited by the coupling of signal sensing, DNA binding, TF abundance and promoter output. Here we establish chimeric induced cooperativity (CIC), a modular architecture that separates LBD, DBD and AD functions and links them to promoters with tunable basal and maximal output. Module parameters can be recombined to predict new CIC-TF configurations and guide design before construction. Ligand-induced cooperativity reduces basal DNA occupancy while increasing induced occupancy, and effective DBDs combine low OFF-state activity with strong ON-state promoter occupancy rather than binding strength alone. Synthetic promoters independently control occupancy gain and output range. The same framework extends to repression and can be recalibrated with limited measurements in mammalian cells. In yeast, CIC-12 achieved a mean fold induction of 298-fold across 12 orthogonal sensors; an earlier CIC-10 chassis enabled model-guided optimization of an eight-gene vitamin B5 biosynthetic pathway. CIC establishes a programmable, model-guided design space for eukaryotic transcriptional control.

synthetic biology↗

bioRxiv2026

Spinotrode: long-term intraspinal electrophysiological recordings to unravel dorsal horn neuron dynamics in behaving mice

Recording single-unit neural activity in the spinal cord in freely moving rodents is crucial for understanding spinal network dynamics but remains challenging due to specific biomechanical constraints. So far, the vast majority of studies have been conducted in anesthetized or restrained animals, limiting the correlation of neuronal activity with naturalistic behaviours. Here we introduce the Spinotrode, a vertebral implant able to stably record signals (over several weeks) at the single-cell level in the bilateral dorsal horns of adult mice. It is engineered to minimize postural constraints and interrogate spinal activity during sensory stimulation and motor behaviours. No functional impairment or tissue damage was apparent. Spinotrode recordings allowed identification of distinct functional types of neurons associated with paw withdrawal, revealed dorsal horn activity during locomotor behaviour distinct from proprioception and touch, and uncovered contralateral sensory activation upon nociceptive reflex responses, which forces reassessment of data obtained in anesthetized animals.

neuroscience↗

bioRxiv2026

Influenza A virus initiates genome selection through promoter-dependent nuclear export

Influenza A virus replicates its segmented RNA genome in the nucleus in the context of viral ribonucleoprotein (vRNP) complexes. Newly synthesised vRNPs are exported to the cytoplasm for virion assembly, whereas structurally similar complementary RNPs (cRNPs), which function as replication intermediates, are not incorporated into virions. The molecular basis for this selectivity remains unclear. Here, combining promoter mutagenesis, single-molecule fluorescence in situ hybridisation (smFISH), virus-like particle (VLP) assays and cryo-electron microscopy (cryo-EM), we find that cRNPs are retained in the nucleus and that export competence is encoded by promoter architecture, with the length of the single-stranded 3' promoter region as the principal contributing feature and promoter sequence and duplex architecture further modulating export efficiency. cRNPs carrying export-competent promoters are incorporated into virus-like particles, demonstrating a functional link between nuclear export and packaging competence. Cryo-EM analyses reveal that both 3' vRNA and cRNA promoters bind a common polymerase surface site but are associated with distinct polymerase conformational landscapes, with only the vRNA promoter being compatible with an encapsidase conformation of the polymerase. Together, our findings identify a promoter-dependent checkpoint that links RNA promoter architecture and polymerase conformation to RNP export and packaging. These results demonstrate that influenza virus initiates genome selection in the nucleus and reveal nuclear export as an early step in genome selection.

microbiology↗