Biology subjects

Zhou, R.

Publications and source records attributed to Zhou, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Plastome convergence across heterotrophic plant lineages: genome reduction, extreme AT bias, high substitution rates, and functional persistence in the endoparasitic Mitrastemonaceae

The loss of photosynthesis triggers extreme plastid genome (ptDNA) decay, including complete genome loss. Of the multiple transitions to heterotrophy among angiosperms, the ptDNA status remains poorly defined in lineages such as the endophytic Mitrastemonaceae (Ericales). Adopting a panplastome perspective, we characterized genomic variation across Mitrastemon yamamotoi individuals, assembling two complete circular ptDNAs and re-evaluating all available genomic resources for the genus. Our results reveal a highly minimized ptDNA (18-26 kb) with extreme AT content (>77%) and loss of the typical quadripartite architecture. Despite the absence of the stabilizing inverted repeats, the Mitrastemon panplastome exhibits remarkable structural stability and collinearity among individuals. The reduced suite of 26 genes, which includes accD, infA, clpP, ycf1, ycf2, and the essential tetrapyrrole precursor trnE-UUC, exhibit elevated substitution rates. Evolutionary rate analyses (dN/dS) demonstrate that the core ribosomal suite remains under strong purifying selection ({omega}<1), confirming the organelles functional status. Furthermore, transcriptomic analysis identified a nearly complete set of nuclear-encoded DNA-RRR genes, with the notable exception of the MUTS2 surveillance system. The convergent loss of these homologs in Mitrastemon and another holoparasitic lineage may be linked to the shared structural instability and mutational bias. Our findings demonstrate that despite extreme genome compaction, accelerated substitution rates, and severe AT-bias, the Mitrastemon panplastome remains quite stable, providing a definitive genomic framework for understanding plastid evolution within the endoparasitic Mitrastemonaceae.

evolutionary biology↗

bioRxiv2026

PRISM: A High-Throughput Simulation Infrastructure for CADD Agents

Despite rapid progress in AI agents for computer-aided drug design (CADD), protein-ligand simulation workflows remain fragmented across disparate tools, creating a major bottleneck for scalable candidate evaluation. Here, we present PRISM (Protein-Receptor Interaction Simulation Modeler), a Python platform built on GROMACS that unifies ligand parameterization across multiple force fields, automated system construction, enhanced sampling, multi-tier binding free energy estimation, and trajectory analysis within a single workflow. Through the Model Context Protocol (MCP), PRISM further serves as the computational infrastructure for CADD-Agent, an expert-workflow-driven AI agent designed to orchestrate hierarchical drug screening pipelines. As a pilot application, we applied PRISM to riboflavin synthase and demonstrated end-to-end automation from candidate library assembly to binding pocket characterization, identifying a potential allosteric inhibition site at the oligomerization interface. Together, these results establish PRISM as a high-throughput simulation infrastructure for agent-enabled CADD.

biophysics↗

bioRxiv2026

Dynasore, the dynamin inhibitor, modulates longitudinal bone growth in a hormetic manner.

BackgroundLongitudinal bone growth occurs via the process of endochondral ossification, involving a complex interplay of chondrocyte proliferation, differentiation, and matrix remodelling. As with all mammalian cells, chondrocytes require dynamin for mitochondrial fission, to shuttle vesicles from the Golgi apparatus, and for both clathrin- and caveolin-mediated endocytosis. Here, we aimed to test the functions of dynamin on bone growth. To do so, we applied dynasore - a small molecule that is a reversible dynamin inhibitor - to mouse metatarsal bones cultured ex vivo. We assessed gross changes using bone length measurements and histomorphometry, and combined this with EdU detection, immunostaining, super-resolution microscopy and transmission electron microscopy. ResultsDynasore induced a dose-dependent hormetic effect on bone elongation: while high concentrations (220 {micro}M) impaired growth and abolished chondrocyte proliferation, low-dose treatment (40 {micro}M) significantly increased longitudinal bone growth. Histological analysis demonstrated that low dose dynasore augmented epiphyseal cartilage expansion and matrix accumulation, particularly within the resting and proliferative zones, while reducing chondrocyte proliferation. Immunostaining indicated that 40 {micro}M dynasore preserved collagen type X synthesis, activated mTORC1 signalling, and blocked autophagy, based on SQSTM1 accumulation. Low dose dynasore treatment expanded the thickness of the filamentous actin layer at the plasma membrane and deepened collagen fiber-containing endocytic pits, indicating that impaired cartilage remodelling was associated with growth-associated matrix accumulation. ConclusionsThis study reveals that dynasore exerts hormetic effects on growth plate chondrocytes, wherein low doses stimulate bone elongation, and high doses impair chondrocyte function.

physiology↗

bioRxiv2026

Rewiring of 3D Enhancer-Promoter Interactome Underlies Diabetic Endothelial Dysfunction

BackgroundDiabetic vascular complications are driven by endothelial dysfunction, yet the role of 3D genome organization in this process is unknown. We sought to define the alterations in chromatin architecture in diabetic endothelium and identify the key regulators involved. MethodsWe generated a high-resolution 3D epigenomic atlas of diabetic endothelial cells from mouse models and human subjects using H3K27ac HiChIP, complemented by ChIP-seq, ATAC-seq, and RNA-seq. A human cohort was used to assess protein expression in diabetic versus non-diabetic endothelial cells. To identify JUNB-interacting proteins, we performed rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME), with protein-protein interaction validated by co-immunoprecipitation. Functional validation was performed using in vitro, ex vivo, and in vivo approaches, including endothelial-specific knockdown in a diabetic hindlimb ischemia model. ResultsMulti-omics profiling revealed extensive enhancer reprogramming in diabetic endothelium, with AP-1 binding motifs being consistently and selectively enriched in downregulated enhancers across three distinct diabetic models. Analysis of a human cohort confirmed significantly reduced JUNB protein levels in diabetic endothelial cells. We identified widespread disruption of JUNB-anchored enhancer-promoter interactions, which underlies transcriptional repression of key endothelial genes. RIME and co-immunoprecipitation established the E3 ubiquitin ligase RBBP6 as a direct JUNB interactor that promotes its polyubiquitination and proteasomal degradation in response to hyperglycemia. Human cohort analysis further showed reciprocal elevation of RBBP6 in diabetic endothelial cells. Either JUNB overexpression or RBBP6 knockdown restored enhancer-promoter connectivity, reactivated vasoprotective transcriptional programs, and rescued endothelial function. Critically, endothelial-specific knockdown of Rbbp6 in diabetic mice restored endothelium-dependent vasorelaxation and improved perfusion recovery after hindlimb ischemia, independent of systemic glucose levels. ConclusionsOur study unveils a novel mechanism whereby hyperglycemia induces enhancer reprogramming and disrupts endothelial 3D genome architecture through RBBP6-mediated degradation of JUNB. The RBBP6-JUNB axis is established as a crucial link between metabolic stress and epigenomic reprogramming in vascular disease, presenting a promising therapeutic target for diabetic vasculopathy.

genomics↗

bioRxiv2026

A biofidelic Goat Model of Traumatic Optic Neuropathy with Optic Canal Fracture via Transnasal Endoscopy

Traumatic optic neuropathy (TON) is a major cause of irreversible vision loss following blunt cranial trauma, yet the absence of clinically relevant large animal models that faithfully recapitulate human TON has significantly impeded translational research. Current rodent models do not reproduce optic canal fracture, a key injury mechanism in many patients with TON. Here, we combined high-fidelity finite element analysis (FEA) with iterative engineering to establish a reproducible goat model of TON. We first built a high-resolution human-head finite element model to characterize force transmission to the optic nerve. Across clinically relevant periorbital impacts, stress preferentially concentrated in the intracanalicular segment, reaching a peak force density of approximately 500 N/m2 at 50.6 ms, about fivefold higher than in the intraorbital segment. Simulations further showed that direct optic canal impact reproduced comparable intracanalicular stress with a markedly lower input force: 195 N, compared with 3900 N for periorbital impact. Guided by these insights, we developed transnasal endoscopic impact systems capable of inducing optic canal fractures in goats. TON was confirmed within 24 hours by a characteristic relative afferent pupillary defect (RAPD), and at 1 month post-injury goats (n = 14) exhibited a 10%-20% reduction in ganglion cell complex (GCC) thickness and 40%-65% reductions in flash visual evoked potential (FVEP) and pattern electroretinogram (PERG) amplitude ratios (all P [≤] 0.001), with structural and functional preservation of the fellow eye. This study presents a robust, standardized, and clinically relevant large-animal platform for investigating TON pathophysiology.

neuroscience↗

bioRxiv2026

Tunable Chemical and Optical Control of ER-Plasma Membrane Contact Site Geometry and Dynamics with High-Fidelity Visualization

Endoplasmic reticulum-plasma membrane (ER-PM) contact sites are essential signaling hubs that regulate lipid transport, calcium homeostasis, and spatially organized signal transduction. Emerging evidence indicates that not only the presence but also the dynamics, stability, and geometry of ER-PM contacts critically shape cellular functions; however, tools that enable simultaneous high-fidelity visualization and reversible, quantitative control of these contacts in living cells remain limited. Here, we introduce a modular toolkit for inducible ER-PM contact-site reconstitution based on complementary chemical and optical dimerization strategies. We develop a nontoxic and reversible abscisic acid (ABA)-inducible system using the plant-derived ABIcs/PYLcs pair, and a rapidly reversible optogenetic system based on the iLID/SspB module, both of which allow robust visualization and dose-dependent control over contact-site formation kinetics, increasing contact-site density and total area fraction per cell without altering the size of individual contacts. In contrast, systematic variation of rigid -helical linker length or inducible tether abundance selectively tunes the lateral growth, stability, and lifetime of individual contact sites, without changing their density. By combining these two orthogonal strategies, we achieve independent control of both individual contact-site size and overall contact-site density, providing complementary mechanisms to adjust total contact area per cell. This versatile platform enables quantitative dissection of ER-PM contact site structure-function relationships and offers broad utility in studies of lipid exchange, calcium signaling, membrane repair, metabolic regulation, and disease-relevant dysregulation.

bioengineering↗

bioRxiv2026

Multi-Omics Reveals Activated Fibroblasts with Dual Functional Roles in Repair and Negative Barrier in the CD8+ T Cell Cytotoxic Niche for Lung Cancer Neoadjuvant Therapy

A major challenge in elucidating immune activation and tolerance is that single-omics technologies are inherently limited. Since single-cell transcriptomics lacks spatial information and spatial transcriptomics lacks resolution or depth, neither can adequately model the multidimensional tumor immune microenvironment (TiME) features. We present NICHE (Niche Integrated Cellular Heterogeneity Elucidator), an integrative multi-omics framework. By aligning physical cell-cell interactions with single-cell ligand-receptor (L-R) expression, NICHE leverages single-cell transcriptomics, spatial proteomics, and AI modeling to systematically decode the composition, spatial interactions, and communications within immune functional niches. To validate NICHEs capabilities, we applied it to human tonsil tissue. The framework successfully identified key structural and functional units and deeply elucidated the cell-cell interactions and molecular crosstalk within them. Furthermore, these results were validated through orthogonal methods, including single-cell spatial transcriptomics and multiplexed immunofluorescence, which confirmed the accuracy and reproducibility of our analyses. In non-small cell lung cancer (NSCLC) patients undergoing neoadjuvant immunotherapy, CD8+ T cell cytotoxic niches mediate tumor clearance with variable outcomes, to define the cellular and molecular drivers behind this functional spectrum, we utilized NICHE to analyze the TiME from patients with complete versus partial pathological response, both pre- and post-treatment. We found that neoadjuvant immunotherapy may induce the activation of CXCL12+, NECTIN2+, POSTN+, and COL6A1+ fibroblasts through the activation of cytotoxic T cells. Paradoxically, these fibroblasts support tissue repair but also establish an immunosuppressive niche that protects residual tumor cells, ultimately attenuating treatment efficacy. Our work establishes a multidimensional framework for dissecting dynamic immune activity, with direct implications for understanding tumor immunology and identifying novel therapeutic targets.

immunology↗

bioRxiv2026

Prolyl tRNA Synthetase Is Required for Mammarenavirus Multiplication

Several mammarenaviruses (MaAv), chiefly Lassa virus (LASV) in Western Africa and Junin virus (JUNV) in the Argentinean Pampas, cause severe disease in humans and pose important public health problems in their endemic regions. In addition, the globally distributed MaAv lymphocytic choriomeningitis virus (LCMV) is an underrecognized human pathogen of clinical significance especially in congenital infections and LCMV poses a serious risk for immunocompromised individuals. There are no FDA-approved MaAv vaccines or antivirals and current anti-MaAv therapy is limited to an off-label use of ribavirin whose efficacy remains controversial. This highlights an urgent unmet need for developing antivirals against human pathogenic MaAv. Halofuginone (HF), a derivative of the natural alkaloid febrifugine, has been shown to exhibit antiviral activity against several RNA viruses. Here, we present evidence that HF exhibits a potent dose-dependent antiviral activity against LCMV, and the hemorrhagic fever causing MaAv LASV and JUNV. HF binds to the bifunctional enzyme glutamyl-prolyl-tRNA synthetase 1 (EPRS1) and specifically inhibits its prolyl-tRNA synthetase (PRS) activity, resulting in translation inhibition via the amino acid starvation (AAS) response with preferential impact on proline-rich proteins. HF anti-LCMV activity was prevented by the addition of exogenous proline supporting that inhibition of PRS activity plays a critical role on the anti-MaAv activity of HF. We found that HF did not affect LCMV cell entry, modestly (twofold) reduced the activity of the virus ribonucleoprotein (vRNP) but strongly inhibited (>90%) Z budding activity, a process involving the Z proline-rich late domain motifs.

microbiology↗

bioRxiv2026

Gn1a rice promotes symbiotic fish growth via reprogramming soil microbiome

Rice-fish symbiotic ecosystems significantly contribute to world food supply. Mutation in rice (Oryza sativa) quantitative trait locus Gn1a, encoding a cytokinin oxidase/dehydrogenase (OsCKX2), leads to cytokinin accumulation in plant, which promotes tillering and panicle branching to achieved higher yield and also shows a selective effect on soil microbial composition. Given that the growth of aquatic animals can be shaped by their surrounding microbial communities, we asked whether adjusting rice cytokinin levels might synergistically boosts both rice yield and fish growth. Herein, we co-cultured common carp (Cyprinus carpio) with ckx2 rice plants to determine the effect of cytokinins on fish. Surprisingly, compared to wild-type plants, the ckx2 plants enhanced nearly 10% fish growth and improved fish antibacterial capacity against Aeromonas hydrophila and Edwardsiella tarda. In fact, the growth-promoting effect on fish requires mediation by the soil microbiota. Mechanistically, ckx2 plants secreted more cytokinins into soil to reprogram the microbial composition, which subsequently translocated to fish gut and modulated the keystone microbes in gut to facilitate short-chain fatty acid production and carbohydrate degradation. These findings provide the first evidence that rice-derived cytokinins exert a cross-kingdom growth-promoting effect on fish, providing a boosting dual-production strategy for advancing rice-fish symbiotic ecosystem.

plant biology↗

bioRxiv2026

Reshaping Organellar Translation and tRNA Metabolism: The Consequences of Photosynthesis Loss and Massive Horizontal Gene Transfer

The transition to holoparasitism in plants precipitates the loss of photosynthesis, fundamentally altering the selective landscape acting on organellar genomes. These changes raise questions about the mechanisms by which the essential, coevolved machinery of translation responds to extreme genomic erosion and metabolic dependency. Integrating comparative genomics, tRNA sequencing, and subcellular localization assays, we elucidate the extensive rewiring of organellar translation systems and the tRNA-dependent tetrapyrrole biosynthesis pathway in the holoparasitic angiosperm family Balanophoraceae, which exhibits extreme reduction of tRNA content in plastid and mitochondrial genomes. We identified a rare evolutionary event: the putative intracellular transfer of the plastid initiator tRNA (tRNA-iMet) to the nucleus, which compensates for its loss from the plastid genome. We also demonstrate that the unusual UAG-to-Trp reassignment in the Balanophora plastid genetic code is driven by the loss of release factor pRF1 and the recruitment of a mutated nuclear tRNA-Trp. Furthermore, we reveal that the retention of organellar nuclear-encoded aminoacyl-tRNA synthetases is dictated by the presence/absence of cognate organellar tRNAs, which appear to be functional regardless of their foreign (horizontal transfer from the host plant) or native origins. Finally, we uncover a striking evolutionary asymmetry in nuclear-encoded ribosomal proteins: while plastid subunits exhibit elevated substitution rates consistent with relaxed selection and compensatory coevolution, mitochondrial subunits display high sequence conservation, likely maintaining compatibility with the extensive horizontal gene transfer observed in this lineage. Collectively, these findings represent some of the most extreme changes ever identified in the anciently conserved machinery of plant organellar translation.

evolutionary biology↗

bioRxiv2026

A Unified and Interpretable Framework for Evaluating Fluorescence Trace Quality in Transcription Kinetics

Quantifying transcriptional dynamics from fluorescence traces is a powerful approach to understanding gene regulation, but such analysis critically depends on the quality of the fluorescence signal. Experimental researchers often lack an objective and computationally simple way to assess trace quality before kinetic modeling. In this study, we fill in this gap via systematically investigating two key factors (i.e., signal-to-noise ratio (SNR) and trace length) using synthetic data generated from a composite-state Hidden Markov Model (cpHMM) simulator. By analyzing thousands of simulated traces, we identified quantitative thresholds (SNR [≥] 30 dB and length [≥] 360) beyond which transcriptional dynamics can be reliably captured for kinetic inference. Building on these findings, we further discovered a unified and easily computable quality indicator based on the difference between the first two autocorrelation lags. A threshold value of approximately 0.07 effectively separates reliable from low quality traces, providing a simple yet robust criterion for data selection. Together, these results establish a practical framework for assessing fluorescence trace reliability, offering experimental researchers an interpretable and computationally efficient tool to ensure data quality prior to transcription kinetics modeling.

bioinformatics↗

bioRxiv2026

'Zipper' Grammar of CTD Governs the Spatial Programing of the Transcription Cycle of RNA Polymerase II

RNA polymerase II transcribes all protein-coding genes in eukaryotes, with its C-terminal domain (CTD) acting as a regulatory platform throughout the transcription cycle. Despite its simple sequence, the conserved heptad repeats encode a regulatory grammar critical for transcription initiation, elongation, and termination. Using structural analysis, single-molecule imaging, and synthetic CTD-engineered Pol II constructs, we defined the minimal sequence requirements across transcriptional stages. We show that while SP motifs are essential phosphorylation sites, flanking residues tolerate variability. In contrast, the periodic positioning of tyrosine residues is indispensable for pre-initiation complex (PIC) assembly through interactions with the Mediator, which are disrupted upon Ser5 phosphorylation triggering promoter escape. This supports a "zipper" model where sequential tyrosine engagement stabilizes PIC assembly and progressive phosphorylation propels Pol II escape. Site-specific Ser2/5 phosphorylation orchestrates 3-end processing factor recruitment. These findings redefine the functional grammar of the Pol II CTD and explain how a low-complexity sequence achieves regulatory specificity.

cell biology↗

bioRxiv2025

Quantitative Network Classification with CLaSSiNet Reveals Nanoscale Organizational Principles of the Membrane Skeleton

Quantitative analysis of nanoscale biological network architectures remains challenging in super-resolution fluorescence imaging, where cytoskeletal and network-like structures often appear as sparse localization clusters rather than continuous filaments. We introduce CLaSSiNet, a first-of-its-kind modular computational pipeline that integrates connectivity, 1D periodicity, and 2D regularity classifiers to automatically segment, classify, and map nanoscale network architectures with unprecedented classification resolution ([~]256 nm) in single-molecule localization microscopy datasets. CLaSSiNet uniquely distinguishes four organizational states (1D periodic networks, 2D polygonal ordered networks, disordered networks, and non-network states) and is robust to experimental noise and compatible with both node- and link-based labeling strategies. Using CLaSSiNet, we achieve the first spatially resolved, quantitative mapping of organizational heterogeneity in the actin-spectrin membrane-associated periodic skeleton (MPS), a broadly conserved membrane scaffold in animal cells. We uncover previously unrecognized subcellular patterning, with ordered 1D and 2D networks enriched at cell edges and junctions, while non-network states dominate the cell body. CLaSSiNet further reveals mechanical coupling principles: actin stress fibers bias the formation and orientation of 1D periodic networks and enrich nearby non-network regions, suggesting coordination between spectrin lattices and contractile actin bundles. Comparative analysis across cell types shows that neurons favor 1D periodic architectures in neurites and 2D polygonal networks in somas, whereas U2OS and 3T3 cells adopt these architectures to a lesser extent, highlighting cell-type-specific tuning of spectrin network design. Together, these results establish CLaSSiNet as a generalizable platform for quantitative network-state mapping and provide new biological insights into how spectrin-based architectures adapt to local mechanical environments.

cell biology↗

bioRxiv2025

Membrane-associated periodic skeleton regulates major forms of endocytosis in neurons through a signaling-driven positive feedback loop

Endocytosis is an evolutionarily conserved process that enables neurons to internalize signaling receptors and membrane proteins, maintaining cellular homeostasis and supporting rapid responses to extracellular cues. The neuronal membrane-associated periodic skeleton (MPS), a lattice-like cytoskeletal structure composed of actin and spectrin, has been shown to restrict clathrin-mediated endocytosis (CME) at the axon initial segment (AIS) of neurons, by gating clathrin-coated pit (CCP) formation through membrane-localized "clearing" structures that are devoid of MPS. However, the extent to which the MPS regulates diverse forms of endocytosis across neuronal compartments, and how it is dynamically remodeled to permit trafficking on demand, remain unknown. While CME is relatively well characterized in neurons, the subcellular localization and physiological relevance of caveolin-mediated endocytosis, flotillin-mediated endocytosis, and fast endophilin-mediated endocytosis (FEME) have remained largely unclear. Here, we show that all four major endocytic pathways--CME, caveolin-, flotillin-, and FEME-- are spatially gated by the MPS and occur specifically within MPS-free "clearing" zones distributed across both axonal and somatodendritic compartments of mature neurons. These results, for the first time, map the spatial landscape of these lesser-understood pathways in neurons and reveal a unifying principle of cytoskeletal gating across endocytic mechanisms. Disruption of the MPS markedly enhances both basal and ligand-induced endocytosis across all four pathways, establishing its broad inhibitory role in pit initiation. We further discover that endocytosis can, in turn, remodel the MPS through a novel signaling-driven feedback loop: ligand-triggered endocytosis activates ERK signaling, which promotes calpain- and caspase-mediated spectrin cleavage. This targeted cytoskeletal degradation facilitates further rounds of endocytosis, forming a self-reinforcing circuit that couples membrane trafficking with cortical architecture remodeling. Finally, we show that the MPS limits amyloid precursor protein (APP) endocytosis and thereby suppresses amyloid-{beta} 1-42 (A{beta}42) production and neuronal apoptosis, implicating MPS integrity in the regulation of neurodegenerative processes such as Alzheimers disease. Together, our findings establish the MPS as a dynamic, signal-responsive modulator of endocytosis and neuronal health. This work uncovers a general spatial gating mechanism that applies to diverse endocytic pathways, introduces a cytoskeleton-centered feedback loop for signal-dependent remodeling, and expands the functional significance of the MPS from passive structural support to active regulation of neuronal homeostasis and disease susceptibility. TeaserMembrane skeleton gates endocytosis and remodels in response to signals, linking membrane dynamics to neuronal health and Alzheimers risk.

cell biology↗

bioRxiv2025

Neural mechanisms of handedness for precision drawing: hand-dependent engagement of cortical networks for bimanual control and tool use

Neural mechanisms underlying handedness remain poorly understood. We used functional magnetic resonance imaging (fMRI) to study performance of a visually guided drawing task with each hand. We hypothesized that the left superior parietal lobule supports drawing with either hand, and individuals with chronic peripheral nerve injury (PNI) to the dominant hand use the same mechanism as healthy adults. Thirty-three right-handed adults (23 healthy, 10 patients) underwent fMRI while performing a precision drawing task, alternating between the right hand (RH) and left hand (LH). BOLD magnitude and functional connectivity (FC) modulation via generalized psychophysiological interaction were analyzed in 12 a priori regions of interest, followed by additional exploratory areas identified via whole brain magnitude analysis. During LH drawing (compared to RH drawing), contralateral primary motor cortex showed lower BOLD magnitude but greater FC with two networks: First, a left motor-premotor network with increased FC and equal-or-greater magnitude during LH drawing. Second, a right parietal network characterized by increased FC during LH drawing but increased magnitude during RH drawing. Exploratory whole-brain analyses supported and extended these motor and parietal networks, and additionally suggested that RH drawing may involve greater magnitude and FC within a bilateral parieto-premotor network centered on right paracingulate cortex. Patient group (PNI vs. control) did not interact with these effects. These results describe the first proposed mechanisms for LH precision drawing, both of which depend on differential engagement of bimanual control networks: a left hemisphere motor-premotor network for precision motor control, which engages intrahemispherically (directly) during RH drawing and interhemispherically (indirectly) during LH drawing; and a right hemisphere parietal network with greater distributed coordination during LH drawing. These mechanisms did not differ between PNI patients and healthy adults, highlighting these mechanisms potential as neuromodulatory targets to enhance LH performance after RH impairment.

neuroscience↗

bioRxiv2025

Variants in Cas9 and nanos regulatory elements modulate activity and reduce resistance allele formation in homing gene drive

Gene drive is a novel approach for controlling vector borne disease via either population modification or suppression. Even with high efficiency, though, overall drive performance can be reduced by somatic Cas9 expression and by maternal deposition of Cas9, leading to resistance allele formation. The nanos promoter for Cas9 shows very little leaky somatic expression, but it causes high rates of embryo resistance allele formation in Drosophila melanogaster. By truncating the promoter, we reduced rates of embryo resistance to undetectable levels, but germline cutting in females decreased by over half. Germline cutting and successful drive conversion was eventually lost when only the 5' UTR was present, though males still retained moderate germline drive efficiency. Several additional methods were tested to improve performance, including additional suppressor elements to the 3' UTR and introns to increase expression level. The most successful of these was the addition of a second nuclear localization signal, which substantially increased activity when coupled with a full-length or truncated nanos promoter. Overall, these experiments show the potential to modulate Cas9 regulatory elements to achieve desired expression for gene drive applications, while also showcasing the difficulty of obtaining an optimal activity profile.

genetics↗

bioRxiv2025

Integrative genomic insights into parallel local adaptation to Danxia and Karst edaphic islands in the endangered tree Firmiana danxiaensis

Uncovering the genetic basis of local adaptation is a central goal in evolutionary biology. Edaphic islands, such as Karst (KL) and Danxia (DL) landforms, provide ideal natural laboratories for this endeavor. However, the mechanisms underlying parallel adaptation to contrasting edaphic extremes within a single species remain poorly understood. Firmiana danxiaensis, an endangered tree endemic to both KL and DL in the Nanling Mountains, offers a rare opportunity to address this question. We integrated a chromosome-level genome assembly, population genomic analysis of 225 individuals from 20 populations across its entire range, and genotype-environment association (GEA) with high-resolution soil and climate data. The relatively large genome of F. danxiaensis (1.51 Gb) reveals two ancient whole-genome duplications and a Quaternary burst of LTR retrotransposons, which, together with significant expanded drought-related transcription factor (TF) families, together constitute its genomic basis of adaptation. Population structure resolved four genetic lineages with distinct demography and inbreeding patterns. GEA identified stronger local adaptation in DL than KL, driven mainly by soil factors (e.g., cadmium, zinc), while climate variables (e.g., Bio9, Bio11) predominated in KL. Despite these divergent drivers, drought stress and elevated metal ion acted as major selective pressures in both landforms. Furthermore, six key TFs (e.g., NAC090, bHLH42, MAPKKK20) under both local adaptation and positive selection in DL are involved in drought response and metal ion binding, facilitating survival in stressful habitats. Our findings provide novel insights into parallel local adaptation to contrasting edaphic islands and offer concrete genomic guidance for the conservation of F. danxiaensis. Significance statementThe genetic basis of parallel local adaptation to contrasting environments remains unclear. Using the endangered tree Firmiana danxiaensis, we uncover genomic mechanisms enabling its adaptation to both Karst and Danxia edaphic islands. We demonstrate that adaptation is primarily driven by soil factors in Danxia and climate in Karst, generating divergent genomic signatures yet converge on drought response. These findings establish a framework for understanding parallel local adaptation and offer concrete genomic guidance for conservation.

evolutionary biology↗

bioRxiv2025

Development of an efficient PEG-Mediated protoplast transformation system for the medicinal fungus Ophiocordyceps xuefengensis

Ophiocordyceps xuefengensis is a newly identified medicinal fungus with significant pharmacological and economic value, but its genetic manipulation has been impeded by the lack of an efficient transformation system. Here, we established the first stable and highly efficient polyethylene glycol (PEG)-mediated protoplast transformation platform for O. xuefengensis using hygromycin B as a selectable marker. Through systematic optimization of critical parameters such as enzyme composition, enzyme concentration, mycelial age, and digestion conditions, we developed an optimized protocol for protoplast preparation. A high protoplast yield of 9.42x107 CFU/mL was achieved using 4-day-old mycelia with 1.5% lywallzyme 1 and 1.5% snailase digested at 34{whitebullet}C with shaking at 130 rpm for 3.5 h. PY medium containing 0.6 M mannitol significantly enhanced protoplast regeneration. Stable plasmid integration and robust hygR gene expression were confirmed through PCR detection and sustained antibiotic resistance over four successive generations. Furthermore, a controllable expression system was established by using the endogenous promoter that drove the stable expression of the glycoside hydrolase gene cbhI. The result of enzymatic assay confirmed the functional production of CBHI enzyme, demonstrating the credibility of this system. This work provides a reliable genetic toolbox for functional genomics studies, targeted gene manipulation, and strain engineering in O. xuefengensis, facilitating fundamental research and sustainable utilization of this valuable medicinal species. IMPORTANCEThe conservation and sustainable utilization of medicinal fungi represents a critical challenge in biotechnology and natural product research. Ophiocordyceps xuefengensis, a newly identified species with significant pharmacological potential, exemplifies this challenge: its wild resources are diminishing while artificial cultivation remains restricted by limited understanding of its fundamental biology. The lack of genetic tools has impeded progress in elucidating its biosynthetic pathways, regulating fruiting body development, and enhancing metabolite production. We established a highly efficient PEG-mediated transformation system that directly addresses this technological gap. In addition, we demonstrated that this transformation system can support heterologous gene expression using endogenous promoters. This platform enables reliable genetic manipulation in O. xuefengensis, permitting functional genomics studies and targeted bioactive compounds synthesis.

microbiology↗