Biology subjects

Jia, X.

Publications and source records attributed to Jia, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

A confined gene drive for population modification in the malaria vector Anopheles stephensi

Gene drives are genetic elements that bias their own inheritance to spread desired traits in target populations, enabling population modification or suppression. Although homing-based drives can propagate efficiently, their potential for uncontrolled spread may present a challenge for field deployment. Thus, confined drive systems are needed. Here, we developed a confined modification drive, called Toxin-Antidote Recessive Embryo (TARE) drive, in the globally important malaria vector Anopheles stephensi. This drive works by cleaving and disrupting wild-type alleles in the germline or early embryo from maternally deposited Cas9. Disrupted alleles are recessive lethal, thus increasing the drive in a frequency-dependent manner. Inheritance bias was moderate in crosses between drive heterozygote mosquitoes, possibly due to low gRNA activity and thus moderate germline cleavage rates. Single-release cage trials confirmed the TARE drives ability to spread, although the drive ultimately declined due to fitness costs and resistance alleles associated with repetitive elements. Nonetheless our modelling analysis indicate that this TARE system could achieve population spread if the resistance issue is addressed. These findings demonstrate a functional prototype TARE drive in Anopheles stephensi and highlight key parameters governing its performance. Minor design optimizations could substantially improve efficiency and integrity, enabling rapid but confined population modification.

genetics↗

bioRxiv2026

CLEAR: Concise List Enrichment Analysis Reducing Redundancy

MotivationHigh-throughput experiments generate genome-wide measurements for thousands of genes, which are often tested marginally. Biological processes are driven by coordinated groups of genes rather than individual genes, making gene set enrichment analysis an essential post hoc interpretation tool. Traditional approaches such as Over-Representation Analysis and Gene Set Enrichment Analysis test gene sets independently, which ignores the hierarchical and overlapping structure of gene set collections such as the Gene Ontology, and often leads to redundant enrichment results. Set-based approaches such as MGSA address this issue by modeling multiple gene sets simultaneously, but they rely on binary gene activation states derived from arbitrary thresholds on gene-level statistics. ResultsWe introduce Concise List Enrichment Analysis Reducing Redundancy (CLEAR), a Bayesian gene set enrichment framework that jointly models gene sets while incorporating continuous gene-level statistics such as test statistics or p-values. CLEAR extends model-based gene set analysis by replacing threshold-based gene activation with a probabilistic model for continuous gene-level statistics. This approach preserves the redundancy-reduction advantages of set-based enrichment methods while avoiding the information loss introduced by binarization. Using both simulated datasets and human gene expression data, we show that CLEAR improves sensitivity compared with existing enrichment approaches while producing a more concise and interpretable set of enriched gene sets. Availability and implementationThe source code, data, and a brief tutorial are freely available at https://github.com/jiatuya/CLEAR

bioinformatics↗

bioRxiv2026

Nanosecond laser-driven proton FLASH spares normal tissue cells by sustaining mitochondrial homeostasis and attenuating ferroptosis

Radiotherapys clinical utility remains fundamentally constrained by the collateral damage to healthy tissues. Ultra-high-dose-rate (UHDR) irradiation, or, FLASH-radiotherapy (FLASH-RT) has emerged as a transformative paradigm to mitigate such toxicity. However, the biological effects of FLASH-RT on the high-efficiency of tumor killing and normal tissue sparing remain poorly understood. In this work, we utilized a petawatt-class laser-plasma acceleration (LPA) platform to deliver discrete 12.9-nanosecond proton pulses at an extreme instantaneous dose rate of 1.94x107 Gy/s. This temporal singularity achieved a profound sparing effect in normal bronchial epithelial cells, evidenced by a nine-fold reduction in the lethal coefficient (from 0.47 to 0.05 Gy-1), while maintaining full tumoricidal potency against lung adenocarcinoma. Mechanistically, we demonstrated that LPA-FLASH could effectively bypass the ATF3-mediated stress response and circumvent the subsequent ferroptotic cascade. This molecular evasion could preserve the mitochondrial cristae integrity and trigger an adaptive bioenergetic ATP surge--a hallmark of metabolic resilience exclusively in healthy tissue cells. Therefore, our findings identify ferroptosis-mediated mitochondrial integrity as a unifying framework for selective normal-tissue protection at the physical limits of radiation delivery, and establish LPA-FLASH-RT as a potent, compact modality for next-generation oncology.

cell biology↗

bioRxiv2026

vToxiNet: a biologically constrained deep learning framework for interpretable prediction of drug-induced hepatotoxicity

Hepatotoxicity remains a leading cause of drug attrition and post-marketing withdrawal, resulting from diverse and complex toxicity mechanisms. Traditional in vitro models can only capture a limited subset of toxicity pathways, and animal studies face translational and ethical limitations. Regulatory agencies have therefore promoted new approach methodologies, including human-relevant assays, omics technologies, and computational models to improve predictive toxicology and support evidence-based decision-making. However, most machine learning models for hepatotoxicity either rely solely on chemical structure or operate as black boxes, limiting mechanistic interpretability and broader applicability. Here, we introduce the virtual toxicity network (vToxiNet), a biologically constrained deep learning framework that embeds systems toxicology knowledge directly into neural network architecture for interpretable hepatotoxicity prediction. vToxiNet integrates chemical descriptors, high-throughput assay responses, transcriptomic signatures, and Reactome pathway hierarchy to construct a virtual adverse outcome pathway network. Across cross-validation and multiple external validation datasets, vToxiNet demonstrates robust predictive performance and generalizes to previously unseen chemicals. Importantly, interpretation of vToxiNet enables gene and pathway-level attribution, supporting mechanism-informed hazard characterization and chemical prioritization. These results demonstrate that encoding biological hierarchy as architectural constraints enables both predictive accuracy and mechanistic insight, establishing a generalizable framework for modeling complex biological outcomes.

pharmacology and toxicology↗

bioRxiv2026

Endocardial TIE1 synergizes with TIE2 to regulate the atrial internal muscular network assembly

Atrial cardiomyopathy is characterized by altered atrial structures, yet its underlying genetic basis remains inadequately explored. TIE1 mutations are reported in lymphedema patients, but whether they exhibit cardiac defects alongside lymphatic abnormalities remains unknown. Here, single-cell RNA sequencing showed high Tie1 and Tek expression in atrial endocardial cells. TIE1 deficiency severely disrupted atrial morphogenesis, with only minor ventricular defects. Bulk RNA-seq showed reduced transcripts for endothelial development and cardiac trabeculation in Tie1 mutants. Separate RNA-seq analysis of the atria and ventricles further confirmed these findings, revealing a more pronounced downregulation of trabecular genes, including Tek, in the atria upon Tie1 loss. Endothelial deletion of Tek impaired trabeculation, particularly in atria. Consistently, Tie1 loss combined with a single null Tek allele disrupted both atrial and ventricular trabeculation. Strikingly, atrial morphogenesis defects appeared within 48 hours of induced endothelial Tie1 loss coupled with Tek heterozygous deletion, implying a critical endocardial role in organizing the atrial muscular network. The synergy of TIE1 and TIE2 in remodeling atrial trabeculae was confirmed postnatally, whereas TIE1 insufficiency alone had no effect. Together, TIE1 is differentially required for atrial versus ventricular development, acting synergistically with TIE2 to regulate endocardial cell-coordinated assembly of atrial internal muscular network.

developmental biology↗

bioRxiv2025

Angle-resolved Measurements Reveal the Origin of Signal Anisotropy in Pump-probe Microscopy

Nonlinear optical microscopy modalities have become widely used in applications ranging from material characterization to tissue diagnosis. In complex systems, multiple mechanisms often contribute to the signal; for example, two-color pump-probe microscopy provides rich molecular signatures of the samples based on several nonlinear processes. Here we uncover a surprising complication, that in many cases the detection direction drastically alters the signal components and the overall amplitude. To understand the origin of this signal anisotropy, we first calculate and measure a simple case, the pump-probe signal of gold nanoshells at various detection angles, attributing the effect to scattering changes due to the sample refractive index change; we then extend this analysis, showing a striking directional dependence arising from distinct scattering profiles of two dominant nonlinear processes. These results demonstrate that comparing epi (backward) and transmission (forward) signals provides additional information, enabling cleaner separation of nonlinear contributions in pump-probe measurements.

biophysics↗

bioRxiv2025

Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data

BackgroundOxford Nanopore sequencing enables long-read sequencing across diverse applications, yet the experimental artifacts introduced by Nanopore barcoding are not well characterized. These artifacts can affect demultiplexing accuracy and downstream analyses. ResultsWe performed a rapid barcoding experiment on 66 diagnostic samples and found that 83% of reads carried the expected single-barcode pattern, while 17% contained multiple barcodes or other artifacts. Current demultiplexers, including the widely used Dorado, fail to correctly handle these complex cases, leaving approximately 7% of reads partially trimmed and contaminated with adapter fragments. Additional issues include the presence of two barcodes at the same read end--either identical, originating from the same sample, or different, introduced after pooling. The latter can lead to barcode bleeding when the outer barcode is incorrectly selected. To address these challenges, we developed Barbell, a pattern-aware demultiplexer that detects all barcode configurations. Barbell reduces trimming errors by three orders of magnitude, minimizes barcode bleeding, and supports custom experimental setups such as shorter barcodes, dual-end barcodes, and custom flank sequences. ConclusionsOur results highlight the impact of complex barcode attachments in Nanopore sequencing and demonstrate that Barbell drastically reduces their effects on downstream analyses. Barbell is open source and available at https://github.com/rickbeeloo/barbell.

bioinformatics↗

bioRxiv2025

Lymphatics unload VEGFR3 in response to the endothelial stress upon VEGFR2 insufficiency

Vascular endothelial growth factor receptor 2 (VEGFR2) is a key target for regulating the endothelial cell lineage and angiogenesis. It is also expressed by lymphatic endothelial cells (LEC) while its participation in the process of lymphangiogenesis remains inadequately characterized. We show in this study that VEGFR2 is highly expressed in dermal initial lymphatic vessels and valves. The induced deletion of pan-endothelial Vegfr2 at the neonatal stage produced a potent suppression of dermal lymphatic growth, including the thinner lymphatic diameter, the decrease of LEC number and lymphatic valves. Mechanistically, the VEGFR2 insufficiency led to a dramatic decrease of lymphatic VEGFR3, a key regulator mediating signals for lymphatic growth and remodeling. The RNA sequencing analysis revealed that GO terms enriched for the downregulated genes included biological processes related to the EC development while pathways related to the hematopoiesis and immune responses were upregulated in the skin of Vegfr2 mutants compared with the littermate controls. This was further confirmed by the RNA-seq analysis of dermal tissues 48 hours after the endothelial Vegfr2 deletion. Consistently, an inhibitory effect on the dermal lymphatic growth was also observed by targeting Vegfr2 in PROX1+ cells, manifesting a similarly altered transcriptome signature. The alteration of lymphatic gene expression was further validated by the siRNA mediated knockdown of Vegfr2 in primary lymphatic endothelial cells, showing a transcriptional trend of LEC to hematopoietic transition. Findings from this study imply that VEGFR2 is required for the maintenance of endothelial identity and its insufficiency may trigger the alteration of lymphatic transcriptional programs to diminish the VEGFR3-mediated lymphangiogenesis.

developmental biology↗

bioRxiv2025

Finding the perfect promoter: Correlating single-cell transcriptome data with gene drive performance

Gene drive can control pathogen transmission or suppress vector populations by spreading drive alleles with super-Mendelian inheritance. CRISPR homing drive currently represents the most powerful type, and regulating Cas9 expression with specific promoters has been effective for improving drive performance. However, selecting these is often a major challenge. Here, we evaluated 35 Cas9 constructs driven by distinct promoters in different gene drive systems and identified associations between drive performance and single-cell RNA expression patterns of the promoter-associated genes. Our results indicate that higher drive conversion is significantly associated with elevated expression of the promoter-associated gene in the respective reproductive cells, but embryo resistance allele formation correlates with excessive female germline expression. For males, early germline expression produces superior performance. Thus, we find that optimal drive performance requires restricting Cas9 expression to a tight quantitative and spatiotemporal window. In addition, found that in situ integrated rhino-Cas9 constructs significantly reduce somatic expression, underscoring the importance of genomic locus. On the basis of these results, we propose criteria for selecting promoters, providing a theoretical rationale and practical guidance for optimization of promoter elements in homing gene drive systems.

genetics↗

bioRxiv2025

Progenitor T cells drive chronic pulmonary type 2 inflammation

Type 2 inflammation unfolds over time and is coordinated by remarkably durable CD4+ Th2 cell responses, standing in contrast to the collapse of adaptive immunity seen in chronic infection and malignancy. In experimental models, short-lived Th2 effector cells and type 2 innate lymphocytes (ILC2) contribute to acute type 2 inflammation, yet the cellular architecture that drives chronic type 2 inflammation and prevents exhaustion remains poorly understood. To define the Th2 landscape in chronic type 2 inflammation, we established a mouse model of long-term pulmonary allergen exposure and found that type 2 inflammation was broadly sustained over at least 4 months despite chronic stimulation. Th2 cells in the lung parenchyma during chronic inflammation were distinct from acute inflammation and resting memory phases, and included an expanded T cell factor-1 (TCF1)-expressing progenitor-like Th2 population. Tissue Th2 progenitors were absent in the nose and in helminth infections, suggesting that type 2 immunopathology is context-specific. Transcriptomic deconstruction of acute and chronic pulmonary Th2 responses defined divergent effector programs as well as the transcriptional signature of a tissue Th2 memory population that resembled human Th2 progenitors. Integrated transcriptomic analysis comparing type 2 inflammation to chronic viral infection revealed a distinct stemness module underlying chronic Th2 inflammation that was separable from a common core memory module. In vivo, lung Th2 progenitors coupled self-renewal with effector cell differentiation and could be sustained for weeks without antigen persistence or contribution from the lymph node. Maintenance of Th2 progenitors was partially dependent on lung parenchymal B cells and associated with bronchus-associated lymphoid tissue formation. Moreover, Th2 progenitors, in contrast to Th2 effectors and ILC2s, were sufficient to both initiate and sustain type 2 inflammation. Thus, we define tissue Th2 progenitors as a distinct cellular state that arises during chronic type 2 inflammation and establish the central role of these cells in maintaining the architecture of Th2 responses over time.

immunology↗

bioRxiv2025

Evolutionary history and recurrent host adaptation in ancient Salmonella enterica

Salmonella enterica subsp. enterica is an extremely diverse bacterial pathogen causing frequent infections and foodborne disease among human populations. More than 1500 different bacterial strains (serovars) have been described, many with a wide host range. A small number of serovars are adapted to infect specific hosts: of these, serovars Typhi and Paratyphi A, B, and C cause primate-specific systemic infections (typhoid and paratyphoid fever). Although Paratyphi C is one of the rarest human-specific serovars today, it was once widespread, and all ancient Salmonella genomes published to date belong to or are ancestral to this lineage. Here, we present 53 new ancient Salmonella genomes spanning Eurasia and dating between 3500 BCE and 1300 CE. This rich genomic dataset allows us to reconstruct the evolutionary history of this pathogen in unprecedented detail. We identify multiple extinct prehistoric lineages that caused infections throughout Eurasia. Multiple lineage replacement events are observed throughout prehistoric and historic times, and Bayesian phylogenetic analysis is used to date and identify host adaptation events within this lineage. We find that host-adapted sublineages Paratyphi C, Choleraesuis, and Typhisuis continued to evolve host specificity independently from each other. We reconstruct signals of convergent host adaptation in the studied lineages and other host-adapted strains by analysing shared pseudogenes and recurrent gene gain and loss events. This analysis demonstrates a role for host interactions as a particular target of selection, highlighting the gradual adaptation of this S. enterica lineage to humans that coincides with the intensification of animal husbandry in pastoralist and sedentary farming societies.

genetics↗

bioRxiv2025

Bacterial community adaptation after freshwater and seawater coalescence

Microbial community coalescence, the merging of entire microbial communities, is common across ecosystems, particularly in estuaries where freshwater and seawater mix. The complexity of these habitats makes the in situ study of community dynamics after coalescence challenging, highlighting the need for controlled experiments to unravel the factors influencing the coalescence in the estuary. To study these processes, we combined natural freshwater and seawater bacterial communities at five different mixing ratios and incubated them in parallel microcosms containing freshwater or seawater incubation media. Forty mixed communities were tracked over six passages using Nanopore full-length 16S rRNA gene sequencing. In the original field samples, freshwater hosted more diverse communities than seawater. While the communities were structurally distinct, shared bacterial families accounted for approximately 95% of total reads. Many low-abundance taxa were lost upon laboratory incubation, while potentially faster-growing ones were enriched. We found that the coalescence outcome was strongly shaped by the incubation media, whereas the mixing ratio had a minor influence. Mixed communities converged toward the source community native to the incubation media, with increasing similarity at a higher source community proportion. In freshwater, a 25% inoculum of the freshwater community was sufficient to re-establish a near-native freshwater community, whereas in seawater, similarity to the native seawater community depended on the inoculation ratio. Network analysis showed a tightly connected module of seawater families, reflecting their shared habitat preference or cooperation, whereas freshwater families were more loosely connected. We also observed that most families were unaffected by mixing ratios or temporal dynamics, with only a few showing mixing ratio dependence. For instance, the freshwater family Comamonadaceae and seawater families Marinomonadaceae and Pseudoalteromonadaceae were dominant in their respective native environments, and increased in mixed communities in proportion to their initial source proportion. Overall, environmental filtering had a stronger impact than the mixing ratio of source communities on coalesced communities, with habitat-specific taxa further modulating the outcome. These findings advanced our understanding of microbial responses to coalescence and provided insights into microbial community assembly in dynamic estuarine systems. HighlightsO_LIEnvironmental filtering outweighs the microbial source community ratio in shaping coalescence outcomes. C_LIO_LIAsymmetric resilience: freshwater communities require a lower inoculum to re-establish than seawater communities. C_LIO_LIModularity of the seawater source community was observed during coalescence. C_LIO_LIFull-length 16S rRNA gene profiling with a custom dual-barcoding Nanopore protocol enables cost-effective bacterial community tracking. C_LIO_LIControlled coalescence experiments offer mechanistic insights into estuarine microbial community transitions. C_LI

ecology↗

bioRxiv2025

Impact of 2'-deoxyribo-purine substrates on nonenzymatic RNA template-directed primer extension

The composition of the primordial genetic material remains uncertain. Studies of duplex structure and stability, and of nonenzymatic template copying chemistry, provide insight into the viability of potentially primordial genetic polymers. Recent work suggests that 2'- deoxyribo-purine nucleotides may have been generated together with ribonucleotides on the early Earth. Since DNA/RNA duplexes are known to be less stable than RNA/RNA duplexes, we have examined the impact of dA, dI, and dG substitutions on RNA structure and nonenzymatic template copying. We find that single 2'-deoxyribo-purine substitutions reduce RNA duplex stability, as expected. Crystallographic studies show that such substitutions lead to minimal structural changes but point to diminished solvation as a likely reason for duplex destabilization. Kinetic studies show that dI and dG substrates exhibit slightly weaker template binding and slower rates of template-directed primer extension than the corresponding ribo-purine substrates. In contrast, dA substrates exhibit much slower reaction kinetics but higher template affinity than rA substrates. Our results suggest that a mixed RNA/DNA primordial genetic polymer would have suffered from moderately slower rates of template copying, but that this could have been offset by an advantage due to more facile strand separation or exchange. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/673048v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@15bd09aorg.highwire.dtl.DTLVardef@dc49d4org.highwire.dtl.DTLVardef@730d20org.highwire.dtl.DTLVardef@162b84f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Capturing trophectoderm-like stem cells enables step-wisely remodeling of placental development

The trophectoderm produced from totipotent blastomeres initiates trophoblast development, while placental deficiencies can cause pregnancy disorders. Yet, a culture system that fully recapitulates the entire placenta development is still lacking, greatly limiting related studies. Here, we captured mouse trophectoderm-like stem cells (TELSCs), which can give rise to all trophoblast lineages and be applied to generate trophoblast organoids. We achieved the induction and maintenance of TELSCs from totipotent blastomere-like stem cells or early embryos through a Hippo-YAP/Notch-to-TGF{beta}1 signaling switch. At the molecular level, TELSCs resemble E4.5 trophectoderm and are distinct from all previously known trophoblast-like stem cells. Functionally, TELSCs can generate all trophoblast lineages in both teratoma and chimera assays. We further applied TELSCs to generate trophoblast organoids containing various mature trophoblasts and a self-renewing extraembryonic ectoderm (ExE)-like progenitor population. Interestingly, we observed transiently formed rosette-like structures that rely on Itgb1, which are essential to induce ExE-like progenitors and to generate organoids eventually. Thus, the capture of TELSCs enables comprehensive insights into placental development. HighlightsO_LITELSCs were robustly induced and long-term maintained from TBLCs and early embryos using a newly developed Hippo-YAP/Notch-to-TGF{beta}1 signaling switch strategy C_LIO_LITELSCs resemble E4.5 trophectoderm at the molecular level and generate all trophoblast lineages both in vivo and in vitro functionally C_LIO_LITELSCs can be applied to generate trophoblast organoids containing multiple mature subtypes and a self-renewing ExE-like population C_LIO_LIRosette structure formation that relies on Itgb1 is critical to induce ExE-like progenitors and to eventually form trophoblast organoids C_LI

cell biology↗

bioRxiv2025

Single-nucleus transcriptome analyses uncover a dynamic transcriptional landscape of soybean roots in response to soybean cyst nematode infection

Soybean cyst nematode (SCN, Heterodera glycines) causes substantial yield losses by inducing the formation of specialized feeding structure called syncytia, which arise from extensive reprogramming of host root cells. Despite their pivotal role in SCN parasitism, the molecular mechanisms governing syncytium formation and function remain poorly understood, largely due to the technique challenges in precisely isolating these rare cell types. Here, we employed single-nucleus RNA sequencing (snRNA-seq) to generate a comprehensive, high-resolution transcriptomic atlas of SCN-infected soybean roots, comparing two resistant cultivars (PI 88788 and Forrest) with a susceptible cultivar (Williams 82) across multiple infection stages. By leveraging the well-characterized syncytium marker GmSNAP18, we successfully identified and transcriptionally profiled syncytial cells, and validate the spatial expression of known SCN-resistant genes. Our analyses revealed strong induction of resistance-associated genes specifically enriched in syncytia from resistant cultivars. Functional validation further demonstrated that overexpression of three novel candidate genes significantly suppressed SCN development. Pseudotime trajectory analyses traced syncytium development back to procambial cell origins, uncovering distinct, cultivar-specific developmental pathways. Collectively, this work provides a foundational single cell transcriptomic resource, advances our understanding of syncytial biology and SCN resistance mechanisms, and identifies promising molecular targets for engineering nematode-resistant soybean varieties.

plant biology↗

bioRxiv2025

Evaluating nongenetic maternal transmission and post-weaning persistence of gut microbiota in cross-fostering rabbits

Gut microbiota is widely recognized as an important source contributing to phenotypic variation of diverse host traits in livestock. In this regarding, it is promising to improve offspring production traits through direct selection on parental individuals with the desirable gut microbiota, and this is termed microbiome breeding. However, the extent of nongenetic maternal transmission of gut microbiota and its post-weaning persistence remains poorly understood. To fill this gap, we cross-fostered 120 newborn rabbits that are offspring of 20 does in this study, and compared gut microbiota of all kits at the weaning (35 days of age) and two weeks post-weaning, respectively. Based on variance component analysis, we found that the large proportions of phenotypic variation of four alpha diversity metrics for kits at weaning can be explained by the nursing does, ranging from 0.218 {+/-} 0.106 for Evenness index to 0.464 {+/-} 0.125 for the number of observed features. The significant effect of nursing does was supported further by comparing three beta diversity metrics among different relationships, using Kruskal-Wallis test and Dunns post-hoc comparisons. In contrast, the biological does showed no significant effect on gut microbiota composition of pre-weaning kits. In post-weaning kits, the influence of nursing does on gut microbiota was not obviously decreased, despite there was increasing contributions of additive genetic effects. In conclusion, this study provides direct evidence in rabbits that offspring gut microbiota is predominantly shaped by the nongenetic maternal transmission, with these maternal influences persisting post-weaning. These results indicate the possibility that the direct selection on parental gut microbiota will alter offspring gut microbiota.

microbiology↗

bioRxiv2025

Changes in endophytic microbial diversity and function in the root system affect the growth of continuously planted Casuarina equisetifolia

Withdrawal StatementThe authors have withdrawn this manuscript because additional experimental data are necessary to strengthen the conclusions and improve the overall quality of the study. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

microbiology↗

bioRxiv2025

Potentially Prebiotic Isocyanide Activation Chemistry Drives RNA Assembly via both Nonenzymatic and Ribozyme-catalyzed Ligation

Nonenzymatic assembly of activated RNA building blocks, such as phosphorimidazolides, would have been essential for the emergence of ribozymes on the early Earth. We previously showed that ribonucleoside monophosphates can be activated to phosphorimidazolides via a prebiotically relevant phospho-Passerini reaction involving 2-aminoimidazole, 2-methylbutyraldehyde, and methyl isocyanide, and that these activated nucleotides enable template-directed nonenzymatic RNA polymerization in the same reaction mixture. Here, we demonstrate that the same chemistry activates oligoribonucleotides and drives both nonenzymatic and ribozyme-catalyzed RNA ligation within the same reaction environment. By demonstrating a continuous path from prebiotic activation chemistry to RNA template copying by both nonenzymatic and ribozyme-catalyzed ligation, our results provide a more integrated and realistic model for RNA assembly on the early Earth.

biochemistry↗