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Abstract BackgroundTransfer RNA (tRNA) modifications are essential for structural integrity, decoding fidelity, and stress adaptation, yet their evolutionary dynamics remain poorly characterized in archaea. Here, we apply Ordered Two-Template Relay sequencing (OTTR-seq), a high-throughput approach that captures full-length tRNAs and modification-sensitive reverse transcription signatures, to systematically profile tRNA modification landscapes across diverse archaeal species. ResultsAcross nine archaeal species spanning thermophilic, acidophilic, halophilic, and mesophilic environments, we identify position-specific and clade-dependent patterns of tRNA modifications. We detect coordinated and mutually exclusive methylation at acceptor stem positions 6 and 67 in hyperthermophiles, as well as clade-specific co-modification at positions 10 and 26, which are typically known as tRNA modification anti-determinants. Comparative analyses also reveal lineage-specific divergence in the domain architectures of tRNA methyltransferases, including Trm1, Trm10, Trm11, and Trm14, linking enzymatic evolution to substrate specificity. We further refine known identity elements, such as the G10oU25 pairing, and identify novel structural features that may facilitate or prevent modification. ConclusionsThese findings exemplify the co-evolution of tRNAs and their modifying enzymes, providing new insights into how archaea may fine-tune translation in extreme environments. The broad scope of data and comparative analyses establishes a multispecies framework for future biochemical, mechanistic, and predictive modeling efforts. 

Abstract RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio. 

This study presents the first 3D two-way coupled fluid structure interaction (FSI) simulation of a hybrid anechoic wind tunnel (HAWT) test section with modeling all important effects, such as turbulence, Kevlar wall porosity and deflection, and reveals for the first time the complete 3D flow structure associated with a lifting model placed into a HAWT. The Kevlar deflections are captured using finite element analysis (FEA) with shell elements operated under a membrane condition. Three-dimensional RANS CFD simulations are used to resolve the flow field. Aerodynamic experimental results are available and are compared against the FSI results. Quantitatively, the pressure coefficients on the airfoil are in good agreement with experimental results. The lift coefficient was slightly underpredicted while the drag was overpredicted by the CFD simulations. The flow structure downstream of the airfoil showed good agreement with the experiments, particularly over the wind tunnel walls where the Kevlar windows interact with the flow field. A discrepancy between previous experimental observations and juncture flow-induced vortices at the ends of the airfoil is found to stem from the limited ability of turbulence models. The qualitative behavior of the flow, including airfoil pressures and cross-sectional flow structure is well captured in the CFD. From the structural side, the behavior of the Kevlar windows and the flow developing over them is closely related to the aerodynamic pressure field induced by the airfoil. The Kevlar displacement and the transpiration velocity across the material is dominated by flow blockage effects, generated aerodynamic lift, and the wake of the airfoil. The airfoil wake increases the Kevlar window displacement, which was previously not resolved by two-dimensional panel-method simulations. The static pressure distribution over the Kevlar windows is symmetrical about the tunnel mid-height, confirming a dominantly two-dimensional flow field. 

Abstract RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world’s largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.