RNA and protein synthesis mechanisms

This paper develops new RNA folding nearest neighbor parameters for sequences containing 1-methyl-pseudouridine, showing it stabilizes RNA folding and improves tRNA ensemble modeling.

This study investigates how E. coli recovers from growth arrest by analyzing the role of RimM in ribosome maturation and recovery mechanisms.

The paper shows that non-optimal codons are preferentially used in sex-biased genes of Drosophila melanogaster and are linked to protein disorder.

The paper investigates the regulation of tRNA intron levels across different organisms and environmental conditions, revealing family-specific turnover mechanisms and stress responses.

The paper investigates the cellular response to puromycin-induced translation stress and identifies ribosome dimerization mediated by rRNA expansion segments as a conserved stress response mechanism.

The paper describes a cell-free assay using wheat germ extract and firefly luciferase to assess IRES-mediated translation and evaluate mRNA modifications.

The paper shows that eIF4G cleavage products can either rescue or repress translation, revealing the closed-loop mRNP's role in translational silencing rather than initiation.

SIRIUS generates maximally divergent DNA sequences for a given protein, reducing shared subsequences compared to existing methods.

RNApdbee 3.0 provides a unified web server for RNA secondary structure annotation using 3D coordinates, integrating 2D and 3D data and standardizing inputs to PDBx/mmCIF.

The paper develops a theoretical model to study how ionic interactions influence subunit rotation in the yeast ribosome, showing that ion concentration changes significantly affect the energy landscape and kinetics of rotation.

The paper introduces a fast k-mer based algorithm to identify new genetic code variations in bacteria and archaea from assembled genomes.

The paper shows that synonymous coding affects domain swapping in myoglobin during co-translational folding in E. coli.

The paper reanalyzes data showing codon-dependent differences in backbone conformation in E. coli, using corrected statistical methods and finding consistent small p-values.

The paper investigates human mitochondrial translation initiation on leaderless mRNAs, revealing two pathways involving mtIF2 and fMet-tRNAMet, with implications for regulation by mtIF3.

This study determines the structure of the hibernating F. tularensis ribosome and shows RaiA and antibiotics bound to it, offering insights for therapeutic intervention.

The paper shows translation fidelity varies across cell types and developmental stages, with brain and muscle having the highest accuracy, and demonstrates its role in neuronal differentiation.

This study identifies Rei1 and Reh1 as facilitators of eL24 loading onto pre-60S ribosomal subunits in yeast.

HalluCodon designs species-specific coding sequences using multimodal language models trained on plant omics data, generating codons that match host-specific usage and support high expression.

mRNA-GPT is a generative model that optimizes full-length mRNA sequences by jointly optimizing all three regions, achieving Pareto-optimal designs and outperforming existing methods.

This study shows tRNA synthetase activity is required for ribosome runoff during stress to drive RNP granule assembly, but not for stress granule or P-body formation.

This study identifies snR37 as a bifunctional H/ACA snoRNP that both pseudouridylates rRNA and scaffolds ribosome assembly during pre-60S intermediate formation.

This study introduces NanoRibolyzer, a long-read nanopore sequencing method to map pre-rRNA processing and modification at single-nucleotide resolution, revealing cleavage sites and modification patterns.

The paper introduces an analysis pipeline using mdsa-tools to study ribosomal CAR-site dynamics through molecular dynamics simulations and unsupervised learning.

The paper uses single-molecule techniques to study tRNA structural dynamics before and during interaction with the pseudouridine synthase Pus4, revealing conformational changes and remodeling effects.

This study shows 5-AzaC incorporation into mRNAs disrupts translation, causes ribosome collisions, and activates stress responses, contributing to its cytotoxicity beyond DNA hypomethylation.

ARNy Plotter provides a web-based platform for analyzing and visualizing RNA structural ensembles, offering tools for dynamic analysis and result sharing.

The paper develops a transformer model to predict codon sequences from amino acids, improving rare codon prediction and linking sequence variation to protein function.

This paper demonstrates the application of plant RNA ThermoSwitches in Agrobacterium-mediated transient expression systems for temperature-controlled protein synthesis.

The paper uses direct RNA sequencing to analyze rRNA modifications in E. coli ribosome assembly intermediates and mature subunits, showing stress-dependent reprogramming of specific modifications.