Engineered the plant-colonizing yeast Yarrowia lipolytica to produce and deliver double-stranded RNAs targeting key genes of the gray mold fungus Botrytis cinerea produced a ‘living factory’ that con...

AbstractRibonucleic acid (RNA) modifications, with over 170 identified types, play diverse roles in cellular processes. The past decade has witnessed a surging demand for accurate identification and localization of RNA modifications in both endogenous and synthetic therapeutic RNAs. With accurate spectral annotation for RNA, tandem mass spectrometry (MS/MS) can meet this demand. Here, we present RNabel, a user-friendly software tool for in-depth annotation of MS/MS spectra of RNA oligonucleotides. RNabel considers a full set of backbone-cleavage ions (a, b, c, d, a-B, w, x, y, z) in which the ribonucleotide unit could be A, U, C, G, Y (pseudouridine), or I (Inosine). Additionally, RNabel considers 196 modifications on the base, the phosphoribose linkage, the 5′ or the 3′ terminus, or the detachment of a subnucleotide fragment as a neutral or charged group. Users can create new components if needed, including ribonucleotides, modifications, and neutral or charged groups that could detach from a ribonucleotide. RNabel efficiently processes large data sets in four acceptable formats including .mgf, .raw, .txt from msConvert, and RNabel batch files. Multiple statistical metrics are provided for quality assessment of spectral annotation. To accelerate RNA modification analysis, RNabel is made freely available for Mac and Windows users at https://github.com/songge1111/RNabel/releases.

A new understanding of transfer RNA biology means researchers can assign up to 34 codons to amino acids of their choosing

Abstract. Endogenous RNAs orchestrate cellular processes through precise spatiotemporal regulation, and live-cell imaging of these molecules is essential f

The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...

Abstract. Current breast cancer biomarkers rely predominantly on protein-coding transcriptomes, leaving the regulatory information encoded by enhancer RNAs

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Anthropic announced that its Claude AI model conducted a large-scale genome search, discovering an unknown enzyme system in bacteriophages. The identified system is flanked by CRISPR-like repetitive DNA sequences, and it was confirmed that short RNAs are produced from them. The search involved numerous agent sessions using Claude, successfully analyzing vast amounts of sequence data in a short time. However, repeating the same search ten times failed to rediscover similar sequences, highlighting the challenge of ensuring reproducibility in AI agent-driven exploration. While experts praise this as an exciting example of AI contributing to biological discoveries, the exact functions and utility remain unclear. Future efforts will focus on clarifying the biological functions of this unknown enzyme system through experiments, including its potential to lead to new gene editing mechanisms.

Positive-sense RNA viruses using subgenomic RNAs (sgRNAs) cause severe crop losses, yet this conserved feature has rarely been exploited for antiviral engineering. Here, we constructed a virus-activat...

Background: Uveitis is a complex disease involving inflammation of the iris, ciliary body, and choroid. The Standardization of Uveitis Nomenclature working group has developed classification criteria for 25 of the most common uveitis entities based on a number of descriptor terms. Due to the broad range of causes of uveitis and the different treatment modalities depending on etiology, investigative aids are vital in expediting accurate diagnosis and management. MicroRNAs, small noncoding RNAs, have exciting potential as biomarkers of disease. They function to alter gene expression at the posttranscriptional level. Other biomarkers of inflammatory disease include cytokines and chemokines. With a substantial proportion of uveitis being classified as “idiopathic,” biomarker #Research may provide important diagnostic clues and subsequently improve patient outcomes globally. Scoping reviews represent a format for systematically searching the literature. We will use a formal framework for conducting scoping reviews and the Joanna Briggs Institute guidelines. Objective: The aim of this review #Protocol is to lay the foundation for identifying what biomarkers have been studied in various uveitis subtypes, including cytokines, chemokines, and multiomic data, with particular focus on microRNAs, thus guiding the selection of biomarkers that may be of interest in future #Research. Methods: Studies will be included if they have human participants with a defined diagnosis of a uveitis subtype who are of any age, gender, or ethnicity and from any country or health care setting; assess molecular biomarkers (including but not limited to microRNAs, cytokines, chemokines, human leucocyte antigen types, gene variants, and multiomics) using any sample type (including but not limited to blood, peripheral blood mononuclear cells, aqueous humor, vitreous humor, cerebrospinal fluid, and urine), are primary #Research studies, are written in English or with an English translation, and were published in any year. Studies will be excluded if they have animal participants, investigate therapeutics in uveitis only, are review articles or letters to the editor, are #Research in progress, or are not in English. The MEDLINE, Embase, and Scopus databases will be searched from inception to June 8, 2026. Results will be descriptively analyzed and presented in the form of a data extraction chart. Results: The proposed scoping review is currently in the screening stage. The start date for this project was January 6, 2026. The projected completion date is in October 2026. A total of 946 articles were subject to title and abstract screening using Covidence software. One reviewer screened all papers, while a second reviewer screened 20% of the papers. Conclusions: The findings from this scoping review will highlight the broad range of molecular biomarkers currently studied in uveitis and identify gaps in the field, guiding the selection of biomarkers, with a particular focus on microRNAs, for future laboratory analysis in our #Research group. Trial Registration: OSF Registries N5HJR; https://osf.io/n5hjr/overview

The capless self-amplifying mRNA (CLsamRNA) platform recently reported by Kim et al.1 in this issue of Molecular Therapy represents the latest advance in the remarkable development of protein-coding RNAs as active pharmaceutical ingredients (APIs) for vaccines and therapeutics. The rationale for using RNA as an API has long been recognized, with evidence that in-vitro-transcribed RNA can direct protein translation reported as early as 19892 and 1990.3 Initially, clinical translation of this technology was hampered by inefficient delivery of RNA, its instability, and the tendency for exogenous RNA to provoke unwanted inflammatory responses.