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Antisense oligonucleotide (AON)-mediated exon skipping is a promising therapeutic approach for Duchenne muscular dystrophy (DMD) patients to restore dystrophin expression by reframing the disrupted op...

Amaranth, FD&C Red No. 2, E123, C.I. Food Red 9, Acid Red 27, Azorubin S, or C.I. 16185 is a modified red azo dye used as a food dye and to color cosmetics. Although it is not from the Amaranth…

Source: https://pubs.acs.org/accacs/article/doi/10.1021/acscatal.6c06722/5457813/Gallium-Containing-ZSM-5-Zeolites-Improve At a glance Adding gallium oxide to ZSM-5 can shift polyolefin hydrocracki...

A Surfline cam captures a huge shark breaching right behind a woman near Marina State Beach as California’s so-called Sharktober season kicks into gear.

A recent study in Biochar by Feng Wang and colleagues reveals that integrating manganese-modified biochar into solid-state fermentation systems substantially accelerates the artificial humification of agricultural lignocellulose waste

Sugar, Glucose Syrup, Acidity Regulators: Malic Acid, Citric Acid; Vegetable Oils (palm, Palm Kernel), Anti-caking Agents: Stearic Acid, Magnesium Stearate, Magnesium Carbonate; Modified Starch, Sodiu...

Conventional microscopic diagnosis of Trichomonas spp. in vaginal discharge specimens relies entirely on organism motility. Herein, we established a novel modified methyl green-acid fuchsin staining method to differentiate Trichomonas vaginalis from leukocytes and epithelial cell nuclei based on staining characteristics, rather than motility. To evaluate the performance of this novel method, 2133 vaginal discharge specimens were subjected to clinical testing using safranin staining microscopy,...

Proteolysis limits the therapeutic use of peptide antibiotics. Wang et al. develop C12RP7, a fatty-acid-modified Arg-Pro lipopeptide that resists proteases, kills antibiotic-resistant bacteria, shows low toxicity and resistance propensity, and provides oral efficacy through bacterial membrane disruption and host metabolic modulation.

Cell-surface glycoRNAs participate in diverse biological processes, but they were investigated as pooled populations and the protein interactome of individual glycoRNA species remain unresolved. Here we develop GlycoRNA-Map, a programmable photocatalytic proximity-labeling method that maps proteins surrounding sequence-defined endogenous glycoRNAs on living cells. A sialic-acid-binding aptamer and an RNA-hybridization probe jointly recruit a fluorophore-modified oligonucleotide through dual recognition of the glycan and RNA moieties of glycoRNAs. Light-activated biotinylation followed by quantitative mass spectrometry identified 200-418 enriched proteins for each of five glycoRNAs in A549 cells. Comparison of these proteomes revealed limited overlap among different glycoRNA sequences and across cell types, demonstrating that glycoRNA-associated protein environments depend on both RNA identity and cellular context. Transforming growth factor-{beta} receptors 1 and 2 (TGFBR1 and TGFBR2) were identified in the proximal proteomes of multiple glycoRNAs. Removal of cell-surface RNAs enhanced TGF-{beta} receptor signaling and promoted cell migration, demonstrating that glycoRNAs can functionally regulate extracellular signaling by interacting with their protein neighborhoods. GlycoRNA-Map thus provides an accessible strategy for resolving sequence-specific glycoRNA-protein interactome and discovering their roles in membrane signaling.

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.

AbstractPost-transcriptional RNA modifications are key regulators of fundamental cellular processes. Yet, their precise biological functions remain largely unresolved. A major challenge is their reliable detection. While sequencing-based approaches are limited to a small subset of RNA modifications, mass spectrometry has the potential to directly identify various modified nucleotides within their sequence context. However, existing tools for nucleic acid analysis offer severely constrained functionality. Here, we introduce a set of algorithmic innovations implemented in SpectrSeqTools, an open-source LC-MS/MS-based software platform that enables fully automated de novo RNA sequencing together with comprehensive modification profiling of short RNA fragments directly from raw data. We further validated prediction accuracy and robustness using experimental and simulated data. As such, SpectrSeqTools effectively broadens the scope of nucleic acid mass spectrometry, enabling the read-out of up to 144 RNA modifications within their sequence context.

Source: https://advanced.onlinelibrary.wiley.com/doi/10.1002/adfm.78520 At a glance An Adelaide University-led team placed isolated Ni–S₄ sites on CdS nanorods to photoreform poly(lactic acid), or ...

We identify ellagic acid (EA) as a compound that binds to YTHDF proteins and disrupts their interaction with N6-methyladenosine (m6A)-modified RNAs.