60 research outputs found

    MicroRNAs from the same precursor have different targeting properties

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    UnlabelledBackgroundThe processing of a microRNA results in an intermediate duplex of two potential mature products that derive from the two arms (5' and 3') of the precursor hairpin. It is often suggested that one of the sequences is degraded and the other is incorporated into the RNA-induced silencing complex. However, both precursor arms may give rise to functional levels of mature microRNA and the dominant product may change from species to species, from tissue to tissue, or between developmental stages. Therefore, both arms of the precursor have the potential to produce functional mature microRNAs.ResultsWe have investigated the relationship between predicted mRNA targets of mature sequences derived from the 5' and 3' arms of the same pre-microRNAs. Using six state-of-the-art target prediction algorithms, we find that 5'/3' microRNA pairs target different sites in 3' untranslated regions of mRNAs. We also find that these pairs do not generally target overlapping sets of genes, or functionally related genes.ConclusionsWe show that alternative mature products produced from the same precursor microRNAs have different targeting properties and therefore different biological functions. These data strongly suggest that developmental or evolutionary changes in arm choice will have significant functional consequences

    In-Situ atomic level studies of Gd atom release and migration on graphene from a metallofullerene precursor

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    We show how Gd based metallofullerene (Gd3N@C80) molecules can be used to create single adatoms and nanoclusters on a graphene surface. An in-situ heating holder within an aberration corrected scanning transmission electron microscope is used to track the adhesion of endohedral metallofullerenes (MFs) to the surface of graphene, followed by Gd metal ejection and diffusion across the surface. Heating to 900oC is used to promote adatom migration and metal nanocluster formation, enabling direct imaging of the assembly of nanoclusters of Gd. We show that hydrogen can be used to reduce the temperature of MF fragmentation and metal ejection, enabling Gd nanocluster formation on graphene surfaces at temperatures as low as 300oC. The process of MF fragmentation and metal ejection is captured in-situ and reveals that after metal release, the C80 cage opens further and fuses with the surface monolayer carbon glass on graphene, creating a highly stable carbon layer for further Gd adatom adhesion. Small voids and defects (~1nm) in the surface carbon glass act as trapping sites for Gd atoms, leading to atomic self-assembly of 2D monolayer Gd clusters. These results show that MFs can adhere to graphene surfaces at temperatures well above their bulk sublimation point, indicating that the surface bound MFs have strong adhesion to dangling bonds on graphene surfaces. The ability to create dispersed single Gd adatoms, and Gd nanoclusters on graphene may have impact in spintronics and magnetism

    RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

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    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 2021: secondary structure integration, improved sequence search and new member databases.

    Get PDF
    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

    RNAcentral : a hub of information for non-coding RNA sequences

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    RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences, collating information on ncRNA sequences of all types from a broad range of organisms. We have recently added a new genome mapping pipeline that identifies genomic locations for ncRNA sequences in 296 species. We have also added several new types of functional annotations, such as tRNA secondary structures, Gene Ontology annotations, and miRNA-target interactions. A new quality control mechanism based on Rfam family assignments identifies potential contamination, incomplete sequences, and more. The RNAcentral database has become a vital component of many workflows in the RNA community, serving as both the primary source of sequence data for academic and commercial groups, as well as a source of stable accessions for the annotation of genomic and functional features. These examples are facilitated by an improved RNAcentral web interface, which features an updated genome browser, a new sequence feature viewer, and improved text search functionality. RNAcentral is freely available at https://rnacentral.org

    A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)

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    Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon
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