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Related Concept Videos

Viruses with RNA Genomes01:29

Viruses with RNA Genomes

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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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Experimental RNAi02:15

Experimental RNAi

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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

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Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the...
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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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High-throughput Screening for Broad-spectrum Chemical Inhibitors of RNA Viruses
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Using artificial intelligence to document the hidden RNA virosphere.

Xin Hou1, Yong He2, Pan Fang2

  • 1National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.

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Summary
This summary is machine-generated.

A new deep learning tool, LucaProt, identifies highly divergent RNA viruses by analyzing RNA-dependent RNA polymerase sequences. This discovery expands our understanding of the global virosphere and virus diversity across ecosystems.

Keywords:
RNA virusartificial intelligencedeep learningevolutionmetatranscriptomicsprotein language modelviromevirus discovery

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Area of Science:

  • Virology
  • Bioinformatics
  • Genomics

Background:

  • Metagenomic tools often fail to detect highly divergent RNA viruses.
  • RNA-dependent RNA polymerase (RdRP) is a key enzyme for RNA virus replication.

Purpose of the Study:

  • To develop a novel computational tool for discovering highly divergent RNA virus sequences.
  • To characterize the diversity and distribution of novel RNA viruses in various global ecosystems.

Main Methods:

  • Development of LucaProt, a deep learning algorithm integrating sequence and structural information.
  • Analysis of 10,487 metatranscriptomes from diverse global environments.
  • Validation of novel viral sequences using RT-PCR and RNA/DNA sequencing.

Main Results:

  • Identification of 161,979 potential RNA virus species and 180 RNA virus supergroups.
  • Discovery of exceptionally long RNA virus genomes (up to 47,250 nucleotides) and complex genomic structures.
  • Detection of novel RNA viruses in diverse environments like air, hot springs, and hydrothermal vents.

Conclusions:

  • LucaProt significantly enhances the discovery of divergent RNA viruses.
  • The study reveals the vast scale of the global RNA virosphere and its ecological distribution.
  • Computational tools are crucial for comprehensive documentation of the global RNA virome.