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Related Concept Videos

Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Complementation Tests00:49

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A complementation test is a simple cross to identify whether the two mutations are located on the same gene or different genes. It was first performed by Edward Lewis in the 1940s while working on fruit flies. He developed the test to identify the location and arrangement of different mutations on chromosomes.
Organisms heterozygous for different mutations are crossed pairwise in all combinations. If present on different genes, the mutations can complement each other by providing the missing...
Real Time RT-PCR02:57

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...

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Error threshold in RNA quasispecies models with complementation.

Josep Sardanyés1, Santiago F Elena

  • 1Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Ingeniero Fausto Elio s/n, 46022 València, Spain. josep.sardanes@upf.edu

Journal of Theoretical Biology
|May 25, 2010
PubMed
Summary

Complementation between viral genomes and their replicases, including defective interfering particles (DIPs), can alter the error threshold. This phenomenon affects viral dynamics and the conditions for error catastrophe, impacting master sequence survival.

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Area of Science:

  • Virology
  • Theoretical Biology
  • Population Genetics

Background:

  • Quasispecies models traditionally assume genotype fitness is sequence-dependent.
  • Biological reality suggests fitness is linked to encoded proteins, like replicases.
  • In viral populations, genomes and their encoded proteins can interact non-exclusively (complementation).

Purpose of the Study:

  • To investigate how complementation affects the error threshold in viral quasispecies models.
  • To analyze the impact of both coded replicase variation and defective interfering particles (DIPs) on viral population dynamics.

Main Methods:

  • Development and analysis of simple quasispecies mean-field models.
  • Modeling scenarios with master/mutant genomes coding for different replicases.
  • Modeling defective interfering particles (DIPs) utilizing master replicase.

Main Results:

  • Complementation influences the error threshold, affecting the transition to error catastrophe.
  • Error-threshold transitions exhibit transcritical-like bifurcations, indicating continuous phase transitions.
  • Defective interfering particles (DIPs) reduce the parameter space for master sequence survival.

Conclusions:

  • Complementation is a crucial factor in viral dynamics, modifying error threshold predictions.
  • The presence of DIPs significantly impacts viral population stability and survival.
  • Models incorporating complementation provide a more biologically realistic view of viral evolution.