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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Leaky Scanning

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 stands for...
Viral Mutations00:36

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive...
Genetic Variation01:25

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
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Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
11:10

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

Differential trends in the codon usage patterns in HIV-1 genes.

Aridaman Pandit1, Somdatta Sinha

  • 1Mathematical Modeling and Computational Biology Group, Centre for Cellular & Molecular Biology (CSIR), Hyderabad, Andhra Pradesh, India.

Plos One
|January 5, 2012
PubMed
Summary

Human Immunodeficiency Virus (HIV) evolution shows gene-specific codon bias, driven by translational selection. This adaptation to host-preferred codons influences HIV-1

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Area of Science:

  • Evolutionary biology
  • Virology
  • Genomics

Background:

  • Host-pathogen interactions drive continuous genetic adaptation in pathogens and hosts.
  • Codon bias, influenced by mutation, selection, and drift, is crucial in host-pathogen evolution.
  • Human Immunodeficiency Virus (HIV) evolution involves complex intra-host positive selection and inter-host neutral processes.

Purpose of the Study:

  • To investigate evolutionary signatures in HIV-1 genomes.
  • To analyze codon usage patterns and their temporal dynamics in HIV-1.
  • To understand the role of translational selection in HIV-1 evolution.

Main Methods:

  • Analysis of HIV-1 genomes from diverse subtypes and clades over 23 years.
  • Examination of codon usage patterns across different HIV-1 genes.
  • Investigation of temporal correlations in codon bias.

Main Results:

  • Unique temporal correlations were observed in the codon bias of three HIV-1 genes.
  • Evidence of differential adaptation of HIV-1 genes towards host-preferred codons.
  • Gene-specific codon usage patterns indicate adaptation to host molecular resources.

Conclusions:

  • Translational selection is a significant force shaping HIV-1 evolution at the population level.
  • Codon usage patterns provide insights into the adaptive evolution of HIV-1.
  • Understanding gene-specific adaptation is key to deciphering pathogen evolution and disease dynamics.