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Rewiring the keyboard: evolvability of the genetic code
The genetic code evolved in two distinct phases. First, the 'canonical' code emerged before the last universal ancestor; subsequently, this code diverged in numerous nuclear and organelle lineages.Expand
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Early fixation of an optimal genetic code.
The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. One hypothesis is that the arrangement of amino acid/codon assignments results fromExpand
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The molecular basis of nuclear genetic code change in ciliates
BACKGROUND The nuclear genetic code has changed in several lineages of ciliates. These changes, UAR to glutamine and UGA to cysteine, imply that eukaryotic release factor 1 (eRF1), the protein thatExpand
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A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
BackgroundCorrelations between genome composition (in terms of GC content) and usage of particular codons and amino acids have been widely reported, but poorly explained. We show here that a simpleExpand
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Molecular computation: RNA solutions to chess problems
We have expanded the field of "DNA computers" to RNA and present a general approach for the solution of satisfiability problems. Expand
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RNA-mediated epigenetic programming of a genome-rearrangement pathway
Genome-wide DNA rearrangements occur in many eukaryotes but are most exaggerated in ciliates, making them ideal model systems for epigenetic phenomena. During development of the somatic macronucleus,Expand
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The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development
Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathwayExpand
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The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes
With more chromosomes than any other sequenced genome, the macronuclear genome of Oxytricha trifallax has a unique and complex architecture, including alternative fragmentation and predominantlyExpand
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Piwi-Interacting RNAs Protect DNA against Loss during Oxytricha Genome Rearrangement
Genome duality in ciliated protozoa offers a unique system to showcase their epigenome as a model of inheritance. In Oxytricha, the somatic genome is responsible for vegetative growth, whereas theExpand
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How Mitochondria Redefine the Code
Abstract. Annotated, complete DNA sequences are available for 213 mitochondrial genomes from 132 species. These provide an extensive sample of evolutionary adjustment of codon usage and meaningExpand
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