Other research by G.A-B.

Art Work

THE "FUNCTIONAL ANARCHY" OF GENOMES

CONTENTS.

MINDSET

INTRODUCTION
  • The "functional anarchy" of genomes.
  • The conversion of genome hazards into genome perturbations
  • The conversion of perturbations into creative forces
  • The result: An exquisitely functional and creative anarchy
    •
    SYMMETRIES AND UNIVERSAL GENOME PROPERTIES CREATED BY 'RECKLESS' MUTATIONS.

  • The universal intra-strand symmetry - the work of countless inversions and inverted transpositions.
  • Chargaff's rules
  • The conundrum
  • The quantitation of the validity of the rule
  • The evidence for the almost universal validity
  • Compliance with Chargaff's second parity rule as a function of sequence length.
  • Violations of Chargaff's second parity rule by many mitochondrial genomes
  • An explanation
  • The asymptotic equalization of strand properties through the actions of countless inversions and inverted transposions.
  • Visual illustration of the increasing equalization
  • Mathematical illustration of the increasing equalization
  • SIGNIFICANCE FOR 'FUNCTIONAL ANARCHY' OF GENOMES
  • Equalisation of physical properties of the strands
  • Continuation of the process in perpetuity
  • Invariance against the major other mechanisms of variation
  • Is there a selective advantage?
  • The universal triplet spectrum (majorityn distribution) - also the work of countless inversions and inverted transpositions.

  • The infinity of conceivable triplet distributions.
  • The actual number of triplet distributions: only 3(!)
  • The hypothetical evolution of the majority profile.
  • The quite understandable mechanism of profile conversion.
  • SIGNIFICANCE FOR 'FUNCTIONAL ANARCHY' OF GENOMES
  • General implications of the existence of the majority profile
  • Does the majority profile facilitate horizontal gene transfer?
  • Is the evolutionary appearance of new orders linked to local changes of triplet distributions of the common ancestor?
  • Genome signatures (local deviations from the majority distribution) - evolutionary markers for new orders?

  • Signatures: Local deviations from the majority profile
  • Profile signatures.
  • Conservation of profile signatures
  • Profile signatures as markers of chromosome rearrangements and synteny.
  • Total fraction of bursts (TFB)
  • Profile signatures as the result of local AT changes (universal sigmoid curve)
  • An explanation of the sigmoid curve based on the spectra and mechanisms of point mutations
  • SIGNIFICANCE FOR 'FUNCTIONAL ANARCHY' OF GENOMES
  • The creation of new bursts during the course of evolution.
  • Is the creation of new bursts linked to the appearance of new orders?
  • The spectrum of point mutations - consistent with auto-mutagenesis.

  • What is the meaning of 'random point mutations'?
  • The use of 'punctuated' repetitive sequences to determine the spectrum of point mutations.
  • How many kinds of point mutations are there?
  • The spectra of vertebrate point mutations.
  • The auto-mutagenic mechanisms that may explain the spectra.
  • SIGNIFICANCE FOR 'FUNCTIONAL ANARCHY' OF GENOMES
  • Do the spectra have genome-wide validity?
  • Point mutations - yet another case of self-inflicted 'anarchy'?
  • The Evolution of Alu-mutations - a clever defense.

  • The deadly threat of Alu-elements and other retro-transposons.
  • The genome pixel image (GPxI) of Alu-elements and their mutations.
  • The universal frequency distribution of Alu-mutants.
  • The decision, which of 2 Alu-elements is more similar to the 'original' based on their mutant distribution.
  • A mathematical model of the dynamics of Alu mutations
  • The calibration of the evolutionary age of Alu-elements.
  • SIGNIFICANCE FOR 'FUNCTIONAL ANARCHY' OF GENOMES
    • APPENDIX

  • The Genome Pixel Image (GPxI)- A different way of looking at genomes.
  • Bibliography
  • Respond by e-mail.
  • Acknowledgement
  • About the author

    • opened :        7/7/2009
    last updated:  4/16/2012