PhD Talk: Gene Assembly in Ciliates

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PhD TalkGene Assembly in Ciliates

• Robert Brijder
• Fundamental Computer Science

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Ciliates

• Ciliates form a large group of unicellular
  organisms.
• Ciliates have a property that is interesting from
  a computational point of view.

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Preliminaries

• All organisms (except ciliates) have one kind of
  nuclei.
• This nuclei consists of a number of chromosomes.
  A chromosome is a enormously long DNA molecule.
• A gene is a specific sequence in a DNA molecule.
  A gene is a building plan for a protein.

Gene 2
Gene 1
Gene 3
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Micronucleus

• Ciliates have two kinds of nuclei the
  micronucleus and the macronucleus.
• The micronucleus consist of chromosomes.
• The genes are silent in the micronucleus the
  gene is divided into parts, which are dispersed
  along one or more chromosomes.
• Gene parts for the actin protein of Sterkiella
  nova

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Macronucleus

• The macronucleus consist of a large number of
  short DNA molecules. Each DNA molecule contains a
  single gene in the appropriate order.

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Gene

• During cell mating, a daughter micronucleus is
  formed. A copy is transformed into the
  macronucleus. This is called gene assembly.

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Example of Sterkiella nova

• Micronucleus

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Gene Assembly
Macronucleus
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Gene
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Nuclear DualismandGene Assembly
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Gene Assembly

• The gene assembly process is done using molecular
  operations.
• How do these operations know how these parts need
  to be glued together? Answer pointers.

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Actually
Double linked list!
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Gene Assembly

• The gene assembly process is accomplished using
  three molecular operations
• Loop recombination
• Hairpin recombination
• Double-loop recombination

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Gene Assembly

• Loop recombination

• Hairpin recombination

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Gene Assembly

• Double-loop recombination

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Modeling Gene Assembly

• Allows us to gain more insight and to prove
  facts.
• State results in terms of the model. Translation
  back to real world is possible.
• Different models used MDS-PRS, S-PRS, G-PRS.
• All models are equivalent, and are assumed to be
  a correct model of the reality.
• Model the layout of the gene parts.
• Model the molecular operations.

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Modeling Gene Assembly
SPRS
legal string

• Loop recombination

Hairpin recombination
Double-loop recombination
where
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Modeling Gene Assembly
Legal string
or

• corresponds to a successful assembled gene.
  
• Non-deterministic process.
• No deadlocks.
• Finite process. Pointers are removed in every
  step.

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What can we prove?

• Given a legal string, is it possible to reduce
  this string without using snr operations (loop
  recombination)? Already proved.
• Given a legal string, how many parallel steps are
  needed to reduce this string? Open question!
• ..

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Questions?