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PhD Talk:
Gene Assembly in
Ciliates
Robert Brijder
Fundamental Computer Science
Ciliates
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Ciliates form a large group of unicellular organisms.
Ciliates have a property that is interesting from a
computational point of view.
Preliminaries
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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 1
Gene 2
Gene 3
Micronucleus
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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:
3
4
6
5
7
9
2
1
8
Macronucleus
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The macronucleus consist of a large number of
short DNA molecules. Each DNA molecule
contains a single gene in the appropriate order.
1
2
3
4
5
6
7 8
9
Gene
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During cell mating, a daughter micronucleus is
formed. A copy is transformed into the
macronucleus. This is called gene assembly.
Example of Sterkiella nova
Micronucleus
3
4
6
5
7
9
2
Gene Assembly
Macronucleus
1
2
3
4
5
Gene
6
7 8
9
1
8
Nuclear Dualism
and
Gene Assembly
Gene Assembly
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The gene assembly process is done using
molecular operations.
How do these operations know how these
parts need to be glued together? Answer:
pointers.
3
1
2
4
Actually
Double linked list!
3
4
b
2
3
2
4
e
Gene Assembly
The gene assembly process is accomplished
using three molecular operations:
• Loop recombination
• Hairpin recombination
• Double-loop recombination
Gene Assembly
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Loop recombination
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Hairpin recombination
Gene Assembly
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Double-loop recombination
Modeling Gene Assembly
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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, GPRS.
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.
Modeling Gene Assembly
3
4
b
2
3
2
SPRS
legal string
Loop recombination:
Hairpin recombination:
Double-loop recombination:
where
4
e
Modeling Gene Assembly
Legal string
or
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corresponds to a successful assembled gene.
• Non-deterministic process.
b
• No deadlocks.
• Finite process. Pointers are removed in every step.
e
What can we prove?
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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!
..
Questions?