Download Project Outline

Affinity Based Model of Temporal
Regulation
Oisín Mac Aodha 4ECE
Project Specification
This project will investigate if it is possible to model
the heterchoronic process at a genetic using evolved
affinities.
A simple gene regulatory model will be created
whose genes encode temporal regulatory
information.
Evolution will determine
1.
2.
configuration of the genome
protein affinities/interaction
Affinity Based Model of Temporal Regulation
Genetic Algorithm
GAs are inspired from the principals of evolution and
natural selection.
Affinity Based Model of Temporal Regulation
Gene Regulatory Network
Our GRN is a biological model of development. It
contains proteins, genes and cells.
Affinity Based Model of Temporal Regulation
Ones Max
Used a GA to evolve the genes of and individual to all
go to one.
Affinity Based Model of Temporal Regulation
Temporal Regulation
Temporal regulation allows us to controls for protein
rate, duration and onset.
Affinity Based Model of Temporal Regulation
Temporal Regulation
Transcription places protein ‘4’ on onset queue.
Affinity Based Model of Temporal Regulation
Temporal Regulation
Protein ‘4’ is moved to the duration queue when onset
counts down to 0.
4
Affinity Based Model of Temporal Regulation
Temporal Regulation
Protein ‘4’ remains in cell while duration != 0. Can bind
with cis-sites on genes.
Affinity Based Model of Temporal Regulation
Affinity Matrix Concept
Onset and Rate will be
determined by the interaction
strength of the transcription
factors with the cis-sites
When a gene is active the
TF interaction strength on the
cis-sites will determine the onset
and duration values
Affinity Based Model of Temporal Regulation
Project Plan
•
•
•
•
Literature review
Create GA to evolve Affinity Matrix
Design and test single gene regulatory model
Expand simple model to allow for multicellular
development
• Integrate GA with developmental process
• Modify to include aspects of protein rate, duration and
onset
• Demonstrate temporal regulation at multicellular level
Affinity Based Model of Temporal Regulation
Questions
Affinity Based Model of Temporal Regulation