Lambda Switch

1
Lambda Switch

• A Quantitative Analysis
• Group C Simon Janssen
• Leroy de Leeuw
• Yuriy Savelyev
• Frenkel Smeijers

2
Overview

• Research Questions
• Biological Model
• SpiCO Model
• SPiM Model
• SpiCO vs. SPiM
• Conclusions

3
Research Questions

• What is a ? switch and can we reproduce the
  switch in SpiCO?
• How does SpiCO compare to SPiM?

4
Biological Model

• Two pathways of ? infected Escherichia coli
  bacterium lysogeny and lytic growth

5
Biological Model
6
SpiCO Model

• Numbers taken from experiments and literature
• Includes cooperation, negative feedback,
• self inhibition
• No external event ? no induction ?
• no lytic growth

7
SpiCO Model

• 'cro' object(
• with()
• profile('monomer'
• sum(
• send(channelscroDimerize sync 'dimer')
• receive(channelscroDimerize sync 0) ) )
• profile('dimer'
• new(crates()
• sum(
• sequence(
• send(channelsproDock bind(c))
• receive(c return(op))
• send(op specCro)
• 'bound'(op) )
• sequence(
• receive(channelscroDimerBreak sync)
• parallel(
• 'monomer'
• 'monomer' ) ) ) ) )

8
SpiCO Model

• Bindings of RNAP on PRM and PR

9
SPiM Model

• External event triggered

10
SpiCO vs. SPiM

• p-calculus
• Lots of numbers and text
• No documentation

• p-calculus
• Graphical output
• Documentation

11
Conclusions

• The lysogeny state is very stable and usually
  needs an external event to change to the lytic
  growth
• SpiCO is still under development ? no
  documentation, no nice output
• We are among the very first external users of
  SpiCO

12
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