1 / 12

Comparison of λ Switch Models: SpiCO vs SPiM in λ-Infected E. coli Dynamics

This study explores the λ switch in Escherichia coli, comparing two models: SpiCO and SPiM. We investigate the biological implications of lysogeny versus lytic growth pathways in λ-infected bacteria. The SpiCO model incorporates experimental data and biological interactions, while the SPiM model utilizes π-calculus for external event-triggered dynamics. Key research questions include the reproducibility of the λ switch in SpiCO and its comparative performance against SPiM. Our conclusions highlight the stability of the lysogeny state and the ongoing development of the SpiCO model.

angelica-figueroa
Télécharger la présentation

Comparison of λ Switch Models: SpiCO vs SPiM in λ-Infected E. coli Dynamics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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 λ switch and can we reproduce the switch in SpiCO? • How does SpiCO compare to SPiM?

  4. Biological Model • Two pathways of λinfected 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(channels#croDimerize sync 'dimer') receive(channels#croDimerize sync 0) ) ) profile('dimer' new(c:rates() sum( sequence( send(channels#proDock bind(c)) receive(c return(op)) send(op specCro) 'bound'(op) ) sequence( receive(channels#croDimerBreak sync) parallel( 'monomer' 'monomer' ) ) ) ) ) profile('bound'(op) send(op unbind 'dimer‘ ) ) ) ) )

  8. SpiCO Model Bindings of RNAP on PRM and PR

  9. SPiM Model • External event triggered

  10. π-calculus Lots of numbers and text No documentation π-calculus Graphical output Documentation SpiCO vs. SPiM

  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

More Related