2IF35: Formal Modelling in Cell Biology Lambda switch in GINsim Fall 2007 Mohammed El-Kebir Koen Schuurmans Monique Hendriks Tim Muller

Outline Genetic toggle switch GINsim Bacteriophage Lambda phage GINsim model Comparison Conclusion Monique t/m GINsim, Mohammed vanaf Bacteriophage

Genetic toggle switch Two genes: b and c Promoters pb and pc Resulting proteins: B and C Transcription factors: A, B, C A promotes expression of gene b and c B inhibits expression of gene c C inhibits expression of gene b A, B en C heten transcriptiefactoren Als A op ene promoter, dan blockt B de andere Als A op andere promoter, dan blockt C de ene Blijft na keuze vastzitten in 1 toestand, stabiel, alleen door invloed van buitenaf weer switchen

GINsim GINsim is made for modeling genetic regulatory networks Building blocks are genes, genes have Basal expression level Maximal expression level Genes can be connected with each other, for Activation Inhibition Abstractie naar genetisch niveau, dus alleen interactie tussen genen (die expressieniveau beinvloeden) Basal = zonder binding van transcriptiefactoren

GINsim (ctn.) Genetic switch model: State space generation (a = 1, b = 0, c = 0): GINsim gebaseerd op petrinet-aanpak Transcriptie van a leidt tot A (transcriptiefactor). Qualtitatief

GINsim (ctn.) Internally GINsim is based on petri-nets. It is possible to export the regulatory network as a petrinet (PNML) Unfortunately, exported PNMLs are incorrect Every gene corresponds with a place #Tokens in a place denote the expression level Transitions are the various modi of the gene (inhibited, activated, basal, etc.) Gene products: eiwitten

Bacteriophage Virus that only infects bacteria A phage consists of: Etymology: eater of bacteria A phage consists of: Head with DNA or RNA Tail for attachment to cell membrane and penetration

Bacteriophage (ctn.) A bacteriophage may have a Lytic cycle Virus keeps on reproducing, ultimately causing lysis of host cell Lysogenic cycle DNA of phage is merged with DNA of host. Peaceful coexistence with the host.

Lambda phage Lambda phage is a bacteriophage Infects the E. coli bacterium Has both a lytic and a lysogenic cycle The choice of the cycle depends on the environment: If the environment is not supporting the growth of more potential hosts, then there is no reason to reproduce If the environment is right for potential hosts, then reproduction will result in more infected cells. The choice is regulated by the lambda switch Extremely stable (transition to lytic growth once every 5000 years) But upon environmental change: lytic growth

Lambda phage (cnt.) Lysogenic cycle CII CI2 CII CI CI CIII CII binds to promoter Pre Gene cI is expressed CI binds to PI Gene cIII is expressed Stabilization CIII prevents destruction of CII Dimerized CI binds to Or1 and Or2 prevents expression of cro and enhances expression of cI CI Pijltjes zijn excitatory en vierkantjes zijn inhibitory. CIII

Lambda phage (cnt.) Lytic cycle CII Cro Cro Cro2 CII degraded by protease before reaching Pre In absence of CII Pr is weakly active Gene cro is expressed Stabilization Dimer Cro2 binds to Or2 and Or1 prevents expression of cI and enhances expression of cro Pijltjes zijn excitatory en vierkantjes zijn inhibitory.

Lambda phage (cnt.) Lambda switch [CII]  A As soon as cI or cro is expressed, the switched is locked (just like with the expression of b or c) CII Pijltjes zijn excitatory en vierkantjes zijn inhibitory.

Comparison Maude PRISM GINsim Qualitative Yes Quantitative No Model checking LTL TPCTL Path finding Limitations Purely qualitative State explosion for realistic models Only regulatory genetic networks