1. 1 Using JigCell and other BioSPICE Tools to Understand the Regulation of Cell Growth and Division John J. Tyson Virginia Polytechnic Institute and State University

2. 2 The Virginia Tech Team: Kathy Chen & Jill Sible (Biology) Cliff Shaffer & Layne Watson (CS) Collaborators: Fred Cross (Rockefeller Univ) Bela Novak (Tech Univ Budapest)

3. 3 Outline The biological problem BioSPICE tools, especially JigCell Future needs

4. 4 The fundamental goal of molecular cell biology

5. 5 Hanahan & Weinberg (2000)

6. 6 Kurt Kohn (1999) mitosis (M phase) DNA replication (S phase) cell division G1 G2

7. 7 Getting in Touch with Your Inner Yeast Kurt Kohn (1999)

8. 8 Fission Yeast

9. 9 wild type cdc25 - wee1 - Mutant Phenotypes 14  m Short G1 Long G2 Size control at G2/M 7  m Long G1 Short G2 Size control at G1/S Very long cells Stuck in G2 Never divide Lethal

10. 10

11. 11 The Modeling Cycle Data Notebook Wiring Diagram Differential Equations Parameter Values Simulation Analysis Comparison Data Notebook ExperimentalDatabases Literature

12. 12 The Modeling Cycle Data Notebook Wiring Diagram Differential Equations Parameter Values Simulation Analysis Comparison Data Notebook ExperimentalDatabases Literature MONODWarehouse

13. 13 The Modeling Cycle Data Notebook Wiring Diagram Differential Equations Parameter Values Simulation Analysis Comparison Data Notebook ExperimentalDatabases Literature JDesigner PathwayBuilder

14. 14 The Modeling Cycle Data Notebook Wiring Diagram Differential Equations Parameter Values Simulation Analysis Comparison Data Notebook ExperimentalDatabases Literature JarnacModelBuilder

15. 15 The Modeling Cycle Data Notebook Wiring Diagram Differential Equations Parameter Values Simulation Analysis Comparison Data Notebook ExperimentalDatabases Literature RunManager

16. 16 The Modeling Cycle Data Notebook Wiring Diagram Differential Equations Parameter Values Simulation Analysis Comparison Data Notebook ExperimentalDatabases Literature LSODA XPP BioNetS Oscill8

17. 17 The Modeling Cycle Data Notebook Wiring Diagram Differential Equations Parameter Values Simulation Analysis Comparison Data Notebook ExperimentalDatabases Literature BioSenS Comparator

18. 18 The Modeling Cycle Data Notebook Wiring Diagram Differential Equations Parameter Values Simulation Analysis Comparison Data Notebook ExperimentalDatabases Literature CRNT AUTO Virtual Cell Gepasi WinPP

19. 19 JigCell Nick AllenMark Vass Jason ZwolakTom Panning Ranjit RandhawaBob Ball

20. 20 Project Manager JigCell tools

21. 21 Model Builder

22. 22 Run Manager mutant

23. 23Comparator Viability = true G1 duration = 35.2 min Mass at division = 1 Viability = false Arrest state = G1 # cycles before arrest = 0

24. 24

25. 25

26. 26 Wild-type Cell birth bud S M A division

27. 27 GAL-CLN2 cdh1  bud?S M A division

28. 28 Model Builder Run Manager Comparator Parameter Values Parameter Optimizer Optimum Parameter Values

29. 29 Local Gradient Search (Levenberg-Marquardt)

30. 30 Global DIRECT Search (DIViding RECTangles)

31. 31 Global DIRECT Search (DIViding RECTangles)

32. 32

33. 33

34. 34 Outline The biological problem BioSPICE tools, especially JigCell Future needs –Bifurcation analysis –Spatial modeling

35. 35 Fission Yeast G1 M S/G2 M M

36. 36 Fission yeast – wild type cell mass Active MPF stable steady state (G1) stable steady state (S-G2) unstable steady state (M) stable oscillation max min

37. 37 0 1 2 3 4 5 mass/nucleus P Cdk1 CycB Cdk1 CycB CKI Cdh1 Cdc20 Wee1 Cdc25 Time (min) SG2MG1S G2MG1S abscissa ordinate

38. 38 Fission yeast – wild type cell mass Active MPF stable steady state (G1) stable steady state (S-G2) unstable steady state (M) stable oscillation max min SNIC

39. 39 Genetic control of cell size at cell division in yeast Paul Nurse Department of Zoology, West Mains Road, Edinburgh EH9 3JT, UK Nature, Vol, 256, No. 5518, pp. 547-551, August 14, 1975 wild-type wee1 

40. 40 0.00.51.01.52.0 1e-5 1e-4 1e-3 1e-2 1e-1 Fission yeast wee1  wild type cell mass Active MPF SNIC

41. 41 cell mass (a.u.) wee1 gene expression wild-type wee1  heterozygote diploid wee1 OP Locus of SNICs GENETICS! PHYSIOLOGY! Two-parameter Bifurcation Diagram

42. 42 Wild type cdc13  cdc13 +/  2 param bifn diag for Cdc13 mitotic cycles endoreplication cell mass (a.u.) Cyclin gene expression ?? Oscill8: Emery Conrad

43. 43 Growth Patterns in Fission Yeast OE NE NE OE NETO actin “patches” “orb” mutants “tea” mutants

44. 44 - - - + + + - - - + + + Reaction + Diffusion + Convection Tubulin (  dimer) Microtubule Motor (Tea2) Landmark (Tea1, Arp2/3) G actin (globular) F actin (filamentous) Growth material Turing pattern Bias Cdc2 CycB

45. 45 time space OE NE NETO

46. 46 orb bipolar NETO monopolar cell length (μm) A. with microtubules

47. 47 T-shaped orb curled monopolar tripolar bipolar cell length (μm) orb bipolar NETO monopolar cell length (μm) A. with microtubulesB. without microtubules CFDRC: Andrzej Przekwas

48. 48 The End