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Using JigCell and other Using JigCell and other BioSPICE Tools to BioSPICE Tools to
Understand the Regulation Understand the Regulation of Cell Growth and Divisionof Cell Growth and Division
John J. TysonVirginia Polytechnic Institute
and State University
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The Virginia Tech Team:The Virginia Tech Team:
Kathy Chen & Jill Sible (Biology)
Cliff Shaffer & Layne Watson (CS)
Collaborators:Collaborators:
Fred Cross (Rockefeller Univ)
Bela Novak (Tech Univ Budapest)
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OutlineOutline
• The biological problem
• BioSPICE tools, especially JigCell
• Future needs
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The fundamental goal of The fundamental goal of molecular cell biologymolecular cell biology
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5Hanahan & Weinberg (2000)
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6Kurt Kohn (1999)
mitosis(M phase)
DNA replication(S phase)
cell division
G1
G2
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Getting in Touch with Your Inner Yeast
Getting in Touch with Your Inner Yeast
Kurt Kohn (1999)
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wild type cdc25 -wee1 -
Mutant Phenotypes
14 mShort G1Long G2
Size controlat G2/M
7 mLong G1Short G2
Size controlat G1/S
Very long cellsStuck in G2Never divide
Lethal
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dCycBT
dt = k1 . M - (k2' + k2" . Cdh1 +k2'" . Cdc20A) . CycBT
dpMPFdt = kwee
. (CycBT - pMPF) - k25 . pMPF - (k2' + k2" . Cdh1 + k2'" . Cdc20A) . pMPF
dIEdt = k9
. MPF . 1- IE
J9 +1- IE - k10 .
IE J10 + IE
dSlp1dt = k7
. IE . 1 - Slp1
J7 + 1 - Slp1 - k8 .
Slp1 J8 + Slp1 - k6
. Slp1
dSte9dt = k3'
. 1 - Ste9
J3 + 1 - Ste9 - (k4' . SK + k4
. MPF) . Ste9
J4 + Ste9dRum1T
dt = k11 - (k12 + k12' . SK + k12" . MPF) . Rum1T
dSKdt = k13' + k13" . M - k14
. SK
dMdt = . M
[Trimer] = 2 [CycBT] [CKIT]
[CycBT] + [CKIT] + Keq-1 + ([CycBT] + [CKIT] + Keq
-1) 2 - 4 [CycBT] [CKIT]
kwee = kwee' + (kwee" - kwee') . GK(Vawee, Viwee' + Viwee" . MPF, Jawee, Jiwee)
k25 = k25' + (k25" - k25') . GK(Va25' + Va25" . MPF, Vi25, Ja25, Ji25)
MPF = (CycBT - pMPF) . (CycBT - Trimer)
CycBT
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The Modeling CycleThe Modeling Cycle
Data NotebookData Notebook
Wiring DiagramWiring Diagram
Differential EquationsDifferential Equations Parameter ValuesParameter Values
SimulationSimulationAnalysisAnalysis
ComparisonComparison
Data NotebookData Notebook
ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature
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The Modeling CycleThe Modeling Cycle
Data NotebookData Notebook
Wiring DiagramWiring Diagram
Differential EquationsDifferential Equations Parameter ValuesParameter Values
SimulationSimulationAnalysisAnalysis
ComparisonComparison
Data NotebookData Notebook
ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature
MONOD Warehouse
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The Modeling CycleThe Modeling Cycle
Data NotebookData Notebook
Wiring DiagramWiring Diagram
Differential EquationsDifferential Equations Parameter ValuesParameter Values
SimulationSimulationAnalysisAnalysis
ComparisonComparison
Data NotebookData Notebook
ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature JDesigner PathwayBuilder
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The Modeling CycleThe Modeling Cycle
Data NotebookData Notebook
Wiring DiagramWiring Diagram
Differential EquationsDifferential Equations Parameter ValuesParameter Values
SimulationSimulationAnalysisAnalysis
ComparisonComparison
Data NotebookData Notebook
ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature
Jarnac ModelBuilder
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The Modeling CycleThe Modeling Cycle
Data NotebookData Notebook
Wiring DiagramWiring Diagram
Differential EquationsDifferential Equations Parameter ValuesParameter Values
SimulationSimulationAnalysisAnalysis
ComparisonComparison
Data NotebookData Notebook
ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature
RunManager
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The Modeling CycleThe Modeling Cycle
Data NotebookData Notebook
Wiring DiagramWiring Diagram
Differential EquationsDifferential Equations Parameter ValuesParameter Values
SimulationSimulationAnalysisAnalysis
ComparisonComparison
Data NotebookData Notebook
ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature
LSODAXPP
BioNetS
Oscill8
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The Modeling CycleThe Modeling Cycle
Data NotebookData Notebook
Wiring DiagramWiring Diagram
Differential EquationsDifferential Equations Parameter ValuesParameter Values
SimulationSimulationAnalysisAnalysis
ComparisonComparison
Data NotebookData Notebook
ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature
BioSenS Comparator
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The Modeling CycleThe Modeling Cycle
Data NotebookData Notebook
Wiring DiagramWiring Diagram
Differential EquationsDifferential Equations Parameter ValuesParameter Values
SimulationSimulationAnalysisAnalysis
ComparisonComparison
Data NotebookData Notebook
ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature
CRNTAUTO
Virtual Cell Gepasi
WinPP
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JigCell
Nick Allen Mark VassJason Zwolak Tom PanningRanjit Randhawa Bob Ball
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Project ManagerProject Manager
JigCelltools
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Model BuilderModel Builder
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Run ManagerRun Manager
mutant
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ComparatorComparator
Viability = trueG1 duration = 35.2 min
Mass at division = 1
Viability = falseArrest state = G1
# cycles before arrest = 0
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Wild-type CellWild-type Cell
birth
bud S M
A
division
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GAL-CLN2 cdh1GAL-CLN2 cdh1
bud?S M
A
division
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Model Builder
Run Manager
Comparator
Parameter Values
ParameterOptimizer
Optimum Parameter Values
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Local Gradient Search(Levenberg-Marquardt)
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Global DIRECT Search(DIViding RECTangles)
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Global DIRECT Search(DIViding RECTangles)
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OutlineOutline
• The biological problem
• BioSPICE tools, especially JigCell
• Future needs– Bifurcation analysis– Spatial modeling
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Fission Yeast
mass/ DNA
0.0 0.5 1.0 1.5
Cdc2
/Cdc1
3
10-5
10-4
10-3
10-2
10-1
100
G1
Mmass/ DNA
0 1 2
Cdc2
/Cdc1
3
10-3
10-2
10-1
100
S/G2
M
mass/ DNA
0.0 0.5 1.0 1.5 2.0
Cdc2
/Cdc1
3
0.1
1
M
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360 1 2 3 4
1e-5
1e-4
1e-3
1e-2
1e-1
1e+0
Fission yeast – wild type
cell mass
Act
ive
MP
F
stable steady state (G1)
stable steady state (S-G2)
unstable steady state (M)
stab
le o
scill
atio
n
max
min
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370 50 100 150 200 250 300
0
1
2
3
4
5
mass/nucleus
P Cdk1
CycB
Cdk1
CycB
CKI
Cdh1
Cdc20
Wee1
Cdc25
Time (min)
S G2 MG1 S G2 MG1 S
abscissa
ordinate
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380 1 2 3 4
1e-5
1e-4
1e-3
1e-2
1e-1
1e+0
Fission yeast – wild type
cell mass
Act
ive
MP
F
stable steady state (G1)
stable steady state (S-G2)
unstable steady state (M)
stab
le o
scill
atio
n
max
min
SNIC
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Genetic control of cell size at cell division in yeastPaul NurseDepartment of Zoology, West Mains Road, Edinburgh EH9 3JT, UK
Nature, Vol, 256, No. 5518, pp. 547-551, August 14, 1975
wild-type wee1
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400.0 0.5 1.0 1.5 2.0
1e-5
1e-4
1e-3
1e-2
1e-1
Fission yeast
wee1
0 1 2 3 41e-5
1e-4
1e-3
1e-2
1e-1
1e+0
wild type
cell mass
Act
ive
MP
FA
ctiv
e M
PF
SNIC
SNIC
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0 1 2 3 4 5 60.0
0.2
0.4
0.6
0.8
1.0
cell mass (a.u.)
wee
1 ge
ne e
xpre
ssio
n
wild-type
wee1
heterozygote diploid
wee1OP
Locus ofSNICs
GE
NE
TIC
S!
GE
NE
TIC
S!
PHYSIOLOGY!
PHYSIOLOGY!
Two-parameter Bifurcation DiagramTwo-parameter Bifurcation Diagram
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Wild type
cdc13
cdc13 +/
0 1 2 3 4 5 6
0.000
0.005
0.010
0.015
0.020
0.025
0.030
2 param bifn diag for Cdc13
mitoticcycles
endoreplication
cell mass (a.u.)
Cyc
lin g
ene
expr
essi
on
??
Oscill8: Emery Conrad
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Growth Patterns in Fission Yeast
OE NE NE OE NETO
actin “patches”
“orb” mutants “tea” mutants
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-
--
+
+
+
-
--
+
+
+
t
CReaction + Diffusion + Convection
Tubulin ( dimer)
MicrotubuleMotor (Tea2)
Landmark (Tea1, Arp2/3)
G actin (globular)
F actin (filamentous)
Growth material
Turing pattern Bias
Cdc2
CycB
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time
space
OENE
NETO
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46
0 5 10 15 20 45
orb
bipolar
NETOmonopolar
cell length (μm)
A. with microtubules
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0 5 10 15 20 45
T-shaped
orb
curled
monopolar
tripolar
bipolar
cell length (μm)0 5 10 15 20 45
orb
bipolar
NETOmonopolar
cell length (μm)
A. with microtubules B. without microtubules
CFDRC: Andrzej Przekwas