1 using jigcell and other biospice tools to understand the regulation of cell growth and division...

1

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

2

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)

3

OutlineOutline

• The biological problem

• BioSPICE tools, especially JigCell

• Future needs

4

The fundamental goal of The fundamental goal of molecular cell biologymolecular cell biology

5Hanahan & Weinberg (2000)

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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Fission Yeast

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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

11

The Modeling CycleThe Modeling Cycle

Data NotebookData Notebook

Wiring DiagramWiring Diagram

Differential EquationsDifferential Equations Parameter ValuesParameter Values

SimulationSimulationAnalysisAnalysis

ComparisonComparison

Data NotebookData Notebook

ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature

12

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

13

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

14

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

15

The Modeling CycleThe Modeling Cycle

Data NotebookData Notebook

Wiring DiagramWiring Diagram

Differential EquationsDifferential Equations Parameter ValuesParameter Values

SimulationSimulationAnalysisAnalysis

ComparisonComparison

Data NotebookData Notebook

ExperimentalExperimentalDatabasesDatabasesLiteratureLiterature

RunManager

16

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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25

26

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

35

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

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

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

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

39

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

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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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

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The End