Presentation - JigCell

Report
DARPA BioComp PI Meeting, 2001
“The Eukaryotic Cell Cycle as a Test Case
for Modeling Cellular Regulation in a
Collaborative Problem Solving Environment”
PI: John J. Tyson (Biology, Virginia Tech)
CoPIs: Cliff Shaffer & Layne Watson (CS, Virginia Tech)
With collaborators at
Rockefeller University
University of Kentucky Medical School
Budapest University of Technology and Economics
G1
cyclin-dependent
kinase
Anaphase
S
Cdc2
Cdc13
DNA
replication
cyclin
G2
Metaphase
Three Objectives
• Modeling
• Experimental Validation
• Software Tools
DoD Relevance
The cell cycle is central to all processes of
biological growth, development and reproduction.
•
•
•
•
•
•
Wound healing
Nerve regeneration
Radiation damage
Eukaryotic pathogens
Tissue culture
Cancer
Kurt Kohn (1999) Mol Biol Cell
Sister chromatid
separation
Cdc20
Lte1
PPX
Esp1
Budding
Esp1
Pds1
Esp1
Bub2
Cdc15
Cln2
SBF
Tem1
Net1P
Unaligned chromosomes
SBF
Pds1
Net1
RENT
Mcm1
Unaligned chromosomes
Cdh1
Mcm1
Cdc20
Cln3
Mad2
Cln2
Clb2
Cdc14
Cdc20
Cdc15
and
Clb5
Bck2
Mcm1
APC
Clb2
Cdc14
growth
CDKs
Swi5
Sic1
Cdc14
?
MBF
DNA synthesis
P
Cdc20
Clb5
Esp1
Sic1
SCF
Cdh1
d CDK
= k1 - (v2’ + v2” . Cdh1 ) . CDK
dt
k1 = 0.0013, v2’ = 0.001, v2” = 0.17,
d Cdh1 (k3’ + k3” . Cdc20A) (1 - Cdh1) (k4’ + k4” . CDK . M) Cdh1
=
dt
J3 + 1 - Cdh1
J4 + Cdh1
k3’ = 0.02, k3” = 0.85, k4’ = 0.01, k4” = 0.9,
J3 = 0.01, J4 = 0.01, k9 = 0.38, k10 = 0.2,
d IEP
= k9 . CDK . M . (1 – IEP ) – k10 . IEP
dt
k5’ = 0.005, k5” = 2.4, J5 = 0.5, k6 = 0.33,
d Cdc20T
(CDK . M)4
= k5’ + k5” 4
- k6 . Cdc20T
dt
J5 + (CDK . M)4
k7 = 2.2, J7 = 0.05, k8 = 0.2, J8 = 0.05,
…
d Cdc20A k7 . IEP (Cdc20T - Cdc20A) k8 . MAD Cdc20A
=
- k6 . Cdc20T
dt
J7 + Cdc20T - Cdc20A
J8 + Cdc20A
Differential equations
Parameter values
Table 6. Properties of clb, sic1, and hct1 mutants
mass at
birth
mass at
SBF 50%
mass at
DNA repl.
mass at
bud ini.
mass at
division
TG1
(min)
84
changed
parameter
Comments
1
wild type
(daughter)
0.71
1.07
(71’)
1.15
(84’)
1.15
(84’)
1.64
(146’)
CT 146 min
(time of occurrence of event)
2
clb1 clb2
0.71
1.07
1.16
1.16
No mit
3
clb1 clb2
1X GAL-CLB2
0.65
1.10
1.19
1.19
1.50
105
k's,b2 = 0.1
k"s,b2 = 0
Surana 1993 Fig 4, 1X GAL-CLB2 is OK, 4X GAL-CLB2
(or 1X GAL-CLB2db) causes telophase arrest.
4
clb5 clb6
0.73
1.07
(65’)
1.30
(99’)
1.17
(80’)
1.70
(146’)
99
k's,b5 = 0
k"s,b5 = 0
Schwob 1993 Fig 4, DNA repl begins 30 min after SBF
activation.
5
clb5 clb6
GAL-CLB5
0.61
0.93
0.92
0.96
1.41
73
k's,b5 = 0.1
k"s,b5 = 0
6
sic1
0.66
1.00
(73’)
0.82
(37’)
1.06
(83’)
1.52
(146’)
38
k's,c1 = 0
k"s,c1 = 0
Schneider 1996 Fig 4, sic1 uncouples S phase from
budding.
7
sic1 GAL-SIC1
0.80
1.07
1.38
1.17
1.86
94
k's,c1 = 0.1
k"s,c1 = 0
Verma 1997 Fig3B, Nugroho & Mendenhall 1994 Fig 2,
most cells are viable.
8
hct1
0.73
1.08
1.17
1.18
1.69
82
9
sic1 hct1
0.71
No SBF
0.72
No bud
No mit
10
sic1 GAL-CLB5
first cycle
second cycle
0.71
0.52
0.74
0.73
No repl
0.76
1.20
k's,b2 = 0
k"s,b2 = 0
Surana 1991 Table 1, G2 arrest.
Schwob 1993 Fig 6, DNA repl concurrent with SBF
activation in both GAL-CLB5 and GAL-CLB5db.
k"d,b2 = 0.01 Schwab 1997 Fig 2, viable, size like WT, Clb2 level high
throughout the cycle.
k's,c1 = 0
Visintin 1997, telophase arrest.
k"d,b2 = 0.01
k's,b5 = 0.1
k"s,b5 = 0
k's,c1 = 0
Schwob 1994 Fig 7C, inviable.
First cycle OK, DNA repl advanced; but pre-repl complexes
cannot form and cell dies after the first cycle.
S/G2/M
Start
Clb/Cdk1
activity
Finish
G1
A/B
A + Cln2
B+Cdc20
Predictions: Budding Yeast
1. Rate constants
Mendenhall (U Kentucky)
2. Hysteresis
Cross (Rockefeller U)
3. Mutants
Cross & Mendenhall
Predictions: Frog Eggs
1. Rate constants (1993)
Confirmed
Kumagai & Dunphy (1995)
2. Hysteresis (1993)
Confirmed
Moore (unpubl)
Sible & Sha (VA Tech)
3. Bifurcation diagram (1998)
Under test
Sible & Sha (VA Tech)
4. Cdk2/Cyclin E (in ppn)
Under test
Sible (VA Tech)
Software Requirements
Experimental Database
Wiring Diagram
Differential Equations
Analysis
Parameter Values
Simulation
Visualization-Translation
Experimental Database
Bifurcation diagram
Cdk1 activity
1
.
0
Cdk1
Clb2,5
0
.
5
M
Sic1
Cdh1
0
.
0
0
G1
1
cell mass
2
Cln2
Parameter Estimation
Simulation
Comparator
Database
Prop 1
Good fit
Prop 1
Prop 2
Bad fit
Prop 2
...
...
...
Error Function (parameters)
Parameter Estimation
Jones’ direct search global optimizer
trust region Levenburg Marquardt
Milestones
Year One
Year Two
Year Three
Modeling
Full model of bud yeast
Sensitivity analysis
Cdk2/cyclin E in frog
Morpho checkpoint
a-factor signalling
Revisions
Comprehensive model
of budding yeast
Comprehensive model
of frog egg
Experiment
Absolute prot concen in
budd yeast
Hysteresis in frog extr
and in budd yeast
Kinetic & thermody
properties
Hopf & SNIPER
bifns in frog extr
Mutants
Complex bifns in
budd yeast & frog
Checkpoint signals
Software
Model builder
Steady-state finder
Comparator
Param optimization in
frog egg model
Numer bifn analysis
Working PSE for cell
cycle modeling
Run management
Simul analysis
Param optimization in
yeast cell model
Deliverables
Year One
Year Two
Year Three
Modeling
2 publications
budding yeast
frog egg develop
1 publication
morpho checkpt
2 tech reports
3 publications
a-factor signalling
compreh yeast
compreh frog
Experiment
2 publications
yeast (Cross)
frog (Sible)
1 tech report (Menden)
Some combination of
publications and
technical reports on
experiments
3 publications
irrev trans in yeast
kinet & thermo par
bifns in frog extr
Software
3 software tools
model builder
steady-state finder
param optimizer
Publications
Software tools for
run management
bifn analysis
comparisons
deter global search
Publications
Suites of integrated
software tools for a
complete cell-cycle
problem-solvingenvironment
Personnel
VT Faculty
VT Students
Collaborators
Modeling
Tyson (25%)
Chen (25%)
Ciliberto (25%) Novak (20%)
Yi (25%)
Pataki (100%)
Experiment
Sible (15%)
Sha (50%)
Software
Shaffer (15%) Zwolak (100%)
Watson (15%) Vass (100%)
Ramak. (10%) Allen (100%)
Cross (25%)
Liu (100%)
Menden. (25%)
GRA (100%)

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