Transcript Modelkey: VUA-TB, WP Effect-3

Modelkey: VUA-TB, WP Effect-3
Bas Kooijman
Dept theoretical biology
Vrije Universiteit Amsterdam
[email protected]
http://www.bio.vu.nl/thb/
Palma, 2005/03/02-04
Research effort by VUA-TB
2005/02 – 2009/02: PhD student (vacancy!!)
Primary task:
modelling effects in canonical communities/ biofilms
support in experimental design and data analysis
collaboration with
UFZ (Mechthild Schmitt Janssen, Christina Klünder)
ECT (Thomas Knacker, Markus Liebig)
2006/02 – 2008/02: Postdoc (vacancy)
Primary task:
modelling effects in food chains
support in decisions what to measure and data analysis
collaboration with
VUA (Bert van Hattum)
Education effort by VUA-TB
2005/02 – 04: DEB tele course
Topic: metabolic organization of organisms
2005/03/07 – 12: DEBtox crash course
Topic: effects of toxicants on metabolic organisation
Participation:
Mechthild Schmitt Janssen, Christina Klünder, Markus Liebig, Bert van Hattum
DEB = Dynamic Energy Budget
Modes of action of toxicants
 assimilation
food
 maintenance costs
defecation
feeding
faeces

 growth costs
assimilation
 reproduction costs
reserve
somatic
maintenance

maint
1-
7

growth

structure
u

tumour
6
 hazard to embryo
maturity
maintenance
maturation
reproduction
maturity
offspring

6
tumour induction
7
endocr. disruption
8
lethal effects:
hazard rate
Mode of action affects
translation to pop level
Models for toxic effects
Tree model components:
• kinetics
external concentration  internal concentration
example: one-compartment kinetics
• change in target parameter(s)
internal concentration  value of target parameter(s)
example: linear relationship
• physiology
value of parameter  endpoint (survival, reproduction)
example: DEB model
Hazard rate
Definition: instantaneous death rate (dim: time-1)
Interpretation of hazard rate times time increment:
probability of death, given to be alive
Relationship with survival probability for
Examples for
:
:
DEB-based effects on reproduction
Indirect effects
indicator: effects on onset of reproduction
• decrease of assimilation rate (food intake, digestion)
• increase of specific maintenance costs
• increase of costs for synthesis of biomass (structural)
Direct effects
indicator: no effects on onset of reproduction
• increase of costs for the synthesis of offspring
• decrease of survival probability at birth
Escherichia coli
Dictyostelium
time, h
cell vol, m3
glucose
mg. ml-1
X0(0)
0.433
X1(0)
0.361
X2(0)
0.084
mm3.ml-1
e1(0)
1
e2(0)
1
-
XK1
0.40
XK2
0.18
g1
0.86
g2
4.43
μg mm3
,
ml ml
-
kM1
0.008
kM2
0.16
h-1
kE1
0.67
kE2
2.05
h-1
jXm1
0.65
jXm2
0.26
mg
, h 1
mm 3h
h = 0.064 h-1, Xr = 1mg ml-1, 25 °C
Data from Dent et al 1976
cell vol, m3
mm3/ml
mm3/ml
mg/ml
Food chains n=2
time, h
Kooijman & Kooi,1996
Nonlin. World 3: 77 - 83
1-species mixotroph community
Mixotrophs are
producers, which live
off light and nutrients
as well as
decomposers, which live
off organic compounds
which they produce by
aging
Simplest community with
full material cycling
Canonical community
Short time scale:
Mass recycling
in a community
closed for mass
open for energy
Long time scale:
Nutrients leaks and influxes
Memory is controlled by
life span (links to body size)
Spatial coherence is controlled by
transport (links to body size)
biomass
biomass
Total carbon
nutrient
1-species:
mixotroph
community
producer
Total carbon
nutrient
consumer
Total nitrogen
Total nitrogen
1-spec. vs canon. community
consumer
producer
nutrient
decomposer
Total carbon
Total nitrogen
3-species:
canonical
community