Bas KooijmanDept theoretical biology

Vrije Universiteit AmsterdamBas@bio.vu.nl

http://www.bio.vu.nl/thb/

The dynamics of isotopes in the standard DEB model

Nantes, 2008/05/22

Macrochemical reaction eq

Notation

Reshuffling

Fractionation from pools & fluxes

Examples• uptake of O2, NH3, CO2 (phototrophs)• evaporation of H2OMechanism• velocity e = ½ m c2

• binding probability to carriers

Examples• anabolic vs catabolic aspects assimilation, dissipation, growthMechanism• binding strength in decomposition

Fractionation from pools & fluxes

Oxygenic photosynthesisCO2 + 2 H2O CH2O + H2O + O2

Reshuffling of 18O

Fractionation of 13C

C4 plantsFractionation• weak in C4 plants• strong in C3 plants

Standard DEB scheme 3

1- maturitymaintenance

maturityoffspring

maturationreproduction

food faecesassimilation

reserve

feeding defecation

structurestructure

somaticmaintenance

growth

Macrochemical reaction eq

Isotopes in products

Product flux: fixed fractions of assimilation, dissipation, growth

Assumptions:• no fractionation at separation from source flux• separation is from anabolic sub-flux

catabolic flux

anabolic flux

product flux

reserve structure

Change in isotope fractionsFor mixed pool j = E, V (reserve, structure)

For non-mixed product j = Ø (otolith)

Isotopes in biomass & otolith

time, d

time, d

time, d time, d

time, d

otolith length otolith length otolith length otolith length

otolith length

bo

dy

len

gth

bo

dy

len

gth

op

aci

ty

tem

pe

ratu

re

f,e

0.00

1

0.00

1

0.00

1

0.00

1

0.00

1

DEB tele course 2009http://www.bio.vu.nl/thb/deb/

Free of financial costs; some 250 h effort investment

Program for 2009: Feb/Mar general theory April 18-22 symposium in Brest Sept/Oct case studies & applications

Target audience: PhD students

We encourage participation in groups that organize local meetings weekly

Software package DEBtool for Octave/ Matlab freely downloadable

Slides of this presentation are downloadable from http://www.bio.vu.nl/thb/users/bas/lectures/

Cambridge Univ Press 2009

Marianne: thank you of the organisation

Audience: thank you for your attention

Dynamic Energy Budget theoryfor metabolic organisation

S.A.L.M. Kooijman Third Edition

Toc for DEB31 BASIC CONCEPTS Individuals as dynamic systems; homeostasis is key to life; body size and composition; metabolic modes; effects of temperature on rates. 2 STANDARD DEB MODEL IN TIME, LENGTH & ENERGY Assimilation; reserve dynamics follows from homeostasis; the k-rule for allocation to soma; dissipation excludes overheads of assimilation and growth; growth of structure; reproduction exports reserve; estimation of parameter values I. 3 CHEMICAL TRANSFORMATIONS IN CELLS A weird world at small scale; classes of compounds in organisms; macrochemical reaction equations; enzyme kinetics revisited; classification of types of processing and of compounds; number of SUs affects transformation rates; inhibition and co- metabolism; supply versus demand kinetics; networking via handshaking.} 4 UNIVARIATE DEB MODELS Changing feeding conditions; changing shapes; conservation of elements; carbon, water, dioxygen and nitrogen balance; conservation of energy; thermodynamic aspects; micro-chemical reaction equations; isotope dynamics; product formation; parameter estimation II; trajectory reconstruction. 5 MULTIVARIATE DEB MODELS Extensions to more than one substrate, reserve and structural mass. Photosynthesis and plant development, simultaneous nutrient limitation, calcification. 6 EFFECTS OF NON-FOOD COMPOUNDS Ageing; uptake kinetics; energetics affects kinetics; toxicants affect energetics; 7 EXTENSIONS OF DEB MODELS Details of specific processes, such as feeding, digestion, cell wall synthesis, organelle-cytosol interactions, pupae; changing parameter values; adaptation; mother-foetus interactions. 8 CO-VARIATION OF DEB PARAMETER VALUES Intra- and inter-specific parameter variations; interactions between QSARs and body size scaling relationships; allocation strategies. 9 LIVING TOGETHER Trophic interactions between organisms; population dynamics; food chains and webs, canonical communities; system earth and climate. 10 EVOLUTION Before the first cells; early substrates and taxa; evolution of individuals as dynamic systems; merging of individuals in steps; multicellularity and body size; from supply to demand systems; life builds on life. 11 EVALUATION Conceptual aspects of energetics; DEB models have many empirical models as special cases; comparison with other approaches.

ERC Advanced grant

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• 34 % of budget for Life Sciences, 517 M€ budget for first call

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