Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam 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 O 2, NH 3, CO 2 (phototrophs) evaporation of H 2 O Mechanism velocity e = ½ m c 2 binding probability to carriers Examples anabolic vs catabolic aspects assimilation, dissipation, growth Mechanism binding strength in decomposition

Fractionation from pools & fluxes

Oxygenic photosynthesis CO H 2 O  CH 2 O + H 2 O + O 2 Reshuffling of 18 O Fractionation of 13 C

C 4 plants Fractionation weak in C 4 plants strong in C 3 plants

Standard DEB scheme 3 1-  maturity maintenance maturity offspring maturation reproduction foodfaeces assimilation reserve feeding defecation structure somatic maintenance 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 reservestructure

Change in isotope fractions For mixed pool j = E, V (reserve, structure) For non-mixed product j = Ø (otolith)

Isotopes in biomass & otolith time, d otolith length body length opacity temperature f,ef,e 

DEB tele course Free of financial costs; some 250 h effort investment Program for 2009: Feb/Mar general theory April 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 Cambridge Univ Press 2009 Marianne: thank you of the organisation Audience : thank you for your attention

Dynamic Energy Budget theory for metabolic organisation S.A.L.M. Kooijman Third Edition

Toc for DEB3 1 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 776 Life Science proposals, max 3.5 M€/ proposal 34 % of budget for Life Sciences, 517 M€ budget for first call Prob: 0.34 × 517/ 776 × 3 = First selection medio June, final selection early Sept, ID panel meeting end Sept DEBtheory proposal: 50 man-year, 5 year run-time, 3.4 M€ 2 PD + 4 PhD A’dam, 2 PD + 1 PhD Lisbon, 1 PD + 2 PhD Marseille DEB helpdesk (AQUAdeb): 30 % of workload + 10 % Tjalling (DEBtox) 150 k€ for symposia/courses