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The dynamics of isotopes in the standard DEB model

The dynamics of isotopes in the standard DEB model. Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Bas@bio.vu.nl http://www.bio.vu.nl/thb /. Nantes, 2008/05/22. Macrochemical reaction eq. Notation. Reshuffling. Fractionation from pools & fluxes. Examples

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The dynamics of isotopes in the standard DEB model

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  1. The dynamics of isotopes in the standard DEB model Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Bas@bio.vu.nl http://www.bio.vu.nl/thb/ Nantes, 2008/05/22

  2. Macrochemical reaction eq

  3. Notation

  4. Reshuffling

  5. Fractionation from pools & fluxes • Examples • uptake of O2, NH3, CO2(phototrophs) • evaporation of H2O • Mechanism • velocity e = ½ m c2 • binding probability to carriers • Examples • anabolic vs catabolic aspects • assimilation, dissipation, growth • Mechanism • binding strength in decomposition

  6. Fractionation from pools & fluxes

  7. Oxygenic photosynthesis CO2 + 2 H2O CH2O + H2O + O2 Reshuffling of 18O Fractionation of 13C

  8. C4 plants • Fractionation • weak in C4 plants • strong in C3 plants

  9. defecation feeding food faeces assimilation reserve somatic maintenance maturity maintenance  1- maturation reproduction growth maturity offspring structure Standard DEB scheme 3

  10. Macrochemical reaction eq

  11. 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 product flux anabolic flux reserve structure

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

  13. Isotopes in biomass & otolith body length temperature f,e time, d time, d time, d 0.001 0.001 body length time, d otolith length time, d 0.001 0.001 0.001 opacity otolith length otolith length otolith length otolith length

  14. DEB tele course 2009 http://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

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

  16. 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.

  17. 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 = 0.075 • 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

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