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The dynamics of isotopes in the standard DEB model

Explore the mechanisms and fractionation of isotopes in the DEB model, examining metabolic processes like growth, assimilation, and dissipation. Learn about the energy budget theory, chemical transformations, univariate and multivariate DEB models, and parameter estimation.

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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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