the dynamics of isotopes in the standard deb model
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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
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
Standard DEB scheme 3
1- maturitymaintenance
maturityoffspring
maturationreproduction
food faecesassimilation
reserve
feeding defecation
structurestructure
somaticmaintenance
growth
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
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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
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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
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.
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