1. Dynamic Energy Budget theory
1 Basic Concepts
2 Standard DEB model
3 Metabolism
4 Univariate DEB models
5 Multivariate DEB models
6 Effects of compounds
7 Extensions of DEB models
8 Co-variation of par values
9 Living together
10 Evolution
11 Evaluation

2. Evolution of DEB systems 10.3
variable
structure
composition
strong
homeostasis
for structure
internalisation of
maintenance as
demand process
delay of use of
internal substrates
increase of
maintenance costs
installation of
maturation program 1 2 3 4 5 6
prokaryotes 7 9
plants
This scheme presents an evolutionary scenario for the metabolic organisation of an individual.
Only 2 of several reserves are shown.
Stacked dots (upper left) represent sloppy coupling between the various structural components
1: originally, strong homeostasis hardly applied and the various compounds from structure where formed from substrates, possibly will little transformation
2: the development of homeostasis comes with stoichiometric constraints on the uptake of substrates
3: since growth can only occur if all required substrates are present, and substrate concentrations vary in time, reserves develop, originally by delaying the processing of internalised substrates.
4: the increase of efficiency of protein-mediated substrate uptake involves maintenance costs.
The increased uptake efficiency increases the reserve pools, and the necessity developed to convert and store reserve (in polymers, or nutrients in vacuoles)
5: since substrates vary in concentration and are continuously required for maintenance, the payment of maintenance is internalised and done from mobilised reserve
6: size control comes with a need for a maturation program; defense systems are fuelled from maturity maintenance
Under starvation conditions, where maturity maintenance cannot be paid, rejuvenation occurs, and the hazard rate is increased.
Failure of paying somatic maintenance leads to shrinking of structure, but is a threshold is exceeded, death is instantaneous.
This situation applies to modern bacteria and many protoctists
7: The animal-line of development, which feed on other organisms, increased homeostasis and the number of reserves shrinks to 1.
8: Reproduction evolved and the juvenile stage gave rise to an embryo (no assimilation) and an adult stage (no maturation, but reproduction)
9: The plant-line of development increased the number of structures (roots and shoots), with specialised assimilation tasks
Reproduction evolved also here, typically in the shoot, and translocation evolved: a fraction of mobilised reserve is allocated to the other structure. 8
animals
Kooijman & Troost 2007
Biol Rev, 82, 1-30
reproduction
juvenile  embryo + adult
strong homeostasis
for reserve
specialization
of structure

3. Evolution of DEB systems 10.3a
Start: variable biomass composition, passive uptake
Strong homeostasis  stoichiometric constraints
Reserves: delay of use of internalised substrates  storage, weak homeostasis
Maintenance requirements: turnover (e.g. active uptake by carriers), regulation
Maintenance from reserve instead of substrate; increase reserve capacity
Control of morphology via maturation; -rule  cell cycle
Diversification of assimilation (litho-  photo-  heterotrophy)
Eukaryotisation: heterotrophic start; unique event?
Syntrophy & compartmentalisation: mitochondria, genome reorganisation
Phagocytosis, plastids (acquisition of phototrophy)
Animal trajectory: biotrophy
Reduction of number of reserves
Emergence of life stages
Further increase of maintenance costs
Further increase of reserve capacity
Socialisation
Supply  demand systems
Plant trajectory: site fixation
Differentiation of root and shoot
Emergence of life stages
Increase of metabolic flexibility (draught)
Nutrient acquisition via transpiration
Symbioses with animals, fungi, bacteria
(e.g. re-mineralisation leaf litter, pollination)

4. Maternal and Paternal Lineages in Cross-Breeding Bovine Species.
wisent = ♀ ox  ♂ bison
Verkaar, E.L.C., Nijman, I.J., Beeke, M., Hanekamp, E. & Lenstra, J.A. 2004
Maternal and Paternal Lineages in Cross-Breeding Bovine Species.
Has Wisent a Hybrid Origin? Molecular Biology and Evolution 21:

5. Eukaryotic chromosome 10.3.4a

6. Mitosis b
MT = micro-tubercule

7. Mitosis – Meiosis c
Gametes
mitosis
meiosis

8. Mendel d

9. Ames test e
Liver extract is added,
because the enzymes
can transform compounds
The metabolites can have
a different mutagenicity
This makes the test more relevant
for mammals (humans)
Ames produced mutants of Salmonella typhimurium that cannot synthesize histidine
The medium has all required nutrients, but only enough histidine for some 4 divisions
Only if back-mutation occurs during growth can colonies continue to grow and be counted
The inoculum size is 108. Genome size is 4.85 Mbp.
What is the expected survival probability in case of 100 revertant colonies?
We expect 4.85 mutations per genome in the case of random mutations and so high mortality
The survival probability turns out to be typically 100 %, so back-mutation is not random

10. Heterotrophic Hepatophyta 10.4
Cryptothallus mirabilis

11. Please open Ch 10 Part IV