Dynamic Energy Budget Theory for Metabolic Organisation, Third Edition

Half-title......Page 3
Title......Page 5
Copyright......Page 6
Summary of contents......Page 7
Contents......Page 9
Support of this book......Page 17
Set-up of this book......Page 18
Acknowledgements......Page 20
1.1.2 Vague boundaries: the cell–population continuum
......Page 21
1.1.3 Why reserves apart from structure?......Page 22
Embryo......Page 24
Juvenile......Page 25
Adult......Page 27
1.2 Homeostasis is key to life......Page 28
1.2.1 Strong homeostasis: stoichiometric constraints......Page 29
1.2.3 Structural homeostasis: isomorphy......Page 30
Shape coefficients convert physical to volumetric lengths......Page 31
Shape at the subcellular level: membrane-cytosol interactions......Page 32
1.2.4 Thermal homeostasis: ecto-, homeo- and endothermy......Page 33
1.2.5 Acquisition homeostasis: supply and demand
......Page 35
1.3.1 Arrhenius temperature......Page 37
1.3.2 Coupling of rates in single reserve systems......Page 38
1.3.3 States can depend on temperature via rates......Page 39
1.3.4 Patterns in Arrhenius temperatures......Page 40
1.3.6 Temperature tolerance range......Page 41
1.3.8 Uncoupling of rates in multiple reserve systems......Page 42
1.4 Summary......Page 43
2 Standard deb model in time, length and energy......Page 44
2.1.1 Food availability is per volume or surface area of environment......Page 45
2.1.2 Food transport is across surface area of individual......Page 46
2.1.3 Feeding costs are paid from food directly......Page 51
2.1.4 Functional response converts food availability to ingestion rate......Page 53
2.1.5 Generalisations: differences in size of food particles......Page 55
2.2 Assimilation......Page 56
2.3 Reserve dynamics......Page 57
2.3.1 Partitionability follows from weak homeostasis......Page 58
2.3.2 Mergeability is almost equivalent to partitionability......Page 60
2.3.3 Mechanism for mobilisation and weak homeostasis......Page 61
2.4 The kappa-rule for allocation to soma
......Page 62
Volume-linked maintenance costs......Page 64
Surface-area-linked maintenance costs......Page 65
2.5.2 Maturation for embryos and juveniles......Page 67
2.5.3 Maturity maintenance: defence systems......Page 70
2.6 Growth: increase of structure......Page 71
2.6.1 Von Bertalanffy growth at constant food......Page 72
2.6.2 States at birth and initial amount of reserve......Page 74
Special case e → ∞: foetal development
......Page 83
2.6.3 States at puberty......Page 86
2.6.4 Reduction of the initial amount of reserve......Page 87
2.7 Reproduction: excretion of wrapped reserve......Page 89
2.7.1 Cumulative reproduction......Page 91
2.7.2 Buffer handling rules......Page 93
2.8 Parameter estimation I: numbers, lengths and time......Page 94
Growth and reproduction at a single food level: debtool/animal/get_pars_r......Page 95
2.9 Summary of the standard deb model......Page 96
3.1 Energy and entropy......Page 99
3.2.1 Mass quantified as gram......Page 101
3.2.3 Composition of biomass......Page 103
3.3 Classes of compounds in organisms......Page 105
Nitrogenous waste......Page 106
3.3.2 Organic compounds......Page 107
Products......Page 108
Storage materials......Page 109
Storage deposits......Page 110
3.4 Conversions of energy, mass and volume......Page 112
3.5 Macrochemical reaction equations......Page 114
3.6 Isotopes dynamics: reshuffling and fractionation......Page 115
3.6.1 Reshuffling......Page 116
3.6.2 Fractionation......Page 117
Fractionation from pools......Page 118
Fractionation from fluxes......Page 119
3.7 Enzyme-mediated transformations based on fluxes......Page 120
3.7.1 From substrate to product......Page 121
3.7.2 Rejection vs. Synthesising Units......Page 122
3.7.3 Four basic classes of transformations......Page 124
Number of SUs......Page 125
Supply kinetics......Page 126
3.7.5 Co-metabolism......Page 127
3.8.1 Trophic modes: auto-, hetero- and mixotrophy......Page 129
3.8.2 Central metabolism......Page 131
3.9 Summary......Page 133
4.1.1 Scatter structure of weight data......Page 134
4.1.3 Mild starvation......Page 136
4.1.4 Prolonged starvation......Page 138
4.1.5 Shrinking and the turnover of structure......Page 141
4.1.7 Dormancy......Page 142
4.1.8 Emergency reproduction......Page 143
4.2.1 V0-morphs......Page 144
4.2.2 V1-morphs......Page 146
Exponential growth at constant food density......Page 149
Yield of biomass on substrate at constant food......Page 150
4.2.3 Static mixtures of morphs: rods......Page 152
Crusts......Page 154
Flocs and tumours......Page 156
Roots and shoots......Page 157
4.3.1 Three basic fluxes......Page 158
Partitioning of mass fluxes......Page 160
4.3.2 State versus flux......Page 161
4.3.4 Composition of reserves and structural mass......Page 162
rRNA
belongs to reserve......Page 163
Composition changes during starvation......Page 165
4.4 Respiration......Page 167
4.4.1 Respiration Quotient......Page 169
4.5 Nitrogen balance......Page 171
4.5.1 Urination Quotient......Page 172
4.6 Water balance......Page 173
4.6.1 Plant–water relationships......Page 174
4.7.1 Three contributions to isotope fluxes......Page 175
Dissipation......Page 176
4.7.2 Changes in isotope fractions......Page 177
4.7.3 Effects of temperature......Page 178
4.7.5 Doubly labelled water......Page 179
4.8.1 Energy balance: dissipating heat......Page 180
Convection and radiation......Page 181
4.8.2 Indirect calorimetry: aerobic conditions......Page 182
4.8.3 Substrate-dependent heat dissipation......Page 183
4.9 Products......Page 185
4.9.1 Fermentation......Page 186
4.10 Parameter estimation II: mass, energy and entropy......Page 188
4.10.1 Composition parameters......Page 189
4.11.1 Reconstruction of food intake from growth data......Page 190
4.11.2 Reconstruction of body temperature from growth data......Page 193
4.11.3 Reconstruction from reproduction data......Page 195
4.11.4 Reconstruction from otolith data......Page 200
4.12 Summary......Page 202
5 Multivariate deb models......Page 204
5.1.1 Diet and preference......Page 205
5.1.2 Pseudo-faeces and variations in half-saturation coefficients......Page 208
5.1.3 Oxygenic photosynthesis......Page 209
Pigment systems......Page 210
Photorespiration......Page 211
Photoinhibition and photoadaptation......Page 212
5.1.4 Calcification......Page 213
5.2 Several reserves......Page 214
5.2.2 Reserve dynamics and excretion......Page 215
5.2.3 Simultaneous nutrient limitation......Page 216
5.2.4 Non-limiting reserves can dam up......Page 217
5.2.5 Dioxygen flux......Page 219
5.2.6 Ammonia–nitrate interactions......Page 220
5.3.1 Static generalisation of the kappa
-rule......Page 222
5.3.2 Dynamic generalisation of the kappa
-rule......Page 224
5.3.3 Roots and shoots: translocation......Page 227
5.4 Summary......Page 232
6.1 Ageing: effects of ROS
......Page 234
Weibull model for small Gompertz ageing rates......Page 238
Gompertz model for small Weibull ageing rates......Page 239
6.1.2 Ageing in unicellulars: stringent response......Page 240
6.2 Toxins and toxicants......Page 241
6.3 One-compartment kinetics is the standard......Page 243
6.3.1 Ionisation affects kinetics......Page 244
Steady-flux approximation......Page 246
6.4 Energetics affects toxicokinetics......Page 247
6.4.1 Dilution by growth......Page 248
6.4.2 Changes in lipid content......Page 249
6.4.3 Metabolic transformations......Page 253
6.5 Toxicants affect energetics......Page 254
6.5.1 No effects......Page 256
6.5.3 Effects on survival......Page 257
Direct effects on reproduction......Page 260
Indirect effects on reproduction......Page 261
6.5.5 Receptor-mediated effects......Page 264
Ames test......Page 265
6.5.7 Effects of mixtures......Page 267
Necs of mixtures......Page 268
6.5.8 Population consequences of effects......Page 270
6.6 Summary......Page 272
7.1.1 Handshaking protocols for carriers......Page 275
Closed protocol......Page 276
Comparison......Page 277
7.1.2 Handshaking protocols for chains......Page 278
Closed handshaking at all nodes......Page 279
Open handshaking at all nodes......Page 280
7.2.1 Food deposits and claims......Page 281
7.2.2 Fast food intake after starvation: hyperphagia......Page 282
7.2.3 Digestion parallel to food searching: satiation......Page 283
7.2.4 Social interaction......Page 284
Homogeneous mantle......Page 286
Mantle with barrier......Page 288
Non-homogeneous mantle......Page 289
Intracellular digestion......Page 290
Social digestion......Page 291
Solitary digestion......Page 292
7.3.1 Smoothing and satiation......Page 293
7.3.2 Gut residence time......Page 295
7.3.3 Gut as a plug flow reactor......Page 296
7.4 Division......Page 299
7.5 Cell wall and membrane synthesis......Page 301
7.7 Mother--foetus system......Page 302
7.8.1 Pupa and imago......Page 304
7.8.2 Metamorphosis in juvenile fish......Page 307
7.9 Changing parameter values......Page 308
7.9.2 Suicide reproduction......Page 309
7.9.4 Diauxic growth: inhibition and preference......Page 311
Minimum food density......Page 313
8 Covariation of parameter values......Page 315
8.1.1 Genetics and parameter variation......Page 316
8.1.2 Geographical size variations......Page 317
8.2 Inter-specific parameter variations......Page 319
8.2.1 Primary scaling relationships......Page 320
Somatic maintenance rate coefficient......Page 321
Body weight......Page 322
Respiration......Page 323
Length at birth and initial amount of reserve......Page 325
Water loss from eggs......Page 326
Minimum embryonic period......Page 327
Maximum ingestion rate......Page 329
Speed......Page 330
Maximum diving depth......Page 331
Von Bertalanffy growth rate......Page 332
Minimum juvenile period......Page 342
Time till death by starvation......Page 343
Life span......Page 344
Abundance......Page 345
Population growth rate......Page 346
8.3.1 Kinetics as a function of partition......Page 347
8.3.2 Film models......Page 349
8.3.3 Bioconcentration coefficient......Page 350
8.3.4 Effects as a function of partition coefficients......Page 352
8.4 Interactions between qsars and body size scaling relationships......Page 353
8.5 Summary......Page 355
9.1 Trophic interactions......Page 356
9.1.2 Syntrophy......Page 357
Indirect transfer......Page 359
Products for a favour......Page 360
Phototroph–heterotroph associations......Page 361
9.1.5 Predation and saprotrophy......Page 366
9.2 Population dynamics......Page 367
9.2.1 Non-structured populations......Page 369
Lotka–Volterra model......Page 370
Lotka-Volterra, Monod, Marr–Pirt, Droop and DEB models
......Page 371
Death......Page 372
Reserves and expo-logistic growth......Page 375
9.2.2 Structured populations......Page 377
Discrete individuals......Page 378
Population growth rates and division intervals......Page 379
Population structure......Page 380
Synchronisation......Page 381
Variation between individuals......Page 383
9.2.3 Mass transformation in populations......Page 385
Propagation through reproduction......Page 386
Propagation through division......Page 389
Steady-state situations for division......Page 391
9.3 Food chains and webs......Page 392
Asymptotic behaviour......Page 393
Closed nutrient–producer–consumer system......Page 395
9.3.2 Stability and invasion......Page 396
9.4 Canonical Community......Page 397
9.4.1 Mass transformations in communities......Page 398
9.5 Summary......Page 402
10 Evolution......Page 404
10.1 Before the first cells......Page 405
10.2 Early substrates and taxa......Page 407
10.2.1 Evolution of central metabolism......Page 408
10.2.2 Phototrophy......Page 410
10.2.3 Diversification and interactions......Page 412
Strong homeostasis induces stoichiometric constraints......Page 413
Reserves relax stoichiometric constraints......Page 414
Excretion: imbalance between availability and requirements......Page 415
Turnover of structure enhances maintenance......Page 416
Defence systems increases maintenance costs......Page 417
kappa-rule and emergence of cell cycles......Page 418
Syntrophy and lateral gene exchange......Page 419
First steps in modular recombination: mitochondria......Page 420
Membrane plasticity......Page 422
Plastids......Page 424
Genome reorganisation......Page 425
10.4 Merging of individuals in steps......Page 426
10.4.1 Reciprocal syntrophy......Page 429
10.4.2 Spatial clustering......Page 431
10.4.3 Physical contact: epibionts......Page 432
10.4.5 Strong homeostasis for structure......Page 435
10.4.6 Coupling of assimilation pathways......Page 437
10.4.9 Cyclic endosymbiosis by specialisation......Page 438
10.5 Multicellularity and body size......Page 439
10.5.1 Differentiation and cellular communication......Page 440
10.5.4 Ageing and sleeping......Page 441
10.6 Control over local conditions......Page 442
10.7.1 Water......Page 444
10.7.2 Carbon dioxide......Page 445
10.7.3 Methane......Page 446
10.7.5 Albedo......Page 447
10.9 Summary......Page 448
11.2 A weird world at small scales......Page 450
11.3 Static Energy Budgets......Page 453
11.4 Net production models......Page 455
11.5 Summary......Page 457
References......Page 458
Glossary......Page 507
Symbols......Page 514
Expressions......Page 516
Units, dimensions and types......Page 517
List of frequently used symbols......Page 518
Taxonomic index......Page 524
Index......Page 529