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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,Criteria for general energy models,Quantitativ
2、e Based on explicit assumptions that together specify all quantitative aspects to allow for mass and energy balancing Consistency Assumptions should be consistent in terms of internal logic, with physics and chemistry, as well as with empirical patterns Simplicity Implied model(s) should be simple (
3、numbers of variables and parameters) enough to allow testing against data Generality The conditions species should fulfill to be captured by the model(s) must be explicit and make evolutionary sense Explanatory The more empirical patterns are explained, the better the model,From Sousa et al 2010 Phi
4、l. Trans. R. Soc. Lond. B 365: 3413-3428,Empirical special cases of DEB 11.1,Empirical patterns: stylised facts,Feeding During starvation, organisms are able to reproduce, grow and survive for some time At abundant food, the feeding rate is at some maximum, independent of food density Growth Many sp
5、ecies continue to grow after reproduction has started Growth of isomorphic organisms at abundant food is well described by the von Bertalanffy For different constant food levels the inverse von Bertalanffy growth rate increases linearly with ultimate length The von Bertalanffy growth rate of differe
6、nt species decreases almost linearly with the maximum body length Fetuses increase in weight approximately proportional to cubed time Reproduction Reproduction increases with size intra-specifically, but decreases with size inter-specifically,Respiration Animal eggs and plant seeds initially hardly
7、use O2 The use of O2 increases with decreasing mass in embryos and increases with mass in juveniles and adults The use of O2 scales approximately with body weight raised to a power close to 0.75 Animals show a transient increase in metabolic rate after ingesting food (heat increment of feeding) Stoi
8、chiometry The chemical composition of organisms depends on the nutritional status (starved vs well-fed) The chemical composition of organisms growing at constant food density becomes constant Energy Dissipating heat is a weighted sum of 3 mass flows: CO2, O2 and N-waste,From Sousa et al 2008 Phil. T
9、rans. R. Soc. Lond. B 363:2453 -2464,Empirical patterns 1 11.1a,From Sousa et al 2008 Phil. Trans. R. Soc. Lond. B 363:2453 -2464,Empirical patterns 2 11.1b,From Sousa et al 2008 Phil. Trans. R. Soc. Lond. B 363:2453 -2464,Topological alternatives 11.1c,From Lika & Kooijman 2011 J. Sea Res 66: 381-3
10、91,Test of properties 11.1d,From Lika & Kooijman 2011 J. Sea Res, 66: 381-391,Applications of DEB theory 11.1e,bioproduction: agronomy, aquaculture, fisheries pest control biotechnology, sewage treatment, biodegradation (eco)toxicology, pharmacology medicine: cancer biology, obesity, nutrition biolo
11、gy global change: biogeochemical climate modeling conservation biology; biodiversity economy; sustainable development,Innovations by DEB theory 11.1f,Unifies all life on earth (bacteria, protoctists, fungi/animals, plants) Links levels of organisation Explains body size scaling relationships Deals w
12、ith energetic and stoichiometric constraints Individuals that follow DEB rules can merge smoothly into a symbiosis that again follows DEB rules Method for determining entropy of living biomass Biomass composition depends on growth rate Product formation has 3 degrees of freedom Explains indirect cal
13、orimetry Explains how yield of biomass depends on growth rate Quantitative predictions have many practical applications,DEB theory reveals unexpected links 11.1g,Length, mm,O2 consumption, l/h,1/yield, mmol glucose/ mg cells,1/spec growth rate, 1/h,Daphnia,Streptococcus,respiration length in individ
14、ual animals & yield growth in pop of prokaryotes have a lot in common, as revealed by DEB theory Reserve plays an important role in both relationships, but you need DEB theory to see why and how,Weird world at small scale 11.2a,Almost all transformations in cells are enzyme mediated Classic enzyme k
15、inetics: based on chemical kinetics (industrial enzymes) diffusion/convection law of mass action: transformation rate product of conc. of substrates larger number of molecules constant reactor volume Problematic application in cellular metabolism: definition of concentration (compartments, moving or
16、ganelles) transport mechanisms (proteins with address labels, targetting, allocation) crowding (presence of many macro-molecules that do not partake in transformation) intrinsic stochasticity due to small numbers of molecules liquid crystalline properties surface area - volume relationships: membran
17、e-cytoplasm; polymer-liquid connectivity (many metabolites are energy substrate dilution by growth) Alternative approach: reconstruction of transformation kinetics on the basis of cellular input/output kinetics,Diffusion cannot occur in cells 11.2b,Self-ionization of water in cells 11.2c,A cell of v
18、olume 0.25 mm3 and pH 7 at 25C has m = 14 protons N = 8 109 water molecules,confidence intervals of pH 95, 90, 80, 60 %,pH,cell volume, m3,modified Bessel function,7,Crowding affects transport 11.2d,cytoskeletal polymers,ribosomes,nucleic acids,proteins,ATP generation & use 11.2e,5 106 ATP molecules
19、 in bacterial cell enough for 2 s of biosynthetic work Only used if energy generating & energy demanding transformations are at different site/time If ADP/ATP ratio varies, then rates of generation & use varies, but not necessarily the rates of transformations they drive,Processes that are not much
20、faster than cell cycle, should be linked to large slow pools of metabolites, not to small fast pools DEB theory uses reserve as large slow pool for driving metabolism,Classic energetics 11.3,Anabolism: synthetic pathways Catabolism: degradation pathways Duality: compounds as source for energy and bu
21、ilding blocks In DEB: from food to reserve; from reserve to structure,From: Mader, S. S. 1993 Biology, WCB,This decomposition occurs at several places in DEBs,Classic energetics 11.3a,From: Duve, C. de 1984 A guided tour of the living cell, Sci. Am. Lib., New York,heterotroph,autotroph,The classic c
22、oncept on metabolic regulation focusses on ATP generation and use. The application of this concept in DEB theory is problematic.,Static Energy Budgets 11.3b,From: Brafield, A. E. and Llewellyn, M. J. 1982 Animal energetics, Blackie, Glasgow,C energy from food P production (growth) F energy in faeces
23、 U energy in urine R heat,Numbers: kJ in 28 d,Basic difference with dynamic budgets: Production is quantified as energy fixed in new tissue, not as energy allocated to growth: excludes overheads Heat includes overheads of growth, reproduction and other processes, it does not quantify maintenance cos
24、ts,Static vs Dynamic Budgets 11.4,Net production models time-dependent static models no demping by reserve,Assimilation models dynamics by nature reserve damps food fluctuations,Static Energy Budgets (SEBs) 11.4a,Differences with DEBs overheads interpretation of respiration interpretation of urinati
25、on metabolic memory life cycle perspective change in states,gross ingested,faeces,urine,apparent assimilated,gross metabolised,net metabolised,spec dynamic action,work,maintenance,somatic maintenance,activity,thermo regulation,production,growth,products,reproduction,Production model 11.4c,food,faece
26、s,assimilation,feeding,defecation,Production models 11.4d,no accommodation for embryonic stage; require additional state variables (no food intake, still maintenance costs and growth) no metabolic memory, no growth during starvation require switches in case of food shortage (reserves allocated to re
27、production used for maintenance) no natural dynamics for reserve; descriptive rules for growth vs reprod. no explanation for body size scaling of metabolic rates, changes in composition of biomass, metabolic memory require complex regulation modelling for fate of metabolites (ATP vs building blocks;
28、 consistency problem with lower levels of org.) dividing organisms (with reserve) cannot be included typically have descriptive set points for allocation, no mechanisms (weight-for-age rules quantify allocation to reproduction),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,