Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory

The Dynamic Energy Budget (DEB) theory quantifies the metabolic organisation of organisms on the basis of mechanistically inspired assumptions. We here sketch a scenario for how its various modules, such as maintenance, storage dynamics, development, differentiation and life stages could have evolved since the beginning of life. We argue that the combination of homeostasis and maintenance induced the development of reserves and that subsequent increases in the maintenance costs came with increases of the reserve capacity. Life evolved from a multiple reserves - single structure system (prokaryotes, many protoctists) to systems with multiple reserves and two structures (plants) or single reserve and single structure (animals). This had profound consequences for the possible effects of temperature on rates. We present an alternative explanation for what became known as the down-regulation of maintenance at high growth rates in microorganisms; the density of the limiting reserve increases with the growth rate, and reserves do not require maintenance while structure-specific maintenance costs are independent of the growth rate. This is also the mechanism behind the variation of the respiration rate with body size among species. The DEB theory specifies reserve dynamics on the basis of the requirements of weak homeostasis and partitionability. We here present a new and simple mechanism for this dynamics which accounts for the rejection of mobilised reserve by busy maintenance/growth machinery. This module, like quite a few other modules of DEB theory, uses the theory of Synthesising Units; we review recent progress in this field. The plasticity of membranes that evolved in early eukaryotes is a major step forward in metabolic evolution; we discuss quantitative aspects of the efficiency of phagocytosis relative to the excretion of digestive enzymes to illustrate its importance. Some processes of adaptation and gene expression can be understood in terms of allocation linked to the relative workload of metabolic modules in (unicellular) prokaryotes and organs in (multicellular) eukaryotes. We argue that the evolution of demand systems can only be understood in the light of that of supply systems. We illustrate some important points with data from the literature.     

Mobility of synaptic vesicles in different pools in resting and stimulated frog motor nerve terminals

We used fluorescence recovery after photobleaching (FRAP) to measure the mobility of synaptic vesicles in frog motor nerve terminals. Vesicles belonging to the recycling pool or to the reserve pool were selectively labeled with FM1-43. In resting terminals, vesicles in the reserve pool were immobile, while vesicles in the recycling pool were mobile. Nerve stimulation increased the mobility of reserve pool vesicles. Treatment with latrunculin A, which destroyed actin filaments, had no significant effect on mobility, and reducing the temperature likewise had little effect, suggesting that recycling pool vesicles move by simple diffusion. Application of okadaic acid caused vesicle mobility in both pools to increase to the same level. We could model these and others' results quantitatively by taking into account the relative numbers of mobile and immobile vesicles in each pool, and vesicle packing density, which has a large effect on mobility.     

The adaptive dynamics of altruism in spatially heterogeneous populations

Abstract.— We study the spatial adaptive dynamics of a continuous trait that measures individual investment in altruism. Our study is based on an ecological model of a spatially heterogeneous population from which we derive an appropriate measure of fitness. The analysis of this fitness measure uncovers three different selective processes controlling the evolution of altruism: the direct physiological cost, the indirect genetic benefits of cooperative interactions, and the indirect genetic costs of competition for space. In our model, habitat structure and a continuous life cycle makes the cost of competing for space with relatives negligible. Our study yields a classification of adaptive patterns of altruism according to the shape of the costs of altruism (with decelerating, linear, or accelerating dependence on the investment in altruism). The invasion of altruism occurs readily in species with accelerating costs, but large mutations are critical for altruism to evolve in selfish species with decelerating costs. Strict selfishness is maintained by natural selection only under very restricted conditions. In species with rapidly accelerating costs, adaptation leads to an evolutionarily stable rate of investment in altruism that decreases smoothly with the level of mobility. A rather different adaptive pattern emerges in species with slowly accelerating costs: high altruism evolves at low mobility, whereas a quasi-selfish state is promoted in more mobile species. The high adaptive level of altruism can be predicted solely from habitat connectedness and physiological parameters that characterize the pattern of cost. We also show that environmental changes that cause increased mobility in those highly altruistic species can beget selection-driven self-extinction, which may contribute to the rarity of social species.     

Bi-trophic food chain dynamics with multiple component populations

Food web models describe the patterns of material and energy flow in communities. In classical food web models the state of each population is described by a single variable which represents, for instance, the biomass or the number of individuals that make up the population. However, in a number of models proposed recently in the literature the individual organisms consist of two components. In addition to the structural component there is an internal pool of nutrients, lipids or reserves. Consequently the population model for each trophic level is described by two state variables instead of one. As a result the classical predator-prey interaction formalisms have to be revised. In our model time budgets with actions as searching and handling provide the formulation of the functional response for both components. In the model, assimilation of the ingested two prey components is done in parallel and the extracted energy is added to a predators reserve pool. The reserves are used for vital processes; growth, reproduction and maintenance. We will explore the top-down modelling approach where the perspective is from the community. We will demonstrate that this approach facilitates a check on the balance equations for mass and energy at this level of organization. Here it will be shown that, if the individual is allowed to shrink when the energy reserves are in short to pay the maintenance costs, the growth process has to be 100% effective. This is unrealistic and some alternative model formulations are discussed. The long-term dynamics of a microbial food chain in the chemostat are studied using bifurcation analysis. The dilution rate and the concentration of nutrients in the reservoir are the bifurcation parameters. The studied microbial bi-trophic food chain with two-component populations shows chaotic behaviour.     

Dominance, Pleiotropy and Metabolic Structure

It is a common observation that most mutants have similar dominance relations for all the characters they are known to affect. As a model of pleiotropic effects we investigate a branched pathway where the two outputs represent two characters whose variation is affected by changes in any of the genetically specified enzymes in the system. We consider the effects on the phenotype (fluxes or intermediate metabolites) of substitutions at one locus represented by enzyme activities of the two homozygotes (mutant and wild type) and that of the heterozygote. Dominance indices for the characters pleiotropically connected by the metabolic system are calculated. We show that if enzymes behave 'linearly,' (first order), that is if saturation and feedback inhibition or other nonlinearities are absent, all fluxes and pools have identical dominance relations. The presence of such nonlinearity, however, leads to differences in dominance between different characters and we define the conditions where such differences can be important.     

A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions

Flux balance models of metabolism generally utilize synthesis of biomass as the main determinant of intracellular fluxes. However, the biomass constraint alone is not sufficient to predict realistic fluxes in central heterotrophic metabolism of plant cells because of the major demand on the energy budget due to transport costs and cell maintenance. This major limitation can be addressed by incorporating transport steps into the metabolic model and by implementing a procedure that uses Pareto optimality analysis to explore the trade‐off between ATP and NADPH production for maintenance. This leads to a method for predicting cell maintenance costs on the basis of the measured flux ratio between the oxidative steps of the oxidative pentose phosphate pathway and glycolysis. We show that accounting for transport and maintenance costs substantially improves the accuracy of fluxes predicted from a flux balance model of heterotrophic Arabidopsis cells in culture, irrespective of the objective function used in the analysis. Moreover, when the new method was applied to cells under control, elevated temperature and hyper‐osmotic conditions, only elevated temperature led to a substantial increase in cell maintenance costs. It is concluded that the hyper‐osmotic conditions tested did not impose a metabolic stress, in as much as the metabolic network is not forced to devote more resources to cell maintenance.     

Untersuchungen zur Überproduktion von Tryptophan und anderer Indolderivate durch Hansenula henricii

The cell pools of tryptophan and anthranilate, the excretion of indole-containing metabolites, and the levels of the enzymes of aromatic amino acid biosynthesis have been determined in regulatory mutants of Hansenula henricii. The strain Hg 48-2-M8 produces indoles with a maximum specific productivity of 0.37 mg/g · h at a maximum specific production value of 21 mg/g dry cell weight. This methyl-tryptophan resistant mutant possess an anthranilate synthase, whose inhibition by tryptophan is reduced. The best conditions for production of indoles are the following: 1% glucose as C-source; ammonium as N-source; pH value smaller than 4. We found that under various growth conditions 25–60% synthesized indole-containing metabolites consists of tryptophan.     

Strong influence of regional species pools on continent-wide structuring of local communities

There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use a continent-wide dataset of local ant communities and implement ecologically explicit source pool definitions to examine the relative importance of regional species pools and local interactions for shaping community structure. Then we assess which factors underlie systematic variation in the structure of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong.     

Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis

Here, we describe our updated mathematical model of Arabidopsis thaliana Columbia metabolism, which adds the glucosinolates, an important group of secondary metabolites, to the reactions of primary metabolism. In so doing, we also describe the evolutionary origins of the enzymes involved in glucosinolate synthesis. We use this model to address a long-standing question in plant evolutionary biology: whether or not apparently defensive compounds such as glucosinolates are metabolically costly to produce. We use flux balance analysis to estimate the flux through every metabolic reaction in the model both when glucosinolates are synthesized and when they are absent. As a result, we can compare the metabolic costs of cell synthesis with and without these compounds, as well as inferring which reactions have their flux altered by glucosinolate synthesis. We find that glucosinolate production can increase photosynthetic requirements by at least 15% and that this cost is specific to the suite of glucosinolates found in A.?thaliana, with other combinations of glucosinolates being even more costly. These observations suggest that glucosinolates have evolved, and indeed likely continue to evolve, for herbivory defense, since only this interpretation explains the maintenance of such costly traits.     

Proline metabolism in pollen: degradation of proline during germination and early tube growth

Proline degradation inPetunia pollen germinated in vitro was studied in cultures supplemented with [¹⁴C]proline labeled at different positions. Despite its abundance in the cell, this amino acid is only a minor substrate for respiration. Proline is partially converted via the citrate cycle into metabolites which can be traced in the ethanol-insoluble fraction of the cellular constituents. The fact that this conversion is much more extensive than the use of proline in respiration indicates that, in germinating pollen, the citrate cycle serves mainly for synthetic purposes. There are no indications that proline carbon is used for feeding of other amino-acid pools used for protein synthesis.     

Monitoring Escherichia coli growth in M63 media by ultrasonic noninvasive methods and correlation with spectrophotometric and HPLC techniques

A low-intensity ultrasonic technique (that is noninvasive, nondestructive, and online) has been developed to monitor the growth of Escherichia coli in glucose minimal media under aerobic and anaerobic conditions. Ultrasonic time of flight (TOF) variations were correlated with microorganism growth and the disappearance of nutrients and their subsequent conversion into different metabolites. Spectrophotometric growth data and high-performance liquid chromatography (HPLC) analysis of released and consumed metabolites were compared with the ultrasonic data demonstrating that the ultrasound device presented can provide supplementary real-time noninvasive information about the metabolic processes taking place in the culture. A semiempirical model under aerobic conditions was developed to explain the TOF variations as a function of the glucose concentration and was modified to take into account the growth inhibition due to the initial glucose concentration. The inhibition effect was obtained by fitting HPLC measurements to the logistic function of Boltzmann. Under aerobic and anaerobic culture conditions, the metabolic processes were correlated with TOF experimental variations through a theoretical approach based on ultrasonic propagation in ternary mixtures.     

Costs of Refuge Use Affect Escape Decisions of Iberian Rock Lizards Lacerta monticola

Theoretical models of anti-predator escape behaviour suggest that prey may adjust their escape response such that the optimal flight distance is the point at which the costs of staying exceed the costs of fleeing. Anti-predatory decisions should be made based also on consequences for long-term expected fitness, such as the costs of refuge use. For example, in lizards, the maintenance of an optimal body temperature is essential to maximize physiological processes. However, if unfavourable thermal conditions of refuges can decrease the body temperature of lizards, their escape decision should be influenced by refuge conditions. Analyses of the variation in flight distances and emergence latency from a refuge for the lizard Lacerta monticola under two different predation risk levels, and their relationship with the thermal environment, supported these predictions. When risk increased, lizards had longer emergence latencies, and thus costs of refuge use increased (a greater loss of time and body temperature). In the low-risk situation, lizards that were farther from the refuge had longer flight distances, whereas thermal conditions were less important. When risk increased, lizards had longer flight distances when refuges were farther off, but also when the external heating rate and the refuge cooling rate were lower. The results suggest that, in addition to the risk of predation, expected long-term fitness costs of refuges can also affect escape decisions.     

Reserve pool neuron transmitter respecification: Novel neuroplasticity

The identity of the neurotransmitters expressed by neurons has been thought to be fixed and immutable, but recent studies demonstrate that changes in electrical activity can rapidly and reversibly reconfigure the transmitters and corresponding transmitter receptors that neurons express. Induction of transmitter expression can be achieved by selective activation of afferents recruited by a physiological range of sensory input. Strikingly, neurons acquiring an additional transmitter project to appropriate targets prior to transmitter respecification in some cases, indicating the presence of reserve pools of neurons that can boost circuit function. We discuss the evidence for such reserve pools, their likely locations and ways to test for their existence, and the potential clinical value of such circuit-specific neurotransmitter respecification for treatments of neurological disorders.     

Lineage Selection and the Maintenance of Sex

Sex predominates in eukaryotes, despite its short-term disadvantage when compared to asexuality. Myriad models have suggested that short-term advantages of sex may be sufficient to counterbalance its twofold costs. However, despite decades of experimental work seeking such evidence, no evolutionary mechanism has yet achieved broad recognition as explanation for the maintenance of sex. We explore here, through lineage-selection models, the conditions favouring the maintenance of sex. In the first model, we allowed the rate of transition to asexuality to evolve, to determine whether lineage selection favoured species with the strongest constraints preventing the loss of sex. In the second model, we simulated more explicitly the mechanisms underlying the higher extinction rates of asexual lineages than of their sexual counterparts. We linked extinction rates to the ecological and/or genetic features of lineages, thereby providing a formalisation of the only figure included in Darwin''s “The origin of species”. Our results reinforce the view that the long-term advantages of sex and lineage selection may provide the most satisfactory explanations for the maintenance of sex in eukaryotes, which is still poorly recognized, and provide figures and a simulation website for training and educational purposes. Short-term benefits may play a role, but it is also essential to take into account the selection of lineages for a thorough understanding of the maintenance of sex.     

Increased signalling effort when survival prospects decrease: male-male competition ensures honesty

For signalling to be honest the handicap principle claims that signals must impose fitness costs so that only the best individuals can afford the most exaggerated signals. The cost of signalling in terms of reduced survival decreases, however, towards the end of an individual's lifetime, which can induce an increase in signalling effort as a terminal effort. I show for the three-spined stickleback, Gasterosteus aculeatus, that a decrease in survival prospects through impaired condition leads to an increase in red nuptial coloration that makes the signal less reliable as an indicator of male parental ability. Males in poor condition with a large signal sometimes cannibalized all the eggs they received, probably to start a new breeding cycle with a higher energy reserve. However, the inclusion of socially imposed costs of signalling through male-male competition during courtship increased the honesty of the signal, as some males in poor condition and of poor parental ability decreased their signal expression. Some cheaters still occurred, but the signalling system was honest on average. This implies that socially imposed costs are important in the maintenance of honest sexual signalling. Dishonesty may occur under favourable conditions when the cost of signalling is reduced. This emphasizes the importance of considering the environmental conditions experienced by individuals when investigating the evolution and maintenance of honest sexual signals. Copyright 2000 The Association for the Study of Animal Behaviour.     

Decreased Rubisco activity leads to dramatic changes of nitrate metabolism,amino acid metabolism and the levels of phenylpropanoids and nicotine in tobacco antisense RBCS transformants

Tobacco transformants that express an antisense RBCS construct were used to investigate the consequences of a lesion in photosynthetic carbon metabolism for nitrogen metabolism and secondary metabolism. The results show that an inhibition of photosynthesis and decrease in sugar levels leads to a general inhibition of nitrogen metabolism, and dramatic changes in the levels of secondary metabolites. The response was particularly clear in plants that received excess nitrogen. In these conditions, a decrease of Rubisco activity led to an inhibition of nitrate reductase activity, accumulation of nitrate, a decrease of amino acid levels that was larger than the decrease of sugars, and a large decrease of chlorogenic acid and of nicotine, which are the major carbon- and nitrogen-rich secondary metabolites in tobacco leaves, respectively. Similar changes were seen when nitrogen-replete wild-type tobacco was grown in low light. The inhibition of nitrogen metabolism was partly masked when wild-type plants and antisense RBCS transformants were compared in marginal or in limiting nitrogen, because the lower growth rate of the transformants alleviated the nitrogen deficiency, leading to an increase of amino acids. In these conditions, chlorogenic acid always decreased but the decrease of nicotine was ameliorated or reversed. When the changes in internal pools are compared across all the genotypes and growth conditions, two conclusions emerge. First, decreased levels of primary metabolites lead to a dramatic decrease in the levels of secondary metabolites. Second, changes of the amino acid : sugar ratio are accompanied by changes of the nicotine:chlorogenic acid ratio.     

Application of Multi-Objective Optimization to Pooled Experiments of Next Generation Sequencing for Detection of Rare Mutations

In this paper we propose some mathematical models to plan a Next Generation Sequencing experiment to detect rare mutations in pools of patients. A mathematical optimization problem is formulated for optimal pooling, with respect to minimization of the experiment cost. Then, two different strategies to replicate patients in pools are proposed, which have the advantage to decrease the overall costs. Finally, a multi-objective optimization formulation is proposed, where the trade-off between the probability to detect a mutation and overall costs is taken into account. The proposed solutions are devised in pursuance of the following advantages: (i) the solution guarantees mutations are detectable in the experimental setting, and (ii) the cost of the NGS experiment and its biological validation using Sanger sequencing is minimized. Simulations show replicating pools can decrease overall experimental cost, thus making pooling an interesting option.     

Maintenance of the 2μm Circle Plasmid of Saccharomyces Cerevisiae by Sexual Transmission: An Example of a Selfish DNA

Many eukaryotic mobile elements have been identified, but few have any obvious function. This has led to the proposal that many such elements may be parasitic DNA. We have used the 2 micron circle plasmid of Saccharomyces cerevisiae as a model system to investigate the maintenance of a cryptic genetic element. We find that under certain conditions this plasmid can spread through experimental populations despite demonstrable selection against it. This spread is dependent upon outbreeding, suggesting that cell to cell transmission of the plasmid during the yeast sexual cycle can counterbalance selection, and maintain the plasmid in populations. This result provides experimental support for the idea that some mobile elements may be parasitic DNA.     

Optimal medium use for continuous high density perfusion processes

For maintenance of high cell density in continuous perfusion processes not only feeding with substrates but also removal of inhibitors and toxic waste products are of special interest. High perfusion rates cause large volumes of product containing medium which have to be processed in product isolation. In order to minimize these volumes concentrated feed solutions of optimized medium are used. On the other hand, such media may cause high concentrations of toxic or inhibitory metabolites which can negatively influence cell growth and product formation. Especially, if the spent medium (or special parts of it) is used again after product isolation, the removal or even better the control of inhibitor production is of highest importance. We have developed a continuous fermentation concept and system (continuous medium cycle bioreactor, cMCB) in which both limitation and inhibition effects can be generated to identify special substances as limiting or inhibitory components. With the results from those experiments it was possible to lower the total perfusion rate during serum-free perfusion cultures of hybridoma cells and to obtain an optimal substrate utilization. The advantages for decreasing the production costs (for media, special supplements and product isolation) are obvious. The other aim of this study was to identify secreted metabolic waste products as inhibitor or toxic metabolite.