Tânia Sousa

From empirical patterns to theory: a formal metabolic theory of life

The diversity of life on Earth raises the question of whether it is possible to have a single theoretical description of the quantitative aspects of the organization of metabolism for all organisms. However, similarities between organisms, such as von Bertalanffys growth curve and Kleibers law on metabolic rate, suggest that mechanisms that control the uptake and use of metabolites are common to all organisms. These and other widespread empirical patterns in biology should be the ultimate test for any metabolic theory that hopes for generality. The present study (i) collects empirical evidence on growth, stoichiometry, feeding, respiration and energy dissipation and exhibits it as stylized biological facts; (ii) formalizes assumptions and propositions in a metabolic theory that is fully consistent with the Dynamic Energy Budget theory; and (iii) proves that these assumptions and propositions are consistent with the stylized facts.

Dynamic energy budget theory restores coherence in biology

We present the state of the art of the development of dynamic energy budget theory, and its expected developments in the near future within the molecular, physiological and ecological domains. The degree of formalization in the set-up of the theory, with its roots in chemistry, physics, thermodynamics, evolution and the consistent application of Occams razor, is discussed. We place the various contributions in the theme issue within this theoretical setting, and sketch the scope of actual and potential applications.

From food-dependent statistics to metabolic parameters, a practical guide to the use of dynamic energy budget theory.

The standard model of the dynamic energy budget theory for metabolic organisation has variables and parameters that can be quantified using indirect methods only. We present new methods (and software) to extract food‐independent parameter values of the energy budget from food‐dependent quantities that are easy to observe, and so facilitate the practical application of the theory to enhance predictability and extrapolation. A natural sequence of 10 steps is discussed to obtain some compound parameters first, then the primary parameters, then the composition parameters and finally the thermodynamic parameters; this sequence matches a sequence of required data of increasing complexity which is discussed in detail. Many applications do not require knowledge of all parameters, and we discuss methods to extrapolate parameters from one species to another. The conversion of mass, volume and energy measures of biomass is discussed; these conversions are not trivial because biomass can change in chemical composition in particular ways thanks to different forms of homeostasis. We solve problems like “What would be the ultimate reproduction rate and the von Bertalanffy growth rate at a specific food level, given that we have measured these statistics at abundant food?” and “What would be the maximum incubation time, given the parameters of the von Bertalanffy growth curve?”. We propose a new non‐destructive method for quantifying the chemical potential and entropy of living reserve and structure, that can potentially change our ideas on the thermodynamic properties of life. We illustrate the methods using data on daphnids and molluscs.

Physics of metabolic organization.

We review the most comprehensive metabolic theory of life existing to date. A special focus is given to the thermodynamic roots of this theory and to implications that the laws of physics-such as the conservation of mass and energy-have on all life. Both the theoretical foundations and biological applications are covered. Hitherto, the foundations were more accessible to physicists or mathematicians, and the applications to biologists, causing a dichotomy in what always should have been a single body of work. To bridge the gap between the two aspects of the same theory, we (i) adhere to the theoretical formalism, (ii) try to minimize the amount of information that a reader needs to process, but also (iii) invoke examples from biology to motivate the introduction of new concepts and to justify the assumptions made, and (iv) show how the careful formalism of the general theory enables modular, self-consistent extensions that capture important features of the species and the problem in question. Perhaps the most difficult among the introduced concepts, the utilization (or mobilization) energy flow, is given particular attention in the form of an original and considerably simplified derivation. Specific examples illustrate a range of possible applications-from energy budgets of individual organisms, to population dynamics, to ecotoxicology.

Cytotoxic bile acids, but not cytoprotective species, inhibit the ordering effect of cholesterol in model membranes at physiologically active concentrations.

Submillimolar concentrations of cytotoxic bile acids (BAs) induce cell death via apoptosis. On the other hand, several cytoprotective BAs were shown to prevent apoptosis in the same concentration range. Still, the mechanisms by which BAs trigger these opposite signaling effects remain unclear. This study was aimed to determine if cytotoxic and cytoprotective BAs, at physiologically active concentrations, are able to modulate the biophysical properties of lipid membranes, potentially translating into changes in the apoptotic threshold of cells. Binding of BAs to membranes was assessed through the variation of fluorescence parameters of suitable derivatized BAs. These derivatives partitioned with higher affinity to liquid disordered than to the cholesterol-enriched liquid ordered domains. Unlabeled BAs were also shown to have a superficial location upon interaction with the lipid membrane. Additionally, the interaction of cytotoxic BAs with membranes resulted in membrane expansion, as concluded from FRET data. Moreover, it was shown that cytotoxic BAs were able to significantly disrupt the ordering of the membrane by cholesterol at physiologically active concentrations of the BA, an effect not associated with cholesterol removal. On the other hand, cytoprotective bile acids had no effect on membrane properties. It was concluded that, given the observed effects on membrane rigidity, the apoptotic activity of cytotoxic BAs could be potentially associated with changes in plasma membrane organization (e.g. modulation of lipid domains) or with an increase in mitochondrial membrane affinity for apoptotic proteins.

Stylized facts in microalgal growth: interpretation in a dynamic energy budget context

A dynamic energy budget (DEB) model for microalgae is proposed. This model deviates from the standard DEB model as it needs more reserves to cope with the variation of assimilation pathways, requiring a different approach to growth based on the synthesizing unit (SU) theory for multiple substrates. It is shown that the model is able to accurately predict experimental data in constant and light-varying conditions with most of the parameter values taken directly from the literature. Also, model simulations are shown to be consistent with stylized facts (SFs) concerning N∶C ratio. These SFs are reinterpreted and the general conclusion is that all forcing variables (dilution rate, temperature and irradiance) impose changes in the nitrogen or carbon limitation status of the population, and consequently on reserve densities. Model predictions are also evaluated in comparison with SFs on chlorophyll concentration. It is proposed that an extra structure, more dependent on the nitrogen reserve, is required to accurately model chlorophyll dynamics. Finally, SFs concerning extracellular polymeric substances (EPSs) production by benthic diatoms are collected and interpreted and a formulation based on product synthesis and rejection flux is proposed for the EPSs production rate.

Deoxycholic acid modulates cell death signaling through changes in mitochondrial membrane properties

Cytotoxic bile acids, such as deoxycholic acid (DCA), are responsible for hepatocyte cell death during intrahepatic cholestasis. The mechanisms responsible for this effect are unclear, and recent studies conflict, pointing to either a modulation of plasma membrane structure or mitochondrial-mediated toxicity through perturbation of mitochondrial outer membrane (MOM) properties. We conducted a comprehensive comparative study of the impact of cytotoxic and cytoprotective bile acids on the membrane structure of different cellular compartments. We show that DCA increases the plasma membrane fluidity of hepatocytes to a minor extent, and that this effect is not correlated with the incidence of apoptosis. Additionally, plasma membrane fluidity recovers to normal values over time suggesting the presence of cellular compensatory mechanisms for this perturbation. Colocalization experiments in living cells confirmed the presence of bile acids within mitochondrial membranes. Experiments with active isolated mitochondria revealed that physiologically active concentrations of DCA change MOM order in a concentration- and time-dependent manner, and that these changes preceded the mitochondrial permeability transition. Importantly, these effects are not observed on liposomes mimicking MOM lipid composition, suggesting that DCA apoptotic activity depends on features of mitochondrial membranes that are absent in protein-free mimetic liposomes, such as the double-membrane structure, lipid asymmetry, or mitochondrial protein environment. In contrast, the mechanism of action of cytoprotective bile acids is likely not associated with changes in cellular membrane structure.

Characterization of a Squaraine/Chitosan System for Photodynamic Therapy of Cancer.

In this work, a squaraine dye CS5 was characterized and evaluated for its potential in photodynamic therapy. The studies were performed in ethanol and also in a powdered biopolymer, in this case chitosan. Ground state absorption, absolute fluorescence quantum yields, fluorescence lifetimes, and transient absorption were determined in order to evaluate the advantage of adsorbing the dye onto a biopolymer. Several concentrations of the dye, adsorbed onto chitosan, were prepared in order to evaluate the concentration effect on the photophysical parameters under study. A remarkable increase in the fluorescence quantum yield and lifetimes was detected when compared with the dye in solution. Also, a very clear dependence of the fluorescence quantum yield on the concentration range was found. A lifetime distribution analysis of these systems fluorescence evidenced the entrapment of the dye onto the chitosan environment with a monoexponential decay which corresponds to the monomer emission in slightly different environments. The transient absorption spectrum was obtained without sensitization indicating the existence of a triplet state which takes special importance in the generation of phototoxic species namely singlet oxygen. The subcellular localization of a photosensitizer is critical for efficient photoinduced cell death, in this way, colocalization studies were performed within HeLa cell line (human cervical carcinoma) through confocal microscopy. Toxicity in the dark and phototoxicity of CS5 were also evaluated for the same cellular model.

Comment on “Energy Uptake and Allocation During Ontogeny”

Hou et al. (Reports, 31 October 2008, p. 736) presented a model for energy uptake and allocation over an organism’s growth and development. However, their model does not account for allocation to reproduction (essential to adults) and growth without assimilation (essential to embryos) and is therefore only applicable to organisms growing with abundant food in the juvenile stage.

Life engine - creating artificial life for scientific and entertainment purposes

The Dynamic Energy Budget (DEB) theory has become a fundamental tool in modeling the metabolic behaviour of organisms. Its capacity to describe the biological aspect of life alone justifies its applicability in Artificial Life. Aware of this potential, the DEB research group in Instituto Superior Tecnico (IST) in Lisbon has joined the videogame company Biodroid Entertainment in the Life Engine project. This project aims to develop a library for scientific purposes but also to create a biology engine for videogames. From the scientific point-of-view, this library is intended to be the standard tool for DEB researchers and, at the same time, to popularize DEB theory in other scientific communities, such as the AL community.