ESS analysis of mechanistic models for territoriality: the value of scent marks in spatial resource partitioning

In this paper elements of game theory are used to analyse a spatially explicit home range model for interacting wolf packs. The model consists of a system of nonlinear partial differential equations whose parameters reflect the movement behavior of individuals within each pack and whose solutions describe the patterns of space-use by each pack. By modifying the behavioral parameters, packs adjust their patterns of movement so as to maximize their reproductive output. This involves a tradeoff between maximizing prey intake and minimizing conflict with neighbors. Evolutionarily stable choices of the behavioral parameters yields territories that are immune to invasion by groups with alternate behaviors.     

A game theoretical approach to conspecific brood parasitism

We constructed a game theoretical model to predict optimal patternsof egg laying in systems where individuals lay in the nestsof others as well as in their own nests. We show that decreasingthe effect of position within an egg-laying sequence on theworth of an egg should lead to reduced parasitism. Indeed,parasitism can only flourish if the worth of an egg to its biological parent declines with the total number of eggs laid in that nest.Further, we found that increasing the intrinsic costs of eggproduction should lead to an increased propensity for conspecificbrood parasitism. The model also predicts that variation inhosts' ability to reject parasitic eggs has little effect on parasitism until this ability is well developed.     

A game theoretical model of kleptoparasitism with incomplete information

Kleptoparasitism, the stealing of food from one animal by another, is a common natural phenomenon that has been modelled mathematically in a number of ways. The handling process of food items can take some time and the value of such items can vary depending upon how much handling an item has received. Furthermore this information may be known to the handler but not the potential challenger, so there is an asymmetry between the information possessed by the two competitors. We use game-theoretic methods to investigate the consequences of this asymmetry for continuously consumed food items, depending upon various natural parameters. A variety of solutions are found, and there are complex situations where three possible solutions can occur for the same set of parameters. It is also possible to have situations which involve members of the population exhibiting different behaviours from each other. We find that the asymmetry of information often appears to favour the challenger, despite the fact that it possesses less information than the challenged individual. The research was supported by EPSRC grant EP/E043402/1 and NSF 0634182.     

DNA methyltransferases: mechanistic models derived from kinetic analysis

The sequence-specific transfer of methyl groups from donor S-adenosyl-L-methionine (AdoMet) to certain positions of DNA-adenine or -cytosine residues by DNA methyltransferases (MTases) is a major form of epigenetic modification. It is virtually ubiquitous, except for some notable exceptions. Site-specific methylation can be regarded as a means to increase DNA information capacity and is involved in a large spectrum of biological processes. The importance of these functions necessitates a deeper understanding of the enzymatic mechanism(s) of DNA methylation. DNA MTases fall into one of two general classes; viz. amino-MTases and [C5-cytosine]-MTases. Amino-MTases, common in prokaryotes and lower eukaryotes, catalyze methylation of the exocyclic amino group of adenine ([N6-adenine]-MTase) or cytosine ([N4-cytosine]-MTase). In contrast, [C5-cytosine]-MTases methylate the cyclic carbon-5 atom of cytosine. Characteristics of DNA MTases are highly variable, differing in their affinity to their substrates or reaction products, their kinetic parameters, or other characteristics (order of substrate binding, rate limiting step in the overall reaction). It is not possible to present a unifying account of the published kinetic analyses of DNA methylation because different authors have used different substrate DNAs and/or reaction conditions. Nevertheless, it would be useful to describe those kinetic data and the mechanistic models that have been derived from them. Thus, this review considers in turn studies carried out with the most consistently and extensively investigated [N6-adenine]-, [N4-cytosine]- and [C5-cytosine]-DNA MTases.     

A game theoretical model of deforestation in human-environment relationships

We studied a two-person game regarding deforestation in human-environment relationships. Each landowner manages a single land parcel where the state of land-use is forested, agricultural, or abandoned. The landowner has two strategies available: forest conservation and deforestation. The choice of deforestation provides a high return to the landowner, but it degrades the forest ecosystem services produced on a neighboring land parcel managed by a different landowner. Given spatial interactions between the two landowners, each landowner decides which strategy to choose by comparing the expected discounted utility of each strategy. Expected discounted utility is determined by taking into account the current and future utilities to be received, according to the state transition on the two land parcels. The state transition is described by a Markov chain that incorporates a landowner's choice about whether to deforest and the dynamics of agricultural abandonment and forest regeneration. By considering a stationary distribution of the Markov chain for land-use transitions, we derive explicit conditions for Nash equilibrium. We found that a slow regeneration of forests favors mutual cooperation (forest conservation). As the forest regenerates faster, mutual cooperation transforms to double Nash equilibria (mutual cooperation and mutual defection), and finally mutual defection (deforestation) leads to a unique Nash equilibrium. Two different types of social dilemma emerge in our deforestation game. The stag-hunt dilemma is most likely to occur under an unsustainable resource supply, where forest regenerates extremely slowly but agricultural abandonment happens quite rapidly. In contrast, the prisoner's dilemma is likely under a persistent or circulating supply of resources, where forest regenerates rapidly and agricultural abandonment occurs slowly or rapidly. These results show how humans and the environment mutually shape the dilemma structure in forest management, implying that solutions to dilemmas depend on environmental properties.     

Comparative analysis of two dynamic mechanistic models of beef cattle growth

The INRA Growth Model (IGM) and the Davis Growth Model (DGM) are two dynamic mechanistic models developed to predict protein and fat deposition in growing cattle whatever the production system. Both models depend on animal genotype and age, metabolizable energy intake (MEI) and knowledge of previous growth. The aim of this paper was (i) to identify in which situations DGM and/or IGM provide reliable estimations of body protein and fat, (ii) to give insight on the improvements needed in each model and (iii) to discuss the usefulness of comparative analysis for improvement of mechanistic models. We performed a comparative analysis of DGM and IGM with three datasets from published experiments on Salers heifers, Angus-Hereford steers and Charolais bulls. Each model was fitted independently to each dataset. Both models gave accurate and precise predictions of body protein. They also performed well for body fat in Charolais bulls growing continuously. However, DGM tended to underestimate body fat deposition during feeding restriction periods with Salers heifers. This suggests that DGM overestimated heat production during periods of low MEI. IGM was not sensitive enough to MEI as it overestimates body fat at low MEI and it underestimates body fat at high MEI in Angus-Hereford steers. Presently, IGM does not take into account metabolizable energy concentration (MEC) of the diet and thus does not simulate different growth trajectories for same MEI but different MEC. These results suggest that model's structure and equations for protein accretion in DGM and IGM are valid. Future improvements will focus on prediction of heat production during feed restriction periods for DGM and on mathematical formulation of feed energy utilisation for fat synthesis in IGM in order to improve model sensitivity to MEI. Comparative analysis provides meaningful information on the models behaviour for further improvement of processes simulations.     

Resource holding potential, subjective resource value, and game theoretical models of aggressiveness signalling

Empirical evidence suggests that aggressiveness (willingness to enter into, or escalate an aggressive interaction) may be more important than the ability to win fights in some species. Both empirical and theoretical traditions treat aggressiveness as a distinct property from the ability (RHP) or motivation (subjective resource value) to win a fight. I examine how these three traits are clearly distinct when modelled using a simple strategic model of escalation. I then examine game theoretical models of agonistic communication and demonstrate that models in which aggressiveness is signalled require: (1) a trait, aggressiveness, which is neither a correlate, nor consequence of RHP or motivation, (2) a handicap which negates any benefit to be gained through the use of a particular signal, and (3) the absence of any other asymmetry which could be used to assign roles to players. I conclude that it is unlikely that these assumptions are ever met, and that empirical examples of "aggressiveness" are far more likely to represent long-term differences in subjective resource value.     

Esterolytic antibodies as mechanistic and structural models of hydrolases-a quantitative analysis

Understanding enzymes quantitatively and mimicking their remarkable catalytic efficiency is a paramount challenge. Here, we applied esterolytic antibodies (the D-Abs) to dissect and quantify individual elements of enzymatic catalysis such as transition state (TS) stabilization, nucleophilic reactivity and conformational changes. Kinetic and mutagenic analysis of the D-Abs were combined with existing structural evidence to show that catalysis by the D-Abs is driven primarily by stabilization of the tetrahedral oxyanionic intermediate of ester hydrolysis formed by the nucleophilic attack of an exogenous (solution) hydroxide anion. The side-chain of TyrH100d is shown to be the main H-bond donor of the D-Abs oxyanion hole. The pH-rate and pH-binding profiles indicate that the strength of this H-bond increases dramatically as the neutral substrate develops into the oxyanionic TS, resulting in TS stabilization of 5-7 kcal/mol, which is comparable to oxyanionic TS stabilization in serine hydrolases. We show that the rate of the exogenous (intermolecular) nucleophilic attack can be enhanced by 2000-fold by replacing the hydroxide nucleophile with peroxide, an alpha-nucleophile that is much more reactive than hydroxide. In the presence of peroxide, the rate saturates (k(cat)(max)) at 6 s(-1). This rate-ceiling appears to be dictated by the rate of the induced-fit conformational rearrangement leading to the active antibody-TS complex. The selective usage of negatively charged exogenous nucleophiles by the D-Abs led to the identification of a positively charged channel. Imprinted by the negatively-charged TS-analogue against which these antibodies were elicited, this channel presumably directs the nucleophile to the antibody-bound substrate. Our findings are discussed in comparison with serine esterases and, in particular, with cocaine esterase (cocE), which possesses a tyrosine based oxyanion hole.     

A game theoretical approach to the evolution of structured communication codes

Structured meaning-signal mappings, i.e., mappings that preserve neighborhood relationships by associating similar signals with similar meanings, are advantageous in an environment where signals are corrupted by noise and sub-optimal meaning inferences are rewarded as well. The evolution of these mappings, however, cannot be explained within a traditional language evolutionary game scenario in which individuals meet randomly because the evolutionary dynamics is trapped in local maxima that do not reflect the structure of the meaning and signal spaces. Here we use a simple game theoretical model to show analytically that when individuals adopting the same communication code meet more frequently than individuals using different codes—a result of the spatial organization of the population—then advantageous linguistic innovations can spread and take over the population. In addition, we report results of simulations in which an individual can communicate only with its K nearest neighbors and show that the probability that the lineage of a mutant that uses a more efficient communication code becomes fixed decreases exponentially with increasing K. These findings support the mother tongue hypothesis that human language evolved as a communication system used among kin, especially between mothers and offspring.     

Animal models for the mechanistic study of systemic lymphangiomatosis

The systematic study of focused animal models has produced an explosion of information regarding the mechanisms governing lymphatic development and the diseases associated with lymphatic dysfunction. Nevertheless, the pathogenesis of systemic lymphangiomatosis has, thus far, eluded mechanistic comprehension. In this review, recent molecular advances in lymphatic vascular development are considered within the context of the animal models that have produced evolving insights. The emerging role of the zebrafish within lymphatic investigation is discussed. Specific models of the human disease pathology are considered in detail. While much has been learned about the molecular framework that surrounds normal lymphatic vascular development, the defect responsible for systemic lymphangiomatosis remains elusive. Development of more robust, recapitulative models will also be invaluable to investigate new and emerging therapeutics for the often devastating disease of systemic lymphangiomatosis.     

A mechanistic investigation on the formation and rearrangement of silaspiropentane: A theoretical study

The formation of silaspiropentane from addition of singlet silacyclopropylidene 1 and silacyclopropylidenoid 8 to ethylene has been investigated separately at the B3LYP, X3LYP, WB97XD, and M05–2X theories using the 6–31+G(d,p) basis set. The silacycloproylidenoid addition follows a stepwise route. In contrast, a concerted mechanism occurs for silacyclopropylidene addition. Moreover, the intramolecular rearrangements of silaspiropentane 9 to methylenesilacyclobutane 11 and 2-silaallene?+?ethylene 12 have been studied extensively. The required energy barrier for the isomerization of 9 to 10 was determined to be 44.0 kcal mol^?1 at the B3LYP/6–31+G(d,p) level. After formation of 10, the rearrangement to methylenesilacyclobutane 12 is highly exergonic by ?15.9 kcal mol^?1, which makes this reaction promising. However, the conversion of 9 to 11 is calculated to be quite endergonic, by 26.5 kcal mol^?1.     

A theoretical study of receptor site models for trimethylammonium group interaction

A model system, depicting the interactions of the trimethylammonium and ammonium groups with possible receptor features has been constructed. The interaction energies of these two onium groups with seven receptor models have been calculated, using the interaction energy procedure of Claverie &; Rein (1969). The change of the energy of binding due to the structural change has been predicted for each receptor model. A ranking of receptor models has been constructed on this basis. The relationship of this change of binding energy to loss of potency of drug molecules containing these two structural features has been examined.     

Towards mechanistic models of plant organ growth

Modelling and simulation are increasingly used as tools in the study of plant growth and developmental processes. By formulating experimentally obtained knowledge as a system of interacting mathematical equations, it becomes feasible for biologists to gain a mechanistic understanding of the complex behaviour of biological systems. In this review, the modelling tools that are currently available and the progress that has been made to model plant development, based on experimental knowledge, are described. In terms of implementation, it is argued that, for the modelling of plant organ growth, the cellular level should form the cornerstone. It integrates the output of molecular regulatory networks to two processes, cell division and cell expansion, that drive growth and development of the organ. In turn, these cellular processes are controlled at the molecular level by hormone signalling. Therefore, combining a cellular modelling framework with regulatory modules for the regulation of cell division, expansion, and hormone signalling could form the basis of a functional organ growth simulation model. The current state of progress towards this aim is that the regulation of the cell cycle and hormone transport have been modelled extensively and these modules could be integrated. However, much less progress has been made on the modelling of cell expansion, which urgently needs to be addressed. A limitation of the current generation models is that they are largely qualitative. The possibilities to characterize existing and future models more quantitatively will be discussed. Together with experimental methods to measure crucial model parameters, these modelling techniques provide a basis to develop a Systems Biology approach to gain a fundamental insight into the relationship between gene function and whole organ behaviour.     

Testing mechanistic models of growth in insects

Insects are typified by their small size, large numbers, impressive reproductive output and rapid growth. However, insect growth is not simply rapid; rather, insects follow a qualitatively distinct trajectory to many other animals. Here we present a mechanistic growth model for insects and show that increasing specific assimilation during the growth phase can explain the near-exponential growth trajectory of insects. The presented model is tested against growth data on 50 insects, and compared against other mechanistic growth models. Unlike the other mechanistic models, our growth model predicts energy reserves per biomass to increase with age, which implies a higher production efficiency and energy density of biomass in later instars. These predictions are tested against data compiled from the literature whereby it is confirmed that insects increase their production efficiency (by 24 percentage points) and energy density (by 4 J mg⁻¹) between hatching and the attainment of full size. The model suggests that insects achieve greater production efficiencies and enhanced growth rates by increasing specific assimilation and increasing energy reserves per biomass, which are less costly to maintain than structural biomass. Our findings illustrate how the explanatory and predictive power of mechanistic growth models comes from their grounding in underlying biological processes.     

Observability analysis of biochemical process models as a valuable tool for the development of mechanistic soft sensors

By enabling the estimation of difficult‐to‐measure target variables using available indirect measurements, mechanistic soft sensors have become important tools for various bioprocess monitoring and control scenarios. Despite promising higher process efficiencies and increased process understanding, widespread application of soft sensors has been stalled by uncertainty about the feasibility and reliability of their estimations given present process analytical constraints. Observability analysis can provide an indication of the possibility and reliability of soft sensor estimations by analyzing the structural properties of first‐principle (mechanistic) models. In addition, it can provide a criteria for selection of suitable measurement methods with respect to their information content; thereby leading to successful implementation of soft sensors in bioprocess development and manufacturing environments. We demonstrate the utility of observability analysis for two classes of upstream bioprocesses: the processes involving growth and ethanol formation by Saccharomyces cerevisiae and the process of penicillin production by Penicillium chrysogenum. Results obtained from laboratory‐scale cultivations in addition to in‐silico experiments enable a comparison of theoretical aspects of observability analysis and the real‐life performance of soft sensors. By taking the expected error of measurements provided to the soft sensor into account, an innovative scaling approach facilitates a higher degree of comparability of observability results among various measurement configurations and process conditions. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1703–1715, 2015     

Basic models for differential inhibition of enzymes

The possible preferential action exerted by an inhibitor on the transformation of one of two agonist substrates catalyzed by the same enzyme has recently been reported in studies on aldose reductase inhibition. This event was defined as “intra-site differential inhibition” and the molecules able to exert this action as “differential inhibitors”. This work presents some basic kinetic models describing differential inhibition. Using a simple analytic approach, the results show that differential inhibition can occur through either competitive or mixed type inhibition in which the inhibitor prevalently targets the free enzyme. The results may help in selecting molecules whose differential inhibitory action could be advantageous in controlling the activity of enzymes acting on more than one substrate.     

A mechanistic analysis of enzymatic degradation of organohalogen compounds

Enzymes that catalyze the conversion of organohalogen compounds have been attracting a great deal of attention, partly because of their possible applications in environmental technology and the chemical industry. We have studied the mechanisms of enzymatic degradation of various organic halo acids. In the reaction of L-2-haloacid dehalogenase and fluoroacetate dehalogenase, the carboxylate group of the catalytic aspartate residue nucleophilically attacked the α-carbon atom of the substrates to displace the halogen atom. In the reaction catalyzed by DL-2-haloacid dehalogenase, a water molecule directly attacked the substrate to displace the halogen atom. In the course of studies on the metabolism of 2-chloroacrylate, we discovered two new enzymes. 2-Haloacrylate reductase catalyzed the asymmetric reduction of 2-haloacrylate to produce L-2-haloalkanoic acid in an NADPH-dependent manner. 2-Haloacrylate hydratase catalyzed the hydration of 2-haloacrylate to produce pyruvate. The enzyme is unique in that it catalyzes the non-redox reaction in an FADH(2)-dependent manner.     

Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage

Small RNAs have a variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify previously unknown rice (Oryza sativa) microRNAs (miRNAs) and those regulated by environmental stress, 62 small RNA libraries were constructed from rice plants and used for deep sequencing with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. More than 94 million genome-matched reads were obtained, resulting in more than 16 million distinct small RNA sequences. This allowed an evaluation of ~400 annotated miRNAs with current criteria and the finding that among these, ~150 had small interfering RNA-like characteristics. Seventy-six new miRNAs were found, and miRNAs regulated in response to water stress, nutrient stress, or temperature stress were identified. Among the new examples of miRNA regulation were members of the same miRNA family that were differentially regulated in different organs and had distinct sequences Some of these distinct family members result in differential target cleavage and provide new insight about how an agriculturally important rice phenotype could be regulated in the panicle. This high-resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae.     

A mechanistic analysis of light and carbon use efficiencies

We explore the extent to which a simple mechanistic model of short-term plant carbon (C) dynamics can account for a number of generally observed plant phenomena. For an individual, fully expanded leaf, the model predicts that the fast-turnover labile C, starch and protein pools are driven into an approximate or moving steady state that is proportional to the average leaf absorbed irradiance on a time-scale of days to weeks, even under realistic variable light conditions, in qualitative agreement with general patterns of leaf acclimation to light observed both temporally within the growing season and spatially within plant canopies. When the fast-turnover pools throughout the whole plant (including stems and roots) also follow this moving steady state, the model predicts that the time-averaged whole-plant net primary productivity is proportional to the time-averaged canopy absorbed irradiance and to gross canopy photosynthesis, and thus suggests a mechanistic explanation of the observed approximate constancy of plant light-use efficiency (LUE) and carbon-use efficiency. Under variable light conditions, the fast-turnover pool sizes and the LUE are predicted to depend negatively on the coefficient of variation of irradiance. We also show that the LUE has a maximum with respect to the fraction of leaf labile C allocated to leaf protein synthesis ( a_lp ), reflecting a trade-off between leaf photosynthesis and leaf respiration. The optimal value of a_lp is predicted to decrease at elevated [CO₂] _a , suggesting an adaptive interpretation of leaf acclimation to CO₂. The model therefore brings together a number of empirical observations within a common mechanistic framework.     

A theoretical analysis of the effects of sonication on differential absorption flattening in suspensions of membrane sheets.

A theoretical analysis is presented for the flattening of absorption and circular dichroic spectra of suspensions of membrane sheets containing proteins. Equations are presented to describe the dependence of this artifact on the size of the sheets. Values for the flattening coefficients QA and QB are calculated both as a function of absorptivity and sheet size. These studies show that sonication in an inadequate procedure for eliminating flattening in these samples.