Selection-mutation balance models with epistatic selection

We present an application of birth-and-death processes on configuration spaces to a generalized mutation4 selection balance model. The model describes the aging of population as a process of accumulation of mu5 tations in a genotype. A rigorous treatment demands that mutations correspond to points in abstract spaces. 6 Our model describes an infinite-population, infinite-sites model in continuum. The dynamical equation which 7 describes the system, is of Kimura-Maruyama type. The problem can be posed in terms of evolution of states 8 (differential equation) or, equivalently, represented in terms of Feynman-Kac formula. The questions of interest 9 are the existence of a solution, its asymptotic behavior, and properties of the limiting state. In the non-epistatic 10 case the problem was posed and solved in [Steinsaltz D., Evans S.N., Wachter K.W., Adv. Appl. Math., 2005, 11 35(1)]. In our model we consider a topological space X as the space of positions of mutations and the influence of epistatic potentials

Mechanisms of inverse agonist action at D-2 dopamine receptors

1 Mechanisms of inverse agonist action at the D-2(short) dopamine receptor have been examined. 2 Discrimination of G-protein-coupled and -uncoupled forms of the receptor by inverse agonists was examined in competition ligand-binding studies versus the agonist [H-3]NPA at a concentration labelling both G-protein-coupled and -uncoupled receptors. 3 Competition of inverse agonists versus [H-3] NPA gave data that were fitted best by a two-binding site model in the absence of GTP but by a one-binding site model in the presence of GTP. K-i values were derived from the competition data for binding of the inverse agonists to G-protein-uncoupled and -coupled receptors. K-coupled and K-uncoupled were statistically different for the set of compounds tested ( ANOVA) but the individual values were different in a post hoc test only for (+)-butaclamol. 4 These observations were supported by simulations of these competition experiments according to the extended ternary complex model. 5 Inverse agonist efficacy of the ligands was assessed from their ability to reduce agonist-independent [S-35]GTPγ S binding to varying degrees in concentration-response curves. Inverse agonism by (+)-butaclamol and spiperone occurred at higher potency when GDP was added to assays, whereas the potency of (-)-sulpiride was unaffected. 6 These data show that some inverse agonists ((+)-butaclamol, spiperone) achieve inverse agonism by stabilising the uncoupled form of the receptor at the expense of the coupled form. For other compounds tested, we were unable to define the mechanism.

Investigation of the mechanism of agonist and inverse agonist action at D-2 dopamine receptors

This study investigated, for the D-2 dopamine receptor, the relation between the ability of agonists and inverse agonists to stabilise different states of the receptor and their relative efficacies. K-i values for agonists were determined in competition, versus the binding of the antagonist [H-3]spiperone. Competition data were fitted best by a two-binding site model (with the exception of bromocriptine, for which a one-binding site model provided the best fit) and agonist affinities for the higher (K-h) (G protein-coupled) and lower affinity (K-l) (G protein-uncoupled) sites determined. Ki values for agonists were also determined in competition versus the binding of the agonist [H-3]N-propylnorapomorphine (NPA) to provide a second estimate of K-h,. Maximal agonist effects (E-max) and their potencies (EC50) were determined from concentration-response curves for agonist stimulation of guanosine-5'-O-(3-[S-32] thiotriphosphate) ([S-35]GTPgammaS) binding. The ability of agonists to stabilise the G protein-coupled state of the receptor (K-l/K-h, determined from ligand-binding assays) did not correlate with either of two measures of relative efficacy (relative E-max, Kl/EC50) of agonists determined in [S-35]GTPgammaS-binding assays, when the data for all of the compounds tested were analysed For a subset of compounds, however, there was a relation between K-l/K-h and E-max.. Competition-binding data versus [H-3]spiperone and [H-3]NPA for a range of inverse agonists were fitted best by a one-binding site model. K-i values for the inverse agonists tested were slightly lower in competition versus [H-3]NPA compared to [H-3]spiperone. These data do not provide support for the idea that inverse agonists act by binding preferentially to the ground state of the receptor. (C) 2004 Elsevier Inc. All rights reserved.

Analysis of molecular determinants of affinity and relative efficacy of a series of R- and S-2-(dipropylamino)tetralins at the 5-HT1A serotonin receptor

1 Factors influencing agonist affinity and relative efficacy have been studied for the 5-HT1A serotonin receptor using membranes of CHO cells expressing the human form of the receptor and a series of R-and S-2-(dipropylamino)tetralins (nonhydroxylated and monohydroxylated (5-OH, 6-OH, 7-OH, 8-OH) species). 2 Ligand binding studies were used to determine dissociation constants for agonist binding to the 5HT(1A) receptor: (a) K-i values for agonists were determined in competition versus the binding of the agonist [H-3]-8-OH DPAT. Competition data were all fitted best by a one-binding site model. (b) K-i values for agonists were also determined in competition versus the binding of the antagonist [H-3]-NAD-199. Competition data were all fitted best by a two-binding site model, and agonist affinities for the higher (K-h) and lower affinity (K-1) sites were determined. 3 The ability of the agonists to activate the 5-HT1A receptor was determined using stimulation of [S-35]-GTPgammaS binding. Maximal effects of agonists (E-max) and their potencies (EC50) were determined from concentration/response curves for stimulation of [S-35]-GTPgammaS binding. 4 K-1/K-h determined from ligand binding assays correlated with the relative efficacy (relative Em) of agonists determined in [S-35]-GTPgammaS binding assays. There was also a correlation between K-1/K-h and K-1/EC50 for agonists determined from ligand binding and [S-35]-GTPgammaS binding assays. 5 Simulations of agonist binding and effect data were performed using the Ternary Complex Model in order to assess the use of K-1/K-h for predicting the relative efficacy of agonists. British Journal of Pharmacology (2003) 138, 1129-1139. doi: 10. 1038/sj.bjp.705085.

Population subdivision and molecular sequence variation: Theory and analysis of Drosophila ananassae data

Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to Mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter Theta to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of Theta, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

Mechanisms of inverse agonist action at D-2 dopamine receptors

1 Mechanisms of inverse agonist action at the D-2(short) dopamine receptor have been examined. 2 Discrimination of G-protein-coupled and -uncoupled forms of the receptor by inverse agonists was examined in competition ligand-binding studies versus the agonist [H-3]NPA at a concentration labelling both G-protein-coupled and -uncoupled receptors. 3 Competition of inverse agonists versus [H-3] NPA gave data that were fitted best by a two-binding site model in the absence of GTP but by a one-binding site model in the presence of GTP. K-i values were derived from the competition data for binding of the inverse agonists to G-protein-uncoupled and -coupled receptors. K-coupled and K-uncoupled were statistically different for the set of compounds tested ( ANOVA) but the individual values were different in a post hoc test only for (+)-butaclamol. 4 These observations were supported by simulations of these competition experiments according to the extended ternary complex model. 5 Inverse agonist efficacy of the ligands was assessed from their ability to reduce agonist-independent [S-35]GTPγ S binding to varying degrees in concentration-response curves. Inverse agonism by (+)-butaclamol and spiperone occurred at higher potency when GDP was added to assays, whereas the potency of (-)-sulpiride was unaffected. 6 These data show that some inverse agonists ((+)-butaclamol, spiperone) achieve inverse agonism by stabilising the uncoupled form of the receptor at the expense of the coupled form. For other compounds tested, we were unable to define the mechanism.

Pharmacological evidence for beta(2)-adrenoceptor in right atria from stressed female rats

The purpose of the present study was to demonstrate a physiological response to TA2005, a potent beta(2)-adrenoceptor (beta(2)-AR) selective agonist, in right atria isolated from stressed female rats under the influence of the estrous cycle. We obtained concentration-response curves to the agonist in the presence and in the absence of selective antagonists in right atria isolated from female rats submitted to three daily foot-shock sessions (30 min duration, 120 pulses of 1.0 mA, 1.0 s, applied at random intervals of 5-25 s) and sacrificed at estrus or diestrus. Our results showed that the pD(2), values of TA2005 were not influenced by estrous cycle phase or foot-shock stress. However, in right atria from stressed rats sacrificed during diestrus, the concentration-response curve to TA2005 was biphasic, with a response being obtained at concentrations of 0.1 nM, whereas during estrus no response was observed at doses lower than 3 nM. ICI118,551, a beta(2)-AR antagonist, abolished the response to nanomolar concentrations of TA2005 in right atria from stressed rats at diestrus, with no changes in a,agonist pot values in right atria from control rats (7.47 +/- 0.09, p > 0.05) but a 3-fold decrease in pD(2), values of TA2005 in right atria from foot shock stressed rats (7.90 +/- 0.07, p less than or equal to 0.05). Concentration-response curves to TA2005 in the presence of ICI118,551 were best fitted by a one-site model equation. The beta(1)-AR antagonist, CGP20712A, shifted to the right only the second part of the concentration-response curves to the agonist, unmasking the putative Pz-AR-mediated response to the agonist in tissues isolated from stressed rats at diestrus. Under this condition, concentration-response curves to the agonist were best fitted by a two-site model equation. pot and maximum response of TA2005 interaction with beta(1)- and putative Pz-adrenoceptor components were calculated. Schild analyses gave a pK(B) value for CGP20712A that was typical for the interaction with beta(1)-AR in each experimental group. pK(B), values for ICI118,551 could not be obtained in stressed rats sacrificed at diestrus since Schild plot slopes were lower than 1.0. In right atria from control rats, ICI118,551 pK(B), values were similar to reported values for the interaction of the antagonist with beta(1)-AR. These results confirm that a heterogenous PAR population mediating the chronotropic response to catecholamines can be demonstrated in right atria from foot shock stressed female rats sacrificed at diestrus. The stress-induced response seems to be mediated by the beta(2)-AR subtype. Right atria from rats sacrificed during estrus are protected against stress-induced alterations on the homogeneity of PAR population.

A new biophysics approach using photoacoustic spectroscopy to study the DNA-ethidium bromide interaction

We have examined the binding processes of ethidium bromide interacting with calf thymus DNA using photoacoustic spectroscopy. These binding processes are generally investigated by a combination of absorption or fluorescence spectroscopies with hydrodynamic techniques. The employment of photoacoustic spectroscopy for the DNA-ethidium bromide system identified two binding manners for the dye. The presence of two isosbestic points (522 and 498 nm) during DNA titration was evidence of these binding modes. Analysis of the photoacoustic amplitude signal data was performed using the McGhee-von Hippel excluded site model. The binding constant obtained was 3.4 x 10(8) M(bp)(-1), and the number of base pairs excluded to another dye molecule by each bound dye molecule (n) was 2. A DNA drug dissociation process was applied using sodium dodecyl sulfate to elucidate the existence of a second and weaker binding mode. The dissociation constant determined was 0.43 mM, whose inverse value was less than the previously obtained binding constant, demonstrating the existence of the weaker binding mode. The calculated binding constant was adjusted by considering the dissociation constant and its new value was 1.2 x 10(9) M(bp)(-1) and the number of excluded sites was 2.6. Using the photoacoustic technique it is also possible to obtain results regarding the dependence of the quantum yield of the dye on its binding mode. While intercalated between two adjacent base pairs the quantum yield found was 0.87 and when associated with an external site it was 0.04. These results reinforce the presence of these two binding processes and show that photoacoustic spectroscopy is more extensive than commonly applied spectroscopies.

Study of water and dimethylformamide interaction by computer simulation

Monte Carlo simulations of water-dimethylformamide (DMF) mixtures were performed in the isothermal and isobaric ensemble at 298.15 K and 1 atm. The intermolecular interaction energy was calculated using the classical 6-12 Lennard-Jones pairwise potential plus a Coulomb term. The TIP4P model was used for simulating water molecules, and a six-site model previously optimised by us was used to represent DMF. The potential energy for the water-DMF interaction was obtained via standard geometric combining rules using the original potential parameters for the pure liquids. The radial distribution functions calculated for water-DMF mixtures show well characterised hydrogen bonds between the oxygen site of DMF and hydrogen of water. A structureless correlation curve was observed for the interaction between the hydrogen site of the carbonyl group and the oxygen site of water. Hydration effects on the stabilisation of the DMF molecule in aqueous solution have been investigated using statistical perturbation theory. The results show that energetic changes involved in the hydration process are not strong enough to stabilise another configuration of DMF than the planar one.

Pharmacological evidence for β2-adrenoceptor in right atria from stressed female rats

The purpose of the present study was to demonstrate a physiological response to TA2005, a potent β2-adrenoceptor (β2-AR) selective agonist, in right atria isolated from stressed female rats under the influence of the estrous cycle. We obtained concentration-response curves to the agonist in the presence and in the absence of selective antagonists in right atria isolated from female rats submitted to three daily foot-shock sessions (30 min duration, 120 pulses of 1.0 mA, 1.0 s, applied at random intervals of 5- 25 s) and sacrificed at estrus or diestrus. Our results showed that the pD2 values of TA2005 were not influenced by estrous cycle phase or foot-shock stress. However, in right atria from stressed rats sacrificed during diestins, the concentration-response curve to TA2005 was biphasic, with a response being obtained at concentrations of 0.1 nM, whereas during estrus no response was observed at doses lower than 3 nM. ICI118,551, a β2-AR antagonist, abolished the response to nanomolar concentrations of TA2005 in right atria from stressed rats at diestrus, with no changes in agonist pD2 values in right atria from control rats (7.47 ± 0.09, p > 0.05) but a 3-fold decrease in pD2 values of TA2005 in right atria from foot shock stressed rats (7.90 ± 0.07, p ≤ 0.05). Concentration-response curves to TA2005 in the presence of ICI118,551 were best fitted by a one-site model equation. The β1-AR antagonist, CGP20712A, shifted to the right only the second part of the concentration-response curves to the agonist, unmasking the putative β2-AR-mediated response to the agonist in tissues isolated from stressed rats at diestrus. Under this condition, concentration-response curves to the agonist were best fitted by a two-site model equation, pD2 and maximum response of TA2005 interaction with β1- and putative β2-adrenoceptor components were calculated. Schild analyses gave a pK(B) value for CGP20712A that was typical for the interaction with β1-AR in each experimental group, pK(B) values for ICI118,551 could not be obtained in stressed rats sacrificed at diestins since Schild plot slopes were lower than 1.0. In right atria from control rats, ICI118,551 pK(B) values were similar to reported values for the interaction of the antagonist with β1-AR. These results confirm that a heterogenous β1-AR population mediating the chronotropic response to catecholamines can be demonstrated in right atria from foot shock stressed female rats sacrificed at diestins. The stress-induced response seems to be mediated by the β2-AR subtype. Right atria from rats sacrificed during estrus are protected against stress-induced alterations on the homogeneity of β-AR population.

Investigação geoambiental com tomada de decisão em campo utilizando o piezocone de resistividade como ferramenta de alta resolução: Marcos Tanaka Riyis. -

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Acionamento de dois sistemas de bombeamento alimentados por uma central de microgeração fotovoltaica

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

An Optimal Control Framework for Resources Management in Agriculture

An optimal control framework to support the management and control of resources in a wide range of problems arising in agriculture is discussed. Lessons extracted from past research on the weed control problem and a survey of a vast body of pertinent literature led to the specification of key requirements to be met by a suitable optimization framework. The proposed layered control structure—including planning, coordination, and execution layers—relies on a set of nested optimization processes of which an “infinite horizon” Model Predictive Control scheme plays a key role in planning and coordination. Some challenges and recent results on the Pontryagin Maximum Principle for infinite horizon optimal control are also discussed.

Investigação geoambiental de áreas contaminadas com elaboração do modelo conceitual em campo utilizando ferramentas de alta resolução (HRSC)

The Brazilian geo-environmental site characterizations usually do not provide a suitable Conceptual Site Model (CSM). Site assessments are mostly inappropriate and there is a lack of knowledge about the subsurface environment, generated by inconsistent data that will guide risk analyses and remediation projects full of uncertainties, causing delay on closing cases, inefficient remediation and higher global projects costs. The step of data collection must have high priority to develop a suitable CSM,, and it demands more effective high resolution site characterization (HRSC) tools than the traditional ones and, preferably, the decision-making have to be done in the field. This paper presents and discusses two geo-environmental site characterization results, in which the decision-making was done in the field based on high resolution site characterization (HRSC) used together with the traditional ones. These site investigations provided a significant time saving, allowed the detection of subsoil heterogeneities, a proper understanding of the subsurface environmental, and have generated a solid CSM in real-time. These CSM can subsidize remediation projects based on a more reliable data than those that would be obtained in traditional site investigations, concerned just in following the rules established by the environmental agencies.

Natural tracer profiles across argillaceous formations

Argillaceous formations generally act as aquitards because of their low hydraulic conductivities. This property, together with the large retention capacity of clays for cationic contaminants, has brought argillaceous formations into focus as potential host rocks for the geological disposal of radioactive and other waste. In several countries, programmes are under way to characterise the detailed transport properties of such formations at depth. In this context, the interpretation of profiles of natural tracers in pore waters across the formations can give valuable information about the large-scale and long-term transport behaviour of these formations. Here, tracer-profile data, obtained by various methods of pore-water extraction for nine sites in central Europe, are compiled. Data at each site comprise some or all of the conservative tracers: anions (Cl(-), Br(-)), water isotopes (delta(18)O, delta(2)H) and noble gases (mainly He). Based on a careful evaluation of the palaeo-hydrogeological evolution at each site, model scenarios are derived for initial and boundary pore-water compositions and an attempt is made to numerically reproduce the observed tracer distributions in a consistent way for all tracers and sites, using transport parameters derived from laboratory or in situ tests. The comprehensive results from this project have been reported in Mazurek et al. (2009). Here the results for three sites are presented in detail, but the conclusions are based on model interpretations of the entire data set. In essentially all cases, the shapes of the profiles can be explained by diffusion acting as the dominant transport process over periods of several thousands to several millions of years and at the length scales of the profiles. Transport by advection has a negligible influence on the observed profiles at most sites, as can be shown by estimating the maximum advection velocities that still give acceptable fits of the model with the data. The advantages and disadvantages of different conservative tracers are also assessed. The anion Cl(-) is well suited as a natural tracer in aquitards, because its concentration varies considerably in environmental waters. It can easily be measured, although the uncertainty regarding the fraction of the pore space that is accessible to anions in clays remains an issue. The stable water isotopes are also well suited, but they are more difficult to measure and their values generally exhibit a smaller relative range of variation. Chlorine isotopes (delta(37)Cl) and He are more difficult to interpret because initial and boundary conditions cannot easily be constrained by independent evidence. It is also shown that the existence of perturbing events such as the activation of aquifers due to uplift and erosion, leading to relatively sharp changes of boundary conditions, can be considered as a pre-requisite to obtain well-interpretable tracer signatures. On the other hand, gradual changes of boundary conditions are more difficult to parameterise and so may preclude a clear interpretation.