Evolutionary dynamics of rRNA gene clusters in cichlid fish

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Growth and reproductive dynamics of the South American red shrimp, Pleoticus muelleri (Crustacea: Solenoceridae), from the southeastern coast of Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Dynamics of glyphosate-induced conformational changes of Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) determined by hydrogen-deuterium exchange and electrospray mass spectrometry

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the reaction between shikimate 3-phosphate and phosphoenolpyruvate to form 5-enolpyruvylshikimate 3-phosphate, an intermediate in the shikimate pathway, which leads to the biosynthesis of aromatic amino acids. EPSPS exists in an open conformation in the absence of substrates and/or inhibitors and in a closed conformation when bound to the substrate and/or inhibitor. In the present report, the H/D exchange properties of EPSPS from Mycobacterium tuberculosis (Mt) were investigated for both enzyme conformations using ESI mass spectrometry and circular dichroism (CD). When the conformational changes identified by H/D exchanges were mapped on the 3-D structure, it was observed that the apoenzyme underwent extensive conformational changes due to glyphosate complexation, characterized by an increase in the content of alpha-helices from 40% to 57%, while the beta-sheet content decreased from 30% to 23%. These results indicate that the enzyme underwent a series of rearrangements of its secondary structure that were accompanied by a large decrease in solvent access to many different regions of the protein. This was attributed to the compaction of 71% of alpha-helices and 57% of beta-sheets as a consequence of glyphosate binding to the enzyme. Apparently, MtEPSPS undergoes a series of inhibitor-induced conformational changes, which seem to have caused synergistic effects in preventing solvent access to the core of molecule, especially in the cleft region. This may be part of the mechanism of inhibition of the enzyme, which is required to prevent the hydration of the substrate binding site and also to induce the cleft closure to avoid entrance of the substrates.

Shikimate Kinase (EC 2.7.1.71) from Mycobacterium tuberculosis: Kinetics and Structural Dynamics of a Potential Molecular Target for Drug Development

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Chromosomal organization of the 18S and 5S rRNAs and histone H3 genes in Scarabaeinae coleopterans: insights into the evolutionary dynamics of multigene families and heterochromatin

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The sugarcane borer Diatraea saccharalis (Fabr.) (Lep., Crambidae) and its parasitoids: a synchrony approach to spatial and temporal dynamics

A data set on Diatraea saccharalis and its parasitoids, Cotesia flavipes and tachinid flies, was analysed at five spatial scales-sugarcane mill, region, intermediary, farm and zone-to determine the role of spatial scale in synchrony patterns, and on temporal population variability. To analyse synchrony patterns, only the three highest spatial scales were considered, but for temporal population variability, all spatial scales were adopted. The synchrony-distance relationship revealed complex spatial structures depending on both species and spatial scale. Temporal population variability [SD log(x+1)] levels were highest at the smallest spatial scales although, in the majority of the cases, temporal variability was inversely dependent on sample size. All the species studied, with a few exceptions, presented spatial synchrony independent of spatial scale. The tachinid flies exhibited stronger synchrony dynamics than D. saccharalis and C. flavipes in all spatial scales with the latter displaying the weakest synchrony levels, except when mill spatial scales were compared. In some cases spatial synchrony may at first decay and then increase with distance, but the presence of such patterns can change depending on the spatial scale adopted.

Structure and dynamics of a Cariniana estrellensis (Lecythidaceae) population in a fragment of Atlantic Forest in Minas Gerais, Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Nebular gas drag and co-orbital system dynamics

Aims. We study trajectories of planetesimals whose orbits decay due to gas drag in a primordial solar nebula and are perturbed by the gravity of the secondary body on an eccentric orbit whose mass ratio takes values from mu(2) = 10(-7) to mu(2) = 10(-3) increasing ten times at each step. Each planetesimal ultimately suffers one of the three possible fates: (1) trapping in a mean motion resonance with the secondary body; (2) collision with the secondary body and consequent increase of its mass; or (3) diffusion after crossing the orbit of the secondary body.Methods. We take the Burlirsh-Stoer numerical algorithm in order to integrate the Newtonian equations of the planar, elliptical restricted three-body problem with the secondary body and the planetesimal orbiting the primary. It is assumed that there is no interaction among planetesimals, and also that the gas does not affect the orbit of the secondary body.Results. The results show that the optimal value of the gas drag constant k for the 1: 1 resonance is between 0.9 and 1.25, representing a meter size planetesimal for each AU of orbital radius. In this study, the conditions of the gas drag are such that in theory, L4 no longer exists in the circular case for a critical value of k that defines a limit size of the planetesimal, but for a secondary body with an eccentricity larger than 0.05 when mu(2) = 10(-6), it reappears. The decrease of the cutoff collision radius increase the difusions but does not affect the distribution of trapping. The contribution to the mass accretion of the secondary body is over 40% with a collision radius 0.05R(Hill) and less than 15% with 0.005R(Hill) for mu(2) = 10(-7). The trappings no longer occur when the drag constant k reachs 30. That means that the size limit of planetesimal trapping is 0.2 m per AU of orbital radius. In most cases, this accretion occurs for a weak gas drag and small secondary eccentricity. The diffusions represent most of the simulations showing that gas drag is an efficient process in scattering planetesimals and that the trapping of planetesimals in the 1: 1 resonance is a less probable fate. These results depend on the specific drag force chosen.

Predicting peptides structure with solvation potential and rotamer library dependent of the backbone

In this work, genetic algorithms concepts along with a rotamer library dependent of backbone and implicit solvation potential are used to study the tertiary structure of peptides. We starting from known primary sequence and optimize the structure of the backbone while the side chains allowed adopting the conformations present in a rotamer library. The GA, implemented with two force fields with a growing complexity, was used predict the structure of a polyalanine and a poly-isolueucine. This paper presents good and interesting results about the study of peptides structures and about the development of computational tools to study peptides structures. (C) 2007 Elsevier B.V. All rights reserved.

Dynamics of collapsing and exploding Bose-Einstein condensate

Recently, Donley et al. performed an experiment on the dynamics of collapsing and exploding Bose-Einstein condensates by suddenly changing the scattering length of atomic interaction to a large negative value on a preformed repulsive condensate of Rb-85 atoms in an axially symmetric trap. Consequently, the condensate collapses and ejects atoms via explosions, We show that the accurate numerical solution of the time-dependent Gross-Pitaevskii equation with axial symmetry can explain some aspects of the dynamics of the collapsing condensate. (C) 2002 Published by Elsevier B.V. B.V.

Timelike and spacelike hadron form factors, Fock state components and light-front dynamics

A unified description of spacelike and timelike hadron form factors within a light-front model was successfully applied to the pion. The model is extended to the nucleon to study the role of qq pair production and of nonvalence components in the nucleon form factors. Preliminary results in the spacelike range 0 <= Q(2) <= 10 (GeV/c)(2) are presented.

Relativistic particle dynamics in D=2+1

We propose a SUSY variant of the action for a massless spinning particles via the inclusion of twistor variables. The action is constructed to be invariant under SUSY transformations and tau-reparametrizations even when an interaction field is including. The constraint analysis is achieved and the equations of motion are derived. The commutation relations obtained for the commuting spinor variables lambda(alpha) show that the particle states have fractional statistics and spin. At once we introduce a possible massive term for the non-interacting model.

Noncommutative fluid dynamics in the Snyder space-time

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Scaling properties of the regular dynamics for a dissipative bouncing ball model

Some scaling properties of the regular dynamics for a dissipative version of the one-dimensional Fermi accelerator model are studied. The dynamics of the model is given in terms of a two-dimensional nonlinear area contracting map. Our results show that the velocities of saddle fixed points (saddle velocities) can be described using scaling arguments for different values of the control parameter. (c) 2007 Elsevier B.V. All rights reserved.

Dynamics of two satellites in the 2/1 Mean-Motion resonance: application to the case of Enceladus and Dione

The dynamics of a pair of satellites similar to Enceladus-Dione is investigated with a two-degrees-of-freedom model written in the domain of the planar general three-body problem. Using surfaces of section and spectral analysis methods, we study the phase space of the system in terms of several parameters, including the most recent data. A detailed study of the main possible regimes of motion is presented, and in particular we show that, besides the two separated resonances, the phase space is replete of secondary resonances.