Dynamics of 5S rDNA in the tilapia (Oreochromis niloticus) genome: repeat units, inverted sequences, pseudogenes and chromosome loci

In higher eukaryotes, the 5S ribosomal DNA (5S rDNA) is organized in tandem arrays with repeat units composed of a coding region and a non-transcribed spacer sequence (NTS). These tandem arrays can be found on either one or more chromosome pairs. 5S rDNA copies from the tilapia fish. Oreochromis niloticus, were cloned and the nucleotide sequences of the coding region and of the non-transcribed spacer were deter-mined. Moreover, the genomic organization of the 5S rDNA tandem repeats was investigated by fluorescence in situ hybridization (FISH) and Southern blot hybridization. Two 5S rDNA classes, one consisting of 1.4-kb repeats and another one with 0.5-kb repeats were identified and designated 5S rDNA type I and type II, respectively, An inverted 5S rRNA gene and a 5S rRNA putative pseudogene were also identified inside the tandem repeats of 5S rDNA type I. FISH permitted the visualization of the 5S rRNA genes at three chromosome loci, one of them consisting of arrays of the 5S rDNA type I, and the two others corresponding to arrays of the 5S rDNA type II. The two classes of the 5S rDNA. The presence of pseudogenes, and the inverted genes observed in the O. niloticus genome might be a consequence of the intense dynamics of the evolution of these tandem repeat elements. Copyright (C) 2002 S. Karger AG, Basel.

Evolutionary dynamics of heterochromatin in the genome of Dichotomius beetles based on chromosomal analysis

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

Cytogenetic Mapping of 5S and 18S rRNAs and H3 Histone Genes in 4 Ancient Proscopiidae Grasshopper Species: Contribution to Understanding the Evolutionary Dynamics of Multigene Families

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

Molecular organization of 5S rDNA in sharks of the genus Rhizoprionodon: insights into the evolutionary dynamics of 5S rDNA in vertebrate genomes

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

Seasonal population dynamics and the genetic structure of the mosquito vector Aedes aegypti in São Paulo, Brazil

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

Population dynamics, sex ratio and size at sex change in a protandric simultaneous hermaphrodite, the spiny shrimp Exhippolysmata oplophoroides

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 evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes

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

Dynamics in dumbbell domains II. The limiting problem

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Infrared dynamics in (2+1) dimensions

In this work we study the asymptotic behavior of (2+1)-dimensional quantum electrodynamics in the infrared region. We show that an appropriate redefinition of the fermion current operator leads to an asymptotic evolution operator that contains a divergent Coulomb phase factor and a contribution from the electromagnetic field at large distances, factored from the evolution operator for free fields, and we conclude that the modified scattering operator maps two spaces of coherent states of the electromagnetic field, as in the Kulish-Faddeev model for QED (quantum electrodynamics) in four space-time dimensions.

Bose-Einstein condensation dynamics in three dimensions by the pseudospectral and finite-difference methods

We suggest a pseudospectral method for solving the three-dimensional time-dependent Gross-Pitaevskii (GP) equation, and use it to study the resonance dynamics of a trapped Bose-Einstein condensate induced by a periodic variation in the atomic scattering length. When the frequency of oscillation of the scattering length is an even multiple of one of the trapping frequencies along the x, y or z direction, the corresponding size of the condensate executes resonant oscillation. Using the concept of the differentiation matrix, the partial-differential GP equation is reduced to a set of coupled ordinary differential equations, which is solved by a fourth-order adaptive step-size control Runge-Kutta method. The pseudospectral method is contrasted with the finite-difference method for the same problem, where the time evolution is performed by the Crank-Nicholson algorithm. The latter method is illustrated to be more suitable for a three-dimensional standing-wave optical-lattice trapping potential.

Quantum discrete phase space dynamics and its continuous limit

The main aspects of a discrete phase space formalism are presented and the discrete dynamical bracket, suitable for the description of time evolution in finite-dimensional spaces, is discussed. A set of operator bases is defined in such a way that the Weyl-Wigner formalism is shown to be obtained as a limiting case. In the same form, the Moyal bracket is shown to be the limiting case of the discrete dynamical bracket. The dynamics in quantum discrete phase spaces is shown not to be attained from discretization of the continuous case.

Short-time dynamics of percolation observables

We consider the critical short-time evolution of magnetic and droplet-percolation order parameters for the Ising model in two and three dimensions, through Monte Carlo simulations with the (local) heat-bath method. We find qualitatively different dynamic behaviors for the two types of order parameters. More precisely, we find that the percolation order parameter does not have a power-law behavior as encountered for the magnetization, but develops a scale (related to the relaxation time to equilibrium) in the Monte Carlo time. We argue that this difference is due to the difficulty in forming large clusters at the early stages of the evolution. Our results show that, although the descriptions in terms of magnetic and percolation order parameters may be equivalent in the equilibrium regime, greater care must be taken to interpret percolation observables at short times. In particular, this concerns the attempts to describe the dynamics of the deconfinement phase transition in QCD using cluster observables.

Bose-Einstein condensation dynamics from the numerical solution of the Gross-Pitaevskii equation

We study certain stationary and time-evolution problems of trapped Bose-Einstein condensates using the numerical solution of the Gross-Pitaevskii (GP) equation with both spherical and axial symmetries. We consider time-evolution problems initiated by suddenly changing the interatomic scattering length or harmonic trapping potential in a stationary condensate. These changes introduce oscillations in the condensate which are studied in detail. We use a time iterative split-step method for the solution of the time-dependent GP equation, where all nonlinear and linear non-derivative terms are treated separately from the time propagation with the kinetic energy terms. Even for an arbitrarily strong nonlinear term this leads to extremely accurate and stable results after millions of time iterations of the original equation.

PRODUCTION of THERMAL PHOTONS IN VISCOUS FLUID DYNAMICS WITH TEMPERATURE-DEPENDENT SHEAR VISCOSITY

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