Organization of Repeated DNA Elements in the Genome of the Cichlid Fish Cichla kelberi and Its Contributions to the Knowledge of Fish Genomes

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

Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromis niloticus: Evidences for a differential distribution of repetitive elements in the sex chromosomes

Repetitive DNAs have been extensively applied as physical chromosome markers on comparative studies, identification of chromosome rearrangements and sex chromosomes, chromosome evolution analysis, and applied genetics. Here we report the characterization of repetitive DNA sequences from the Nile tilapia (Oreochromis niloticus) genome by construction and screening of plasmid library enriched with repetitive DNAs, analysis of a BAC-based physical map, and hybridization to chromosomes. The physical mapping of BACs enriched with repetitive sequences and C(o)t-1 DNA (DNA enriched for highly and moderately repetitive DNA sequences) to chromosomes using FISH showed a predominant distribution of repetitive elements in the centromeric and telomeric regions and along the entire length of the largest chromosome pair (X and Y sex chromosomes) of the species. The distribution of repetitive DNAs differed significantly between the p arm of X and Y chromosomes. These findings suggest that repetitive DNAs have had an important role in the differentiation of sex chromosomes. (c) 2007 Elsevier Ltd. All rights reserved.

Cytogenetic Mapping of the Retroelements Rex1, Rex3 and Rex6 among Cichlid Fish: New Insights on the Chromosomal Distribution of Transposable Elements

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

Chromosome spreading of associated transposable elements and ribosomal DNA in the fish Erythrinus erythrinus. Implications for genome change and karyoevolution in fish

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

Body sway and sensory motor coupling adaptation in children: Effects of distance manipulation

The purpose of this investigation was to examine coupling between visual information and body sway in children and young adults at various distances from a moving room front wall. Sixty children (from 4 to 14 years old) and 10 young adults stood upright inside a moving room that was oscillated at .2 and .5 Hz, at distances of .25, .5, 1, and 1.5 m from a front wall. Visual information induced body sway in all participants in all conditions. Young children swayed more than older participants, whether the moving room was oscillated or not. Coupling between visual information and body sway became stronger and the room movement influence became weaker with age. Up to the age of 10, coupling strength between visual information and body sway and the room movement influence were distance dependent. Postural control development appears to be dependent on how children reweight the contribution of varying sensory cues available in environment in order to control body sway. (C) 2007 Wiley Periodicals, Inc.

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

We report a method for studying global DNA methylation based on using bisulfite treatment of DNA and simultaneous PCR of multiple DNA repetitive elements, such as Alu elements and long interspersed nucleotide elements (LINE). The PCR product, which represents a pool of approximately 15000 genomic loci, could be used for direct sequencing, selective restriction digestion or pyrosequencing, in order to quantitate DNA methylation. By restriction digestion or pyrosequencing, the assay was reproducible with a standard deviation of only 2% between assays. Using this method we found that almost two-thirds of the CpG methylation sites in Alu elements are mutated, but of the remaining methylation target sites, 87% were methylated. Due to the heavy methylation of repetitive elements, this assay was especially useful in detecting decreases in DNA methylation, and this assay was validated by examining cell lines treated with the methylation inhibitor 5-aza-2'deoxycytidine (DAC), where we found a 1-16% decrease in Alu element and 18-60% LINE methylation within 3 days of treatment. This method can be used as a surrogate marker of genome-wide methylation changes. In addition, it is less labor intensive and requires less DNA than previous methods of assessing global DNA methylation.

Copy number of P elements, KP/full-sized P element ratio and their relationships with environmental factors in Brazilian Drosophila melanogaster populations

The P transposable element copy numbers and the KP/full-sized P element ratios were determined in eight Brazilian strains of Drosophila melanogaster. Strains from tropical regions showed lower overall P element copy numbers than did strains from temperate regions. Variable numbers of full-sized and defective elements were detected, but the full-sized P and KP elements were the predominant classes of elements in all strains. The full-sized P and KP element ratios were calculated and compared with latitude. The northernmost and southernmost Brazilian strains showed fewer full-sized elements than KP elements per genome, and the strains from less extreme latitudes had many more full-sized P than KP elements. However, no clinal variation was observed. Strains from different localities, previously classified as having P cytotype, displayed a higher or a lower proportion of KP elements than of full-sized P elements, as well as an equal number of the two element types, showing that the same phenotype may be produced by different underlying genomic components of the P-M system.

Losing identity: structural diversity of transposable elements belonging to different classes in the genome of Anopheles gambiae

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A Model Coupling Vibrational and Rotational Motion for the DNA Molecule

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

Strength of the trilinear Higgs boson coupling in technicolor models

We discuss the strength of the trilinear Higgs boson coupling in technicolor (or composite) models in a model independent way. The coupling is determined as a function of a very general ansatz for the technicolor self-energy, and turns out to be equal or smaller than the one of the Standard Model Higgs boson depending on the dynamics of the theory. (c) 2006 Published by Elsevier B.V.

Lambda c(+), Sigma(c), and Lambda(b) hypernuclei in the quark-meson coupling model

Charmed (and bottom) hypernuclei are studied in the quark-meson coupling (QMC) model. This completes systematic studies of charmed (Lambda(c)(+), Sigma(c), Xi(c)), and Lambda(b) hypernuclei in the QMC model. Effects of the Pauli blocking due to the underlying quark structure of baryons, and the Sigma(c)N-Lambda(c)N channel coupling are phenomenologically taken into account at the hadronic level in the same way as those included for strange hypernuclei. Our results suggest that the Sigma(c)(++) and Xi(c)(+) hypernuclei are very unlikely to be formed. while the Lambda(c)(+), Xi(c)(0) and Lambda(b) hypernuclei are quite likely to be formed. For the Sigma(c)(+) hypernuclei, the formation probability is non-zero, though small. A detailed analysis is also made about the phenomenologically introduced Pauli blocking and channel coupling effects for the Sigma(c)(0) hypernuclei.

Cooper pair dispersion relation for weak to strong coupling

Cooper pairing in two dimensions is analyzed with a set of renormalized equations to determine its binding energy for any fermion number density and all coupling assuming a,generic pairwise residual interfermion interaction. Also considered are Cooper pairs (CP's) with nonzero center-of-mass momentum (CMM) and their binding energy is expanded analytically in powers of the CMM up to quadratic terms. A Fermi-sea-dependent linear term in the CMM dominates the pair excitation energy in weak coupling (also called the BCS regime) while the more familiar quadratic term prevails in strong coupling (the Bose regime). The crossover, though strictly unrelated to BCS theory per se, is studied numerically as it is expected to play a central role in a model of superconductivity as a Bose-Einstein condensation of CPs where the transition temperature vanishes for all dimensionality d less than or equal to 2 for quadratic dispersion, but is nonzero for all d greater than or equal to 1 for linear dispersion.

Low-energy direct muon transfer from H to Ne10+, S16+ and Ar18+ using the two-state close-coupling approximation to the Faddeev-Hahn-type equation

We perform a three-body calculation of direct muon-transfer rates from thermalized muonic hydrogen isotopes to bare nuclei Ne10+, S16+ and Ar18+ employing integro-differential Faddeev-Hahn-type equations in configuration space with a two-state close-coupling approximation scheme. All Coulomb potentials including the strong final-state Coulomb repulsion are treated exactly. A long-range polarization potential is included in the elastic channel to take into account the high polarizability of the muonic hydrogen. The transfer rates so-calculated are in good agreement with recent experiments. We find that the muon is captured predominantly in the n = 6, 9 and 10 states of muonic Ne10+, S16+ and Ar18+, respectively.

Lessons of spin and torsion: Reply to Consistent coupling to Dirac fields in teleparallelism

In reply to the criticism made by Mielke in the preceding Comment on our recent paper, we once again explicitly demonstrate the inconsistency of the coupling of a Dirac field to gravitation in the teleparallel equivalent of general relativity. Moreover, we stress that the mentioned inconsistency is generic for all sources with spin and is by no means restricted to the Dirac field. In this sense the SL(4,R)-covariant generalization of the spinor fields in the teleparallel gravity theory is irrelevant to the inconsistency problem.

Freezing of the QCD coupling constant and the pion form factor

The possibility that the QCD coupling constant (alpha(s)) has an infrared finite behavior (freezing) has been extensively studied in recent years. We compare phenomenological values of the frozen QCD running coupling between different classes of solutions obtained through non-perturbative Schwinger-Dyson Equations. With these solutions were computed QCD predictions for the asymptotic pion form factor which, in turn, were compared with experiment.