Transposable elements in Coffea (Gentianales : Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

Transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK beta-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.

Revisiting horizontal transfer of transposable elements in Drosophila

Horizontal transfer ( HT), defined as the transfer of genetic material between species, is considered to be an essential step in the 'life cycle' of transposable elements. We present a broad overview of suspected cases of HT of transposable elements in Drosophila. Hundred-one putative events of HT have been proposed in Drosophila for 21 different elements (5.0% refer to non-long terminal repeat (LTR) retrotransposons, 42.6% to LTR retrotransposons and 52.4% to DNA transposons). We discuss the methods used to infer HT, their limits and the putative vectors of transposable elements. We outline all the alternative hypotheses and ask how we can be almost certain that phylogenetic inconsistencies are due to HT.

Structural and properties of nanocrystalline WO3/TiO2-based humidity sensors elements prepared by high energy activation

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

Distribution of refractory and volatile elements in CoRoT exoplanet host stars

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Ancestral polymorphism and recent invasion of transposable elements in Drosophila species

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

Characterization, feasibility and optimization of Agaricus subrufescens growth based on chemical elements on casing layer

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Expression of beta-human chorionic gonadotropin (beta-hCG) in non-trophoblastic elements of transitional cell carcinoma of the bladder: possible relationship with the prognosis.

Transitional cell carcinoma (TCC) of the bladder is a neoplasm with variability in its clinical behavior. Although there are several studies correlating stage and ABO isoantigen expression with invasiveness, there is no single predictor factor to assess the potential invasiveness, especially in the low grade, non-invasive TCC. In the present study we evaluated the correlation of histological grade plus stage and the expression of beta human chorionic gonadotropin (beta-hCG), in 100 cases of TCC, with the clinical behavior. These features were correlated with tumor progression in patients with at least two years of follow up. We observed more aggressiveness in G4 group (high grade and invasive) (93% had tumor progression) when compared to G1 group (low grade and superficial) (11% had tumor progression). However in 25.5% of the TCC cases (groups G2: low grade and invasive and G3: high grade and superficial) the clinical behavior was intermediate, showing some limitation in using grading and staging only, as a predictive factor. There was an expression of beta-hCG in 21.4% of the cases in up to 25% of the tumor cells without any trophoblastic morphology. These beta-hCG producing TCC had a strong correlation with aggressiveness: 39.1% and 12.8% of the TCC expressed beta-hCG with and without tumor progression, respectively.

Toda and Volterra lattice equations from discrete symmetries of KP hierarchies

The discrete models of the Toda and Volterra chains are being constructed out of the continuum two-boson KP hierarchies. The main tool is the discrete symmetry preserving the Hamiltonian structure of the continuum models. The two-boson currents of KP hierarchy are being associated with sites of the corresponding chain by successive actions of discrete symmetry.

On discrete symmetries of the multi-boson KP hierarchies

We show that the multi-boson KP hierarchies possess a class of discrete symmetries linking them to discrete Toda systems. These discrete symmetries are generated by the similarity transformation of the corresponding Lax operator. This establishes a canonical nature of the discrete transformations. The spectral equation, which defines both the lattice system and the corresponding Lax operator, plays a key role in determining pertinent symmetry structure. We also introduce the concept of the square root lattice leading to a family of new pseudo-differential operators with covariance under additional Bäcklund transformations.

Affine Lie algebraic origin of constrained KP hierarchies

An affine sl(n + 1) algebraic construction of the basic constrained KP hierarchy is presented. This hierarchy is analyzed using two approaches, namely linear matrix eigenvalue problem on hermitian symmetric space and constrained KP Lax formulation and it is shown that these approaches are equivalent. The model is recognized to be the generalized non-linear Schrödinger (GNLS) hierarchy and it is used as a building block for a new class of constrained KP hierarchies. These constrained KP hierarchies are connected via similarity-Bäcklund transformations and interpolate between GNLS and multi-boson KP-Toda hierarchies. Our construction uncovers the origin of the Toda lattice structure behind the latter hierarchy. © 1995 American Institute of Physics.

Constrained KP models as integrable matrix hierarchies

We formulate the constrained KP hierarchy (denoted by cKP K+1,M) as an affine sl(M + K+ 1) matrix integrable hierarchy generalizing the Drinfeld-Sokolov hierarchy. Using an algebraic approach, including the graded structure of the generalized Drinfeld-Sokolov hierarchy, we are able to find several new universal results valid for the cKP hierarchy. In particular, our method yields a closed expression for the second bracket obtained through Dirac reduction of any untwisted affine Kac-Moody current algebra. An explicit example is given for the case sl(M + K + 1), for which a closed expression for the general recursion operator is also obtained. We show how isospectral flows are characterized and grouped according to the semisimple non-regular element E of sl(M + K+ 1) and the content of the center of the kernel of E. © 1997 American Institute of Physics.

Off-diagonal helicity density matrix elements for vector mesons produced in polarized e+e- processes

Final-state qq̄ interactions give origin to nonzero values of the off-diagonal element ρ1,-1 of the helicity density matrix of vector mesons produced in e+e- annihilations, as has been confirmed by recent OPAL data on φ, D*, and K*. New predictions are given for ρ1,-1 of several mesons produced at large XE and small pT - i.e., collinear with the parent jet - in the annihilation of polarized e+ and e-; the results depend strongly on the elementary dynamics and allow further nontrivial tests of the standard model.

Evaluation of DNA polymorphisms amplified by arbitrary primers (RAPD) as genetically associated elements to differentiate virulent and non-virulent Paracoccidioides brasiliensis isolates

Randomly amplified polymorphic DNA (RAPD) analysis of 35 Paracoccidioides brasiliensis isolates was carried out to evaluate the correlation of RAPD profiles with the virulence degree or the type of the clinical manifestations of human paracoccidioidomycosis. The dendrogram presented two main groups sharing 64% genetic similarity. Group A included two isolates from patients with chronic paracoccidioidomycosis; group B comprised the following isolates showing 65% similarity: two non-virulent, six attenuated, five virulent, eight from patients with chronic paracoccidioidomycosis and two from patients with acute paracoccidioidomycosis. The virulent Pb18 isolate and six attenuated or non-virulent samples derived from it were genetically indistinguishable (100% of similarity). Thus, in our study, RAPD patterns could not discriminate among 35 P. brasiliensis isolates according to their differences either in the degree of virulence or in the type of the clinical manifestation of this fungal infection. © 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Short interspersed repetitive elements (SINEs) from the cichlid fish, Oreochromis niloticus, and their chromosomal localization by fluorescent in situ hybridization

In the present study, we describe the cloning and characterization of a new SINE-like element from O. niloticus (ROn-2) and show the distribution of this SINE and a previously isolated SINE, ROn-1, in the chromosomes of O. niloticus. The ROn-2 element is 359 base pairs (bp) in length, contains short direct terminal repeats, a tRNA-related region similar to tRNA Val and tRNA Arg, a tRNA-unrelated region, and a poly-A tail. Analysis of the chromosomal distribution of ROn-1 and ROn-2 by fluorescent in situ hybridization showed that both SINE sequences are present in all chromosomes of tilapia, and organized in small clusters. The only exception was a large cluster of ROn-1 repeats found in the middle of the long arm of chromosome 1. In view of our data we discuss the hypothesis that the absence of large clusters of SINE sequences and the structural composition of these sequences may explain the absence of base-specific fluorochrome bands in the chromosomes of tilapia.