Ancestral polymorphism and recent invasion of transposable elements in Drosophila species

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

Identification and frequency of transposable elements in Eucalyptus

Transposable elements (TE) are major components of eukaryotic genomes and involved in cell regulation and organism evolution. We have analyzed 123,889 expressed sequence tags of the Eucalyptus Genome Project database and found 124 sequences representing 76 TE in 9 groups, of which copia, MuDR and FAR1 groups were the most abundant. The low amount of sequences of TE may reflect the high efficiency of repression of these elements, a process that is called TE silencing. Frequency of groups of TE in Eucalyptus libraries which were prepared with different tissues or physiologic conditions from seedlings or adult plants indicated that developing plants experience the expression of a much wider spectrum of TE groups than that seen in adult plants. These are preliminary results that identify the most relevant TE groups involved with Eucalyptus development, which is important for industrial wood production. Copyright by the Brazilian Society of Genetics.

Transposon display supports transpositional activity of P elements in species of the saltans group of Drosophila

Mobilization of two P element subfamilies (canonical and O-type) from Drosophila sturtevanti and D. saltans was evaluated for copy number and transposition activity using the transposon display (TD) technique. Pairwise distances between strains regarding the insertion polymorphism profile were estimated. Amplification of the P element based on copy number estimates was highly variable among the strains (D. sturtevanti, canonical 20.11, O-type 9.00; D. saltans, canonical 16.4, O-type 12.60 insertions, on average). The larger values obtained by TD compared to our previous data by Southern blotting support the higher sensitivity of TD over Southern analysis for estimating transposable element copy numbers. The higher numbers of the canonical P element and the greater divergence in its distribution within the genome of D. sturtevanti (24.8%) compared to the O-type (16.7%), as well as the greater divergence in the distribution of the canonical P element, between the D. sturtevanti (24.8%) and the D. saltans (18.3%) strains, suggest that the canonical element occupies more sites within the D. sturtevanti genome, most probably due to recent transposition activity. These data corroborate the hypothesis that the O-type is the oldest subfamily of P elements in the saltans group and suggest that the canonical P element is or has been transpositionally active until more recently in D. sturtevanti. © Indian Academy of Sciences.

Report of a chimeric origin of transposable elements in a bovine-coding gene

Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is ∼85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific, mainly in the ruminant lineage. ©FUNPEC-RP.

Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes

Background: Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Results: Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Conclusion: Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins. © 2013 Schneider et al.; licensee BioMed Central Ltd.

Evaluation of Meteorological Elements and Lettuce (lactuca Sativa, L.) Yield Related to Geographic Orientation of Polyethylene Greenhouses

O experimento foi realizado na área experimental do Departamento de Engenharia Rural da Faculdade de Ciências Agronômicas – Unesp/Botucatu, Estado de São Paulo, em duas estufas dispostas em diferentes orientações geográficas, Leste/Oeste e Norte/Sul. A alface (Lactuva sativa L.) cv. Elisa foi cultivada em ambas estufas, sendo semeada em 05/05/99, transplantada em 29/05/99 e colhida em 31/06/99. Utilizou-se tensiômetros para monitorar o potencial de água no solo para realizar o manejo do sistema de irrigação por gotejamento. Microevaporímetros eqüidistantes de 3 m e colocados em 3 alturas, 0.50, 1.00 e 1.50 m, termohigrógrafos e tanques Classe “A” foram instalados nas duas estufas. Através de análise geoestatística, não se observou dependência espacial nem variabilidade espacial da evaporação nas duas estufas. Entretanto, a altura dos evaporímetros apresentou diferenças significativas: a evaporação à altura de 1.50 foi menor que nas outras duas.As médias de temperatura, umidade relativa e déficit de pressão de vapor do arnão diferiram estatisticamente entre as estufas e o ambiente externo. Os valores médios de evaporação de água no tanque Classe A instalado fora das estufas diferiram estatisticamente quando comparados com os instalados no interior das estufas, porém, entre as orientações não se constatou diferença significativa. Pôde-se verificar que não houve diferença significativa das características agronômicas da alface em ambas orientações estudadas. No entanto, houve diferença significativa para essas características entre os canteiros no interior das mesmas, havendo variância espacial para os dados de matéria fresca apenas na estufa N/S.

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

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

Modified routine for decreasing numeric oscillations at associations of lumped elements

Some changes in the application of the numeric trapezoidal integration are analyzed for applications considering pi circuits. It is considered numeric and computational proceedings for improving the numeric results obtained with associations of pi circuits. In numeric integration solutions of the linear systems, it is common to represent these associations of pi circuits by only one matrix. This representation introduces undesirable numeric oscillations in simulations of the dynamics of wave propagation in electrical systems. The proposed changes improve the results of application of cascades of pi circuits associated to the trapezoidal integration, avoiding that the numerical oscillations, or Gibb's oscillations, have high values and are slowly damped. For the carried out simulations, different number of pi circuits and voltage sources are checked, confirming the reduction of the influence of the numeric oscillations on the obtained results. (C) 2014 Elsevier B.V. All rights reserved.

Tropical Africa as a cradle for horizontal transfers of transposable elements between species of the genus Drosophila and Zaprionus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Key participants of the tumor microenvironment of the prostate: An approach of the structural dynamic of cellular elements and extracellular matrix components during epithelial-stromal transition

Cancer is a multistep process that begins with the transformation of normal epithelial cells and continues with tumor growth, stromal invasion and metastasis. The remodeling of the peritumoral environment is decisive for the onset of tumor invasiveness. This event is dependent on epithelial–stromal interactions, degradation of extracellular matrix components and reorganization of fibrillar components. Our research group has studied in a new proposed rodent model the participation of cellular and molecular components in the prostate microenvironment that contributes to cancer progression. Our group adopted the gerbil Meriones unguiculatus as an alternative experimental model for prostate cancer study. This model has presented significant responses to hormonal treatments and to development of spontaneous and induced neoplasias. The data obtained indicate reorganization of type I collagen fibers and reticular fibers, synthesis of new components such as tenascin and proteoglycans, degradation of basement membrane components and elastic fibers and increased expression of metalloproteinases. Fibroblasts that border the region, apparently participate in the stromal reaction. The roles of each of these events, as well as some signaling molecules, participants of neoplastic progression and factors that promote genetic reprogramming during epithelial–stromal transition are also discussed.

The behavior of brazilian senators: analyzing the exchange of votes inside the fixed committees during the 52nd legislature

Using the method of Social Networks Analysis, we’ll try to see if politicians swap votes between them seeking support for their projects, to this end, we’ll first map the behavior, activities and contacts of the Senators of the Brazilian Federative Republic within all the fixed committees which had some vote during the 52nd Legislature, then we can see the most popular and central Senators to each committee. After this analysis we wish to answer the following question: did logrolling exist in the Brazilian Senate? Previously the empirical analysis and response to the problems posed, we’ll present the necessary theoretical introduction understood by reviewing the literature on relevant subjects, whether they are purely theoretical with respect to the exchange of support, or analytical about the Brazilian political system.

Terminal-repeat retrotransposons with GAG domain in plant genomes: a new testimony on the complex world of transposable elements

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Chromosome mapping of retrotransposable elements Rex1 and Rex3 in Leporinus Spix, 1829 species (Characiformes: Anostomidae) and its relationships among heterochromatic segments and W sex chromosome

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

Correlations of trace elements in breast human tissues: Evaluation of spatial distribution using μ-XRF

The aim of this work is to investigate microscopic correlations between trace elements in breast human tissues. A synchrotron X-ray fluorescence microprobe system (μ-XRF) was used to obtain two-dimensional distribution of trace element Ca, Fe, Cu and Zn in normal (6 samples) and malignant (14 samples) breast tissues. The experiment was performed in X-ray Fluorescence beam line at Laboratório Nacional de Luz Síncrotron (LNLS), Campinas, Brazil. The white microbeam was generated with a fine conical capillary with a 20 μm output diameter. The samples were supported on a XYZ table. An optical microscope with motorized zoom was used for sample positioning and choice the area to be scanned. Automatic two-dimensional scans were programmed and performed with steps of 30 μm in each direction (x, y) on the selected area. The fluorescence signals were recorded using a Si(Li) detector, positioned at 90 degrees with respect to the incident beam, with a collection time of 10 s per point. The elemental maps obtained from each sample were overlap to observe correlation between trace elements. Qualitative results showed that the pairs of elements Ca-Zn and Fe-Cu could to be correlated in malignant breast tissues. Quantitative results, achieved by Spearman correlation tests, indicate that there is a spatial correlation between these pairs of elements (p < 0.001) suggesting the importance of these elements in metabolic processes associated with the development of the tumor.