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.

Towards a theory of the small firm: theoretical aspects and some policy implications

Includes bibliography

Fly your kite: a metaphor for a theory of territorial development

Includes bibliography

A Commentary on de Sousa′s towards an Integrative Theory of Consciousness

De Sousa′s comprehensive two-part review of a diversity of contemporary approaches to the study of consciousness is highly welcome. He makes us aware of a proliferation of theoretical and empirical approaches targeting a common theme, but diverging in many ways. He skilfully accomplishes a classification of kinds of approach, identification of the main representatives, their contributions, and respective limitations. However, he does not show how the desired integration could be accomplished. Besides summarising de Sousa′s efficient analytical work, I make critical comments and briefly report my contribution for the integration project.© MSM 2013.

Towards a theory of change

Includes bibliography

Towards a theory of change

Includes bibliography

On the article by Raúl Prebisch, Towards a theory of change": comments"

Includes bibliography

When less is better: Insights from the product mix dilemma from the Theory of Constraints perspective

Perhaps due to its origins in a production scheduling software called Optimised Production Technology (OPT), plus the idea of focusing on system constraints, many believe that the Theory of Constraints (TOC) has a vocation for optimal solutions. Those who assess TOC according to this perspective indicate that it guarantees an optimal solution only in certain circumstances. In opposition to this view and founded on a numeric example of a production mix problem, this paper shows, by means of TOC assumptions, why the TOC should not be compared to methods intended to seek optimal or the best solutions, but rather sufficiently good solutions, possible in non-deterministic environments. Moreover, we extend the range of relevant literature on product mix decision by introducing a heuristic based on the uniquely identified work that aims at achieving feasible solutions according to the TOC point of view. The heuristic proposed is tested on 100 production mix problems and the results are compared with the responses obtained with the use of Integer Linear Programming. The results show that the heuristic gives good results on average, but performance falls sharply in some situations. © 2013 Copyright Taylor and Francis Group, LLC.

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)