Transposons and genome evolution in plants

Although it is known today that transposons comprise a significant fraction of the genomes of many organisms, they eluded discovery through the first half century of genetic analysis and even once discovered, their ubiquity and abundance were not recognized for some time. This genetic invisibility of transposons focuses attention on the mechanisms that control not only transposition, but illegitimate recombination. The thesis is developed that the mechanisms that control transposition are a reflection of the more general capacity of eukaryotic organisms to detect, mark, and retain duplicated DNA through repressive chromatin structures.

Maize as a model for the evolution of plant nuclear genomes

The maize genome is replete with chromosomal duplications and repetitive DNA. The duplications resulted from an ancient polyploid event that occurred over 11 million years ago. Based on DNA sequence data, the polyploid event occurred after the divergence between sorghum and maize, and hence the polyploid event explains some of the difference in DNA content between these two species. Genomic rearrangement and diploidization followed the polyploid event. Most of the repetitive DNA in the maize genome is retrotransposable elements, and they comprise 50% of the genome. Retrotransposon multiplication has been relatively recent—within the last 5–6 million years—suggesting that the proliferation of retrotransposons has also contributed to differences in DNA content between sorghum and maize. There are still unanswered questions about repetitive DNA, including the distribution of repetitive DNA throughout the genome, the relative impacts of retrotransposons and chromosomal duplication in plant genome evolution, and the hypothesized correlation of duplication events with transposition. Population genetic processes also affect the evolution of genomes. We discuss how centromeric genes should, in theory, contain less genetic diversity than noncentromeric genes. In addition, studies of diversity in the wild relatives of maize indicate that different genes have different histories and also show that domestication and intensive breeding have had heterogeneous effects on genetic diversity across genes.

Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer

Two major pathways of recombination-dependent DNA replication, “join-copy” and “join-cut-copy,” can be distinguished in phage T4: join-copy requires only early and middle genes, but two late proteins, endonuclease VII and terminase, are uniquely important in the join-cut-copy pathway. In wild-type T4, timing of these pathways is integrated with the developmental program and related to transcription and packaging of DNA. In primase mutants, which are defective in origin-dependent lagging-strand DNA synthesis, the late pathway can bypass the lack of primers for lagging-strand DNA synthesis. The exquisitely regulated synthesis of endo VII, and of two proteins from its gene, explains the delay of recombination-dependent DNA replication in primase (as well as topoisomerase) mutants, and the temperature-dependence of the delay. Other proteins (e.g., the single-stranded DNA binding protein and the products of genes 46 and 47) are important in all recombination pathways, but they interact differently with other proteins in different pathways. These homologous recombination pathways contribute to evolution because they facilitate acquisition of any foreign DNA with limited sequence homology during horizontal gene transfer, without requiring transposition or site-specific recombination functions. Partial heteroduplex repair can generate what appears to be multiple mutations from a single recombinational intermediate. The resulting sequence divergence generates barriers to formation of viable recombinants. The multiple sequence changes can also lead to erroneous estimates in phylogenetic analyses.

Retrotransposons of rice involved in mutations induced by tissue culture.

Five retrotransposon families of rice (Tos1-Tos5) have been reported previously. Here we report 15 new retrotransposon families of rice (Tos6-Tos20). In contrast to yeast and Drosophila retrotransposons, all of the rice retrotransposons examined appear inactive (or almost inactive) under normal growth conditions. Three of the rice retrotransposons (Tos10, Tos17, and Tos19) are activated under tissue culture conditions. The most active one, Tos17, was studied in detail. The copy number of Tos17 increased with prolonged culture period. In all of the plants regenerated from tissue cultures, including transgenic plants, 5 to 30 transposed Tos17 copies were detected. The transcript of Tos17 was only detected under tissue culture conditions, indicating that the transposition of Tos17 is mainly regulated at the transcriptional level. To examine the target-site specificity of Tos17 transposition, sequences flanking transposed Tos17 copies were analyzed. At least four out of eight target sites examined are coding regions. Other target sites may also be in genes because two out of four were transcribed. The regenerated plants with Tos17-insertions in the phytochrome A gene and the S-receptor kinase-related gene were identified. These results indicate that activation of Tos17 is an important cause of tissue culture-induced mutations. Tissue culture-induced activation of Tos17 may be a useful tool for insertional mutagenesis and functional analysis of genes.

Transposon tools for recombinant DNA manipulation: characterization of transcriptional regulators from yeast, Xenopus, and mouse.

Transposon Tn1000 has been adapted to deliver novel DNA sequences for manipulating recombinant DNA. The transposition procedure for these "tagged" Tn1000s is simple and applicable to most plasmids in current use. For yeast molecular biology, tagged Tn1000s introduce a variety of yeast selective markers and replication origins into plasmids and cosmids. In addition, the beta-globin minimal promoter and lacZ gene of Tn(beta)lac serve as a mobile reporter of eukaryotic enhancer activity. In this paper, Tn(beta)lac was used to localize a mouse HoxB-complex enhancer in transgenic mice. Other tagged transposons create Gal4 DNA-binding-domain fusions, in either Escherichia coli or yeast plasmids, for use in one- and two-hybrid tests of transcriptional activation and protein-protein interaction, respectively. With such fusions, the Saccharomyces cerevisiae Swi6 G1/S-phase transcription factor and the Xenopus laevis Pintallavis developmental regulator are shown to activate transcription. Furthermore, the same transposon insertions also facilitated mapping of the Swi6 and Pintallavis domains responsible for transcriptional activation. Thus, as well as introducing novel sequences, tagged transposons share the numerous other applications of transposition such as producing insertional mutations, creating deletion series, or serving as mobile primer sites for DNA sequencing.

Identification and characterization of putative transposable DNA elements in solanaceous plants and Caenorhabditis elegans.

Several families of putative transposable elements (TrEs) in both solanaceous plants and Caenorhabditis elegans have been identified by screening the DNA data base for inverted repeated domains present in multiple copies in the genome. The elements are localized within intron and flanking regions of many genes. These elements consist of two inverted repeats flanking sequences ranging from 5 bp to > 500 bp. Identification of multiple elements in which sequence conservation includes both the flanking and internal regions implies that these TrEs are capable of duplicative transposition. Two of the elements were identified in promoter regions of the tomato (Lycoperiscon esculentum) polygalacturonase and potato (Solanum tuberosum) Win1 genes. The element in the polygalacturonase promoter spans a known regulatory region. In both cases, ancestral DNA sequences, which represent potential recombination target sequences prior to insertion of the elements, have been cloned from related species. The sequences of the inverted repeated domains in plants and C. elegans show a high degree of phylogenetic conservation. While frequency of the different elements is variable, some are present in very high copy number. A member of a single C. elegans TrE family is observed approximately once every 20 kb in the genome. The abundance of the described TrEs suggests utility in the genomic analysis of these and related organisms.

Increased sensitivity to gamma irradiation in bacteria lacking protein HU.

The heterodimeric HU protein, isolated from Escherichia coli, is associated with the bacterial nucleoid and shares some properties with both histones and HMG proteins. It is the prototype of small bacterial DNA binding proteins with a pleiotropic role in the cell. HU participates in several biological processes like cell division, initiation of DNA replication, transposition, and other biochemical functions. We show here that bacteria lacking HU are extremely sensitive to gamma irradiation. Expression of either one of the subunits of HU in the hupAB double mutant nearly restores the normal survival rate. This shows that the sensitivity is due to the absence of HU rather than being the result of a secondary mutation occurring in the hupAB cells or a modification of the SOS repair system, since SOS genes are induced normally in the absence of HU. Finally, in vitro studies give an indication of its potential role: HU protects DNA against cleavage by gamma-rays.

A conservação da biodiversidade nos discursos expositivos do Zoo de Barcelona

A Educação para a Conservação é um campo de pesquisa que se dedica ao estudo das reflexões éticas e das atitudes humanas direcionadas para com o respeito que se deve ter com o ambiente, principalmente pelo estabelecimento de ações conservacionistas pautadas em interações educativas. Os Zoos, de modo geral, estão inseridos nessa perspectiva, uma vez que se apresentam como instituições de cunho educativo voltadas para a conservação da biodiversidade. No entanto, o discurso expositivo apresentado por esses aparatos culturais no Brasil, muitas vezes, não contempla tais elementos em suas exposições. Por este motivo, buscou-se a análise de exposições zoológicas também no exterior, que contemplassem discursos sobre a conservação da biodiversidade em suas exposições, tendo sido escolhida a exposição do Zoo de Barcelona, Espanha, para a realização desta investigação. A pesquisa teve por objetivos compreender como a conservação da biodiversidade é abordada na exposição deste zoológico catalão, com base na formulação de saberes de referência constituídos a partir de diferentes áreas: os Movimentos Ambientalistas, a Filosofia da Conservação e as Éticas Ambientais. Igualmente, buscou-se compreender como o discurso expositivo sobre conservação encontra-se apresentado nos aparatos expográficos distribuídos ao longo da exposição, bem como em livros e documentos. Compreendendo a investigação como um Estudo de Caso, foram acessados documentos institucionais de acesso público encontrados no site da instituição e textos presentes nos painéis expositivos. As análises foram realizadas com base no referencial teórico da Transposição Didática/Museográfica, que permite o estudo da exposição por ao menos três lógicas: a lógica do discurso; a lógica do espaço; e a lógica do gesto. Além disso, o mesmo referencial prevê o estabelecimento de um saber de referência ou saber sábio pautado no conhecimento epistemológico sobre a conservação da biodiversidade e, nesta pesquisa, no discurso de pesquisadores da área, que foram entrevistados sobre este assunto. Este saber de referência ou saber sábio possibilitou a criação de um conjunto de categorias de análise que pautou a análise do discurso expositivo apresentado pelo Zoo de Barcelona. As categorias criadas foram classificadas em duas dimensões: a dos Valores e a das Ações. Duas categorias, a Antropocêntrica e a Não antropocêntrica constituíram a Dimensão dos Valores e quatro categorias, a Desenvolvimentista, a Sustentabilista, a Sócio-humanística e a Técnico-científica constituíram a Dimensão das Ações. Os resultados apontaram que o discurso expositivo é composto predominantemente por informações Técnico-científicas e Sustentabilistas, ambas as categorias contextualizadas por uma visão não antropocêntrica de valorização da natureza. A forma como o discurso expositivo encontra-se apresentado na parte textual da exposição corrobora a linha conceitual de assuntos abordados nos grandes eventos globais promovidos pela ONU ao longo dos últimos 40 anos, sobre a conservação do meio ambiente. Categorias como a Sócio-humanística, a Antropocêntrica e a Dimensão dos Valores foram pouco abordadas. A categoria Desenvolvimentista não foi encontrada na exposição. Pelas evidências levantadas durante a análise dos dados pode-se concluir que o Zoo de Barcelona apresenta um discurso expositivo conservacionista e que há elementos suficientes na exposição para se apontar o desenvolvimento de uma Educação para a Conservação.

Ureter retrocava : uma anomalia congénita rara

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

La Direttiva 2008/104/CE relativa al lavoro tramite agenzia interinale: aspetti problematici e modelli di implementazione = Directive 2008/104/EC relating to temporary agency work: problematic aspects and implementation models. WP C.S.D.L.E. “Massimo D’Antona”.INT – 101/2013

The problematic gestation of the Directive on temporary agency work shows the presence of several criticalities that there are also in the national transposition in relation to the principle of equal treatment and to the mechanisms for preventing abuse during successive assignments. From a first analysis it can be said that in some EU Member States only the derogations have been implemented and not the general principle of equal treatment. At the same time, the obligation of the Member States, contained in the Directive on temporary agency work, to establish mechanisms for preventing abuse during successive assignments is crucial, especially in the light of the recent case law of the EU Court of Justice in which the Court does not apply to the temporary agency workers the protective rules of the Directive on fixed-term contracts (see C-290/12 , Della Rocca).

The Racial Equality Directive – from law to practice. IES Policy Brief Issue 2013/07/September 2013

The transposition of the Racial Equality Directive (2000/43/EC) has immensely enhanced legal protection against discrimination on the grounds of racial and ethnic origin throughout the EU. More than 10 years after its adoption, the main challenge identified in many Member States is the enforcement of anti-discrimination laws in practice, in particular with regard to access to justice. Ultimately it is up to the domestic courts to ensure effective implementation of anti-discrimination law. Polls regularly show that the discrepancy between the levels of discrimination experienced and discrimination reported by victims must be seriously addressed. Awareness is low not only among the public but also among the members of the legal professions, leading to under-reporting of discrimination cases. In addition, data that reflect the ethnic or racial composition of the population are scarce which makes it difficult to prove discrimination before the competent authorities. Moreover, certain procedural difficulties that affect access to justice and effective enforcement also stem from the short limitation periods foreseen in legislation, lengthy procedures, evidence, high costs and failures in the provision of legal aid, ineffective sanctions, as well as barriers in the form of language and issues relating to legal standing or legitimate interest. The law remains complex and remedies often inadequate.

Dos pombos descoordenados às rãs sem rumo: o ensino do encéfalo através dos manuais escolares de Ciências Naturais (1900-1950)

O objetivo principal deste trabalho é mostrar como o encéfalo foi abordado nos programas e manuais de Ciências Naturais publicados na primeira metade do século XX. Para tal, utilizou-se um método de caráter qualitativo assente no conceito de transposição didática de Chevallard. O conteúdo programático mostrou que o estudo do encéfalo foi sempre associado ao estudo do sistema nervoso. A descrição neuroanatómica e fisiológica do encéfalo nos manuais organizou-se em torno do bolbo raquidiano, cerebelo e cérebro. Os manuais publicados nas primeiras duas décadas do século XX (Aires, 1906, 1920) foram mais exaustivos na abordagem a esses órgãos do que os publicados entre as décadas de 30 e 50 (Primo, 1939; Soeiro, 1930, 1950; Lima & Soeiro,1950). A sua análise mostrou que a transposição didática do conhecimento científico sobre o encéfalo baseou-se na neuroanatomia, e menos na neurofisiologia, o que é revelador do avanço do conhecimento neuroanatómico deste órgão em comparação com a compreensão do seu funcionamento. Todos os autores ilustraram as funções dos órgãos que constituem o encéfalo através de observações e experiências realizadas em animais, como os pombos e as rãs.

Complex Congenital Heart Disease: The Influence of Prenatal Diagnosis

INTRODUCTION: Complex congenital heart disease is a group of severe conditions. Prenatal diagnosis has implications on morbidity and mortality for most severe conditions. The purpose of this work was to evaluate the influence of prenatal diagnosis and distance of residence and birth place to a reference center, on immediate morbidity and early mortality of complex congenital heart disease. MATERIAL AND METHODS: Retrospective study of complex congenital heart disease patients of our Hospital, born between 2007 and 2012. RESULTS: There were 126 patients born with complex congenital heart disease. In 95%, pregnancy was followed since the first trimester, with prenatal diagnosis in 42%. There was a statistically significant relation between birth place and prenatal diagnosis. Transposition of great arteries was the most frequent complex congenital heart disease (45.2%), followed by pulmonary atresia with ventricular septal defect (17.5%) and hypoplastic left ventricle (9.5%). Eighty-two patients (65.1%) had prostaglandin infusion and 38 (30.2%)were ventilated before an intervention. Surgery took place in the neonatal period in 73%. Actuarial survival rate at 30 days, 12 and 24 months was 85%, 80% and 75%, respectively. There was no statistically significant relation between prenatal diagnosis and mortality. DISCUSSION: Most patients with complex congenital heart disease did not have prenatal diagnosis. All cases with prenatal diagnosis were born in a tertiary center. Prenatal diagnosis did not influence significantly neonatal mortality, as already described in other studies with heterogeneous complex heart disease. CONCLUSION: prenatal diagnosis of complex congenital heart disease allowed an adequate referral. Most patients with complex congenital heart disease were not diagnosed prenatally. This data should be considered when planning prenatal diagnosis of congenital heart disease.

Analyse du film Intouchables: pouvons-nous tout transposer dans la traduction audiovisuelle?

Dans ce mémoire, il sera question d’analyser un film français : « Intouchables » d'Olivier Nakache et Eric Toledano. Après plusieurs visionnages aussi bien en français qu’en italien, car ce film peut se lire sur plusieurs niveaux (niveau que nous aurons l’occasion d’aborder plus longuement par la suite), nous pourrons constater que diverses thématiques sont soulevées. Ce dernier aborde des situations quotidiennes avec humour, avec délicatesse et surtout parce qu’en le regardant nous n’avons pas l'impression de ressentir des sentiments, comme par exemple la pitié ou la compassion. En effet, s’il y a bien une chose que le handicap entraîne auprès de bien des personnes, c'est l’inégalité et la pitié, affect qui n’est pas spécialement mélioratif en soi. Intouchables est une comédie qui a été traduite en plusieurs langues. La traduction audiovisuelle est un nouveau genre de traduction qui présente beaucoup de problématiques, car le traducteur doit prendre en considération plusieurs facteurs tels que l'audio et le visuel, donc transmettre le message devient de plus en plus complexe. Ce film présente différents aspects qui peuvent complexifier le travail de traduction, par exemple le langage employé et l’humour.

CemaT1 is an active transposon within the Caenorhabditis elegans genome

The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and T-C transposons, with a distribution thus far limited to a few invertebrate species. In the nematode Caenorhabditis elegans, there are eight copies of CemaT1 that are predicted to encode a functional transposase, with five copies being >99% identical. We present evidence, based on searches of publicly available databases and on PCR-based mobility assays, that the CemaT1 transposase is expressed in C. elegans and that the CemaT transposons are capable of excising in both somatic and germline tissues. We also show that the frequency of CemaT1 excisions within the genome of the N2 strain of C. elegans is comparable to that of the Tc1 transposon. However, unlike T-C transposons in mutator strains of C elegans, maT transposons do not exhibit increased frequencies of mobility, suggesting that maT is not regulated by the same factors that control T-C activity in these strains. Finally, we show that CemaT1 transposons are capable of precise transpositions as well as orientation inversions at some loci, and thereby become members of an increasing number of identified active transposons within the C. elegans genome. (C) 2004 Elsevier B.V. All rights reserved.