Étude de l’évolution des génomes par duplications, pertes et réarrangements

La duplication est un des évènements évolutifs les plus importants, car elle peut mener à la création de nouvelles fonctions géniques. Durant leur évolution, les génomes sont aussi affectés par des inversions, des translocations (incluant des fusions et fissions de chromosomes), des transpositions et des délétions. L'étude de l'évolution des génomes est importante, notamment pour mieux comprendre les mécanismes biologiques impliqués, les types d'évènements qui sont les plus fréquents et quels étaient les contenus en gènes des espèces ancestrales. Afin d'analyser ces différents aspects de l'évolution des génomes, des algorithmes efficaces doivent être créés pour inférer des génomes ancestraux, des histoires évolutives, des relations d'homologies et pour calculer les distances entre les génomes. Dans cette thèse, quatre projets reliés à l'étude et à l'analyse de l'évolution des génomes sont présentés : 1) Nous proposons deux algorithmes pour résoudre des problèmes reliés à la duplication de génome entier : un qui généralise le problème du genome halving aux pertes de gènes et un qui permet de calculer la double distance avec pertes. 2) Nous présentons une nouvelle méthode pour l'inférence d'histoires évolutives de groupes de gènes orthologues répétés en tandem. 3) Nous proposons une nouvelle approche basée sur la théorie des graphes pour inférer des gènes in-paralogues qui considère simultanément l'information provenant de différentes espèces afin de faire de meilleures prédictions. 4) Nous présentons une étude de l'histoire évolutive des gènes d'ARN de transfert chez 50 souches de Bacillus.

Origin and evolution of 3'UTR of flaviviruses: long direct repeats as a basis for the formation of secondary structures and their significance for virus transmission

The 3' untranslated regions (3'UTRs) of flaviviruses are reviewed and analyzed in relation to short sequences conserved as direct repeats (DRs). Previously, alignments of the 3'UTRs have been constructed for three of the four recognized flavivirus groups, namely mosquito-borne, tick-borne, and nonclassified flaviviruses (MBFV, TBFV, and NCFV, respectively). This revealed (1) six long repeat sequences (LRSs) in the 3'UTR and open-reading frame (ORF) of the TBFV, (2) duplication of the 3'UTR of the NCFV by intramolecular recombination, and (3) the possibility of a common origin for all DRs within the MBFV. We have now extended this analysis and review it in the context of all previous published analyses. This has been achieved by constructing a robust alignment between all flaviviruses using the published DRs and secondary RNA structures as "anchors" to reveal additional homologies along the 3'UTR. This approach identified nucleotide regions within the MBFV, NKV (no-known vector viruses), and NCFV 3'UTRs that are homologous to different LRSs in the TBFV 3'UTR and ORF. The analysis revealed that some of the DRs and secondary RNA structures described individually within each flavivirus group share common evolutionary origins. The 3'UTR of flaviviruses, and possibly the ORF, therefore probably evolved through multiple duplication of an RNA domain, homologous to the LRS previously identified only in the TBFV. The short DRs in all virus groups appear to represent the evolutionary remnants of these domains rather than resulting from new duplications. The relevance of these flavivirus DRs to evolution, diversity, 3'UTR enhancer function, and virus transmission is reviewed.

Amphioxus molecular biology: insights into vertebrate evolution and developmental mechanisms

The cephalochordate amphioxus is the best available proxy for the last common invertebrate ancestor of the vertebrates. During the last decade, the developmental genetics of amphioxus have been extensively examined for insights into the evolutionary origin and early evolution of the vertebrates. Comparisons between expression domains of homologous genes in amphioxus and vertebrates have strengthened proposed homologies between specific body parts. Molecular genetic studies have also highlighted parallels in the developmental mechanisms of amphioxus and vertebrates. In both groups, a similar nested pattern of Hox gene expression is involved in rostrocaudal patterning of the neural tube, and homologous genes also appear to be involved in dorsoventral neural patterning. Studies of amphioxus molecular biology have also hinted that the protochordate ancestor of the vertebrates included cell populations that modified their developmental genetic pathways during early vertebrate evolution to yield definitive neural crest and neurogenic placodes. We also discuss how the application of expressed sequence tag and gene-mapping approaches to amphioxus have combined with developmental studies to advance our understanding of chordate genome evolution. We conclude by considering the potential offered by the sequencing of the amphioxus genome, which was completed in late 2004.

Type III secretion homologs are present in Brucella melitensis, B-ovis, and B-suis biovars 1, 2, and 3

Protein sequences from characterized type III secretion (TTS) systems were used as probes in silico to identify several TTS gene homologs in the genome sequence of Brucella suis biovar 1 strain 1330. Four of the genes, named flhB, fliP, fliR, and fliF on the basis of greatest homologies to known flagellar apparatus proteins, were targeted in PCR and hybridization assays to determine their distribution among other Brucella nomen species and biovars. The results indicated that flhB, fliP, fliR and fliF are present in Brucella melitensis, Brucella ovis, and Brucella suis biovars 1, 2 and 3. Similar homologos have been reported previously in Brucella abortus. Using RT-PCR assays, we were unable to detect any expression of these genes. It is not yet known whether the genes are the cryptic remnants of a flagellar system or are actively involved in a process contributing to pathogenicity or previously undetected motility, but they are distributed widely in Brucella and merit further study to determine their role.

A dystrophin-immunoreactive protein in mammalian brain.

Dystrophin is expressed only in muscle and brain, but is absent from all tissues of the adult mdx mouse, a mutant with a single base substitution in the dystrophin gene. The brains of both normal and mdx mice contain a protein of approximately 230 kDa that is recognised by anti-dystrophin antibodies raised to the N-terminal region of the rod-like domain. Although the N-terminal and central rod regions of dystrophin share structural homologies with spectrin, the 230-kDa protein represents neither of the presently described forms of brain spectrin by a variety of criteria (molecular weight, cerebellar localisation, and developmental regulation) and is distinct from the product of the dystrophin gene. Studies of mdx and normal mouse brain show different postnatal developmental regulation of the 230-kDa dystrophin-immunoreactive protein.

Non-lignified parenchyma in Cactaceae and Portulacaceae

This work describes the occurrence and distribution pattern of non-lignified parenchyma in species of Cactaceae and Portulacaceae, of which samples of roots and stems of six species of Cactaceae and four species of Portulacaceae were analysed. The first records of non-lignified parenchyma in Portulacaceae were obtained and, in the case of Cactaceae, an in-depth discussion is given on the characterization of this tissue by various authors, as well as new information on the occurrence and distribution pattern of the non-lignified parenchyma. The terminology used to characterize the non-lignified parenchyma cells in the wood of Cactaceae is extremely diversified and often not very descriptive, which makes it difficult to establish homologies and better characterize this tissue. Non-lignified parenchyma cells in the secondary xylem in Cactaceae and Portulacaceae occur in association with the fibrous phase of the wood, often forming true continuous bands. This resembles what some authors call parenchyma wood. The proposal of this study is to demonstrate that, independent of the distribution pattern of the non-lignified parenchyma cells, the terminology used should follow that of the International Association of Wood Anatomists (IAWA) Committee as non-lignified parenchyma and not refer to a parenchymous phase of the wood. (C) 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159, 322-329.

The Y Chromosome of the Atelidae Family (Platyrrhini): Study by Chromosome Microdissection

In order to study the intergeneric variability of the Y chromosome, we describe the hybridization of the Y chromosome of Brachyteles arachnoides, obtained by microdissection, to metaphases of Ateles belzebuth marginatus, Lagothrix lagothricha, and Alouatta male specimens. Brachyteles arachnoides (Atelinae) has 62 chromosomes and a very small Y chromosome. Our results showed that the Brachyteles arachnoides Y chromosome probe hybridized to Lagothrix lagothricha metaphases yielding one hybridization signal on only the tiny Y chromosome, and when hybridized with Ateles belzebuth marginatus metaphases it yielded one hybridization signal on two thirds of the small acrocentric Y chromosome. However, no hybridization signal was observed in Alouatta metaphases (subfamily Alouattinae), a closely related genus in the Atelidae family. Furthermore, our data support a close phylogenetic relationship among Brachyteles, Ateles, and Lagothrix and their placement in the Atelinae subfamily, but exclude Alouatta from this group indicating its placement as basal to this group. Copyright (C) 2009 S. Karger AG, Basel

As relações de trabalho nas organizações de economia solidária : um paralelo Brasil-França

O objetivo desta pesquisa é o estudo das relações que se estabelecem entre o trabalhador e seu trabalho em organizações não convencionais, isto é, que não se identificam com o modo capitalista de produção e que reivindicam, pelo contrário, a criatividade e a originalidade de um trabalho mais autônomo, mais justo e mais responsável: a economia solidária. O que significa, para o trabalhador, atuar nestas organizações? É a pergunta que orienta este estudo. Dito de outro modo: a experiência vivida no trabalho cotidiano pelo trabalhador da economia solidária manifesta-se mediante práticas profissionais e práticas sociais reveladoras de novas formas de inserção no trabalho e na sociedade? Seria essa experiência fruto de uma transformação que ocorre em alguns segmentos do mundo do trabalho e observável em outros contextos econômicos ou um reflexo da situação particularmente fragilizada dos trabalhadores brasileiros? Tratar-se-á então de entender a singularidade da participação dos trabalhadores a este projeto, seu impacto sobre o desenvolvimento de seu trabalho e das relações estabelecidas com a organização e de estudar as transformações que podem ocorrer nas relações sociais a partir do trabalho. Este será analisado sob uma dimensão subjetiva, como experiência de construção identitária, e sob uma dimensão institucional, como socialização para e pela solidariedade. O conceito de “trabalho solidário”, que reúne essas dimensões, será analisado apoiando-se, em grande parte, na obra de François Dubet e sua teoria do ator, da estrutura social e da socialização. A pesquisa se inscreve numa perspectiva de contribuição à Sociologia do Trabalho e das relações de trabalho sem a pretensão de realizar uma sociologia da economia solidária, nas suas múltiplas relações com a sociedade. O que está em foco é a transformação das relações entre o trabalhador e seu trabalho. O argumento defendido pela pesquisa é que as relações que nascem de uma experiência cotidiana do trabalho nas organizações da economia solidária são peculiares e diversificadas, mas interpelam e desafiam o conjunto das relações sociais. Portanto, o trabalho realizado nessas organizações talvez seria, apesar de suas ambigüidades, suscetível de estimular novas formas de relações sociais por meio de uma socialização assentada na solidariedade. Três tipos de organizações “referências” (tipos ideais) são construídos a partir do tipo de produção dominante e dos valores e objetivos que motivam a ação: organizações de produção, associações culturais e organizações humanitárias. A comparação Brasil – França, através das organizações investigadas em Porto Alegre e Paris, procura homologias, isto é: correspondências na construção da ação apesar de contextos diferentes, assim como a reconstrução de processos e procura de especificidades que possam enriquecer as interações. No decorrer da investigação, o que se encontrou, tanto no Brasil quanto na França, foi de um lado, um discurso “oficial” (mentores, militantes da economia solidária e pesquisadores) que descreve a tarefa que se atribui a economia solidária: a responsabilização de todos para transformar a sociedade. Por outro lado, encontrou-se, através do discurso dos trabalhadores, o relato da realidade quotidiana que aparece como um mundo de tensões e contradições. Para entender essa aparente incompatibilidade, foi preciso recriar os mecanismos de construção do trabalho solidário: em que medida pode-se falar de experiência social e em que medida a socialização para e pela solidariedade é bem sucedida. Para tanto, foi necessário recompor o processo de construção das relações sociais dentro e fora do trabalho, manifestado mediante estratégias dos atores que precisam se posicionar frente às lógicas de ação desenvolvidas pelas organizações. A seguir, analisou-se a possibilidade de encontrar semelhanças e diferenças entre o Brasil e a França na construção deste trabalho solidário. Enfim, procurou-se responder à pergunta que originou esta pesquisa: seria mesmo o trabalho solidário gerador de novas relações sociais no trabalho e no âmbito mais amplo da sociedade?

Characterization of bovine transcripts preferentially expressed in testis and with a putative role in spermatogenesis

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

Uma ecologia de base complexa

This thesis objective systemize and discuss the ecological knowledge constructed by means of tradition knowledge with basis in a complex ecology (MORIN, 2002b). The conception of tradition knowledge (ALMEIDA, 2001c) corresponds to a diversity of knowledgement, of men and women, constructed from heteroclite elements of the geographic way, making use of analogies and homologies which serves as the base for this scientific inquiry. These knowledge are extremely related the context where these people are inserted. To construct an ecology of complex base is to understand that the reality is not given previously, and that its construction assumes indissociability among the elements that composes it, that is, between nature and society, material and immaterial elements. To incorporate the disorder, the uncertainty, the unpredictable and the auto-echo-organization as guide principles of a new ecology, constitutes in a new vision of the biological science and the scientific ecology in direction to a science of complexity. The work focuses the ecological knowledge of the Piató lagoon, municipality of Açu, in the State of Rio Grande do Norte, having as interlocutor of this boarding Mr. Francisco Lucas da Silva (known in the local as Chico Lucas), fisherman and agriculturist, who was born, and lives until today, in the community of Areia Branca, around the lagoon. Having for base the method as strategy (MORIN, 2001a), the research construction was performed through the realization of more than 10 trips carried out between the years of 2005 and 2007. In these trips the ecological aspects of the environments such as, the flora and the fauna, as well as the environmental impacts on the lagoon, were obtained in recorded dialogues and interviews with Chico Lucas, which were later transcripts. The information from there showed a natural and social complex reality, little known by Cartesian science, since it brings a wealth of details of daily life full, over all, for tradition knowing of the people that had lived there and the ones who remain living there. The thesis looks to understand the strategies of thought and the knowledge production referring to traditional knowing and its ability of interchange between different cognitive operators. The ecological knowledge that emerges of these knows reveals a systemic perception of the environment, presenting the beings and phenomena in its peculiarities and its degrees of complexity, but immutable in its indissociability

Binucleate Rhizoctonia sp AG G causing root rot in yacon (Smallanthus sonchifolius) in Brazil

A new rot caused by a binucleate Rhizoctonia sp. affecting the tuberous root cortex of the domesticated yacon (Smallanthus sonchifolius) has been observed in Brazil. Isolates of a binucleate Rhizoctonia sp. were collected from roots with rot symptoms and characterized by the number of nuclei per cell, hyphal anastomosis, RAPD molecular markers, ITS-5.8S rDNA sequence and pathogenicity tests. All isolates had a mean of 1.9-2.2 nuclei per cell and anastomosed with the binucleate Rhizoctonia sp. AG G-tester strain. RAPD analysis was carried out between 11 isolates recovered from yacon and 11 AG (A, Ba, Bb, Bo, C, D, F, G, O, P, Q) standard testers of binucleate Rhizoctonia sp. Genetic similarities of 94.8-100% were observed among isolates of the binucleate Rhizoctonia sp. from yacon and all isolates were genetically more closely related to the AG G tester than other strains according to UPGMA analysis using RAPD markers. Homologies of complete ITS nucleotide sequences were 100% between binucleate isolates of Rhizoctonia sp. from yacon and the AG G tester. According to pathogenicity tests, the isolates caused typical rot symptoms of yacon tubers 90 days after inoculation.

Molecular characterization of two Brazilian isolates of Lettuce mosaic virus with distinct biological properties

Efetuou-se a clonagem e seqüenciamento do gene que codifica a proteína capsidial de dois isolados do vírus do mosaico da alface (Lettuce mosaic virus, LMV) provenientes do estado de São Paulo, previamente caracterizados como pertencentes aos patótipos II (AF198, incapaz de infetar cultivares com os genes de resistência mo1¹ ou mo1²) e IV (AF199, capaz de quebrar a resistência propiciada pelos genes mo1¹ e mo1²), com base na virulência em cultivares diferenciadoras. Análise comparativa das seqüências de nucleotídeos de isolados provenientes da Europa, América do Norte, Oriente Médio e os dois isolados brasileiros não permitiu sua separação em estirpes, pois as porcentagens de homologia foram sempre superiores a 95%. Entretanto, análise filogenética dos isolados sugere uma origem comum entre o isolado AF-198 e os isolados LMV-R e LMV-0 (patótipo II, provenientes dos Estados Unidos e da França, respectivamente). O isolado AF199 apresentou uma alta homologia de seqüência com os isolados LMV-Aud e LMV-13, ambos provenientes da França. Esses isolados também são relacionados a isolados provenientes do Chile, embora uma origem comum não seja proposta. Eventos independentes de mutação podem estar ocorrendo em diferentes partes do mundo, propiciando o surgimento de novas estirpes de LMV capazes de quebrar a resistência conferida pelos genes mo1¹ e mo1².

Characterization of S3Pvac Anti-Cysticercosis Vaccine Components: Implications for the Development of an Anti-Cestodiasis Vaccine

Background: Cysticercosis and hydatidosis seriously affect human health and are responsible for considerable economic loss in animal husbandry in non-developed and developed countries. S3Pvac and EG95 are the only field trial-tested vaccine candidates against cysticercosis and hydatidosis, respectively. S3Pvac is composed of three peptides (KETc1, GK1 and KETc12), originally identified in a Taenia crassiceps cDNA library. S3Pvac synthetically and recombinantly expressed is effective against experimentally and naturally acquired cysticercosis.Methodology/ Principal Findings: In this study, the homologous sequences of two of the S3Pvac peptides, GK1 and KETc1, were identified and further characterized in Taenia crassiceps WFU, Taenia solium, Taenia saginata, Echinococcus granulosus and Echinococcus multilocularis. Comparisons of the nucleotide and amino acid sequences coding for KETc1 and GK1 revealed significant homologies in these species. The predicted secondary structure of GK1 is almost identical between the species, while some differences were observed in the C terminal region of KETc1 according to 3D modeling. A KETc1 variant with a deletion of three C-terminal amino acids protected to the same extent against experimental murine cysticercosis as the entire peptide. on the contrary, immunization with the truncated GK1 failed to induce protection. Immunolocalization studies revealed the non stage-specificity of the two S3Pvac epitopes and their persistence in the larval tegument of all species and in Taenia adult tapeworms.Conclusions/ Significance: These results indicate that GK1 and KETc1 may be considered candidates to be included in the formulation of a multivalent and multistage vaccine against these cestodiases because of their enhancing effects on other available vaccine candidates.

Cyto-, myelo- and chemoarchitecture of the prefrontal cortex of the Cebus monkey

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

Bundle sheath ontogeny in Kranz and non-Kranz species of Cyperaceae (Poales)

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