Submitted by Nadir Basilio (nadirsb@uninove.br) on 2016-06-01T14:43:08Z No. of bitstreams: 1 Valdemar Modolo Junior.pdf: 2802590 bytes, checksum: f3956818acd10efc3244abc007294827 (MD5) / Made available in DSpace on 2016-06-01T14:43:08Z (GMT). No. of bitstreams: 1 Valdemar Modolo Junior.pdf: 2802590 bytes, checksum: f3956818acd10efc3244abc007294827 (MD5) Previous issue date: 2015-06-10 / Among the optimization methods, the Genetic Algorithm (GA) has been producing good results in problems with high order of complexity, such as, for example, the production scheduling problem in job shop environment. The production sequencing problems must be translated into a mathematical representation, so that the AG can act. In this process we came up a problematic, the choice between different ways to represent the solution as some representations have limitations, how to present not feasible and / or redundant solutions. Therefore the aim of this study is to conduct a comparative study between different representations of the solution in the AG in production sequencing problems in job shop environments. Two representations of the solution were analyzed, the priority lists based and based on order of operations and compared with a binary representation, in the context of sequencing problem set defined by Lawrence (1984). The results were evaluated according to the total processing time (makespan), the computational cost and the proportion of generated feasible solutions. It was noticed that the representation of the solution based on order of operations, which produced 100% of feasible solutions, was the one that showed the best results although no convergence to the best known solution to every problem. / Dentre os métodos de otimização, o Algoritmo Genético (AG) vem produzindo bons resultados em problemas com ordem de complexidade elevada, como é o caso, por exemplo, do problema de sequenciamento da produção em ambiente job shop. Os problemas de sequenciamento da produção devem ser traduzidos para uma representação matemática, para que o AG possa atuar. Neste processo surgi uma problemática, a escolha entre as diferentes formas de se representar a solução visto que algumas representações apresentam limitações, como apresentar soluções não factíveis e/ou redundantes. Portanto o objetivo deste trabalho é realizar um estudo comparativo entre diferentes representações da solução no AG em problemas de sequenciamento da produção em ambientes job shop. Duas representações da solução foram analisadas, a baseada em listas de prioridades e a baseada em ordem de operações e comparada com uma representação binária, no contexto do conjunto de problemas de sequenciamento definidos por Lawrence (1984). Os resultados foram avaliados em função do tempo total de processamento (makespan), do custo computacional e da proporção de soluções factíveis geradas. Percebeu-se que, a representação da solução baseada em ordem de operações, a qual produziu 100% de soluções factíveis, foi a que mostrou os melhores resultados apesar de não apresentar convergência para a melhor solução conhecida em todos os problemas.

Résumé : Nous avons d’abord souhaité, dans ce travail de thèse, préciser les mécanismes moléculaires conduisant à l'expression ectopique du récepteur du GIP (glucose-dependent insulinotropic polypeptide receptor, GIPR) dans des adénomes somatotropes provenant de patients présentant une acromégalie avec une réponse paradoxale (stimulation) de l’hormone de croissance au glucose par voie orale. Nous avons montré que l’expression ectopique de GIPR se produit par une activation transcriptionnelle hypomorphe du gène GIPR associée à des anomalies de méthylation dans le corps du gène. L’activation de la voie AMP cyclique par le GIP postprandial dans les adénomes exprimant le GIPR peut représenter un mécanisme alternatif de la tumorigenèse somatotrope en l’absence de mutations de l’oncogène GNAS.Nous rapportons d’autre part une analyse cytogénétique approfondie des adénomes somatotropes, qui nous a permis de définir deux groupes d'adénomes, un groupe à faible altération du nombre de copies et un groupe à forte altération du nombre de copies. Deux tumeurs présentaient des réarrangements chromosomiques complexes avec une signature typique de chromothripsis, et une architecture sous-clonale incluant jusqu’à six populations cellulaires différentes, témoignant d’une hétérogénéité intratumorale importante.Dans une collection d'adénomes hypophysaires invasifs comportant la portion intrasellaire et la portion envahissante le sinus caverneux, nous avons montré par RNA-seq des profils d'expression génique divergents, apportant des arguments supplémentaires en faveur de l'hétérogénéité intratumorale dans ces tumeurs bénignes. Les échantillons tumoraux provenant de portions invasives ont montré une surexpression de la voie de transition épithélio-mésenchymateuse et des marqueurs de cellules souches cancéreuses soulignant leur rôle potentiel dans l’acquisition du phénotype invasif des cellules adénomateuses hypophysaires. / AbstractIn this work, we explored the molecular mechanisms of ectopic glucose-dependent insulinotropic polypeptide receptor (GIPR) expression in somatotroph adenomas from patients with acromegaly displaying a paradoxical GH increase to oral glucose. We showed that ectopic GIPR expression occurs through hypomorphic transcriptional activation of GIPR gene likely driven by DNA methylation changes. Activation of the cAMP pathway by postprandial GIP may represent an alternative tumorigenic mechanism in GIPR expressing somatotroph adenomas without driver mutations in GNAS oncogene. Cytogenetic profiling defined two groups of adenomas, a low-copy-number alteration (CNA) group and a high-CNA group.Two tumor samples displayed complex chromosomal rearrangements compatible with chromothripsis and showed subclonal architecture with up to six distinct cell population in each tumor, demonstrating an important intratumor heterogeneity.In a collection of invasive pituitary adenomas including the non-invasive intrasellar portions and the portions invading the cavernous sinuses, we showed by RNA-seq different gene expression profiles, providing supplemental evidence for the intratumoral heterogeneity in these benign tumors. Tumor samples from invasive portions showed up-regulation of the epithelial-mesenchymal transition pathway and increased expression of cancer stem-cell markers highlighting their potential role in pituitary tumor cell invasive behavior.

Les LPSNC représentent une localisation rare des lymphomes B diffus à grandes cellules (LBDGC), d’immunophénotype post-GC, dont la tumorigenèse reste mal connue.Notre objectif était de caractériser les altérations moléculaires des LPSNC à l’aide de techniques d’analyse haut débit.Notre projet a montré comme principaux résultats : 1/ la haute fréquence de mutations touchant des gènes impliqués dans la voie de signalisation BCR/TLR/NF-κB, en particulier MYD88, CD79B et TBL1XR1 ; 2/ des déséquilibres chromosomiques récurrents, en particulier la perte du 6q22 et du 6p (locus HLA) ; 3/ des mutations du promoteur de TERT et 4/ des transcrits de fusions ETV6-IGH.Plusieurs altérations semblent être des biomarqueurs pronostiques (i.e perte du 6q22 et délétions homozygotes de CDKN2A), prédictifs de réponse au traitement ou des cibles prometteuses pour des thérapies innovantes.En conclusion, il existe une grande similitude entre le profil moléculaire des LPSNC et celui des LBDGC extra-cérébraux avec néanmoins quelques spécificités. Les LPSNC peuvent résulter d’une tumorigenèse propre mais aussi de son microenvironnement singulier. / PCNSL represent a rare extranodal diffuse large B cell lymphoma (DLBCL) with a post-GC phenotype whose tumorigenesis is still poorly unknown.Our objective was to characterize the molecular genetic alterations of PCNSL using high throughput technologies.Results: We demonstrated 1/ a high incidence of somatic mutations in genes involved in the BCR/TLR/NF-κB pathway, especially MYD88, CD79B and TBL1XR1; 2/ recurrent chromosome imbalances such as 6q22 loss and 6q (HLA locus) homozygous deletions; 3/ TERT promoter mutations and 4/ gene fusions such as ETV6-IGH. Several alterations are associated with a prognostic impact (6q22 loss and CDKN2A homozygous deletions) or are promising targets for novel therapies.To conclude, PCNSL and extracerebral DLBCL share many similarities in terms of molecular genetic profile despite some specificities. PCNSL may result from a specific tumorigenesis but also from its peculiar microenvironment.

L’alternance de périodes glaciaires et interglaciaires durant les 20 derniers Ma a mené à des changements environnementaux répétés au niveau du plateau continental antarctique. C’est dans ce contexte que les téléostéens de la famille des Nototheniidae se sont adaptés et diversifiés à travers plusieurs vagues de radiations (dont les Trematominae), dominant l’Ichtyofaune australe. Parmi les Nototheniidae, le groupe « Trematomus » (genres Cryothenia, Pagothenia, Trematomus et Indonotothenia) est celui où l’on observe la plus grande diversité chromosomique, avec des nombres diploïdes de chromosomes allant de 24 à 58, impliquant de nombreux réarrangements ayant accompagné les spéciations. Nous avons cherché à caractériser ces remaniements chromosomiques. Avec un caryotype ancestral inféré de 2n = 48, une conservation des unités chromosomiques entre espèces, et une constance des tailles de génome, l’hypothèse de réarrangements structuraux sans polyploïdisation préalable est la plus probable. Afin de reconstruire l’histoire évolutive de ces événements, nous avons recherché les homologies chromosomiques interspécifiques. Ceci nous a permis de reconstituer les remaniements (majoritairement des fusions) que nous avons repositionnés sur la phylogénie résolue des « Trematomus ». Contrairement à ce qui a été publié pour le genre Notothenia, nos résultats suggèrent des acquisitions multiples et indépendantes. Les éléments transposables (ETs) peuvent être impliqués dans les remaniements chromosomiques par le biais de recombinaisons ectopiques. Ils participent alors à la diversification des lignées au cours de l’évolution. En raison de leur régulation épigénétique, leur mobilisation massive peut être induite en cas de variations environnementales importantes. Nous nous sommes intéressés à trois super-familles d’ETs (DIRS, Gypsy and Copia) dans ces génomes. Les DIRS1 ont montré des patrons d’insertions en points chauds dans les régions centromériques et péricentromériques. Etant donné leur mode de transposition décrit et leur propension à s’insérer dans des copies préexistantes, nous proposons un rôle des éléments DIRS1 comme facilitateurs des fusions observées lors de la diversification des « Trematomus ». / In the last 20 My, multiple glacial-interglacial cycles led to strong and repeated environmental changes on the Antarctic continental shelf. In this changing environment, nototheniid fishes diversified through several rounds of species radiation (one of which within Trematominae), and now constitute the dominant group in Antarctic teleosts. Among Nototheniidae, the group « Trematomus » (genera Cryothenia, Pagothenia, Trematomus and Indonotothenia) exhibits the highest chromosomal diversity, with diploid chromosome numbers ranging between 24 and 58, involving many rearrangements probably linked to speciation. We characterized the nature of these chromosomal repatternings. With an inferred ancestral state of 2n = 48 acrocentric chromosomes, a conserved number of chromosomal structural units, and a constancy of the genomes sizes we measured; the hypothesis of structural modifications is favored rather than a whole genome duplication associated to drastic reductions. In order to reconstruct an evolutionary scenario of such chromosomal rearrangements accompanying the trematomine diversification, we identified interspecific chromosomal homologies. This allowed us to reconstruct the rearrangements events (mostly centric and tandem fusions). We plotted them on a phylogeny we reconstructed based on our own ddRAD-seq data. Contrary to what was reported for the Notothenia, our results are in favor of independent acquisitions. Transposable elements (TEs) can lead to chromosomal rearrangements through ectopic recombination events, hinting at a role as drivers of specific-lineage diversification. Moreover, due to their epigenetic regulation, TEs can be mobilized when thermic changes occur. We focused on three retrotransposon superfamilies (DIRS, Gypsy and Copia) in nototheniid genomes. The DIRS1 showed unexpected accumulation patterns of insertion in the centromeric and pericentromeric regions. Given the mechanism of DIRS1 transposition and their tendency to sometimes insert on pre-existing copies (homing), we suggest a role of DIRS1 elements as facilitators of the fusions that occurred during the trematomine radiation.

No description available.

Paroedura genus includes 17 described species endemic to Madagascar and the Comoros Islands, where they went through a significant adaptive radiation. The genus Paroedura is monophyletic and well supported hypothesis on phylogenetic relationships among its species was published. Species vary considerably in body size and morphology and in preferences for habitat, some species live in sympatry. The genus Paroedura belongs to cytogenetically poorly studied family Gekkonidae which exhibits high variability in modes of sex determination and in comparison with basal gecko lineages, also considerable variability in the chromosome number and morphology. Karyotypes of only two species of the genus (P. picta, P. sp.) have been published. The aim of my thesis was to describe karyotypes of both sexes in all available species of the genus using conventional and molecular cytogenetic methods, to perform the phylogenetic analysis of karyotype evolution and chromosomal rearrangements in the genus, to assess the role of these rearrangements in the speciation of the genus and to detect sex chromosomes. I acquired karyotypes of both sexes in nine species representing the most of major phylogenetic lineages of the genus. According to the results, species can be divided into three groups according to diploid...

Carriers of apparently balanced chromosomal aberrations (BCA) are usually phenotypically normal. However, it has been estimated that up to 27% of these BCA may be associated with an abnormal phenotype, most often caused by cryptic imbalances at the breakpoints, gene disruption by the breakpoint or via the position effect. In contrast to conventional karyotyping, molecular cytogenetic techniques enable more detailed BCA characterization and better correlation between genotype and phenotype of the patient. The aim of this thesis was to evaluate the presence of copy number variants (CNVs) at breakpoints or elsewhere in the genome in patients with abnormal phenotype who carry de novo or inherited BCA. 54 BCA were investigated using array CGH (20 de novo cases, 27 inherited and 7 cases of unknown origin) including 32 reciprocal translocations, 6 robertsonian translocations, 12 inversions and 4 complex chromosomal rearrangements. If possible, the parents were also examined to ascertain the inheritance of the relevant CNVs. In order to specify microarray findings or exclude gene disruption, FISH was used in selected patients. Among the patients included, in 31,5% (17/54) at least one (in 8 patients more than one) significant CNV was detected. Four cases carried cryptic imbalances only at the breakpoints,...

The Araneoidea superfamily is a diverse clade of spiders with a great species diversity. The whole superfamily displays considerable conservativeness of observed karyotypes. Most likely ancestral karyotype in males is 24 acrocentric chromosomes with X1X2 sex determination system. The goal of this study is to explore the karyotype diversity of two araneoid families - Araneidae and Mimetidae. The majority of studied species exhibit the ancestral karyotype. In some species of the aformentioned families was observed sudden increase in chromosome numbers, up to 2n♂ = 52 in Araneidae and up to 2n♂ = 57 in Mimetidae. The latter number is the highest chromosome count observed in Entelegynae so far. Increase in 2n goes hand in hand with increase in sex chromosome numbers, leading up to X1X2X3X40 system in Araneidae and up to X1X2X3X4X5X6X70 in Mimetidae. I suggest polyploidy as a possible mechanism of the increase. To test this hypothesis, I measured the size of the genome using flow cytometry and used fluorescence in situ hybridization for the detection of 18S rRNA and 5S rRNA genes. For one species, probe for U2 snRNA gene was also optimized as part of this thesis. In many species studied, these techniques were used for the first time ever. In the case of the family Mimetidae, the largest genomes in...

Objective: Two chromosomal instability (CIN) pathways are described in glioblastoma multiforme (GBM), type 1 and type 2, which can be observed in up to 70% of the cases. Microsatellite instability (MSI) plays a pathogenic role in sporadic cancers such as colon, gastric and endometrial carcinomas with deficient mismatch repair (MMR). We aimed to perform a comprehensive analysis of the relationship between CIN and MSI mechanisms in sporadic glioblastomas. Methods: 129 GBMs were examined (109 newly diagnosed and 20 relapses) investigating MSI, immunohistochemical expression of MMR proteins as well as sequencing and promoter methylation of hMLH1. We characterized the molecular changes frequently correlated with CIN in MSI+ GBMs and compared them with 26 microsatellite-stable tumors. Results: Low-level MSI was observed in 11 of 129 (8.5%) cases and was higher in relapses than in primary GBMs (25 vs. 5.5%, p = 0.027). High-level MSI was not found in any case. A deficient expression of MLH1 and PMS2 without hMLH1 inactivation was observed only in one giant cell GBM. 55% of the MSI+ GBMs showed a profile which did not correspond to one of the known CIN pathways. An inverse association was observed between MSI and mutations of both p53 and PTEN. Conclusions: Our data suggest that CIN and MSI contribute to the genomic instability in GBMs via independent pathways. Since MSI was significantly more frequent in relapses, it might play a role in the malignant progression of GBM. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

In most bacterial pathogens, the genome is comprised within a single circular chromosome which is typically organized by the origin-to-terminus axis that divides the chromosome into equally-sized arms of replication (replichores). This similarity in length is presumed to be required for the synchronization of the two replication forks to meet at the terminus for efficient chromosome segregation. Transfer of genes between organisms, different from the route of parent to offspring, is called horizontal gene transfer (HGT). Acquiring foreign DNA through HGT is an important factor for the evolution of virulence in bacteria since it provides access to new features such as new toxins and antibiotic resistance genes. Chromosomes of many pathogenic bacteria such as Salmonella spp. carry such horizontally-transferred DNA fragments called pathogenicity islands. However, after such HGT events, the existing organization of chromosome can be disrupted and an imbalance between the two halves of the circular chromosome might occur. The predicted outcome of a replichore imbalance is the retardation of growth which in turn might result in the out-competition by other faster-growing bacteria in the environment. For that reason, we have investigated the association of the fitness cost and the replichore imbalance with isogenic strains with varying degrees of inter-replichore inversions. Our results showed that there is a correlation between the magnitude of replichore imbalance and fitness cost, for example 2.49-fold imbalance (one replichore 2.49-fold longer than the other) resulted in 11% reduction of fitness in comparison with balanced replichores. Therefore, our data suggest that the replichore imbalance could be utilized to predict the fitness cost of HGT events.