Dissertations / Theses: 'Gene orders'

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Goldman, Jacki P. "Regulated accessibility of variable region genes may control developmentally ordered T cell receptor [gamma] gene rearrangement." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/32626.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1995.
On t.p., "[gamma] appears as the lower case Greek letter.
Includes bibliographical references (leaves 155-172).
by Jacki P. Goldman.
Ph.D.

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Zheng, Chunfang, Eric Chen, Victor Albert, Eric Lyons, and David Sankoff. "Ancient eudicot hexaploidy meets ancestral eurosid gene order." BioMed Central, 2013. http://hdl.handle.net/10150/610022.

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BACKGROUND:A hexaploidization event over 125 Mya underlies the evolutionary lineage of the majority of flowering plants, including very many species of agricultural importance. Half of these belong to the rosid subgrouping, containing severals whose genome sequences have been published. Although most duplicate and triplicate genes have been lost in all descendants, clear traces of the original chromosome triples can be discerned, their internal contiguity highly conserved in some genomes and very fragmented in others. To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids, including the retention of a small proportion of the duplicate and triplicate genes and the reconstruction of putative ancestral intermediates between the original hexaploid and modern species, in this case the ancestor of the eurosid clade.RESULTS:We quantitatively trace the fate of gene triples originating in the hexaploidy across seven core eudicot flowering plants, and fit this to a two-stage model, pre- and post-radiation. We also measure the simultaneous dynamics of duplicate orthologous gene loss in three rosids, as influenced by biological functional class. We propose a new protocol for reconstructing ancestral gene order using only gene adjacency data from pairwise genomic analyses, based on repeating MAXIMUM WEIGHT MATCHING at two levels of resolution, an approach designed to transcend limitations on reconstructed contig size, while still avoiding the ambiguities of a multiplicity of solutions. Applied to three high-quality rosid genomes without subsequent polyploidy events, our automated procedure reconstructs the ancestor of the eurosid clade.CONCLUSIONS:The gene loss analysis and the ancestor reconstruction present complementary assessments of post-hexaploidization evolution, the first at the level of individual gene families within and across sister genomes and the second at the chromosome level. Despite the loss of more than 95% of gene duplicates and triplicates, and despite major structural rearrangement, our reconstructed eurosid ancestor clearly identifies the three regions corresponding to each of the seven original chromosomes of the earlier pre-hexaploid ancestor. Functional analysis confirmed trends reported for more recent plant polyploidy events: genes involved with regulation and responses were retained in multiple copies, while genes involved with metabolic processes were lost.

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Silvestre, Daniela. "Seqüenciamento e análise do genoma mitocondrial de Melipona bicolor (Hymenoptera, Apidae, Meliponini)." Universidade de São Paulo, 2002. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-06052002-110339/.

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A seqüência completa do genoma mitocondrial de uma espécie pode ajudar no mapeamento de restrição e desenho de primers para PCR. Estes poderão servir para amplificação e posterior seqüenciamento de regiões específicas de outras espécies e populações relacionadas, para estudos filogenéticos e de dinâmica populacional. Até o momento, temos na literatura a seqüência completa do DNA mitocondrial (DNAmt) de um único himenóptero, Apis mellifera, espécie que é endêmica do Velho Mundo. Nenhum genoma mitocondrial de uma espécie de abelha nativa do Brasil foi até o momento descrito. Com a devastação crescente dos ecossistemas, há a perda de espécies de abelhas ainda pouco estudadas, e talvez até outras ainda não conhecidas. Entre os meliponíneos, há espécies-chave de diversos ecossistemas brasileiros, tendo portanto uma enorme importância ecológica. No decorrer deste projeto, foram amplificados via PCR e seqüenciados 77% do genoma mitocondrial da abelha sem ferrão Melipona bicolor (Apidae, Meliponini), contendo todos os 13 genes mitocondriais codificadores para proteínas, 18 dos 22 genes para RNAt e os dois genes para RNAr (sendo um integral e o outro parcialmente seqüenciado). Além do seqüenciamento, foram realizados neste trabalho: análise da organização do genoma (conteúdo e ordem gênica); análise da tradução dos genes para proteínas e código genético; análise de outras características moleculares (freqüência das bases, códons utilizados, iniciação e terminação de genes, freqüência de aminoácidos etc); e comparação das características acima mencionadas com o genoma mitocondrial de A. mellifera e também com outros insetos. O viés para o uso de bases A+T, bastante evidente em A. mellifera, mostrou-se ainda mais acentuado em M. bicolor. Foram encontradas diferenças no tamanho e composição dos genes. Pelo menos nove rearranjos na ordem gênica mitocondrial foram observados entre as duas espécies de abelhas, um fenômeno raro entre organismos tão próximos. Considerando que essas espécies compartilham um comportamento intrigante, a eussocialidade, esses rearranjos podem servir como um excelente marcador para estudar a origem e a evolução desse comportamento no grupo.
The complete sequence of the mitochondrial genome of a species may help on restriction mapping and to design PCR primers. These can be useful to amplify and sequence specific regions from other species and analyze populations, in phylogenetic and demographic studies. So far, there was reported on literature the mtDNA complete sequence for only one hymenopteran, Apis mellifera, endemic from the Old World. No mitocondrial genome of a Brazilian native bee was ever described. With the increasing devastation of natural environments, several bee species can be led to extinction, including those poorly studied and maybe some unknown species. The meliponines (stingless bees) include key species to several Brazilian ecosystems, so they play an important ecological role. In this project, we have PCR amplified and sequenced 77% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini). The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was only partially sequenced). Besides sequencing, this work consisted of: analysis of genome organization (gene content and order); analysis of gene translation and genetic code; analysis of other molecular features (base frequencies, codon usage, gene initiation and termination, amino acid frequencies etc.); and comparison of the characteristics mentioned above with A. mellifera mitocondrial genome and also other insects. The highly biased A+T content is a typical characteristic of A. mellifera mitochondrial genome, and it is even more extreme on M. bicolor mtDNA. There are length and compositional differences on genes between M. bicolor and A. mellifera. At least nine gene order rearrangements were observed by comparing the mtDNA of these species, what is a rare event on closely related organisms. Considering that both species share an intriguing behavior, eusociality, these gene rearrangements may be used as an excellent marker to study the origin and evolution of that behavior on bees.

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Bernt, Matthias. "Gene order rearrangement methods for the reconstruction of phylogeny." Doctoral thesis, Universitätsbibliothek Leipzig, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-38666.

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The study of phylogeny, i.e. the evolutionary history of species, is a central problem in biology and a key for understanding characteristics of contemporary species. Many problems in this area can be formulated as combinatorial optimisation problems which makes it particularly interesting for computer scientists. The reconstruction of the phylogeny of species can be based on various kinds of data, e.g. morphological properties or characteristics of the genetic information of the species. Maximum parsimony is a popular and widely used method for phylogenetic reconstruction aiming for an explanation of the observed data requiring the least evolutionary changes. A certain property of the genetic information gained much interest for the reconstruction of phylogeny in recent time: the organisation of the genomes of species, i.e. the arrangement of the genes on the chromosomes. But the idea to reconstruct phylogenetic information from gene arrangements has a long history. In Dobzhansky and Sturtevant (1938) it was already pointed out that “a comparison of the different gene arrangements in the same chromosome may, in certain cases, throw light on the historical relationships of these structures, and consequently on the history of the species as a whole”. This kind of data is promising for the study of deep evolutionary relationships because gene arrangements are believed to evolve slowly (Rokas and Holland, 2000). This seems to be the case especially for mitochondrial genomes which are available for a wide range of species (Boore, 1999). The development of methods for the reconstruction of phylogeny from gene arrangement data has made considerable progress during the last years. Prominent examples are the computation of parsimonious evolutionary scenarios, i.e. a shortest sequence of rearrangements transforming one arrangement of genes into another or the length of such a minimal scenario (Hannenhalli and Pevzner, 1995b; Sankoff, 1992; Watterson et al., 1982); the reconstruction of parsimonious phylogenetic trees from gene arrangement data (Bader et al., 2008; Bernt et al., 2007b; Bourque and Pevzner, 2002; Moret et al., 2002a); or the computation of the similarities of gene arrangements (Bergeron et al., 2008a; Heber et al., 2009). 1 1 Introduction The central theme of this work is to provide efficient algorithms for modified versions of fundamental genome rearrangement problems using more plausible rearrangement models. Two types of modified rearrangement models are explored. The first type is to restrict the set of allowed rearrangements as follows. It can be observed that certain groups of genes are preserved during evolution. This may be caused by functional constraints which prevented the destruction (Lathe et al., 2000; Sémon and Duret, 2006; Xie et al., 2003), certain properties of the rearrangements which shaped the gene orders (Eisen et al., 2000; Sankoff, 2002; Tillier and Collins, 2000), or just because no destructive rearrangement happened since the speciation of the gene orders. It can be assumed that gene groups, found in all studied gene orders, are not acquired independently. Accordingly, these gene groups should be preserved in plausible reconstructions of the course of evolution, in particular the gene groups should be present in the reconstructed putative ancestral gene orders. This can be achieved by restricting the set of rearrangements, which are allowed for the reconstruction, to those which preserve the gene groups of the given gene orders. Since it is difficult to determine functionally what a gene group is, it has been proposed to consider common combinatorial structures of the gene orders as gene groups (Marcotte et al., 1999; Overbeek et al., 1999). The second considered modification of the rearrangement model is extending the set of allowed rearrangement types. Different types of rearrangement operations have shuffled the gene orders during evolution. It should be attempted to use the same set of rearrangement operations for the reconstruction otherwise distorted or even wrong phylogenetic conclusions may be obtained in the worst case. Both possibilities have been considered for certain rearrangement problems before. Restricted sets of allowed rearrangements have been used successfully for the computation of parsimonious rearrangement scenarios consisting of inversions only where the gene groups are identified as common intervals (Bérard et al., 2007; Figeac and Varré, 2004). Extending the set of allowed rearrangement operations is a delicate task. On the one hand it is unknown which rearrangements have to be regarded because this is part of the phylogeny to be discovered. On the other hand, efficient exact rearrangement methods including several operations are still rare, in particular when transpositions should be included. For example, the problem to compute shortest rearrangement scenarios including transpositions is still of unknown computational complexity. Currently, only efficient approximation algorithms are known (e.g. Bader and Ohlebusch, 2007; Elias and Hartman, 2006). Two problems have been studied with respect to one or even both of these possibilities in the scope of this work. The first one is the inversion median problem. Given the gene orders of some taxa, this problem asks for potential ancestral gene orders such that the corresponding inversion scenario is parsimonious, i.e. has a minimum length. Solving this problem is an essential component 2 of algorithms for computing phylogenetic trees from gene arrangements (Bourque and Pevzner, 2002; Moret et al., 2002a, 2001). The unconstrained inversion median problem is NP-hard (Caprara, 2003). In Chapter 3 the inversion median problem is studied under the additional constraint to preserve gene groups of the input gene orders. Common intervals, i.e. sets of genes that appear consecutively in the gene orders, are used for modelling gene groups. The problem of finding such ancestral gene orders is called the preserving inversion median problem. Already the problem of finding a shortest inversion scenario for two gene orders is NP-hard (Figeac and Varré, 2004). Mitochondrial gene orders are a rich source for phylogenetic investigations because they are known for more than 1 000 species. Four rearrangement operations are reported at least in the literature to be relevant for the study of mitochondrial gene order evolution (Boore, 1999): That is inversions, transpositions, inverse transpositions, and tandem duplication random loss (TDRL). Efficient methods for a plausible reconstruction of genome rearrangements for mitochondrial gene orders using all four operations are presented in Chapter 4. An important rearrangement operation, in particular for the study of mitochondrial gene orders, is the tandem duplication random loss operation (e.g. Boore, 2000; Mauro et al., 2006). This rearrangement duplicates a part of a gene order followed by the random loss of one of the redundant copies of each gene. The gene order is rearranged depending on which copy is lost. This rearrangement should be regarded for reconstructing phylogeny from gene order data. But the properties of this rearrangement operation have rarely been studied (Bouvel and Rossin, 2009; Chaudhuri et al., 2006). The combinatorial properties of the TDRL operation are studied in Chapter 5. The enumeration and counting of sorting TDRLs, that is TDRL operations reducing the distance, is studied in particular. Closed formulas for computing the number of sorting TDRLs and methods for the enumeration are presented. Furthermore, TDRLs are one of the operations considered in Chapter 4. An interesting property of this rearrangement, distinguishing it from other rearrangements, is its asymmetry. That is the effects of a single TDRL can (in the most cases) not be reversed with a single TDRL. The use of this property for phylogeny reconstruction is studied in Section 4.3. This thesis is structured as follows. The existing approaches obeying similar types of modified rearrangement models as well as important concepts and computational methods to related problems are reviewed in Chapter 2. The combinatorial structures of gene orders that have been proposed for identifying gene groups, in particular common intervals, as well as the computational approaches for their computation are reviewed in Section 2.2. Approaches for computing parsimonious pairwise rearrangement scenarios are outlined in Section 2.3. Methods for the computation genome rearrangement scenarios obeying biologically motivated constraints, as introduced above, are detailed in Section 2.4. The approaches for the inversion median problem are covered in Section 2.5. Methods for the reconstruction of phylogenetic trees from gene arrangement data are briefly outlined in Section 2.6.3 1 Introduction Chapter 3 introduces the new algorithms CIP, ECIP, and TCIP for solving the preserving inversion median problem. The efficiency of the algorithm is empirically studied for simulated as well as mitochondrial data. The description of algorithms CIP and ECIP is based on Bernt et al. (2006b). TCIP has been described in Bernt et al. (2007a, 2008b). But the theoretical foundation of TCIP is extended significantly within this work in order to allow for more than three input permutations. Gene order rearrangement methods that have been developed for the reconstruction of the phylogeny of mitochondrial gene orders are presented in the fourth chapter. The presented algorithm CREx computes rearrangement scenarios for pairs of gene orders. CREx regards the four types of rearrangement operations which are important for mitochondrial gene orders. Based on CREx the algorithm TreeREx for assigning rearrangement events to a given tree is developed. The quality of the CREx reconstructions is analysed in a large empirical study for simulated gene orders. The results of TreeREx are analysed for several mitochondrial data sets. Algorithms CREx and TreeREx have been published in Bernt et al. (2008a, 2007c). The analysis of the mitochondrial gene orders of Echinodermata was included in Perseke et al. (2008). Additionally, a new and simple method is presented to explore the potential of the CREx method. The new method is applied to the complete mitochondrial data set. The problem of enumerating and counting sorting TDRLs is studied in Chapter 5. The theoretical results are covered to a large extent by Bernt et al. (2009b). The missing combinatorial explanation for some of the presented formulas is given here for the first time. Therefor, a new method for the enumeration and counting of sorting TDRLs has been developed (Bernt et al., 2009a).

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Munoz, Adriana, Chunfang Zheng, Qian Zhu, Victor Albert, Steve Rounsley, and David Sankoff. "Scaffold filling, contig fusion and comparative gene order inference." BioMed Central, 2010. http://hdl.handle.net/10150/610198.

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BACKGROUND:There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being published in scaffold or contig form. Rearrangement algorithms, however, including gene order-based phylogenetic tools, require whole genome data on gene order or syntenic block order. How then can we use rearrangement algorithms to compare genomes available in scaffold form only? Can the comparative evidence predict the location of unsequenced genes?RESULTS:Our method involves optimally filling in genes missing from the scaffolds, while incorporating the augmented scaffolds directly into the rearrangement algorithms as if they were chromosomes. This is accomplished by an exact, polynomial-time algorithm. We then correct for the number of extra fusion/fission operations required to make scaffolds comparable to full assemblies. We model the relationship between the ratio of missing genes actually absent from the genome versus merely unsequenced ones, on one hand, and the increase of genomic distance after scaffold filling, on the other. We estimate the parameters of this model through simulations and by comparing the angiosperm genomes Ricinus communis and Vitis vinifera.CONCLUSIONS:The algorithm solves the comparison of genomes with 18,300 genes, including 4500 missing from one genome, in less than a minute on a MacBook, putting virtually all genomes within range of the method.

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Turner, Kyle Hugh. "Commanding officer's standing orders a powerful and unique genre." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 2006. http://library.nps.navy.mil/uhtbin/hyperion/06Jun%5FTurner.pdf.

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Myhre, Susanna. "Genetic re-targeting and de-targeting of adenovirus type 5 in order to create vectors for gene therapy /." Göteborg : Department of Microbiology and Immunology, The Sahlgrenska Academy at Göteborg University, 2007. http://hdl.handle.net/2077/7498.

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Tiwari, Vijay Kumar. "The Epigenetics of Gene Transcription and Higher Order Chromatin Conformation." Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6302.

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It is becoming increasingly clear that long-range control of gene expression is mediated through direct physical interactions between genes and regulatory elements, either intra- or interchromosomally. In addition to transcriptional initiation, formation of active chromatin hubs seem to be crucial for increased transcriptional efficiency as well as insulation from neighbouring heterochromatic environment. Regulatory factors apparently have an important role in organization of such functional modules in a development and differentiated- dependent fashion. The relevance of trans-acting factors in the ‘choice’ process of X-Chromosome Inactivation (XCI) was highlighted by our observations where CTCF was shown to occupy a homologous position on the active mouse and human Xist/XIST promoters and its binding affinity was altered in familial cases of opposite skewed X-inactivation patterns. The paradigm of genomic imprinting, i.e. the Igf2-H19 locus, manifests its imprinted states through the H19 Imprinting Control Region (ICR). The repression of the maternal Igf2 allele depends on the insulator properties of the H19 ICR when this interacts with CTCF. The studies here detected a novel kind of CTCF-dependent tightly closed pocket- like higher order structure exclusively on maternal allele which was found to be essential for imprinted Igf2 expression as well as maintenance of precise epigenetic marks at various Differentially Methylated Regions (DMRs) across this locus. Despite the highly condensed state of the mitotic chromosome, the insulator protein CTCF was found to constitutively occupy its known target sites. Furthermore, pivotal CTCF-dependent long-range regulatory loops within Igf2-H19 locus were found to survive mitotic compaction and such mechanisms might serve as a novel kind of epigenetic memory to minimize transcriptional chaos and to reset proper expression domains in the daughter cells as soon as cells exit mitosis. Our observations also suggest that the epigenetic reprogramming of H19 ICR during spermatogenesis is initiated by a CTCF-dependent recruitment of chromatin remodeling factor Lsh to the H19 ICR followed by completion of the imprint acquisition process by a replacement of CTCF with its closely related paralogue termed BORIS. Overall, this thesis unravels the novel roles for CTCF as an architectural factor in the organization of higher order chromatin conformations and transcriptional regulation.

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Göndör, Anita. "Epigenetic Regulation of Higher Order Chromatin Conformations and Gene Transcription." Doctoral thesis, Uppsala universitet, Zoologisk utvecklingsbiologi, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8296.

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Epigenetic states constitute heritable features of the chromatin to regulate when, where and how genes are expressed in the developing conceptus. A special case of epigenetic regulation, genomic imprinting, is defined as parent of origin-dependent monoallelic expression. The Igf2-H19 locus is considered as paradigm of genomic imprinting with a growth-promoting gene, Igf2, expressed paternally and a growth antagonist, H19 encoding a non-coding transcript, expressed only from the maternal allele. The monoallelic expression patterns are regulated by the epigenetic status at an imprinting control region (ICR) in the 5´-flank of the H19 gene. The chromatin insulator protein CTCF interacts with only the maternal H19 ICR allele to prevent downstream enhancers to communicate with the Igf2 promoters. Mutations of these CTCF binding sites lead to biallelic Igf2 expression, increased size of the conceptus and predisposition for cancer. Reasoning that these effects cannot be explained by the regulation of Igf2 expression alone, a technique was invented to examine long-range chromatin interactions without prior knowledge of the interacting partners. Applying the circular chromosomal conformation capture (4C) technique to mouse neonatal liver cells, it was observed that 114 unique sequences interacted with the H19 ICR. A majority of these interactors was in complex with only the maternal H19 ICR allele and depended on the presence of functional CTCF binding sites. The functional consequence of chromosomal networks was demonstrated by the observation that the maternal H19 ICR allele regulated the transcription of two genes on another chromosome. As the chromosomal networks underwent reprogramming during the maturation of embryonic stem cells, attention was turned to human cancer cells, displaying features common with mouse embryonic stem cells. Subsequently, chromatin folding at the human H19 ICR suggested that stable chromatin loops were organized by synergistic interactions within and between baits and interactors. The presence of these interactions was linked to DNA methylation patterns involving repeat elements. A "flower" model of chromatin networks was formulated to explain these observations. This thesis has unravealed a novel feature of the epigenome and its functions to regulate gene expression in trans. The identified roles for CTCF as an architectural factor in the organization of higher order chromatin conformations may be of importance in understanding development and disease ontogeny from novel perspectives.

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WHEELER, COSETTE MARIE THERESE. "HEPATITIS A VIRUS: GROWTH CHARACTERISTICS, PURIFICATION, AND CAPSID GENE ORDER (PEPTIDES, IMMUNOREACTIVITIES, POLYPEPTIDES)." Diss., The University of Arizona, 1985. http://hdl.handle.net/10150/188108.

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A human isolate of hepatitis A virus (HAV) strain HAS-15 was adapted to rapid growth FRhK-4 cells and a one-step growth curve was determined. Detectable virion production was absent for approximately 20 h post-infection (p.i.) and was followed by a 4-day logarithmic phase of virus production. A maximum intracellular virus titer of 10⁹ radioimmunofocus-forming units (RFU) per milliliter was achieved and remained essentially constant for a period of up to 14 days p.i. An adsorption study with HAV HAS-15 using FRhK-4 cells demonstrated greater than 99.9% of infectious virus adsorbed at 25 C in less than 20 min. Milligram amounts of purified HAV HAS-15 were obtained from persistently-infected RFhK-4 cells. The HAV polypeptides were separated by sodium dodecyl sulfate - polyacrylamide gel electrophoresis and transferred to nitocellulose for detection by an enzyme-linked immunotransfer blot (EITB) procedure. HAV nucleotide-derived amino acid sequence was subjected to computer analysis to identify potential immunogenic regions within the HAV capsid polypeptides. Synthetic peptides corresponding to selected regions of each of the larger putative capsid polypeptides were coupled to keyhole limpet hemocyanin and used to immunize rabbits. EITB reactivities of HAV specific anti-peptide sera have allowed the identification of the gene order for the larger HAV P1 gene products and the determination of the following molecular weights: HAV VP2 or 1B (MW 27,000), HAV VP3 or 1C (MW 29,000), and HAV VP1 or 1D (MW 33,000). The disposition of the HAV capsid polypeptides with respect to the virion external surface was evaluated by EITB reactivity of HAV polypeptides with specific antisera. Hyperimmune rabbit anti-157S HAV and human IgM reacted with VP1, VP2, and VP3, while IgG reacted predominantly with VP1 and VP2. Further evaluation of the HAV virion structure was attempted by examining the relative accessibility of the virion polypeptides to various labeling reagents. Reaction of intact virions with Iodogen resulted in the predominant labeling of VP1 while labeling of VP2 and 3 was barely detectable. Selective labeling of VP1 under controlled conditions, combined with the anti-HAV IgG immunologic reactivity against VP1 and VP2, suggests that these two capsid components are more exposed on the virion surface and may play an important role in the generation of neutralizing antibodies.

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Win, Maung Nyan Parker Carl Stevens Smolke Christina D. "Engineering RNA devices for gene regulation, biosensing, and higher-order cellular information processing /." Diss., Pasadena, Calif. : Caltech, 2008. http://resolver.caltech.edu/CaltechETD:etd-05282008-142750.

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Lefort, Virginie Favrel Joel Beslon Guillaume. "Evolution de second ordre et algorithmes évolutionnaires l'algorithme RBF-Gene /." Villeurbanne : Doc'INSA, 2008. http://docinsa.insa-lyon.fr/these/pont.php?id=mathivet_lefort.

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Seifert, Michael, Khalil Abou-El-Ardat, Betty Friedrich, Barbara Klink, and Andreas Deutsch. "Autoregressive Higher-Order Hidden Markov Models: Exploiting Local Chromosomal Dependencies in the Analysis of Tumor Expression Profiles." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-165328.

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Changes in gene expression programs play a central role in cancer. Chromosomal aberrations such as deletions, duplications and translocations of DNA segments can lead to highly significant positive correlations of gene expression levels of neighboring genes. This should be utilized to improve the analysis of tumor expression profiles. Here, we develop a novel model class of autoregressive higher-order Hidden Markov Models (HMMs) that carefully exploit local data-dependent chromosomal dependencies to improve the identification of differentially expressed genes in tumor. Autoregressive higher-order HMMs overcome generally existing limitations of standard first-order HMMs in the modeling of dependencies between genes in close chromosomal proximity by the simultaneous usage of higher-order state-transitions and autoregressive emissions as novel model features. We apply autoregressive higher-order HMMs to the analysis of breast cancer and glioma gene expression data and perform in-depth model evaluation studies. We find that autoregressive higher-order HMMs clearly improve the identification of overexpressed genes with underlying gene copy number duplications in breast cancer in comparison to mixture models, standard first- and higher-order HMMs, and other related methods. The performance benefit is attributed to the simultaneous usage of higher-order state-transitions in combination with autoregressive emissions. This benefit could not be reached by using each of these two features independently. We also find that autoregressive higher-order HMMs are better able to identify differentially expressed genes in tumors independent of the underlying gene copy number status in comparison to the majority of related methods. This is further supported by the identification of well-known and of previously unreported hotspots of differential expression in glioblastomas demonstrating the efficacy of autoregressive higher-order HMMs for the analysis of individual tumor expression profiles. Moreover, we reveal interesting novel details of systematic alterations of gene expression levels in known cancer signaling pathways distinguishing oligodendrogliomas, astrocytomas and glioblastomas.

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Fries, Anthony Charles. "The molecular evolution of mitochondrial oxidative phosphorylation genes in the Order Passeriformes." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1258557488.

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Hassan, Aamir Ul. "Integration of Genome Scale Data for Identifying New Biomarkers in Colon Cancer: Integrated Analysis of Transcriptomics and Epigenomics Data from High Throughput Technologies in Order to Identifying New Biomarkers Genes for Personalised Targeted Therapies for Patients Suffering from Colon Cancer." Thesis, University of Bradford, 2017. http://hdl.handle.net/10454/17419.

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Colorectal cancer is the third most common cancer and the leading cause of cancer deaths in Western industrialised countries. Despite recent advances in the screening, diagnosis, and treatment of colorectal cancer, an estimated 608,000 people die every year due to colon cancer. Our current knowledge of colorectal carcinogenesis indicates a multifactorial and multi-step process that involves various genetic alterations and several biological pathways. The identification of molecular markers with early diagnostic and precise clinical outcome in colon cancer is a challenging task because of tumour heterogeneity. This Ph.D.-thesis presents the molecular and cellular mechanisms leading to colorectal cancer. A systematical review of the literature is conducted on Microarray Gene expression profiling, gene ontology enrichment analysis, microRNA and system Biology and various bioinformatics tools. We aimed this study to stratify a colon tumour into molecular distinct subtypes, identification of novel diagnostic targets and prediction of reliable prognostic signatures for clinical practice using microarray expression datasets. We performed an integrated analysis of gene expression data based on genetic, epigenetic and extensive clinical information using unsupervised learning, correlation and functional network analysis. As results, we identified 267-gene and 124-gene signatures that can distinguish normal, primary and metastatic tissues, and also involved in important regulatory functions such as immune-response, lipid metabolism and peroxisome proliferator-activated receptors (PPARs) signalling pathways. For the first time, we also identify miRNAs that can differentiate between primary colon from metastatic and a prognostic signature of grade and stage levels, which can be a major contributor to complex transcriptional phenotypes in a colon tumour.

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Seifert, Michael, Khalil Abou-El-Ardat, Betty Friedrich, Barbara Klink, and Andreas Deutsch. "Autoregressive Higher-Order Hidden Markov Models: Exploiting Local Chromosomal Dependencies in the Analysis of Tumor Expression Profiles." Public Library of Science, 2014. https://tud.qucosa.de/id/qucosa%3A28671.

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Changes in gene expression programs play a central role in cancer. Chromosomal aberrations such as deletions, duplications and translocations of DNA segments can lead to highly significant positive correlations of gene expression levels of neighboring genes. This should be utilized to improve the analysis of tumor expression profiles. Here, we develop a novel model class of autoregressive higher-order Hidden Markov Models (HMMs) that carefully exploit local data-dependent chromosomal dependencies to improve the identification of differentially expressed genes in tumor. Autoregressive higher-order HMMs overcome generally existing limitations of standard first-order HMMs in the modeling of dependencies between genes in close chromosomal proximity by the simultaneous usage of higher-order state-transitions and autoregressive emissions as novel model features. We apply autoregressive higher-order HMMs to the analysis of breast cancer and glioma gene expression data and perform in-depth model evaluation studies. We find that autoregressive higher-order HMMs clearly improve the identification of overexpressed genes with underlying gene copy number duplications in breast cancer in comparison to mixture models, standard first- and higher-order HMMs, and other related methods. The performance benefit is attributed to the simultaneous usage of higher-order state-transitions in combination with autoregressive emissions. This benefit could not be reached by using each of these two features independently. We also find that autoregressive higher-order HMMs are better able to identify differentially expressed genes in tumors independent of the underlying gene copy number status in comparison to the majority of related methods. This is further supported by the identification of well-known and of previously unreported hotspots of differential expression in glioblastomas demonstrating the efficacy of autoregressive higher-order HMMs for the analysis of individual tumor expression profiles. Moreover, we reveal interesting novel details of systematic alterations of gene expression levels in known cancer signaling pathways distinguishing oligodendrogliomas, astrocytomas and glioblastomas.

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Love-Gregory, Latisha D. "Investigation of the origin of the Y393N allele in Old Order Mennonite and non-Mennonite maple syrup urine disease patients analysis of the branched chain [alpha]-keto acid dehydrogenase complex E1[alpha] gene : a dissertation ... /." free to MU campus, to others for purchase, 2001. http://wwwlib.umi.com/cr/mo/fullcit?p3012999.

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Franke, Martin [Verfasser]. "The Role of Higher-Order Chromatin Organization at the SOX9 Locus in Gene Regulation and Disease / Martin Franke." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1140487191/34.

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Krimm, Jean-Pierre. "Application des ordres partiels à la génération compositionnelle de systèmes asynchrones." Université Joseph Fourier (Grenoble), 2000. http://www.theses.fr/2000GRE10243.

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La verification formelle permet de garantir qu'un programme verifie un ensemble de proprietes. Pour ce faire, une methode attractive consiste a modeliser son comportement par un systeme de transition etiquetees (ste), puis a evaluer les proprietes sur ce ste par exploration exhaustive. L'interet de cette approche par model-checking est d'etre automatisable dans le cas fini, mais son inconvenient reste la taille du ste, souvent redhibitoire pour des programmes complexes. Pour palier a ce probleme, une solution possible est de considerer un ste reduit qui preserve les proprietes a verifier. Une approche naturelle consiste alors a proceder de maniere compositionelle : on genere independamment les ste associes a differentes parties du systeme global, on reduit ces ste modulo une relation appropriee, puis on compose les ste reduits ainsi obtenus. Cette technique a ete notamment mise en uvre avec succes sur des systemes de processus communiquants par rendez-vous. L'objectif de cette these est d'etendre ces resultats au cas plus difficile ou les communications ont lieu a travers des buffers asynchrones, ce qui correspond au modele d'execution de langages de specification comme sdl ou promela. Pour reduire la taille du ste obtenu lors d'une generation partielle, l'originalite de ce travail consiste alors a utiliser une notion de preordre sur les sequences d'execution du systeme : seules les sequences les plus executables conduisant a un ensemble d'etats caracteristiques de la propriete a verifier sont prises en compte. Deux types de proprietes sont notamment envisagees : l'absence de blocage et la preservation d'un langage observable. Cette approche est formellement justifiee, et un operateur de composition parallele permettant de calculer directement des ste reduits est propose. Cet operateur a ete implemente dans un outil de generation compositionnelle et sa mise en uvre sur des etudes de cas confirme largement l'interet de cette solution.

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Mwinyi, Adina, Achim Meyer, Christoph Bleidorn, Bernhard Lieb, Thomas Bartolomaeus, and Lars Podsiadlowski. "Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida." Universität Potsdam, 2009. http://opus.kobv.de/ubp/volltexte/2010/4491/.

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Background: Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida. Results: The first complete mitochondrial genome of a member of Sipuncula, Sipunculus nudus, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida sensu lato, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida. Conclusion: The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula.

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Nicolas, Antoine. "UNDERSTANDING EVOLUTIONARY RELATIONSHIPS IN THE ANGIOSPERM ORDER APIALES BASED ON ANALYSES OF ORGANELLAR DNA SEQUENCES AND NUCLEAR GENE DUPLICATIONS." VCU Scholars Compass, 2009. http://scholarscompass.vcu.edu/etd/1701.

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I studied evolutionary history in the angiosperm order Apiales, with a special emphasis on interactions between form, time, and space. Four broad categories of problems were addressed: interfamilial relationships in Apiales, the assignment of genera traditionally assigned to the Apiaceae subfamily Hydrocotyloideae, the estimation of divergence times of the major clades, and the reconstruction of the biogeographic history of Apiales. We used molecular markers with different evolutionary properties and rates derived from the plastid (trnD-trnT and rpl16), nuclear (RPB2), and mitochondrial (nad1 intron 2) genomes, from more than 250 species representing all major clades in the order. The nuclear RPB2 region exhibited evidence of at least six duplication events in Apiales and provided a rich source of information for understanding the origins of polyploid lineages, especially in Araliaceae. Sequence comparisons among the copies show that exon regions are highly conserved. All copies appear to be functional but may have undergone subfunctionalization. Phylogenetic analyses of the three genomes suggest that Hydrocotyloideae should be divided into as many as six evolutionary lineages, but that most taxa should be included in subfamilies Azorelloideae and Mackinlayoideae. Relationships among and within the major clades of Azorelloideae need further analyses since many genera appeared non-monophyletic (e.g., Azorella, Schizeilema, and Eremocharis). Mackinlayoideae appeared as the earliest diverging lineage of Apiaceae, but the plastid and nuclear trees were incongruent in the placement of the Platysace clade relative to Mackinlayoideae and the rest of Apiaceae. Among the remaining clades of suborder Apiineae, Myodocapaceae appeared sister to Apiaceae in both plastid and nuclear trees, preceded by the divergence of Araliaceae and then Pittosporaceae. At the base of the gene trees in Apiales, Griseliniaceae and Torricelliaceae formed successive sisters to Apiineae. The placement of Pennantiaceae as sister to the rest of Apiales was confirmed by plastid data, but was not found in the nuclear trees. The order appears to have originated in the Cretaceous, with Apiineae having an age of c. 100 Mya. Australasia appears to be the most likely center of origin for Apiineae and most of its major clades, except Azorelloideae (South America) and Apioideae-Saniculoideae (sub-Saharan Africa).

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Mathivet, Virginie. "Evolution de second ordre et algorithmes évolutionnaires : l'algorithme RBF-Gened." Lyon, INSA, 2007. http://theses.insa-lyon.fr/publication/2007ISAL0042/these.pdf.

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On parle d’évolution de second ordre (ou de sélection indirecte) lorsque les individus sont sélectionnés non pour leur seule adaptation à l’environnement mais aussi pour leur capacité à évoluer « mieux ». Bien qu’un tel mécanisme soit a priori très intéressant en évolution artificielle, la structure des algorithmes évolutionnaires interdit généralement celui-ci car les processus évolutifs sont figés. Nous avons ainsi proposé un nouvel algorithme évolutionnaire, RBF-Gene. Il possède un niveau intermédiaire, le protéome (composé de « protéines »), entre le phénotype d’un individu et son génotype lui permettant de faire varier la structure du génome sans modifier son phénotype sachant que ces variations auront une influence sur les reproductions futures. Nous montrons qu’une sélection de second ordre est bien à l’œuvre dans l’algorithme et qu’elle permet de façonner les génomes, en modifiant la taille des zones non codantes et l’ordre des gènes
Second order evolution (or indirect selection) corresponds to a situation where the individuals are not only selected on their fitness to an environment, but also on their ability to evolve « better ». Even if such a mechanism seems a priori very interesting in artificial evolution, it is not permitted by the structure of evolutionary algorithms because the evolutionary processes are fixed. Therefore, we propose a new evolutionary algorithm, RBFGene. It includes an intermediate level, the proteom (made of « proteins »), between the phenotype of an individual and its genotype, that allows for changes in the structure of the genome without changing the phenotype. These modifications can thereafter have an influence on later reproductions. We show the existence of an indirect selection in our algorithm, acting on genomes by changing the size of the non coding sequences or the order of the genes

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Chapados, Julie. "Comparative genomics: Using the complete genome sequence of Halobacterium salinarum NRC-1 to assess gene order conservation within the Halobacteriaceae." Thesis, University of Ottawa (Canada), 2002. http://hdl.handle.net/10393/6234.

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Comparative mapping and comparative genomics can be used to study genome stability. The genome organization of different strains, species or genera are compared by using physical maps or complete genome sequences. A previous comparative study determined that there was no gene order conservation between Haloferax volcanii and Halobacterium salinarum at a 15-kbp resolution. My research was designed to assess gene order conservation between certain halophiles at a much finer resolution. This was accomplished by using the only available haloarchaeal genome sequence as a reference. Random gene fragments obtained from other related halophiles were compared to the complete genome sequence and the level of gene order conservation was estimated. The hypothesis of this study was that gene order will not be conserved among haloarchaeal genera. Significant linkage (conserved gene fragments) was detected between Halobacterium salinarum NRC-1 and the five analyzed species. The hypothesis was refuted as some gene fragments have maintained similar gene organization in different genera. Furthermore, many genes from the selected halophiles have no homologs in the NRC-1 genome. The use of gene order as a tool to measure phylogeny is discussed.

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McLaughlin, Kathryn Anne. "Role of DNA methylation and Polycomb machineries in directing higher-order chromatin architecture in embryonic stem cell." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31400.

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Mouse embryonic stem cells (mESCs) are an excellent model to study epigenetics and chromatin structure, owing to their self-renewal capabilities and tolerance of dynamic changes to DNA and histone modifications. Culturing conditions impact on the ability of mESCs to effectively recapitulate in vivo developmental states, and this is exemplified by refined culture conditions (termed 2i) that promote a pluripotent ground state. 2i-cultured mESC populations are homogeneous, naïve, and distinct from conventional (serum/LIF-cultured) cells, which exist as a metastable population. Remarkably, 2i-cultured mESCs also display global DNA hypomethylation, with methylation patterns more comparable to the cells of the E3.5 pre-implantation blastocyst. This is distinct from conventional serum-cultured cells, which display DNA methylation profiles that resemble later-stage E6.5 post-implantation epiblasts. The ability to transition between 2i- and serum-culture states is an attractive model for studying the dynamic role of DNA methylation in a variety of processes. DNA hypomethylation has been linked with depletion of the Polycomb-mediated repressive histone mark H3K27me3 from its normal target loci. Polycomb repressive complexes (PRC1 and PRC2) are important developmental regulators that maintain the repression of lineage-specific genes through generating compact higher-order chromatin structures. Polycomb target sites are primarily unmethylated CpG islands (CGIs). However, under conditions of DNA hypomethylation, new (previously methylated) binding sites are unveiled, and Polycomb is redistributed from its normal CGI target regions to intragenic regions. Thus, shifting mESCs to ground state conditions results in both DNA methylation and Polycomb patterns that are quite distinct from their serum-cultured counterparts. In my PhD, I sought to investigate the effect of DNA hypomethylation and Polycomb redistribution on higher-order chromatin structure in the ground state. I used a targeted, single-locus approach (FISH) as well as a genome-wide approach (Hi-C) to analyse differences in chromatin structure between conventionally cultured and ground state mESCs. My work suggests that chromatin structure is globally altered in hypomethylated 2icultured mESCs, with a similar state present in E3.5 mouse blastocysts. Using mESC lines in which DNA methylation levels can be directly manipulated, I was able to dissect the molecular mechanism driving higher-order structure changes in 2i medium, and showed the importance of DNA methylation in directing Polycomb-mediated chromatin compaction. My results may be important in considering the impact of DNA-methylation mediated reprogramming in multiple developmental, disease and regenerative medicine contexts.

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Mains, Christine Marie. "COMPARATIVE MAPPING: HOMOLOGY WITHIN THE ORDER PERISSODACTYLA OF FOUR GENES LOCATED ON EQUUS CABALLUS CHROMOSOME 20." Connect to this title online, 2004. http://lib.uky.edu/ETD/ukyvesc2004t00198/CMThesis.pdf.

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Abouna, Marie Stéphanie. ""Féminisation" du football et constructions des identités sexuées : des dynamiques et accompagnements de(s)-ordres du genre." Brest, 2010. http://www.theses.fr/2010BRES1021.

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Ce travail s’intéresse à la construction des identités de genre par le football. Nous cherchons à saisir comment l’expérience du football au féminin est porteuse de sens. Il s’agit d’abord de caractériser l’espace du football au féminin par une sociologie comparative des données sur ses évolutions historiques, médiatiques et sociodémographiques, ensuite de comprendre comment les footballeuses rendent possibles leur pratique. A travers une approche compréhensive, nous tentons de saisir les expériences féminines à partir d’une observation in situ et d’un corpus d’entretiens biographiques réalisés auprès des footballeuses et d’autres actrices et acteurs issus de deux clubs où cohabitent des équipes féminines et masculines. Nous montrons que les constructions identitaires s’organisent et s’ancrent dans le quotidien décliné dans des formes originales de sociabilités et de rapports sociaux mettant en présence des femmes (jeunes et adultes, mères et filles, compagnes) aux côtés des hommes
This research is interested in the construction of gender identities through football. We will be trying to grasp how the experiment of feminine football is meaningful. First of all, it is about characterizing the space of feminine football by comparing the development of data on its history, media coverage, sociological and demographical effects, then understanding the way in which the female plavers make their participation possible. Through a comprehensive approach, we will try to understand the feminine experiments by starting from “in situ” observations and from a corpus of interviews through biographical stories on female football players and other actors from two clubs where both the feminine and the masculine teams coexist. We will show that the identity constructions are organized and anchored daily in the original forms of sociability and social relationships placing women (young people and adults, mothers and daughters, partners) next to men

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Lima, Paola Goussain de Souza [UNESP]. "As inversões sujeito-verbo e a concordância verbal: um estudo sobre a influência da posposição do sujeito em gêneros escritos de imprensa do português brasileiro." Universidade Estadual Paulista (UNESP), 2011. http://hdl.handle.net/11449/86536.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Este trabalho traz o estudo de estruturas que apresentam posposição do sujeito e a influência das mesmas no processo de concordância verbal em gêneros escritos de imprensa do Português Brasileiro (PB), datados entre 2008 e 2010. Para tanto, selecionamos, como corpus desta pesquisa, os gêneros editorial, carta dos leitores, noticiário, coluna e entrevista – seções que apresentam traços mais informais e subjetivos de seus usuários/leitores, dos jornais Folha de São Paulo, Jornal da Tarde, Notícias Já e Diário de São Paulo e das revistas Istoé Gente, Época, Malu Mulher e Aparecida, por estes serem meios de comunicação de imprensa escrita, direcionados a diferentes leitores e com grande circulação nacional. Fizemos um levantamento das ocorrências de sujeitos pospostos nos gêneros escritos de imprensa, analisamos os dados, levantando, ao final, nossas considerações sobre a relação posição do sujeito X concordância verbal. Trazemos a hipótese de que o sujeito posposto na escrita, assim como ocorre na fala, desfavoreça a CV, pois, por não se apresentar em posição de tópico e não condizer com a definição dada pela Gramática Tradicional, “ser de quem se diz alguma coisa”, características estas principais para a identificação do sujeito em uma oração, o usuário da língua tende a identificá-lo como sendo outro termo da oração, havendo ou não um termo que ocupe a posição inicial da oração em seu lugar, não realizando, com isto, a concordância entre o verbo e este SN sujeito pós-verbal
This research brings a study of structures which present postposition of the subject and the influence of those in the process of verbal agreement in written genres Press of the Brazilian Portuguese (BP), dated between 2008 and 2010. To this end, we selected as a corpus of this research, the gender’s editorial, letter from readers, news, column and interview – sections that have more informal and subjective features of their users / readers, from Folha de São Paulo newspaper, Jornal da Tarde, Notícias Já, Diário de São Paulo and from the magazines Istoé Gente, Época, Malu Mulher and Aparecida, for they being means of printing media, towards different readers and with a large national circulation. We did a survey of the occurrences of subjects postponed in written genres of press. We analyzed the data, increasing, at the end, our thoughts about the relation position of the subject X verbal agreement. We bring the hypothesis that the subject postponed in writing, as well as in speech, does not favour the CV, then, for not present itself in a position of topic and does not match the definition given by the Traditional Grammar, being from whom says to be something” these characteristics are major for the identification of the subject in a sentence. The language user tends to identify it as another word of the sentence, whether there is or not a term that occupies its initial positions in the sentence, without achievement, with that, the agreement between the verb and the post-verbal subject SN

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ROCHA, Patrícia Keytth Lins. "Qual região do DNA mitocondrial reflete a história evolutiva da ordem Lepidoptera?" Universidade Federal de Pernambuco, 2013. https://repositorio.ufpe.br/handle/123456789/13136.

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A ordem Lepidoptera apresenta uma gama de espécimes de importância econômica, algumas são agentes polinizadores e outras são pragas. Vários estudos têm sido realizados com base na morfologia com base em dados moleculares para elucidar a evolução da ordem. O DNA mitocondrial é muito utilizado por proporcionar boa resolução filogenética. Com base em genes mitocondriais informativos, nós propusemos um conjunto de dados que pode ser utilizado em análise filogenética de Lepidoptera obtendo a mesma robustez que a análise com mtDNAs completos. Para isso, as sequências dos mitogenomas de Lepidoptera foram recuperadas no banco de dados do NCBI. Foi identificada a ordem gênica das sequências utilizando o programa MAUVE. As regiões de interesse em D. flavipennella foram sequenciadas para testar a eficiência dos marcadores moleculares em sequência nova. Foi realizada análise de entropia, teste de sinal filogenético e de saturação para verificar características de bons marcadores moleculares e foram realizadas análises filogenéticas nos programas PhyML e MrBayes. Foram realizados também testes com e sem a terceira posição dos códons para verificar a influência da terceira posição nas análises filogenéticas de Lepidoptera. As regiões estudadas foram concatenadas para aumentar os valores de confiança das árvores. Verificamos que com a concatenação dos genes COI, ATP6, COIII, ND3, ND5, CYTB, ND1 e 16S foi possível obter resultados com robustez semelhante a dos mitogenomas completos.

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Legros, Catherine. "Analyse du discours métalinguistique d'étudiants des ordres postsecondaires en situation de repérage d'erreurs d'accords de genre et de nombre." Mémoire, Université de Sherbrooke, 1993. http://hdl.handle.net/11143/9952.

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Les résultats obtenus au Test universitaire de rédaction et de bonne orthographe illustrent bien le fait qu'après un nombre considérable d'années de cours de français, en particulier de grammaire, «plus d'un tiers des étudiants ne satisfont pas aux exigences minimales de qualité en français écrit établies par les universités.» (Roy, 1989). Plusieurs chercheurs (Bibeau, 1975; Bureau, 1976; Roy et Lafontaine, 1990) se sont penchés sur les types d'erreurs commis le plus couramment par les étudiants. Ces spécialistes arrivent à la conclusion que les lacunes apparaissent pratiquement à tous les niveaux du français écrit (syntaxe, orthographe lexicale et orthographe grammaticale) et touchent même des notions de base normalement acquises à l'ordre primaire. Les bilans dressés par ces recherches ont mis en relief le besoin urgent de trouver des solutions. Depuis de nombreuses années, les recherches abondent dans le domaine de la didactique du français en général et dans celui de l'enseignement de la grammaire en particulier, mais les solutions proposées s'avèrent jusqu'à présent peu efficaces. Plusieurs plans d'intervention ont été mis sur pied; des centres d'aide en français sont à la disposition des étudiants du cégep et des cours de rattrapage sont proposés à ceux de l'université. Peu de bénéfices découlent de ces actions, car il s'avère que les notions grammaticales qui posent problème sont enseignées de la même manière et à l'aide des mêmes manuels qu'elles l'ont été lorsque l'étudiant était au primaire ou au secondaire (Roy et a/.,1992). Les résultats obtenus par ces étudiants montrent que cet enseignement de la grammaire ne permet pas à l'apprenant de comprendre le fonctionnement global du français écrit. En fait, il semblerait que dans toutes les tentatives pour changer la situation, un facteur clé ait été négligé. Aucune recherche ne s'est penchée sur la façon dont les notions grammaticales et syntaxiques sont assimilées par les élèves. En bref, il n'y a pas eu d'étude qui ait l'apprenant pour objet de recherche. Nous nous proposons, dans la présente étude, d'analyser le discours métalinguistique émis par des étudiants des ordres postsecondaires au moment où ces étudiants doivent résoudre des difficultés d'accord de genre et de nombre. À ce sujet, Boutet, Gauthier et Saint-Pierre (1985) déclarent qu'il faut faire une différence «entre le savoir-faire linguistique des élèves, savoir qui est acquis à leur arrivée à l'école, et le savoir-dire sur la langue, ou savoir métalinguistique. C'est ce savoir qui devient la tâche de l'enseignement.». Nous convenons avec ces auteures qu'il est temps de prendre en considération le savoir réellement constitué par les apprenants afin de pouvoir envisager des moyens d'intervention auprès de ceux qui ont des difficultés. Nous présentons, dans le premier chapitre, la problématique de recherche en relation avec une revue de littérature concernant le métalinguistique. Nous donnons ensuite un aperçu de l'enseignement des variations d'accords de genre et nombre dispensé par des livres de grammaire utilisés actuellement. Enfin, toujours en rapport avec les variations de genre et de nombre, nous exposons les opérations linguistiques sur lesquelles peuvent reposer les raisonnements des étudiants. À l'issue de ce cheminement, nous définissons clairement nos objectifs de recherche. Le deuxième chapitre est consacré à la méthodologie que nous allons utiliser afin d'avoir accès aux raisonnements des étudiants. Nous présentons notre échantillon et les variables dont nous allons tenir compte. Nous décrivons ensuite la cueillette des données et le corpus que nous analyserons. Pour finir, un aperçu de l'analyse des données est présenté ainsi que les limites de notre démarche. Nous exposons l'analyse des résultats dans le troisième et le quatrième chapitre. Dans un premier temps (troisième chapitre), nous examinons les scores obtenus au mini-Turbo par les sujets de l'échantillon. Ensuite, nous présentons l'analyse des raisonnements émis pendant la passation du mini-Turbo (quatrième chapitre) Cette analyse de type quantitatif s'articule en deux temps : un test d'homogénéité en regard de chaque variable et une analyse des correspondances en regard des deux types de variables (caractéristiques individuelles et types de raisonnements).

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Alcon, Timothy C. "Using a seed-network to query multiple large-scale gene expression datasets from the developing retina in order to identify and prioritize experimental targets." [Ames, Iowa : Iowa State University], 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:1473175.

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Soncco, Álvarez José Luis. "Cálculo da distância de reversão e construção de árvores filogenéticas usando a ordem dos genes." reponame:Repositório Institucional da UnB, 2017. http://repositorio.unb.br/handle/10482/23520.

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Tese (doutorado)—Universidade de Brasília, Instituto de Ciências Exatas, Departamento de Ciência da Computação, 2017.
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O cálculo de distâncias evolutivas, como as distâncias de reversão e double cut and join, entre a ordem dos genes de dois organismos e um problema combinatório complexo. Este cenário pode ficar ainda mais complicado se quisermos construir árvores filogenéticas, visto que a maioria das abordagens da literatura primeiro solucionam o problema da mediana de três genomas, o qual foi demonstrado ser NP-Difícil para vários modelos evolutivos. Neste trabalho propomos vários algoritmos evolutivos para o problema de ordenação de permutações (sem sinal) por reversões, cuja saída e a distancia de reversão. Estes algoritmos são baseados em um algoritmo genético simples, sobre o qual foram incorporados varias heurísticas como busca local, busca por oposição, e eliminação de pontos de quebra. Experimentos foram realizados usando diferentes dados (permutações) baseados na ordem dos genes, os quais foram gerados artificialmente (de forma aleatória) e também a partir de dados biológicos. Dentre estes algoritmos os que melhores resultados tem para casos práticos, ou seja, permutações de comprimento ate 120, são os chamados AMBO e AMBO-Híbrido. Estes resultados foram validados usando testes estatísticos como Friedman e Holm. Adicionalmente, foi implementado um software para construir arvores filogenéticas chamado de HELPHY, que toma como entrada dados baseados na ordem dos genes (permutações com sinal). Primeiro foi proposto um algoritmo guloso para o problema da pequena filogenia, cujo objetivo e calcular o custo de uma determinada árvore. Logo, para o problema da grande filogenia foi proposta uma abordagem baseada em busca em vizinhança variável, cujo objetivo e explorar o espaço de soluções de estruturas de árvores. Experimentos mostraram que HELPHY conseguiu melhorar o tempo de execução para encontrar árvores com bons escores (distância de reversão) para o dataset Campanulaceae; além disso, uma nova árvore tendo o melhor escore (distância double cut and join) na literatura foi encontrado para o dataset Hemiascomycetes.
Calculating evolutionary distances, such as the reversal distance or the double cut and join distance, between the gene orders of two organisms is a complex combinatory problem. This scenario can be even more complicated if we want to build phylogenetic trees, since most of the approaches in the literature first solves the median problem for three genomes, which was shown to be NP-Hard for various evolutionary models. In this work, we are proposing several evolutionary algorithms for the problem of sorting (unsigned) permutations by reversals, whose output is the reversal distance. These algorithms are based on a simple genetic algorithm, on which were embedded different heuristics such as local search, opposition-based learning, and elimination of breakpoints. Experiments were performed using different types of data (permutations) based on gene orders which were generated artificially (in a random way) and also from biological data. From these algorithms, the ones with the best results for practical cases, that is, permutations of length up to 120, are called as AMBO and AMBO-Hibrido. These results were validated by applying the Friedman and Holm statistical tests. Moreover, a software called HELPHY for building phylogenetic trees was implemented, which takes as input data based on gene order (signed permutations). First, an greedy algorithm was proposed for the small phylogeny problem, whose aim is to calculate the cost (score) of a given tree structure. Then, an approach based on variable neighborhood search was proposed for the large phylogeny problem, whose aim is to explore the search space of tree structures. Results of the experiments showed that HELPHY improved the execution time for finding good scores (reversal distance) for the dataset Campanulaceae; besides, a new tree structure with the best score (double cut and join distance) in the literature was found for the dataset Hemiascomycetes.

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Björk, Oscar. "En trädgård, en boksamling och det väl valda ordet : genrepedagogik för skriftspråksutveckling hos framgångsrika respektive mindre framgångsrika skriftspråkare i gymnasiet." Thesis, Södertörns högskola, Institutionen för kultur och lärande, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-24066.

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This is a qualitative analysis that, based on systemic functional linguistics, or SFL, and genre theory, has aimed to study the genre pedagogical implications on written language as they occur in narrative stories and expositions whilst the model is introduced. Systemic functional linguistics is a linguistic theory that views the organisation of language as functional options for meaning; language is a set of resources to channel meaning through realisation. Genre theory elucidates the pragmatic and educational uses of SFL in the categorizing of language in configurations of meanings as they are set and understood in different cultures. The purpose of the survey is to do so with focus on successful and less successful writers by attempting to answer two primal issues: How is development of written language in reference to the introduction of the genre pedagogical model visible in the studied texts? How does genre pedagogical teaching influence successful and less successful writers as visible in their writing with a certain purpose? To answer these issues the survey is based on narratives and expositions written by high school students who have been divided into two groups according to the purpose of the survey. One text in each genre has been written by the students before and after lessons based on the genre pedagogical learning wheel explaining the relevant genres. Thereafter the texts have been analysed, both in accordance to the staging of the relevant genres, but also with an inductive focus on the variations of the texts. The results show that significant development of the texts, after the genre pedagogical lessons, is visible in both student groups in different ways. This demonstrates how the genre pedagogical approach to teaching language is a method that is able to lift students regardless of their prior merits.

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Santana, Juan F. "The Dm-Myb oncoprotein coordinates higher-order chromatin structure to potentiate expression of target genes as well as stabilize facultative heterocrhomatin." Diss., University of Iowa, 2016. https://ir.uiowa.edu/etd/6270.

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Myb is a proto-oncogene that when mutated causes leukemias and lymphomas in birds and mammals. Vertebrates contain three representatives of the Myb gene family consisting of A-, B- and c-Myb, all of which encode DNA-binding factors that are important for the proper expression of genes. Several studies have described Myb’s primary function as a factor that upregulates transcription by binding to promoter regions, thus controlling the expression level of genes adjacent to these sequences. In flies, this regulation has been shown to be accomplished epigenetically such that Myb is only required after initial activation of a gene in order to potentiate this distinct transcriptional state. Here, we further characterize the potentiator role of Myb and show that its absence leads to a reduction in H3K4me3 along promoters and increase RNA polymerase pausing at promoters leading to decrease occupancy across gene bodies, resulting in downregulation of transcription. However, up to now, no other mechanisms have been proposed that account for the thousands of genes whose expression is altered in the absence of Myb, including those that appear to be “repressed” by Myb. Here we uncover a novel and critical role of Myb in demarcating and maintaining silent chromatin domains. We observe that Myb demarcates and stabilizes H3K27me3 domains associated with silent genomic regions, and in its absence, these domains become reduced in length and less enriched for this chromatin mark, promoting an enrichment of H3K4me3 and subsequent derepression of the genes within these domains. We also identify the nucleosome remodeling factor, NURF, to be genetically and physically interacting with Myb. We show that they work in concert to regulate a subset of tissue specific genes. More specifically, they are both needed for proper maintenance of H3K4me3 and RNA polymerase levels of active genes. Finally, we describe a novel function of Myb essential for silencing retrotransposable elements. Myb binds to both 5' and 3' end long terminal repeats (LTRs) and its absence leads to reduction of H3K9me3 levels along these repeats. As a result, derepression and ectopic transcription occurs in different tissues of Myb mutant animals such as brain, salivary glands and wing discs. We observed a significant increase in copy number of retrotransposons in all these tissues indicative of retrotransposition events. In conclusion, we find that genes whose expression levels change in the absence of Myb (~2,000 genes) are directly influenced or regulated by Myb, with virtually no genes showing altered expression through secondary consequences of aberrant transcription factor upregulation, thus providing strong evidence for a chromatin “buffering” effect in cells that helps prevent misprogramming.

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Sun, Xiaoming. "Ki-67 Regulates Cell Cycle Progression and Heterochromatin Organization." eScholarship@UMMS, 2009. http://escholarship.umassmed.edu/gsbs_diss/920.

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A subset of eukaryotic heterochromatin is located around the nucleoli, and this localization is correlated with gene silencing. Although there is some evidence for trans-acting factors organizing genomic loci around the nucleolus, the characterization of proteins and /or RNAs involved in perinculeolar heterochromatin localization and maintenance is incomplete. Notably, the mammalian female inactive X chromosome, a well-studied model of facultative heterochromatin, frequently resides in the perinucleolar regions during mid to late S phase. The disruption of the Xi–nucleolus association results in the erosion of heterochromatin compartment and silencing, which renders it a good model to investigate the mechanism and biological relevance of heterochromatin organization around the nucleolus. This dissertation will present evidence showing that Ki-67 regulates inactive X (Xi) chromosome association with nucleoli, maintains Xi heterochromatic structures, and regulates cell cycle progression, in cell-type-specific manner dependent on checkpoint proficiency. Ki-67 protein plays roles in heterochromatin organization during interphase. Upon Ki-67 depletion, a subset of Xi in human female hTERT-RPE1 moved away from nucleolus and displayed several features of compromised heterochromatin maintenance. These chromatin alterations were limited to Xi chromosomes localized away from the nuclear lamina and were not observed in virally transformed 293T cells upon Ki-67 depletion. Furthermore, I demonstrated that the different Xi heterochromatin alteration responses result from cell-type-specific reduced proportion of cells in S phase upon Ki-67 depletion. In human hTERT-RPE1, WI-38, IMR90, hTERT-BJ cell lines, depletion of Ki-67 slowed entry into S phase and coordinately downregulated genes related to DNA replication. These cell lines are able to induce p21 expression upon Ki-67 depletion. On the contrary, alteration of transcription and cell cycle progression were not observed in tumor-derived HeLa, U2OS and 293T cell lines. These cell lines do not induce p21 expression either. I additionally examined the Ki-67 function in mouse cell cultures. Depletion of Ki-67 neither redistributes inactive X chromosome nor regulates S phase progression in primary female mouse embryonic cells.

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Sun, Xiaoming. "Ki-67 Regulates Cell Cycle Progression and Heterochromatin Organization." eScholarship@UMMS, 2017. https://escholarship.umassmed.edu/gsbs_diss/920.

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A subset of eukaryotic heterochromatin is located around the nucleoli, and this localization is correlated with gene silencing. Although there is some evidence for trans-acting factors organizing genomic loci around the nucleolus, the characterization of proteins and /or RNAs involved in perinculeolar heterochromatin localization and maintenance is incomplete. Notably, the mammalian female inactive X chromosome, a well-studied model of facultative heterochromatin, frequently resides in the perinucleolar regions during mid to late S phase. The disruption of the Xi–nucleolus association results in the erosion of heterochromatin compartment and silencing, which renders it a good model to investigate the mechanism and biological relevance of heterochromatin organization around the nucleolus. This dissertation will present evidence showing that Ki-67 regulates inactive X (Xi) chromosome association with nucleoli, maintains Xi heterochromatic structures, and regulates cell cycle progression, in cell-type-specific manner dependent on checkpoint proficiency. Ki-67 protein plays roles in heterochromatin organization during interphase. Upon Ki-67 depletion, a subset of Xi in human female hTERT-RPE1 moved away from nucleolus and displayed several features of compromised heterochromatin maintenance. These chromatin alterations were limited to Xi chromosomes localized away from the nuclear lamina and were not observed in virally transformed 293T cells upon Ki-67 depletion. Furthermore, I demonstrated that the different Xi heterochromatin alteration responses result from cell-type-specific reduced proportion of cells in S phase upon Ki-67 depletion. In human hTERT-RPE1, WI-38, IMR90, hTERT-BJ cell lines, depletion of Ki-67 slowed entry into S phase and coordinately downregulated genes related to DNA replication. These cell lines are able to induce p21 expression upon Ki-67 depletion. On the contrary, alteration of transcription and cell cycle progression were not observed in tumor-derived HeLa, U2OS and 293T cell lines. These cell lines do not induce p21 expression either. I additionally examined the Ki-67 function in mouse cell cultures. Depletion of Ki-67 neither redistributes inactive X chromosome nor regulates S phase progression in primary female mouse embryonic cells.

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Krona, Theodor, and Kronqvist Emil Virbert. "Employer branding: A way to retain young employees : A qualitative study on how SMEs use employer branding in order to retain young employees in their organization and how it is perceived." Thesis, Högskolan i Halmstad, Akademin för ekonomi, teknik och naturvetenskap, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:hh:diva-39677.

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Problem background: The voluntary turnover of employees is increasing, the baby boomer generation is retiring and the remaining jobs are to be filled with the workforce left behind, a workforce that is smaller in size. These younger generations (generation Y and Z) have different values and attitudes towards work, and they tend to switch jobs more frequently. This means that companies needs to focus on retaining their personnel. This is particularly true for SMEs since they do not have the same resources to spend on attracting potential workers as larger corporations. Purpose: The purpose of this study is to gain a better understanding of how SMEs use employer branding to retain young employees (18-30 years old) in their organization and how it is perceived. Theoretical framework: Consists of theories regarding employer branding and organizational behaviour. These include signaling theory, functional and symbolic attributes, the seven brand value propositions and organizational reputation. Methodology: The authors has used a deductive qualitative approach where a total of 14 semi structured interviews has been conducted. Seven of the interviews were performed on employees between the age of 18-30 years old from three different companies. The remaining seven were performed on management personnel from the same three companies. The respondents answered a questionnaire at the end of each interview. Empirical results: Contains a summary of each company that were involved as well as what was discussed and uncovered in the interviews. Analysis: It connects the empirical results and the theoretical framework. The found discrepancies and similarities are discussed and analyzed with the seven brand value propositions based on the theoretical framework. Conclusion: It was concluded that there exists a discrepancy between Workers and Management when it comes to the time the Workers are willing to stay. It was also uncovered that development was an important aspect when it came to the young employees turnover intention as well as flexible schedules, support from management, salaries and varying work tasks. The reputation of the companies was also not accurate which in turn could affect the matching potential between organization and individual.

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Hochbach, Anne [Verfasser]. "Usability of nuclear single-copy genes compared with plastid DNA on different phylogenetic levels of and within the order Poales : [kumulative Dissertation] / Anne Hochbach." Halle, 2019. http://d-nb.info/1179184432/34.

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Wood, Lynn. "High resolution physical mapping of an 840KB region at the 5' end of the dystrophin gene by construction of ordered phage lambda sublibraries from yeast artificial chromosomes." Thesis, University of Southampton, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242219.

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Tekieh, Farideh. "Towards the Identification of Candidate Gene(s) for Fusarium Head Blight Resistance on the 7EL Chromosome of Thinopyrum elongatum: Design and Use of Genetic Markers." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/35670.

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Triticum aestivum (bread wheat), one of the most globally important cereal crops, is vulnerable to fusarium head blight (FHB). The disease is mainly associated with the pathogen Fusarium graminearum and generates yield losses and mycotoxin contaminated grains with low quality. One possible solution to overcome this problem is the production of FHB resistant wheat varieties by crossing with strongly resistant germplasm from either wheat or closely related species. Thinopyrum elongatum is a wild grass that carries genetic resistance to FHB on the long arm of its chromosome 7E (7EL). In the first part of this research project, five Th. elongatum accessions were characterized for their response to F. graminearum infection. In the second part, BC1F4 progeny derived from the cross CS-ph1b × CS-7E(7D) were characterized to better define the 7E fragments introgressed into the 7D chromosome. Progeny were screened with a series of known 7E-specific genetic markers and for their FHB resistance. Among the 43 wheat plants tested, twelve FHB resistant progeny were shown to carry a similar, smaller 7EL introgressed fragment based on genetic marker screening. To characterize further the introgressed 7EL fragments, additional 7EL-specific markers as well as 7DL-specific markers for homoeologous wheat sequences were designed. As neither wheat nor Th. elongatum genomes were fully sequenced at the time, this made the designing procedure challenging; a cross-walking strategy between wheat and Th. elongatum draft genomic sequences was used. Twelve pairs of markers for homoeologous sequence regions of 7EL and 7DL chromosomes plus six individual 7EL- and four 7DL-specific markers were successfully designed. Nine novel 7EL-specific markers were associated with the smallest 7EL fragment carrying FHB resistance. That smallest introgressed 7EL fragment replaced approximately half of the 7DL chromosome, based on the absence of 7DL markers in some progeny. The novel 7EL- and 7DL-specific markers as well as the proposed genetic order for novel and previously designed markers contributed greatly to the characterization of the introgressed 7EL fragments in the 7DL chromosome. Further analysis of progeny from the next generations of these plants and from other families will be required to confirm the results and possibly obtain much smaller 7EL fragments.

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Belal, Nahla Ahmed. "Two Problems in Computational Genomics." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/26318.

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This work addresses two novel problems in the field of computational genomics. The first is whole genome alignment and the second is inferring horizontal gene transfer using posets. We define these two problems and present algorithmic approaches for solving them. For the whole genome alignment, we define alignment graphs for representing different evolutionary events, and define a scoring function for those graphs. The problem defined is proven to be NP-complete. Two heuristics are presented to solve the problem, one is a dynamic programming approach that is optimal for a class of sequences that we define in this work as breakable arrangements. And, the other is a greedy approach that is not necessarily optimal, however, unlike the dynamic programming approach, it allows for reversals. For inferring horizontal gene transfer, we define partial order sets among species, with respect to different genes, and infer genes involved in horizontal gene transfer by comparing posets for different genes. The posets are used to construct a tree for each gene. Those trees are then compared and tested for contradiction, where contradictory trees correspond to genes that are candidates of horizontal gene transfer.
Ph. D.

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Lima, Paola Goussain de Souza. "As inversões sujeito-verbo e a concordância verbal : um estudo sobre a influência da posposição do sujeito em gêneros escritos de imprensa do português brasileiro /." Araraquara : [s.n.], 2011. http://hdl.handle.net/11449/86536.

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Orientador: Odette Gertrudes L. A. de Souza Campos
Banca: Gladis Maria Barcelos de Almeida
Banca: Rosane de Andrade Berlinck
Banca: Beatriz Nunes de Oliveira Longo
Banca: Maria Beatriz Gameiro
Resumo: Este trabalho traz o estudo de estruturas que apresentam posposição do sujeito e a influência das mesmas no processo de concordância verbal em gêneros escritos de imprensa do Português Brasileiro (PB), datados entre 2008 e 2010. Para tanto, selecionamos, como corpus desta pesquisa, os gêneros editorial, carta dos leitores, noticiário, coluna e entrevista - seções que apresentam traços mais informais e subjetivos de seus usuários/leitores, dos jornais Folha de São Paulo, Jornal da Tarde, Notícias Já e Diário de São Paulo e das revistas Istoé Gente, Época, Malu Mulher e Aparecida, por estes serem meios de comunicação de imprensa escrita, direcionados a diferentes leitores e com grande circulação nacional. Fizemos um levantamento das ocorrências de sujeitos pospostos nos gêneros escritos de imprensa, analisamos os dados, levantando, ao final, nossas considerações sobre a relação posição do sujeito X concordância verbal. Trazemos a hipótese de que o sujeito posposto na escrita, assim como ocorre na fala, desfavoreça a CV, pois, por não se apresentar em posição de tópico e não condizer com a definição dada pela Gramática Tradicional, "ser de quem se diz alguma coisa", características estas principais para a identificação do sujeito em uma oração, o usuário da língua tende a identificá-lo como sendo outro termo da oração, havendo ou não um termo que ocupe a posição inicial da oração em seu lugar, não realizando, com isto, a concordância entre o verbo e este SN sujeito pós-verbal
Abstract: This research brings a study of structures which present postposition of the subject and the influence of those in the process of verbal agreement in written genres Press of the Brazilian Portuguese (BP), dated between 2008 and 2010. To this end, we selected as a corpus of this research, the gender's editorial, letter from readers, news, column and interview - sections that have more informal and subjective features of their users / readers, from Folha de São Paulo newspaper, Jornal da Tarde, Notícias Já, Diário de São Paulo and from the magazines Istoé Gente, Época, Malu Mulher and Aparecida, for they being means of printing media, towards different readers and with a large national circulation. We did a survey of the occurrences of subjects postponed in written genres of press. We analyzed the data, increasing, at the end, our thoughts about the relation position of the subject X verbal agreement. We bring the hypothesis that the subject postponed in writing, as well as in speech, does not favour the CV, then, for not present itself in a position of topic and does not match the definition given by the Traditional Grammar, "being from whom says to be something" these characteristics are major for the identification of the subject in a sentence. The language user tends to identify it as another word of the sentence, whether there is or not a term that occupies its initial positions in the sentence, without achievement, with that, the agreement between the verb and the post-verbal subject SN
Mestre

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42

Frénoy, Antoine. "Second order selection pressures promoting the evolution and maintenance of cooperation in microbial and in silico systems." Thesis, Paris 5, 2014. http://www.theses.fr/2014PA05T050/document.

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Cette thèse s'intéresse aux liens entre l'évolution de la coopération et la sélection de second ordre. Dans une première partie, nous montrons comment des organismes digitaux adaptent leurs génomes pour encoder les gènes liées à la coopération d'une manière plus contrainte (suppression d'évolvabilité), notamment à l'aide d'opérons et d'overlaps impliquant aussi des gènes essentiels. Dans une deuxième partie, nous testons expérimentalement cette vision des overlaps de gènes comme "contrainte évolutive" grâce à des outils d'algorithmique et de biologie synthétique que nous avons développés. Dans une troisième partie, nous utilisons des simulations par agents pour montrer comment une forme de division du travail peut être interprétée comme un système coopératif à la lumière de la théorie évolutive moderne. Dans une dernière partie, nous montrons que la dispersion spatiale des allèles coopératives obtenue par des phénomènes de "genetic hitchiking" joue un rôle important dans l'évolution de la coopération, quand bien même ce mécanisme de dispersion s'applique aussi à des allèles non coopératives, grâce à la "relatedness" (aux loci codant pour la coopération) crée par l'invasion locale de mutations bénéfiques (à des loci non liés à la coopération) et par l'équilibre complexe entre ces mutations bénéfiques et la robustesse mutationnelle. L'ensemble de ces résultats appelle à une prise en compte plus importante des pressions sélectives de second ordre dans l'étude de l'évolution sociale, et au développement de modèles plus réalistes qui permettraient d'intégrer de telles forces évolutives. Nous insistons également sur l'importance du paysage mutationnel dans l'étude des populations bactériennes, et montrons le potentiel croissant de la biologie synthétique comme outil d'étude de ce paysage et de l'évolution microbienne en général
In the first part, I show how digital organisms adapt their genomes to encode cooperation-related genes in a more constrained way (evolvability suppression), especially using operons and overlaps also involving essential genes. In the second part, we experimentally test this view of gene overlaps as an evolutionary constraint, using both algorithmic and synthetic biology tools that we have developed. In the third part, I use agent-based simulations to show how a form of division of labour can be interpreted as a cooperative system in the light of modern evolutionary theory. In the final part, I show that the patterns of dispersal of cooperative alleles due to hitchhiking phenomena play an important role in the evolution of cooperation. The last result holds even though the hitchhiking mechanisms also applies to non-cooperative alleles, thanks to the relatedness (at cooperation-related loci) created by the local invasion of beneficial mutations (at loci not related to cooperation). The beneficial mutations form a complex and interesting equilibrium with mutational robustness, which I investigate using in silico evolution. On the whole, these results call for a more careful consideration of the second-order selection pressures in the study of social evolution, and show the necessity for more realistic models allowing to integrate such evolutionary forces. My thesis research specifically highlights the importance of the mutational landscape in the study of microbial populations and shows the increasing potential of synthetic biology as a tool to study such landscape and microbial evolution in general

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Love-Gregory, Latisha Debrett. "Investigation of the origin of the Y393N allele in old order mennonite and non-mennonite maple syrup urine disease patients : analysis of the branched chain [alpha]-keto acid dehydrogenase complex E1[alpha] gene /." free to MU campus, to others for purchase, 2001. http://wwwlib.umi.com/cr/mo/fullcit?p3012999.

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44

Pilorget, Julie. "Des femmes dans la ville : Amiens (1380-1520)." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUL118.

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Cette thèse de doctorat étudie la place des femmes dans la société urbaine des derniers siècles du Moyen Âge. Son objectif réside en l’examen des multiples opportunités offertes alors aux femmes, tant dans le domaine juridique qu’économique et social. La recherche s’appuie sur l’observatoire privilégié de la ville d’Amiens, capitale régionale dynamique, qui présente l’intérêt d’appartenir à un système coutumier original, particulièrement favorable aux femmes. La caractéristique des coutumes picardes tient essentiellement à ce qu’elles donnent la priorité au ménage sur le lignage. L’institution de la communauté de biens entre époux permet ainsi de considérer les femmes comme de véritables actrices économiques. Leurs différentes occupations révèlent leur présence quotidienne et leur participation constante à la vie économique de la cité. Sur le plan social, elles en retirent une visibilité certaine et font partie intégrante de la communauté des habitants. De plus, l’étude des registres de délibérations et livres de justice démontre qu’elles n’hésitent pas à s’affirmer par la verdeur de leur propos sur la place publique, où tous sont en représentation. L’objectif de ce travail est également d’améliorer notre compréhension des rapports de genre dans le contexte du renforcement de l’ordre social à l’aube des Temps Modernes. Enfin, d’un point de vue méthodologique, ce sujet, centré sur un espace de syncrétisme aux confins des influences flamande et orléano-parisienne, entend réinterroger les périodisations académiques et conduire, par le dialogue entre sciences humaines, au décloisonnement des réflexions
This dissertation examines the place of women in the medieval town of Amiens and demonstrates the continuing significance of women’s participation in diverse aspects of social and economic life during the historical shift from the medieval to the early modern era. This city adhered to a unique legal system called ‘picard-wallon’, which was particularly favourable to women, making them the owners of half of the family patrimony. Since family structures played a determining role in the ideological choices and economic behaviour of family members, the institution of community property between spouses allows us to consider women as legitimate economic agents. The study of women’s activity in the marketplace in particular, shows that we should first rethink the public/private dichotomies that have long been applied to gender studies. This work also highlights the nature of women’s contribution to the medieval society. Public space fostered orality and the production of specific speech acts. The study of women’s involvement in crime shows that they were not afraid of defending their honour if necessary. Therefore, this dissertation sheds light on the reinforcement of the public order at the end of the Middle Ages and its consequences on gender relations at the beginning of the early modern period. Finally, this dissertation makes use of new methodological perspectives. By focusing on a place of syncretism, at the intersection of three different regional areas, this study highlights the multi-cultural influences at work in the city in order to interrogate the relevance of classical periodization and establish the importance of a transdisciplinary approach to medieval studies

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Zanardo, Ana Beatriz Riguetti. "Abundância de fungos entomopatogênicos da ordem Hypocreales e diversidade genética de Metarhizium spp. isolados de amostras de solo de áreas representativas de cinco biomas brasileiros." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/11/11146/tde-22092015-140424/.

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Os fungos entomopatogênicos dos gêneros Metarhizium, Beauveria e Isaria (Ordem Hypocreales), são comumente encontrados em solo onde sobrevivem de maneira saprofítica ou como endofíticos do sistema radicular das plantas. Informações sobre a composição destas espécies bem como sua diversidade, distribuição e associação com diferentes tipos de cultivos e vegetação nativa são escassas no Brasil. O presente estudo foi desenvolvido para comparar a abundância de fungos entomopatogênicos e a diversidade genética de isolados de Metarhizium spp. em amostras de solo de cultivos anuais, perenes e vegetação nativa, em cinco estados brasileiros que representam os biomas Amazônia, Cerrado, Caatinga, Mata Atlântica e Pampa, em duas estações (seca e úmida) nos anos de 2012 e 2013. O isolamento dos fungos foi realizado com meio seletivo e \"Insect bait\" utilizando Galleria mellonella e Tenebrio molitor. Nos estudos de diversidade genética de Metarhizium spp. foram utilizadas sequências de DNA da região MzIGS3. Representantes dos haplótipos revelados nesta análise tiveram a região 5\'-TEF sequenciada para identificação específica. Fungos entomopatogênicos foram isolados de 86% das 1.056 amostras de solo sendo Metarhizium o gênero predominante (66% das amostras de solo), seguido por Beauveria (41,9%) e Isaria (10,8%). Em geral, as maiores densidades de fungos entomopatogênicos foram obtidas nos biomas Amazônia e Cerrado e as menores densidades detectadas no bioma Caatinga. Metarhizium spp. foi detectado em maior número de amostras de solo em vegetação nativa e cultivos anual e perene do Cerrado. A frequência de Isaria spp. foi baixa nas amostras de solo, sendo detectado em maior número de amostras nos solos com cultivos anuais e vegetação nativa na Amazônia e Caatinga. Metarhizium spp. foi geralmente encontrado em um maior número de amostras coletadas na estação úmida em comparação com as coletas da estação seca, por outro lado Beauveria spp. foi superior na estação seca. A diversidade dos isolados de Metarhizium spp. provenientes de áreas de vegetação nativa foi maior do que dos isolados de cultivos anuais e perenes. Seis linhagens foram encontradas neste estudo; M. robertsii, M. anisopliae, M. pingshaense e três espécies indeterminadas. M. robertsii foi a linhagem predominante (65% dos isolados) sendo encontrado em áreas com vegetação nativa e cultivos anual e perene dos cinco biomas. Metarhizium sp. indet. 1 apresentou a maior diversidade haplotípica dentre as linhagens estudadas. Uma nova linhagem, não caracterizada taxonomicamente, Metarhizium sp. indet. 3, foi encontrada predominantemente na Caatinga. Somente na Amazônia foram encontradas todas as linhagens. O conhecimento da composição das populações de fungos entomopatogênicos nativos bem como sobre a filogenia, diversidade e distribuição dos haplótipos de Metarhizium spp. em solos brasileiros, gerado neste estudo, poderá servir como subsídio para o desenvolvimento de estratégias de conservação e maximização do controle biológico natural de pragas.
Entomopathogenic fungi of the genera Metarhizium, Beauveria and Isaria (order Hypocreales) are associated to the soil where they survive saprofitically or as endophytes of the plants root system. Information on the species composition and its diversity, distribution and association of these fungi with different types of crops and native vegetation are scarce in Brazil. The present study was carried out to compare the abundance of entomopathogenic fungi and the genetic diversity of Metarhizium spp. Isolated from soil samples from annual and perennial crops and native vegetation in five Brazilian states that represent the biomes Amazon, Cerrado, Caatinga, Atlantic Forest and Pampa, in two seasons (wet and dry) in the years 2012 and 2013. The isolation of fungi was performed with selective medium and \"Insect bait\" using Galleria mellonella and Tenebrio molitor. DNA sequences of the region MzIGS3 were used in genetic diversity studies of Metarhizium spp. Representatives haplotypes revealed in the diversity analysis had the 5\'-TEF region sequenced for species identification. Entomopathogenic fungi were isolated from 86% of 1,056 soil samples and Metarhizium was the predominant genus (66% of soil samples), followed by Beauveria (41.9%) and Isaria (10.8%). In general, the highest densities of entomopathogenic fungi were obtained in the Amazon and Cerrado biomes and the lowest densities were detected in the Caatinga biome. Metarhizium spp. was detected in a greater number of soil samples from native vegetation and annual and perennial crops of Cerrado. The frequency of Isaria spp. was low in soil samples being detected in a greater number of soils with annual crops and native vegetation in the Amazon and Caatinga. Metarhizium spp. was usually found in a greater number of samples collected during the wet season compared to the collections in the dry season. On the other hand, Beauveria spp. was higher in the dry season. The diversity of isolates of Metarhizium spp. from areas of native vegetation was greater than that obtained from annual and perennial crops. Six lineages were found in this study; M. robertsii, M. anisopliae, M. pingshaense and three indeterminate species. M. robertsii was the predominant (65% of isolates) found in areas with native vegetation and in the annual and perennial crops of the five biomes. Metarhizium sp. indet. 1 showed the greatest haplotype diversity among the strains studied. A new strain, not characterized taxonomically, Metarhizium sp. indet. 3, was found predominantly in the Caatinga. Only in the Amazon, all lineages were found. The knowledge on species composition of entomopathogenic fungi as well as about phylogeny, diversity and distribution of haplotypes of Metarhizium spp. in Brazilian soils, generated in this study, may be useful for the development of strategies for conservation and maximization of natural biological control of pests.

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46

Lebre, Sophie. "Stochastic process analysis for Genomics and Dynamic Bayesian Networks inference." Phd thesis, Université d'Evry-Val d'Essonne, 2007. http://tel.archives-ouvertes.fr/tel-00260250.

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This thesis is dedicated to the development of statistical and computational methods for the analysis of DNA sequences and gene expression time series.

First we study a parsimonious Markov model called Mixture Transition Distribution (MTD) model which is a mixture of Markovian transitions. The overly high number of constraints on the parameters of this model hampers the formulation of an analytical expression of the Maximum Likelihood Estimate (MLE). We propose to approach the MLE thanks to an EM algorithm. After comparing the performance of this algorithm to results from the litterature, we use it to evaluate the relevance of MTD modeling for bacteria DNA coding sequences in comparison with standard Markovian modeling.

Then we propose two different approaches for genetic regulation network recovering. We model those genetic networks with Dynamic Bayesian Networks (DBNs) whose edges describe the dependency relationships between time-delayed genes expression. The aim is to estimate the topology of this graph despite the overly low number of repeated measurements compared with the number of observed genes.

To face this problem of dimension, we first assume that the dependency relationships are homogeneous, that is the graph topology is constant across time. Then we propose to approximate this graph by considering partial order dependencies. The concept of partial order dependence graphs, already introduced for static and non directed graphs, is adapted and characterized for DBNs using the theory of graphical models. From these results, we develop a deterministic procedure for DBNs inference.

Finally, we relax the homogeneity assumption by considering the succession of several homogeneous phases. We consider a multiple changepoint
regression model. Each changepoint indicates a change in the regression model parameters, which corresponds to the way an expression level depends on the others. Using reversible jump MCMC methods, we develop a stochastic algorithm which allows to simultaneously infer the changepoints location and the structure of the network within the phases delimited by the changepoints.

Validation of those two approaches is carried out on both simulated and real data analysis.

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Salaverry, Pietro Barbiani. "Proposta de metodologia de implantação de plano para cada peça e introdução do sistema de abastecimento por kits." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2014. http://hdl.handle.net/10183/127912.

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Esta dissertação contempla uma proposta de metodologia para implantação de Plano Para Cada Peça e introdução do sistema de abastecimento por kits. Contemplados em dois artigos, onde respectivamente no primeiro foi desenvolvida uma ferramenta para captura de dados, um método de como estruturá-los, como organizá-los em um banco de dados e interpretá-los de acordo com as características do produto e produtivas para definição do método de abastecimento. No segundo artigo, foi proposta uma metodologia de introdução do processo de abastecimento por kits, onde de acordo com as características do produto e do processo produtivo, foram definidos: os layouts das áreas de separação e sequenciamento de peças, a quantidade de entradas de abastecimento, a quantidade de peças necessárias em cada kit, a disposição das peças e layout dos kits, o processo de separação de peças e montagem dos kits, assim como os carros de movimentação e abastecimento na linha.
This dissertation includes a methodology proposal for deploying Plan For Every Part and implement the kit line feeding. Conceived respectively in two articles, on the first one was developed a tool for data capture, a method of how to structure, arrange in a database and interpret it according to product and production characteristics for setting the supply method. The second article presents a method to introduce the process by kits supply, which according to the product characteristics and the production process were defined: the parts picking and sequencing area layouts, the amount of supply inputs, the required quantity of parts in each kit, the layout and parts arrangement of kits, the picking process and kits assembly, as well as the handling and supply cars to the assembly line.

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48

Boudier, Valérie. "Des comestibles et d'autres sujets du même ordre. . . : peinture et nourriture dans les scènes de genre de Vincenzo Campi, Bartolomeo Passerotti et Annibale Carracci." Paris, EHESS, 2007. http://www.theses.fr/2007EHES0091.

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L'objet initial de ce travail était de mieux comprendre pourquoi la peinture de genre est encore aujourd'hui mal considérée et mal interprétée. Notre réflexion s'est progressivement orientée vers son émergence, au moment où, autour des années 1580, Vincenzo Campi. Bartolomeo Passerotti et Annibale Carracci inaugurent ce nouveau genre pictural en Italie du Nord. Nous avons ensuite questionné la fonction de l'aliment dans la peinture de genre puisqu'elle figurait alors essentiellement des scènes de marché, de boucherie, de cuisine et de repas, autant de sujets ayant trait à la nourriture et mettant en scène des personnages dont les gestes dépendent des objets alimentaires. Cette thèse propose un ensemble de réflexions attestant l'importance de l'aliment dans l'émergence même de la peinture de genre puisque sa présence en tant que sujet et son traitement pictural engendrent un processus de matérialisation de l'image peinte. Au Cinquecento, la peinture de genre est un espace de liberté, un lieu de réflexion théorique sur l'art où représenter l'aliment est une pratique critique de la peinture
The general aim of the dissertation was to understand why the genre painting is still regarded as a minor style and lacks proper interpretation. We first look at the emergence of the genre painting, in the years 1580 and the innovative work of Vincenzo Campi, Bartolomeo Passerotti, and Annibale Carracci in North Italia. We then question the function of food in the genre painting as this style was mainly representing market, butchery, kitchen, and meal scenes. All these subjets show food and expose characters whom movement are organized by food. Therefore, the dissertation proposes a reflection on the importance of food in the beginning of the genre painting, by showing that both the presence and the pictorial treatment of food give rise to the materialization of the painted image. In the Cinquecento, the genre painting is an area of freedom, a place of theoretical thinking on art, in wich representingfood is a critical practice of painting

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Guillemard, Eléna. "L'adieu aux ordres. Les sécularisations des religieuses au moment de la Réforme (France, Suisse, Angleterre, XVIe siècle)." Thesis, Lyon, 2020. http://www.theses.fr/2020LYSE3020.

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Sur les quelques 200 femmes retrouvées qui quittent les ordres religieux au cours du XVIe siècle en France, en Suisse et en Angleterre, certains itinéraires de vie montrent la difficulté d’une adaptation au siècle, qui prend d’abord une forme économique. En effet, ces femmes, souvent privées d’un soutien familial (elles ont pu sortir contre le gré de leurs familles car leur sortie menaçait les héritages familiaux en les réinstaurant potentiellement parmi les héritières potentielles), seules dans le monde pour la première fois de leur vie, doivent trouver les moyens d’une adaptation séculière. Mais la marge de manœuvre n’est pas toujours large : ainsi, d’un côté, des femmes de la grande noblesse, telle Charlotte de Bourbon, future princesse d’Orange, sortent et retrouvent leur position sociale, profitant de réseaux anciens de solidarité nobles, de l’autre, des femmes inconnues, issues de familles aux origines sociales variées, affrontent le retour au siècle sans relais ni soutiens économiques, amicaux ou familiaux. Se posent alors les questions du devenir de ces femmes : quelles formes prend leur sécularisation ? Si les discours protestants et catholiques acclament ou condamnent le mariage, il semblerait que ce choix ne soit pas le premier fait par ces femmes en rupture de cloître. Ainsi, ces parcours présentent des alternatives multiples, entre l’élaboration d’un foyer conjugal, l’obtention de pensions, de rentes, ou un retour familial. Les anciennes religieuses inventent donc leur itinéraire de vie, dans un contexte d’affrontements confessionnels au sein duquel leur statut d’anciennes religieuses influence et conditionne sans cesse les modalités et les conditions de possibilité de leur retour
Out of the 200 or so women that I found who left the religious orders during the 16th century in France, Switzerland and England, certain life paths suggest the difficulty of adapting to the secular life, especially in terms of economy. Indeed, these women, often deprived of family support (they were able to leave against the will of their families because their exit threatened family legacies by reintroducing them as potential heirs), alone in the world for the first time, had to find the means for a secular adaptation. But their capacity for action was often limited: thus, on the one hand, noble women, such as Charlotte de Bourbon, the future Princess of Orange, left and regained their former social position, with the help of various networks of solidarity; on the other hand, less famous women, from families with various social backgrounds, faced the return to the world without any economic, friendly or family support. A question then arises as to the future of these women: what form does their secularization take? If Protestant and Catholic discourses acclaimed or condemned marriage, it would seem that only some of the women who had escaped from the cloister chose that path. Thus, these paths present multiple alternatives, between forming a conjugal home, obtaining pensions, annuities, or returning to their parents’ home. Through these paths, the former nuns invented their life itineraries, in a context of religious confrontations in which their status as former nuns constantly influenced and conditioned the modalities of their return to the world

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Simon, Elisabeth. "Classe et genre : l’idéal d’une éducation égalitaire pour tous : l’exemple de Fécamp (1806-1906)." Thesis, Normandie, 2017. http://www.theses.fr/2017NORMLH05/document.

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Les promesses d’égalité pour tous dans l’éducation au moment de la Révolution ne se réalisent pas dans les années qui suivent. La France n’a pas les moyens de mettre en œuvre une éducation à la hauteur de ses ambitions. Avec Napoléon puis le retour de la monarchie, les congrégations retrouvent la place privilégiée qu’elles occupaient sous l’Ancien Régime afin de suppléer ces manques. Les deux freins principaux à cette égalité que sont le niveau social et la différence de genre, ainsi que les solutions pour lever ces freins, sont étudiés dans cette thèse en s’appuyant sur l’exemple concret de la cité maritime de Fécamp (Seine-Maritime, France) de 1806 à 1906 où trois congrégations, les sœurs de la Providence de Rouen, les frères des écoles chrétiennes et les sœurs de Saint Vincent de Paul, se partagent l’éducation (au travers des écoles et des orphelinats) avec les maîtres ou personnels laïques
The promise of equality for all in education at the time of the Revolution will not be achieved in the following years. France does not have the means to set up education for its ambitions. With Napoleon and the return of the monarchy, the congregations find the privileged position they held under the old regime to supplement these deficiencies. The two main obstacles to equality that are socially and gender difference, and solutions to address these brakes, are studied in this thesis based on the concrete example of the maritime city of Fécamp (Seine maritime, France) from 1806 to 1906 where three congregations, the sisters of Providence of Rouen, the Christian brothers and the sisters of Saint Vincent de Paul, shared education (through schools and orphanages) with teachers and laic personnel

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Dissertations / Theses on the topic 'Gene orders'

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