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The DNA microarray is a powerful tool to study expression levels of thousands of genes simultaneously. Often, cDNA libraries representing expressed genes of an organism are available, along with expressed sequence tags (ESTs). ESTs are widely used as the probes for microarrays. Designing custom microarrays, rich in genes relevant to the experimental objectives, requires selection of probes based on their sequence. We have designed a probe selection method, called GeneSieve, to select EST probes for custom microarrays. To assign annotations to the ESTs, we cluster them into contigs using PHRAP. The larger contig sequences are then used for similarity search against known proteins in model organism such as Arabidopsis thaliana. We have designed three different methods to assign annotations to the contigs: bidirectional hits (BH), bidirectional best hits (BBH), and unidirectional best hits (UBH). We apply these methods to pine and potato EST sets. Results show that the UBH method assigns unambiguous annotations to a large fraction of contigs in an organism. Hence, we use UBH to assign annotations to ESTs in GeneSieve. To select a single EST from a contig, GeneSieve assigns a quality score to each EST based on its protein homology (PH), cross hybridization (CH), and relative length (RL). We use this quality score to rank ESTs according to seven different measures: length, 3' proximity, 5' proximity, protein homology, cross hybridization, relative length, and overall quality score. Results for pine and potato EST sets indicate that EST probes selected by quality score are relatively long and give better values for protein homology and cross hybridization. Results of the GeneSieve protocol are stored in a database and linked with sequence databases and known functional category schemes such as MIPS and GO. The database is made available via a web interface. A biologist is able to select large number of EST probes based on annotations or functional categories in a quick and easy way. / Master of Science

Les pêcheries de thonidés représentent 7.9% de la production mondiale de produits de la mer. La plupart des stocks de thons sont pleinement exploités, et certains surexploités, et tous font face à une pression de pêche croissante. En raison de l'extension des zones de pêche, les évaluations des stocks dépendent en grande partie des captures commerciales. Toutefois, les données commerciales peuvent varier au cours du temps étant donné que les pêcheurs peuvent investir dans des engins de pêche et de l'équipement, s'établir au large des côtes, ou commencer à pêcher dans de nouvelles zones. Peu d'attention a été portée à la réponse des pêcheurs aux mesures de gestion ou aux conséquences de l'investissement technologique. L'objectif de la présente thèse est d'étudier les effets de stratégies de pêche et les réponses adaptatives des flottes de senneurs sur les thons tropicaux et la faune associée dans l'Océan Atlantic Est et dans l'Océan Pacifique Est. Dans un premier temps, nous montrons comment l'introduction de nouvelles technologies a eu un effet direct en augmentant la puissance de pêche, et un effet indirect en entraînant une modification des zones pêche. Nous étudions les effets de deux fermetures spatio-temporelles sur la dynamique de la flotte de senneurs européens. La première mesure de gestion a diminué les jours où des captures sont réalisées, les carrés avec capture à l'intérieur de la zone partiellement fermée, tandis que la pêche sur DCP a été redistribuée à l'extérieur de la zone et aucun changement n'a pas été enregistré pour la pêche sur banc libre. La seconde fermeture de pêche a entraîné une augmentation de toutes les activités de pêche en dehors de la zone. Dans l'Océan Pacifique Est, la flotte de senneurs mexicains a réagit à la fermeture d'une saison de pêche en diminuant le nombre de jours passés à quai. Par conséquent, le nombre de calées sur bancs associés aux dauphins a augmenté, et les niveaux de capture observés avant la mesure de gestion ont été maintenues. Nous analysons les effets des stratégies de senneurs de l'Union Européenne sur les prises accessoires. Nous mettons en évidence que la composition des espèces de requins capturés sous DCP et les raies capturées sur bancs libres ont changé au cours du temps. Nous estimons également que plusieurs types d'espèces peuvent être capturés par mode de pêche. / Tuna and tuna-like fisheries represent 7.9% of the global production of marine capture fisheries. Most tuna stocks are fully exploited and some overexploited, facing growing fishing pressures. Due to the extent of fishing grounds, stock assessments depend largely in commercial data, which vary over time because fishermen may invest in fishing technology, expand offshore, or start fishing in different areas. However, little attention has received the responses of fishermen facing management regulations or the effects resulting from technological investment. For these reasons the aim of this study was to investigate the effects of fishing strategies developed by purse seine fleets on tropical tunas and on associated fauna in the eastern Atlantic and eastern Pacific oceans. The continuous introduction of new fishing technology in the French fleet in the 1980s and the 1990s evidenced a direct increase in fishing power when large yellowfin in free-swimming school is targeted and likely an indirect effect by modifying the fishing grounds characterizing FAD-fishing on small size categories. The consequences of the two time-area closures on the spatio-temporal dynamics of the European Union fleet were investigated. The regulation on FADs resulted in a decrease in the days with catch and successful squares inside the restricted area, reallocating FAD-fishing outside the area while no change in free-swimming school fishing was observed. The no-take time-area increased all fishing activities outside the restricted area with apparently no gain in terms of protection of juveniles. In the eastern Pacific as a response to a closed season the Mexican fleet reduced days in port and consequently the number of sets on dolphin-associated schools increased, maintaining the catch levels observed before the regulation. The study of the effects of the EU fleet fishing strategies on bycatch over two time periods showed that the species composition of sharks caught on FADs and may be for rays caught on free-swimming schools changed over time. We also estimated the total number of species that can be potentially be caught by fishing mode.

Neste trabalho realizamos um programa de seqüenciamento em larga escala de cDNAs obtidos de bibliotecas construídas a partir de mRNA de células de B. emersonii submetidas ao choque térmico e ao estresse por cádmio. Obtivemos 6350 seqüências expressas (ESTs) de alta qualidade, que representam 2326 seqüências únicas putativas (unigenes) do fungo. Destes unigenes putativos, 1282 genes foram classificados em pelo menos uma das categorias do Consórcio Gene Ontology (GO). A análise do transcriptoma parcial de B. emersonii determinado até o momento permitiu a identificação de 78 unigenes codificando chaperones moleculares de todas as famílias conhecidas. Para avaliarmos a expressão global dos genes em resposta a estresses ambientais, como o choque térmico e o cádmio, realizamos ensaios de microarranjos de DNA nestas condições de estresse. Observamos que em resposta ao choque térmico, B. emersonii induz a expressão de genes que codificam proteínas relacionadas com o enovelamento de proteínas e com a proteólise, o que seria esperado em condições de temperaturas elevadas, assim como genes que codificam proteínas com propriedades antioxidantes, além de proteínas envolvidas no metabolismo de nucleotídeos e no metabolismo de carboidratos. Em resposta ao estresse por cádmio, verificou-se a indução de genes que codificam principalmente proteínas com propriedades antioxidantes, proteínas envolvidas no metabolismo de aminoácidos, proteínas relacionadas com o transporte celular e proteínas envolvidas no enovelamento de proteínas e proteólise. Uma das conseqüências do estresse por cádmio é o aumento do estresse oxidativo e proteínas antioxidantes têm um papel fundamental na resposta a este tipo de estresse. Dentre os genes observados durante o seqüenciamento das ESTs de B. emersonii, observamos dez genes codificando proteínas distintas da família Hsp70. Nove genes hsp70 são expressos em pelo menos um dos estágios do desenvolvimento do fungo e sete apresentam uma indução significativa após o choque térmico. Estes dados sugerem que estes genes desempenham um papel importante durante o desenvolvimento e em resposta ao estresse térmico em B. emersonii. Outro dado interessante obtido neste trabalho foi o enriquecimento de ESTs que continham íntrons em sua seqüência nas bibliotecas de estresse. Portanto, o choque térmico e o estresse por cádmio em B. emersonii diminuem a eficiência de processamento dos íntrons permitindo sua caracterização. O cDNA da proteína Hsp17 foi o que apresentou o maior número de ESTs seqüenciadas nas bibliotecas de estresse. Experimentos de Northern blot indicaram que o gene hsp17 possui um nível de expressão muito baixo durante o ciclo de vida de B. emersonii, no entanto, como esperado sua expressão aumenta drasticamente quando as células de esporulação ou germinação são submetidas a choque térmico. Os níveis da proteína Hsp17 acompanham os níveis do seu mRNA, indicando que o controle da expressão do gene hsp17 deve ocorrer em nível de transcrição. / In this work we realized a large scale, sequencing program of cDNAs libraries obtained from mRNA of B. emersonii cells submitted to heat shock and cadmium stress. A total of 6350 high quality expressed sequence tags (ESTs) were obtained, representing 2326 unique putative genes (unigenes) of this fungus. From these putative unigenes, 1282 genes were classified at least in one of the three Gene Ontology Consortium (GO) categories. The analysis of the partial transcriptome of B. emersonii, determined until now, allowed the identification of 78 unigenes encoding molecular chaperones of all known protein families. To evaluate the global expression of the genes in response to environmental stresses, such as heat shock and cadmium, DNA microarray assays were performed. We observed that in response to heat shock B. emersonii induces the expreession of genes encoding proteins related to protein folding and proteolysis, as expected under high temperature conditions, as well as genes encoding proteins with antioxidant properties and proteins involved in nucleotide and carbohydrate metabolism. In response to cadmium stress, we mainly verified the induction of genes for proteins with antioxidant properties, proteins involved in amino acid metabolism, proteins related to cellular transport and proteins related to protein folding and proteolysis. One of the consequences of the exposure to cadmium is the increase of oxidative stress, and antioxidant proteins have a fundamental role in the response to this kind of injury. Amongst the genes observed during the B. emersonii EST sequencing program, ten genes encoding distinct proteins from the Hsp70 family were observed. Nine of them are expressed at least in one stage of the fungus development and seven genes presented a significant induction during heat shock treatment. These data suggest that the hsp70 genes perform an important role during development and in response to heat stress in B. emersonii. Another interesting result from this work was the enrichment of ESTs containing introns in the stress libraries. Thus, heat shock and cadmium stress decrease the efficiency of intron processing in B. emersonii, allowing for intron characterization. The cDNA for the Hsp17 protein presented the highest number of ESTs sequenced from the stress libraries. Northern blot experiments indicated that the hsp17 gene is expressed at very low levels throughout the life cycle of B. emersonii, however, as expected its expression increases drastically when sporulation or germination cells are submitted to heat shock. Hsp17 protein levels accompany its mRNA levels, indicating that the control of expression of the hsp17 gene occurs at a transcriptional level.

Substanzen der pharmazeutischen und chemischen Industrie müssen nach internationalen Richtlinien auf deren Toxizität gegenüber Mensch und Umwelt geprüft werden. Dazu gehören u. a. Prüfungen zur Vorhersage des embryotoxischen Potentials, die am lebenden Organismus durchgeführt werden. Mit dem Ziel die Anzahl der Tierversuche zu verringern, die notwendig sind um das toxikologische Profil einer Prüfsubstanz zu bestimmen, wurde der Embryonale Stammzelltest (EST) entwickelt. Als Grundlage des EST dienen embryonale Stammzellen (ES-Zellen) einer Zelllinie. ES-Zellen sind Zellen, die sich in der frühen embryonalen Entwicklung in die Zellen der Keimblätter entwickeln können. Daraus wiederum differenzieren die vielen verschiedenen, unterschiedlich spezialisierten Zelltypen des komplexen Organismus. Im EST wird die Konzentration einer Prüfsubstanz bestimmt, bei der die Differenzierung von ES-Zellen zu Herzmuskelzellen zu 50 % inhibiert wird. Zusätzlich wird die Konzentration der Prüfsubstanz bestimm&#176;t, bei der 50 % der ES-Zellen (IC50D3) bzw. Fibroblastenzellen (IC503T3) absterben. Die allgemeine Toxizität ist damit von der spezifischen Toxizität der Prüfsubstanz auf die ES-Zellen und deren Differenzierung unterscheidbar. Die Parameter fliessen in ein biostatistisches Modell zur Prädiktion des embryotoxischen Potentials der Prüfsubstanzen ein. <br><br> Es wurde ein Versuchsprotokoll entwickelt, wonach die ES-Zellen sich verstärkt zu Endothelzellen differenzieren. Die Endothelzellen, die im lebenden Organismus die Wand der späteren Blutgefässe, wie Venen und Arterien bilden, wurden mittels molekularbiologischer Methoden auf der RNA- und der Protein-Ebene nachgewiesen und quantifiziert. Verschiedene Zellkulturmethoden, Wachstumsfaktoren, als auch Wachstumsfaktorkonzentrationen wurden auf deren Vermögen die Differenzierung der ES-Zellen zu Endothelzellen zu induzieren, untersucht. Nach der Etablierung des Differenzierungsprotokolls wurden sieben Substanzen auf deren Vermögen geprüft, die Differenzierung von ES-Zellen zu Endothelzellen zu inhibieren. Die Endothelzellen wurden dabei über die Expression der RNA von zwei endothelzellspezifischen Genen quantifiziert. Im Vergleich dazu wurden die IC50D3 und die IC503T3 der Prüfsubstanz bestimmt, um eine Abschätzung des embryotoxischen Potentials der Prüfsubstanz zu ermöglichen. Die Ergebnisse zeigten, dass eine Abschätzung des embryotoxischen Potentials der sieben Prüfsubstanzen in nicht-, schwach- oder stark embryotoxisch vorgenommen werden konnte. Es ist zu schlussfolgern, dass der weiterentwickelte in vitro Embryotoxizitätsassay sensitiv und reproduzierbar ist. Mit der Verwendung von verschiedenen Differenzierungsendpunkten kann die Prädiktionskraft des Assays deutlich verbessert, und die Anzahl von Tierversuchen verringert werden. Durch die Verwendung von molekularbiologischen Markern kann der Assay einem Hochdurchsatzscreening zugängig gemacht werden und damit die Anzahl von Prüfsubstanzen deutlich erhöht werden. / Compounds of the pharmaceutical and chemical industry need to be tested for their toxicological potential with regard to humans and environment following international guidelines. Tests for the prediction of the embryotoxic potential executed on living organisms are examples of these guidelines. In order to reduce the number of animal experiments necessary for the assessment of the toxicological profile of compounds the embryonic stem cell test (EST) was developed. Embryonic stem cells (ES-cells) of a cell line are used as the basis of the EST. ES-cells are cells which develop at the early embryonic development into cells of the germ layers. Out of these the many different specialized cell types of the complex organism can differentiate. With the EST this concentration of a test compound will be determined where a 50 % inhibition of the differentiation of ES-cells into cardiomyocytes can be detected. Additionally, the concentration of a test compound which is cytotoxic to 50 % of the ES-cells (IC50D3) and to 50 % of fibroblasts (IC503T3) will be determined. Therefore, general toxicity caused by the test compound on ES-cells and its differentiation can be distinguished from specific toxicity of the test compound. Determined parameters will be included into a biostatistical model for the subsequent predicition of the embryotoxic potential of test compounds. <br><br> A protocol was developed whereby the differentiation of ES-cells into endothelial cells is induced. Endothelial cells which make up the walls of blood vessels, such as arteries and veins, were detected and quantified at the RNA and the protein level applying molecular biological methods. Different cell culture methods, growth factors and growth factor concentrations were studied for their ability to induce the differentiation of ES-cells into endothelial cells. Applying the developed differentiation protocol seven compounds were tested for their potential to inhibit the differentiation of ES-cells into endothelial cells. Endothelial cells were quantified by the RNA-expression of two endothelial-specific genes. In comparison to the expression levels the IC50D3 and the IC503T3 were determined in order to assess the embryotoxic potential of the test compound. The results showed that an assessment of the embryotoxic potential of the seven test compounds into non-, weakly- and strongly embroytoxic was possible. It can be concluded that the improved in vitro embryotoxicity assay is sensitive and reproducible. With the use of different differentiation endpoints the power of predicitivity of this assay can be significantly increased and the number of animal experiments can be reduced. With the application of molecular biological markers this assay can be applied as a high througput screening and therefore the number of test compounds can be strongly increased.

Texte remanié de: Thesis Ph. D.--New Delhi--Jawaharlal Nehru University. Titre de soutenance : Social protest and popular movement in medieval Orissa (c. AD 1450-1600). / Bibliogr. p. 213-223.

This work focuses on the use of a genetic algorithm for optimization in a search-based problem. The Genetic Algorithm (GA) is a subset of evolutionary algorithms that models biological processes to optimize highly complex functions. A GA allows a population composed of many individuals to evolve under specified selection rules to a state that maximizes the “fitness” (i.e. minimize the objective function). A major advantage of using GA over most stochastic techniques is its parallelism, which speeds up the simulation results leading to faster convergence. With mutation, the GA is also less likely to get stuck in local minima compared to other stochastic techniques. However, some notable drawbacks of the Standard GA (SGA) include slow convergence and a possibility of being stuck in local optimum solution. The SGA uses a random process to generate parameter values for the initial population generation, crossover and mutation processes. Random number generators are designed to result in either uniform distributions or Gaussian distributions. We conjecture that the evolutionary processes in genetics are driven by a random non-linear deterministic dynamic process rather than a random non-deterministic process. Therefore, in the GA evolutionary process, a chaotic map is incorporated into the initial population generation, the crossover and mutation processes of the SGA; this is termed the Chaotic GA (CGA). The properties of a chaotic system that provides additional benefits over randomly generated solutions are sensitivity to initial conditions, topological density and topological transitivity (robust diversity). These properties ensure that the CGA is able to explore the entire solution space. Introducing chaos into the whole process of a standard genetic algorithm may help improve convergence time and accuracy. Simulation was done using Matlab and Java.

Mémoire (M.E.S.R.)-- Université du Québec à Chicoutimi, 1992. / Document électronique également accessible en format PDF. CaQCU

Diss.--Philosophische Fakultät--Aachen--Rheinisch-Westfälische Technische Hochschule, 1986. / Bibliogr. p. 351-386. Index.