Malaria is one of the deadliest diseases known to mankind. In 2010, 219 million cases were reported, and 666,000 deaths were attributed to this disease. In the past, pyrethroid-treated mosquito nets have shown efficacy in reducing malaria transmission in many malaria endemic regions. However, an upsurge in the mosquito population that is resistant to pyrethroids threatens to compromise the efficacy of pyrethroid-treated bed nets. In an effort to develop another class of insecticide with a different mode of action, we have explored three classes of five membered heterocyclic carbamates (isoxazol-3-yl, pyrazol-5-yl, and pyrazol-4-yl), and 3-oxoisoxazole- 2(3H)-carboxamide as acetylcholinesterase inhibitors (AChE) targeting wild type (G3) and resistant (Akron) malaria mosquito Anopheles gambiae (Ag). Isoxazole carboxamide and carbamates were obtained regioselectively through judicious use of two different protocols. The final products were characterized and identified using ¹H and ¹³C NMR, and mass spectroscopy. In addition, the carboxamide structure was confirmed using X-ray diffraction. Several of the novel carbamates and carboxamides evaluated exhibited excellent toxicity towards susceptible G3 and resistant Akron strain An. gambiae (48f LC₅₀ G3 = 41 μg/mL, LC₅₀ Akron = 58 μg/mL, and 47i LC₅₀ G3 = 38 μg/mL, LC₅₀ Akron = 40 μg/mL). Hence, achieving the resistance- breaking goal. On the contrary, the commercial aryl methylcarbamates currently approved for indoor residual sprays (IRS) showed no potency towards the resistant strain An. gambiae (LC₅₀ G3 = 16-42 μg/mL, and LC₅₀ Akron >5,000 μg/mL). Further, we observed low toxicological cross-resistance ratios (RR) for the toxic isoxazol-3-yl and pyrazol-4-yl carbamates, and 3- oxoisoxazole-2(3H)-carboxamides (RR = 0.5-2.0). Amongst the commercial AChE inhibitors approved for IRS, only aldicarb exhibited such low RR (RR = 0.5), whereas the RR for commercial aryl methylcarbamates exceed 130-fold. The low RR observed for these novel heterocyclic inhibitors would certainly be favorable for a new anticholinesterase-based mosquitocide targeting both the susceptible and resistant strain mosquitoes. Although the overall selectivity (Ag vs human) did not exceed 24-fold, the heterocyclic carbamates and carboxamides synthesized by the author showed appreciable inhibition of resistant AChE (G119S) in comparison to commercial aryl carbamates, which showed no inhibition at all. During the course of this project, the isoxazol-3-yl and pyrazol-5-yl methylcarbamates proved to be unstable, and thus could not be isolated. The synthesis of pyrazol-4-yl methylcarbamates using N-methylcarbamoyl chloride proved particularly challenging due to the formation of by-products called allophanates. The similar Rf of the by-product and the desired final product made the isolation laborious and time-consuming. We have successfully overcome this problem by employing a new protocol, where triphosgene served as the carbonylating agent and N-methylamine in THF was used as the amine source. In addition, we have also developed another one-pot protocol for a safer synthesis of pyrazol-4-yl methylcarbamates utilizing 1,1- carbonyldiimidazole (CDI), and N-methylamine hydrogen chloride salt. With the pyrazol-4-yl core, apart from achieving excellent toxicity towards both strains of An. gambiae, we have also achieved excellent AgAChE vs hAChE selectivity (Ag vs h >100-fold). Due to our continued interest in developing this core, we have devised a convenient, scalable, no-column approach for the synthesis an intermediate 103 that can be utilized to synthesize these compounds more efficiently. / Ph. D.

Malaria continues to cause significant mortality in sub-Saharan Africa and elsewhere, and existing vector control measures are being threatened by growing resistance to pyrethroid insecticides. With the goal of developing new human-safe, resistance-breaking insecticides we have explored several classes of acetylcholinesterase inhibitors. In vitro assay studies demonstrate that tri- and difluoromethyl ketones can potentially inhibit An. gambiae AChE (AgAChE). These compounds inhibit the enzyme by making a covalent adduct with the catalytic serine of AChE. Trifluoromethyl ketones however are poor inhibitors of the G119S resistant mutant of AgAChE. However difluoromethyl ketones can inhibit G119S AgAChE and compound 3-10g showed an IC₅₀ value of 25.1 nM after 23h incubation time. Despite this potent inhibition of AgAChE, the tri-, di-, and (mono)fluoroketones showed very low toxicity to An. gambiae, perhaps due to hydration and rapid clearance. In an attempt to improve An. gambiae toxicity, oximes and oxime ethers of these compounds were prepared as potential prodrugs. These structures identified trifluoromethyl ketone oxime 3-2d as a potent toxin against both wild-type (G3-strain) and a multiply resistant (Akron) strain of An. gambiae. This compound is within 3-fold of the toxicity of propoxur to wild type An. gambiae (LC₅₀ values of 106 and 39 µg/mL, respectively). Most significantly, 3-2d was much more toxic than propoxur to multiply-resistant (Akron) strain An. gambiae (LC₅₀ = 112 and >5,000 µg/mL, respectively). However, thus far we have not been able to link the toxicity of these compounds to a cholinergic mechanism. Pre-incubation studies suggest that significant hydrolysis of these compounds to TFKs does not occur over 22 h at pH 7.7 or 5.5. The mechanism of action of 3-2d remains unknown. Our enzyme inhibition studies have demonstrated that 3-2d does not hydrolyze to the trifluoromethyl ketone 2-9d at pH 7.7. The high Akron toxicity of 3-2d and poor inhibition of G119S AgAChE by 2-9d argue against enzyme mediated conversion of 3-2d to 2-9d within the mosquito. Thus, we can rule out an AChE inhibition mechanism for toxicity. Additional experiments by our collaborator (Dr. Jeffrey Bloomquist, University of Florida) also rule out inhibition of mitochondrial respiration or agonism of the muscarinic acetylcholine receptor. Future work will address other potential insecticidal modes of action. / Ph. D.

Doctor of Philosophy / Department of Entomology / Kun Yan Zhu / Chitin metabolism represents an attractive target site for combating insect pests as insect growth and development are strictly dependent on precisely toned chitin synthesis and degradation and this process is absent in humans and other vertebrates. However, current understanding on this process and the involved enzymes is rather limited in insects. In this study, two chitin synthase genes (AgCHS1 and AgCHS2 or AgCHSA and AgCHSB), and 20 chitinase and chitinase-like genes (groups I-VIII) presumably encoding the enzymes for chitin biosynthesis and degradation, respectively, were identified and characterized in African malaria mosquito, Anopheles gambiae. Immunohistochemistry analysis and developmental stage- and tissue-dependent transcript profiling by using reverse transcription PCR, real-time quantitative PCR, and in situ hybridization revealed new information on these genes. Current understanding on chitin synthases is extended by the expression profiles such as the localization of AgCHS1 and AgCHS2 transcripts in eggs, AgCHS2 transcripts in the posterior larval midgut, AgCHS1 and AgCHS2 proteins in the compound eyes, and AgCHS2 enzyme in pupal inter-segments. Chitinase and chitinase-like genes are highly diverse in their gene structure, domain organization, and stage- and tissue-specific expression patterns. Most of these genes were expressed in several stages. However, some genes are stage- and tissue-specific such as AgCht8 mainly in pupal and adult stages, AgCht2 and AgCht12 specifically in foregut, AgCht13 exclusively in midgut. Functional analysis of each chitin synthase gene was conducted by using the chitosan/dsRNA nanoparticle-based RNA interference (RNAi) through larval feeding. The repression of the AgCHS1 transcripts which are predominantly expressed in carcass initiated from the mosquito larval feeding of dsRNA suggests the systemic nature of RNAi in mosquito larvae. In addition, silencing of AgCHS1 increased larval susceptibilities to diflubenzuron, whereas silencing of AgCHS2 enhanced the peritrophic matrix disruption and thus increased larval susceptibilities to calcofluor white or dithiothreitol. Furthermore, a non-radioactive method was adapted and optimized to examine the chitin synthase activity in mosquitoes. By using this method, diflubenzuron and nikkomycin Z show limited in vitro inhibition on chitin synthase at high concentration in cell free system, whereas no in vivo inhibition was observed.

>Magister Scientiae - MSc / Tsetse flies (Glossina spp) are vectors of African trypanosome (Trypanosoma spp) parasites, causative agents of Human African trypanosomiasis (sleeping sickness) and Nagana in livestock. Research suggests that tsetse fly immunity factors are key determinants in the success and failure of infection and the maturation process of parasites. An analysis of tsetse fly immunity factors is limited by the paucity of genomic data for Glossina spp. Nevertheless, completely sequenced and assembled genomes of Drosophila melanogaster, Anopheles gambiae and Aedes aegypti provide an opportunity to characterize protein families in species such as Glossina by using a comparative genomics approach. In this study we characterize thioester-containing proteins (TEPs), a sub-family of immunity-related proteins, in Glossina by leveraging the EST data for G.morsitans and the genomic resources of D. melanogaster, A. gambiae as well as A.aegypti.A total of 17 TEPs corresponding to Drosophila (four TEPs), Anopheles (eleven TEPs) and Aedes aegypti (two TEPs) were collected from published data supplemented with Genbank searches. In the absence of genome data for G. morsitans, 124 000 G.morsitans ESTs were clustered and assembled into 18 413 transcripts (contigs and singletons). Five Glossina contigs (Gmcn1115, Gmcn1116, Gmcn2398, Gmcn2281 and Gmcn4297) were identified as putative TEPs by BLAST searches. Phylogenetic analyses were conducted to determine the relationship of collected TEP proteins.Gmcn1115 clustered with DmtepI and DmtepII while Gmcn2398 is placed in a separate branch, suggesting that it is specific to G. morsitans.The TEPs are highly conserved within D. melanogaster as reflected in the conservation of the thioester domain, while only two and one TEPs in A. gambiae and A. aegypti thioester domain show conservation of the thioester domain suggesting that these proteins are subjected to high levels of selection. Despite the absence of a sequenced genome for G. morsitans, at least two putative TEPs where identified from EST data.

Le contrôle du paludisme ne semble aujourd'hui envisageable que par stratégies combinées ciblant différents stades du parasite. Chez le vecteur, certains mécanismes de la réponse immunitaire pourraient être manipulés pour bloquer le développement sporogonique du parasite. Cette thèse examine les effets de la diversité du vecteur et du parasite dans le couple le plus important en termes d'épidémiologie, A. gambiae - P. falciparum. Des polymorphismes de gènes de l'immunité du moustique contrôlant le niveau d'infection ont été identifiés par étude d'association. Certains d'entre eux ont un effet spécifique selon les isolats de parasites, suggérant de potentielles interactions génotype X génotype. Nous avons déterminé un déséquilibre de liaison très bas dans les populations naturelles de vecteurs, validant notre approche par gènes candidats. Les caractéristiques et les forces évolutives faisant d'A. gambiae un vecteur du paludisme majeur sont discutées. Les diverses populations de vecteurs et parasites peuvent interagir de manière spécifique. Pour tester cela, des infections par des isolats de parasites sympatriques et allopatriques ont été comparées, montrant des intensités plus faibles dans les couples sympatriques. Les profils d'expression des gènes montrent cependant peu de régulations spécifiques aux populations, mais plutôt des différences extrêmes selon les isolats de parasites. Ces résultats suggèrent des effets importants de la diversité entre populations et individus. En conclusion, cette thèse souligne l'importance de la prise en compte de la diversité naturelle des vecteurs et parasites dans les recherches futures sur leurs interactions. / To achieve malaria control a variety of approaches must be combined targeting different stages of the parasites life cycle. With better understanding of mosquito immunity, it is hoped that aspects of natural resistance can be manipulated to prevent parasite development. This thesis investigates the effect of both mosquito and parasite diversity on the mosquitoes response to malaria using the most important human malaria system; Anopheles gambiae-Plasmodium falciparum in natural/semi-natural conditions. Mosquito loci are identified that significantly control infection phenotype, some of which act in a parasite isolate specific manner, highlighting their potential involvement in genotype by genotype interactions. Such research is moving towards genomewide studies; however, on finding very low linkage disequilibrium in wild mosquitoes, it favors candidate gene association studies. A. gambiae characteristics that make it such a good malaria vector are discussed and the evolutionary forces driving these traits. Selection behind vector-parasite interactions can differ spatially and temporally causing specificities in sympatric couples. Sympatric and allopatric mosquito infections with malaria are compared, showing that sympatric infections develop lower infection intensities suggesting local adaptation. Mosquito gene expression profiles highlight a small number of genes differentially regulated between sympatric and allopatric infections, however extreme differences in gene regulation are observed within populations, probably driven by the variable nature of malaria parasites. This thesis highlights the importance of taking into account natural diversity in future research.

Memory of chirality (MOC) is an emerging strategy for asymmetric synthesis which relies upon the intermediacy of transiently non-racemic reactive species. In these reactions the configuration of the sole stereogenic center of the enantiopure starting material is "memorized" by a chiral non-racemic conformation in the intermediate; trapping then captures the stereochemical information, and generates a new stereogenic center with high fidelity. We experimentally and computationally studied the highly retentive deprotonation/alkylations of 1,4-benzodiazepin-2-ones (BZDs) that rely upon this strategy. We captured a transiently non-racemic BZD enolate intermediate in enantiopure form, then released the enolate and observed its subsequent reaction. This approach allowed the first ever step-wise observation of the stereochemical course of such a MOC process. Approximately 2 million deaths are caused by malaria every year in the world. In total roughly 3.2 billion people are living under the risk of malaria transmission. Current use of anticholinesterase insecticides has been limited by their toxicity to human beings. A major African malaria insect vector, Anopheles gambiae (Ag), was targeted. Based on sequence alignment and homology models of AgAChE, a strategy of dual-site binding was adopted that targets Trp84 in the active site and Cys286 at the peripheral site. Selective AChE inhibitors have been designed and synthesized. / Ph. D.

Female adults of many mosquito species possess distinct physiological features adapting to blood feeding for successful reproduction. The disease pathogens that are transmitted by mosquitoes have evolved to take advantages of the indispensable blood feedings to complete their transmission cycles and to survive attacks from the mosquito's innate immune system. Normal egg development and mosquito immunity are tightly controlled by tissue- and stage-specific gene expression and coordinated by many signal molecules in the mosquito. Understanding gene regulation affecting mosquito reproduction and malaria parasites infection is of paramount importance for developing novel malaria control strategies. A growing body of evidence indicates that microRNAs (miRNAs) are involved in egg maturation and immune reactions against invading pathogens in mosquitoes. However, the molecular mechanisms by which specific miRNAs selectively modulate reproduction and the survival of pathogens are largely unknown. The miRNA-induced gene-silencing pathway in mosquitoes was mostly extrapolated from the studies of flies. To explore the dynamics of miRNAs in reproduction, I used small RNAs sequencing to monitor miRNAs expression and their association with Argonaute 1 (Ago1) and Argonaute 2 (Ago2) in the malaria mosquito Anopheles gambiae (An. gambiae) during the 72-h period immediately after blood feeding. I found the abundance and Ago loading of most of the mature miRNAs were relatively stable after blood ingestion. However, miRNAs of the miR-309/286/2944 cluster were considerably upregulated after blood feeding. I confirmed that miR-309 is essential for normal egg development by depletion of endogenous miR-309 with a specific antagomir. In addition, my results showed that the Ago association of some miRNAs was not proportional to their cellular abundance implying additional regulation at miRNA integration. To investigate the functional roles of miRNAs and define context-dependent miRNA-mRNA interactions during the reproductive process, I have applied an innovative experimental approach to study miRNA-mRNA interactome. CLEAR (covalent ligation of endogenous Argonaute-bound RNAs)-CLIP can generate miRNA-mRNA chimeras from UV-irradiation stabilized Ago-miRNA-mRNA complex. My results have defined tens of thousands of miRNA-mRNA interactions in mosquitoes, including novel targets for mosquito-specific miRNAs. Verification of the predicted interactions using mRNA-seq, ribosome-profiling, and luciferase reporter assay revealed a reliable miRNA-mRNA interaction network. Based on the detected interactions, I refined the paring rules for mosquito miRNAs and illustrated the dynamic pairing between different regions of miRNAs with their targets in vivo. The miRNA-mRNA interactions were compared using this approach at multiple time points before and after blood feeding. Importantly, this study showed that the interactions were dynamic and enriched in genes that are involved in metabolisms, supporting the proposed functions of miRNAs in coordinating the gene regulation in mosquito reproduction. Plasmodium falciparum (P. falciparum) is a major human malaria parasite. To understand the functions of miRNAs in the mosquito resistance to Plasmodium infection, we analyzed the miRNA-mRNA interactions after female mosquitoes taking a P. falciparum-infected blood meal or an uninfected blood meal. Comparison of the interactions revealed enhanced miRNA-mRNA interactions after P. falciparum infection involving a group of immunity-related genes. In summary, this study has provided a systematic view and significantly advanced our understanding of the miRNA functions in mosquito reproduction and P. falciparum infection. / PHD

Bacillus thuringiensis sérotype israelensis (Bti) produit quatre toxines entomocides utilisées à grande échelle pour le biocontrôle des populations de diptères nuisibles et vecteurs de maladies : Cry4Aa, Cry4Ba, Cry11Aa et Cyt1Aa. Chacune de ces toxines présente un effet létal sur différents insectes mais, lorsqu’elles sont combinées, on observe un effet synergique et l’absence de résistance. Bien que cette synergie soit bien documentée par des tests de toxicité, il existe très peu d’information sur son mécanisme aux niveaux cellulaire et moléculaire. À l’aide d’intestins isolés des larves du moustique Aedes aegypti, le principal vecteur du paludisme, et de microélectrodes, nous avons observé une dépolarisation membranaire en présence de Cyt1Aa et de Cry4Aa individuellement. Cette dépolarisation se produit cependant plus rapidement lorsque la Cyt1Aa est utilisée en même temps que la Cry4Aa. D’autre part, des expériences réalisées avec la sonde calcique Fura-2 sur une lignée cellulaire provenant d’Anopheles gambiae (Ag55), ont révélé une forte activité lytique de la Cyt1Aa, mais très peu d’effets des autres Cry, et ce même en combinaison. Nous avons dissocié les cellules de l’épithélium intestinal isolé du moustique pour des expériences de Fura2. Nos résultats, quoique préliminaires, montrent les effets variables de ces toxines lorsqu’elles sont administrées seules sur les cellules dissociées : une augmentation du calcium intracellulaire, ou une fuite de la sonde se traduisant par une perte du signal fluorescent, ou la lyse cellulaire. On observe également en présence de Cyt1Aa et de Cry4Ba, que les effets sont presque instantanés. / Bacillus thuringiensis var israelensis (Bti) produces four insecticidal toxins used around the world to control disease-borne and harmful dipterans populations: Cry4Aa, Cry4Ba, Cry11Aa and Cyt1Aa. They each present their lethal effect on different dipterans, but combined, they generate a synergistic activity and a reduced resistance is observed. Though these synergies are well documented and supported by toxicity bioassays, little is known regarding the cellular and molecular mechanisms of these synergies. Here, by using freshly isolated midguts from the mosquito Aedes aegypti, an important malaria vector, and glass microelectrodes, we measured the electrical potential of the apical membrane when exposed to these toxins alone or in combination. We observed a depolarisation when treated with Cyt1Aa and Cry4Aa. Toxin mixture assays only revealed a faster depolarisation of the membrane when the above two toxins were combined together, and a variety of responses with other toxin mixtures. Microspectrofluometry using the calcium probe Fura-2 on an immortal cell line from Anopheles gambiae (Ag55) showed massive effect of Cyt1Aa, but very little effect of the Cry toxins alone or in mixture. Microspectrofluometry experiments were also conducted on freshly dissociated cells from Aedes aegypti. Though these experiments are innovative and the results preliminary, it was observed that some cells responded differently to Cyt1Aa and Cry4Ba, showing the various ways these toxins affect cells, by inducing either intracellular calcium change, or by entirely losing the probe, or by cell lysis. The mixture of these toxins is very efficient and almost instantaneous.

Submitted by Caroline Falcao (caroline.rfalcao@ufpe.br) on 2017-06-19T17:21:04Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) 2012-Tese-GlaubiaArrudaSilva.pdf: 6824713 bytes, checksum: 821241186cb31ac2e399105bacd70cde (MD5) / Made available in DSpace on 2017-06-19T17:21:04Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) 2012-Tese-GlaubiaArrudaSilva.pdf: 6824713 bytes, checksum: 821241186cb31ac2e399105bacd70cde (MD5) Previous issue date: 2012-08-13 / Os estudos e as pesquisas históricas acerca das doenças constituem-se em caminhos por meio dos quais é possível construir novas perspectivas de análise das sociedades em tempos e espaços diversos. Essa tese de doutorado acerca da epidemia de malária, ocorrida entre os anos de 1937 e 1942, tem como um dos seus enfoques centrais a análise de como a população dos municípios localizados na área denominada Baixo Jaguaribe, no estado do Ceará, vivenciou este surto epidêmico. Outro caminho perseguido foi o de analisar os momentos em que a malária deixava de ser apenas um problema do indivíduo, da família e tornava-se alvo de políticas públicas dos governos municipal, estadual e federal, além disso, passavam também a ser negociadas com uma instituição dos EUA, a Fundação Rockefeller. Dessa forma, outro foco de análise foramas ações empreendidas pelo governo municipal, estadual, federal e pela Fundação Rockefeller nas tentativas de erradicar o mosquito transmissor da doença, Anopheles gambiae,através, por exemplo, de campanhas como o Serviço de Obras Contra a Malária (SOCM) e, posteriormente, pelo Serviço de Malária do Nordeste (SMNE). E, por fim, outra dimensão pesquisada e analisada nessa tese foram as relações estabelecidas entre os moradores locais eum saber institucionalizado pela ciência no combate a doença, confrontando, assim, os tratamentos e os saberes daquela população. / Studies andhistorical researchconcerning thediseases arepathsthrough whichone canbuild newperspectives on society’s analysisindifferenttimes and places. Thisdoctorate thesison themalaria epidemic, which occurred between1937 and1942,has asone of itscentralfocusesthe analysison how thepopulation of the municipalitieslocatedin the area calledBaixo Jaguaribein the state ofCeará,experiencedthisoutbreak. Anotherpath pursuedwas to analyzethe moments in whichmalariawas no longerjust a problem ofthe individual or its familyand becamethe target ofpublic policiesof municipal,state and federal government, also beingnegotiated withaU.S. institution, the Rockefeller Foundation.Thus, another focus of the present analysis was the actions taken by the municipal, state and federal government, and the Rockefeller Foundation in attempts to eradicate the mosquito that transmits the disease, Anopheles gambiae, through, for example, the campaigns such as the Serviço de Obras Contra a Malária (SOCM) and later by theServiço de Malária do Nordeste (SMNE). Finally, another dimension researched and analyzed in this thesis was the relation between local residents and a scientific institutionalized knowledge to fight the disease, thus comparing the treatments and knowledge of that population.

L'incessant augment del nombre de seqüències genòmiques, juntament amb l'increment del nombre de tècniques experimentals de les que es disposa, permetrà obtenir el catàleg complet de les funcions cel.lulars de diferents organismes, incloent-hi la nostra espècie. Aquest catàleg definirà els fonaments sobre els que es podrà entendre millor com els organismes funcionen a nivell molecular. Al mateix temps es tindran més pistes sobre els canvis que estan associats amb les malalties. Per tant, la seqüència en brut, tal i com s'obté dels projectes de seqüenciació de genomes, no té cap valor sense les anàlisis i la subsegüent anotació de les característiques que defineixen aquestes funcions. Aquesta tesi presenta la nostra contribució en tres aspectes relacionats de l'anotació dels gens en genomes eucariotes. Primer, la comparació a nivell de seqüència entre els genomes humà i de ratolí es va dur a terme mitjançant un protocol semi-automàtic. El programa de predicció de gens SGP2 es va desenvolupar a partir d'elements d'aquest protocol. El concepte al darrera de l'SGP2 és que les regions de similaritat obtingudes amb el programa TBLASTX, es fan servir per augmentar la puntuació dels exons predits pel programa geneid, amb el que s obtenen conjunts d'anotacions més acurats d'estructures gèniques. SGP2 té una especificitat que és prou gran com per que es puguin validar experimentalment via RT-PCR. La validació de llocs d'splicing emprant la tècnica de la RT-PCR és un bon exemple de com la combinació d'aproximacions computacionals i experimentals produeix millors resultats que per separat. S'ha dut a terme l'anàlisi descriptiva a nivell de seqüència dels llocs d'splicing obtinguts sobre un conjunt fiable de gens ortòlegs per humà, ratolí, rata i pollastre. S'han explorat les diferències a nivell de nucleòtid entre llocs U2 i U12, pel conjunt d'introns ortòlegs que se'n deriva d'aquests gens. S'ha trobat que els senyals d'splicing ortòlegs entre humà i rossegadors, així com entre rossegadors, estan més conservats que els llocs no relacionats. Aquesta conservació addicional pot ser explicada però a nivell de conservació basal dels introns. D'altra banda, s'ha detectat més conservació de l'esperada entre llocs d'splicing ortòlegs entre mamífers i pollastre. Els resultats obtinguts també indiquen que les classes intròniques U2 i U12 han evolucionat independentment des de l'ancestre comú dels mamífers i les aus. Tampoc s'ha trobat cap cas convincent d'interconversió entre aquestes dues classes en el conjunt d'introns ortòlegs generat, ni cap cas de substitució entre els subtipus AT-AC i GT-AG d'introns U12. Al contrari, el pas de GT-AG a GC-AG, i viceversa, en introns U2 no sembla ser inusual. Finalment, s'han implementat una sèrie d'eines de visualització per integrar anotacions obtingudes pels programes de predicció de gens i per les anàlisis comparatives sobre genomes. Una d'aquestes eines, el gff2ps, s'ha emprat en la cartografia dels genomes humà, de la mosca del vinagre i del mosquit de la malària, entre d'altres. El programa gff2aplot i els filtres associats, han facilitat la tasca d'integrar anotacions de seqüència amb els resultats d'eines per la cerca d'homologia, com ara el BLAST. S'ha adaptat també el concepte de pictograma a l'anàlisi comparativa de llocs d splicing ortòlegs, amb el desenvolupament del programa compi. / El aumento incesante del número de secuencias genómicas, junto con el incremento del número de técnicas experimentales de las que se dispone, permitirá la obtención del catálogo completo de las funciones celulares de los diferentes organismos, incluida nuestra especie. Este catálogo definirá las bases sobre las que se pueda entender mejor el funcionamiento de los organismos a nivel molecular. Al mismo tiempo, se obtendrán más pistas sobre los cambios asociados a enfermedades. Por tanto, la secuencia en bruto, tal y como se obtiene en los proyectos de secuenciación masiva, no tiene ningún valor sin los análisis y la posterior anotación de las características que definen estas funciones. Esta tesis presenta nuestra contribución a tres aspectos relacionados de la anotación de los genes en genomas eucariotas. Primero, la comparación a nivel de secuencia entre el genoma humano y el de ratón se llevó a cabo mediante un protocolo semi-automático. El programa de predicción de genes SGP2 se desarrolló a partir de elementos de dicho protocolo. El concepto sobre el que se fundamenta el SGP2 es que las regiones de similaridad obtenidas con el programa TBLASTX, se utilizan para aumentar la puntuación de los exones predichos por el programa geneid, con lo que se obtienen conjuntos más precisos de anotaciones de estructuras génicas. SGP2 tiene una especificidad suficiente como para validar esas anotaciones experimentalmente vía RT-PCR. La validación de los sitios de splicing mediante el uso de la técnica de la RT-PCR es un buen ejemplo de cómo la combinación de aproximaciones computacionales y experimentales produce mejores resultados que por separado. Se ha llevado a cabo el análisis descriptivo a nivel de secuencia de los sitios de splicing obtenidos sobre un conjunto fiable de genes ortólogos para humano, ratón, rata y pollo. Se han explorado las diferencias a nivel de nucleótido entre sitios U2 y U12 para el conjunto de intrones ortólogos derivado de esos genes. Se ha visto que las señales de splicing ortólogas entre humanos y roedores, así como entre roedores, están más conservadas que las no ortólogas. Esta conservación puede ser explicada en parte a nivel de conservación basal de los intrones. Por otro lado, se ha detectado mayor conservación de la esperada entre sitios de splicing ortólogos entre mamíferos y pollo. Los resultados obtenidos indican también que las clases intrónicas U2 y U12 han evolucionado independientemente desde el ancestro común de mamíferos y aves. Tampoco se ha hallado ningún caso convincente de interconversión entre estas dos clases en el conjunto de intrones ortólogos generado, ni ningún caso de substitución entre los subtipos AT-AC y GT-AG en intrones U12. Por el contrario, el paso de GT-AG a GC-AG, y viceversa, en intrones U2 no parece ser inusual. Finalmente, se han implementado una serie de herramientas de visualización para integrar anotaciones obtenidas por los programas de predicción de genes y por los análisis comparativos sobre genomas. Una de estas herramientas, gff2ps, se ha utilizado para cartografiar los genomas humano, de la mosca del vinagre y del mosquito de la malaria. El programa gff2aplot y los filtros asociados, han facilitado la tarea de integrar anotaciones a nivel de secuencia con los resultados obtenidos por herramientas de búsqueda de homología, como BLAST. Se ha adaptado también el concepto de pictograma al análisis comparativo de los sitios de splicing ortólogos, con el desarrollo del programa compi. / The constantly increasing amount of available genome sequences, along with an increasing number of experimental techniques, will help to produce the complete catalog of cellular functions for different organisms, including humans. Such a catalog will define the base from which we will better understand how organisms work at the molecular level. At the same time it will shed light on which changes are associated with disease. Therefore, the raw sequence from genome sequencing projects is worthless without the complete analysis and further annotation of the genomic features that define those functions. This dissertation presents our contribution to three related aspects of gene annotation on eukaryotic genomes. First, a comparison at sequence level of human and mouse genomes was performed by developing a semi-automatic analysis pipeline. The SGP2 gene-finding tool was developed from procedures used in this pipeline. The concept behind SGP2 is that similarity regions obtained by TBLASTX are used to increase the score of exons predicted by geneid, in order to produce a more accurate set of gene structures. SGP2 provides a specificity that is high enough for its predictions to be experimentally verified by RT-PCR. The RT-PCR validation of predicted splice junctions also serves as example of how combined computational and experimental approaches will yield the best results. Then, we performed a descriptive analysis at sequence level of the splice site signals from a reliable set of orthologous genes for human, mouse, rat and chicken. We have explored the differences at nucleotide sequence level between U2 and U12 for the set of orthologous introns derived from those genes. We found that orthologous splice signals between human and rodents and within rodents are more conserved than unrelated splice sites. However, additional conservation can be explained mostly by background intron conservation. Additional conservation over background is detectable in orthologous mammalian and chicken splice sites. Our results also indicate that the U2 and U12 intron classes have evolved independently since the split of mammals and birds. We found neither convincing case of interconversion between these two classes in our sets of orthologous introns, nor any single case of switching between AT-AC and GT-AG subtypes within U12 introns. In contrast, switching between GT-AG and GC-AG U2 subtypes does not appear to be unusual. Finally, we implemented visualization tools to integrate annotation features for gene- finding and comparative analyses. One of those tools, gff2ps, was used to draw the whole genome maps for human, fruitfly and mosquito. gff2aplot and the accompanying parsers facilitate the task of integrating sequence annotations with the output of homologybased tools, like BLAST.We have also adapted the concept of pictograms to the comparative analysis of orthologous splice sites, by developing compi.