Fraturas cominutivas com grandes perdas ósseas são comuns em animais silvestres, sendo de maior prevalência em aves, devido a traumas, com a crescente urbanização e desmatamento. Um dos problemas para o tratamento dessas fraturas nesses animais é a dificuldade do uso de enxertia autógena, devido os locais de coleta não oferecerem material suficiente e pela alta taxa de morbidade. Assim, a engenharia de biomateriais vem desenvolvendo diversos dispositivos com a intenção de auxiliar nesse tratamento. O uso de cimento ósseo é crescente nesse meio, e tem como objetivo a recuperação e reintrodução do animal a seu habitat. O objetivo deste trabalho foi avaliar o uso do cimento ósseo de hidroxiapatita deficiente em cálcio (HAD) associado ou não a proteína morfogenética óssea (BMP), para o tratamento do defeito crítico (DC) diafisário em ulna de galinhas domésticas. Foram utilizadas 32 aves, separadas em 4 grupos de 8 animais, sendo: controle negativo (GCN), controle positivo (GCP), cimento de HAD (GHAD) e cimento HAD associado a BMP (GHAD+BMP). Todos os animais passaram pelos procedimentos de ostectomia e a fixação dos fragmentos por meio da colocação de um pino intramedular de 1,5mm de forma retrógada, e acompanhados por período de 60 dias. Foram realizados exames radiográficos, análise histopatológica e biomecânica das ulnas. O presente trabalho demonstrou que não houve diferença significativa de consolidação entre os grupos com e sem BMP, porém o HAD+BMP apresentou-se mais eficiente para DC em galinhas na avaliação histopatológica, levando a resposta osteoindutora, por parte do cimento, e osteogênica, pela proteína. / Comminuted fractures with great bone loss are common in wild animals, being more present in birds due to trauma related to growing urbanization and deforestation. One of the problems of the treatment of these kinds of fractures in these animals is the difficulty of using autogenous grafting because collection places do not offer enough material and also because of the high morbidity rate. Therefore, biomaterials engineering has been developing several devices intending to help on this treatment. Therewith, the use of bone cement is increasing in this environment, and has as its goal the recovery and reintroduction of the animal to its habitat. The objective of this work was to evaluate the use of calcium deficient hydroxyapatite bone cement (HAD) for the treatment of diaphysialcritical defect (DC) in ulna of domestic hens. Thirty-two birds were used, divided in four groups of eight animals, being: negative control (GCN), positive control (GCP), HAD cement (GHAD) and HAD cement associated with bone morphogenetic protein (GHAD + BMP). All animals went through the procedure of ostectomy and fixation of the fragments by placing a 1.5mm intramedullary pin in a retrograde way, and assisted for a period of 60 postoperative days. Radiographic examinations, histopathological and biomechanical analysis of the ulna were performed.The present paper demonstrated that there was not a significant consolidation measure between the groups with no BMP, however HAD + BMP presented more efficient results for DC in hens in the histopathological evaluation, leading to an osteoinductive response by cement and osteogenic by the protein.

Fraturas cominutivas com grandes perdas ósseas são comuns em animais silvestres, sendo de maior prevalência em aves, devido a traumas, com a crescente urbanização e desmatamento. Um dos problemas para o tratamento dessas fraturas nesses animais é a dificuldade do uso de enxertia autógena, devido os locais de coleta não oferecerem material suficiente e pela alta taxa de morbidade. Assim, a engenharia de biomateriais vem desenvolvendo diversos dispositivos com a intenção de auxiliar nesse tratamento. O uso de cimento ósseo é crescente nesse meio, e tem como objetivo a recuperação e reintrodução do animal a seu habitat. O objetivo deste trabalho foi avaliar o uso do cimento ósseo de hidroxiapatita deficiente em cálcio (HAD) associado ou não a proteína morfogenética óssea (BMP), para o tratamento do defeito crítico (DC) diafisário em ulna de galinhas domésticas. Foram utilizadas 32 aves, separadas em 4 grupos de 8 animais, sendo: controle negativo (GCN), controle positivo (GCP), cimento de HAD (GHAD) e cimento HAD associado a BMP (GHAD+BMP). Todos os animais passaram pelos procedimentos de ostectomia e a fixação dos fragmentos por meio da colocação de um pino intramedular de 1,5mm de forma retrógada, e acompanhados por período de 60 dias. Foram realizados exames radiográficos, análise histopatológica e biomecânica das ulnas. O presente trabalho demonstrou que não houve diferença significativa de consolidação entre os grupos com e sem BMP, porém o HAD+BMP apresentou-se mais eficiente para DC em galinhas na avaliação histopatológica, levando a resposta osteoindutora, por parte do cimento, e osteogênica, pela proteína. / Comminuted fractures with great bone loss are common in wild animals, being more present in birds due to trauma related to growing urbanization and deforestation. One of the problems of the treatment of these kinds of fractures in these animals is the difficulty of using autogenous grafting because collection places do not offer enough material and also because of the high morbidity rate. Therefore, biomaterials engineering has been developing several devices intending to help on this treatment. Therewith, the use of bone cement is increasing in this environment, and has as its goal the recovery and reintroduction of the animal to its habitat. The objective of this work was to evaluate the use of calcium deficient hydroxyapatite bone cement (HAD) for the treatment of diaphysialcritical defect (DC) in ulna of domestic hens. Thirty-two birds were used, divided in four groups of eight animals, being: negative control (GCN), positive control (GCP), HAD cement (GHAD) and HAD cement associated with bone morphogenetic protein (GHAD + BMP). All animals went through the procedure of ostectomy and fixation of the fragments by placing a 1.5mm intramedullary pin in a retrograde way, and assisted for a period of 60 postoperative days. Radiographic examinations, histopathological and biomechanical analysis of the ulna were performed.The present paper demonstrated that there was not a significant consolidation measure between the groups with no BMP, however HAD + BMP presented more efficient results for DC in hens in the histopathological evaluation, leading to an osteoinductive response by cement and osteogenic by the protein.

Orientador: Carlos Ducatti / Banca: Cyntia Ludovico Martins / Banca: Antonio Celso Pezzato / Banca: Marcos Macari / Banca: Marcelo Zacarias Moreira / Resumo: O objetivo deste trabalho foi identificar a inclusão de níveis crescentes de farinha de vísceras (FV) na alimentação de frangos de corte, usando os isótopos estáveis de carbono e nitrogênio na análise do sangue e músculo peitoral das aves coletados semanalmente. Foram utilizados 560 pintos machos (Cobb), com um dia de idade, distribuídos aleatoriamente em tratamentos: controle (dieta vegetal), os demais tratamentos tiveram a inclusão de 0,5; 1,0; 1,5; 2,0; 2,5; 3,0; 3,5; 4,0 e 8,0% de FV na dieta. A cada 7 dias foram separadas ao acaso oito aves (n = 8) por tratamento e coletados sangue e músculo peitoral para análise da razão isotópica do carbono e nitrogênio. Tanto no sangue quanto no músculo peitoral das aves aos 7 dias de idade a FV foi detectada a partir de 3,5%, valor que é mantido para o sangue aos 14 dias de idade. No músculo peitoral aos 14 dias a detecção foi a partir de 4,0%. Com 21 dias de idade no sangue a FV foi detectada a partir 2,0% e no músculo peitoral acima de 0,5% de inclusão. Aos 28, 35 e 42 dias no sangue foi detectado a partir de 4,0; 2,5 e 3,0%; respectivamente. No músculo peitoral aos 28 e 35 dias de idade foi identificada a FV em nível a partir de 2,0% e oas 42 dias a partir de 1,5%. A coleta de amostras ao longo do período de criação é necessária para acompanhar a variação do nível de inclusão de FV na alimentação de frangos de corte, devido as mudanças de dieta de acordo com as fase de criação de aves. O músculo peitoral comparado ao sangue das aves identifica a FV na alimentação de frangos de corte em menores níveis. A análise estatística linear discriminante é boa ferramenta para identificação de menores níveis de inclusão de FV na alimentação de frangos de corte comparada a análise estatística manova / Abstract: The aim of this paper was to identify the increasing levels of poultry offal meal (POM) in feed for broiler chickens using stable isotopes of carbon and nitrogen in the blood analysis and breast muscle of birds at each week. They were used 560 male chicks (Cobb), one day age. They were randomly assigned to treatments: control (vegetable diet), all other treatments had the inclusion of 0.5, 1.0; 1.5; 2.0; 2.5; 3.0; 3.5; 4.0 and 8.0% of POM in the diet. For analysis of the isotope ratio carbon and nitrogen at every 7 days were separated at random eight birds (n = 8) per treatment and collected blood and breast muscle. Both in blood as in breast muscle at 7 days old POM was detected at 3.5%, which is maintained for the blood at 14 days old. In the breast muscle at 14 days the detection was from 4.0%. Within 21 days of age in the POM blood was detected from 2.0% in the breast muscle and above the 0.5% inclusion. At 28, 35 and 42 days in the blood was detected from 4.0, 2.5 and 3.0%, respectively. In the breast muscle at 28 and 35 days of age was identified in the POM level from 2.0% and 42 days from 1.5%. The collection of samples throughout the growing period is needed to monitor the level of inclusion variação POM in feed for broiler chickens, because of changes in diet according to the phase of poultry. The breast muscle compared to the blood of birds identified the POM in the supply of broilers at lower levels. Statistical analysis of linear discriminant is a good tool for identification of lower levels of inclusion of POM in feed for broiler chickens compared to Manova statistical analysis / Doutor

Fraturas cominutivas com grandes perdas ósseas são comuns em animais silvestres, sendo de maior prevalência em aves, devido a traumas, com a crescente urbanização e desmatamento. Um dos problemas para o tratamento dessas fraturas nesses animais é a dificuldade do uso de enxertia autógena, devido os locais de coleta não oferecerem material suficiente e pela alta taxa de morbidade. Assim, a engenharia de biomateriais vem desenvolvendo diversos dispositivos com a intenção de auxiliar nesse tratamento. O uso de cimento ósseo é crescente nesse meio, e tem como objetivo a recuperação e reintrodução do animal a seu habitat. O objetivo deste trabalho foi avaliar o uso do cimento ósseo de hidroxiapatita deficiente em cálcio (HAD) associado ou não a proteína morfogenética óssea (BMP), para o tratamento do defeito crítico (DC) diafisário em ulna de galinhas domésticas. Foram utilizadas 32 aves, separadas em 4 grupos de 8 animais, sendo: controle negativo (GCN), controle positivo (GCP), cimento de HAD (GHAD) e cimento HAD associado a BMP (GHAD+BMP). Todos os animais passaram pelos procedimentos de ostectomia e a fixação dos fragmentos por meio da colocação de um pino intramedular de 1,5mm de forma retrógada, e acompanhados por período de 60 dias. Foram realizados exames radiográficos, análise histopatológica e biomecânica das ulnas. O presente trabalho demonstrou que não houve diferença significativa de consolidação entre os grupos com e sem BMP, porém o HAD+BMP apresentou-se mais eficiente para DC em galinhas na avaliação histopatológica, levando a resposta osteoindutora, por parte do cimento, e osteogênica, pela proteína. / Comminuted fractures with great bone loss are common in wild animals, being more present in birds due to trauma related to growing urbanization and deforestation. One of the problems of the treatment of these kinds of fractures in these animals is the difficulty of using autogenous grafting because collection places do not offer enough material and also because of the high morbidity rate. Therefore, biomaterials engineering has been developing several devices intending to help on this treatment. Therewith, the use of bone cement is increasing in this environment, and has as its goal the recovery and reintroduction of the animal to its habitat. The objective of this work was to evaluate the use of calcium deficient hydroxyapatite bone cement (HAD) for the treatment of diaphysialcritical defect (DC) in ulna of domestic hens. Thirty-two birds were used, divided in four groups of eight animals, being: negative control (GCN), positive control (GCP), HAD cement (GHAD) and HAD cement associated with bone morphogenetic protein (GHAD + BMP). All animals went through the procedure of ostectomy and fixation of the fragments by placing a 1.5mm intramedullary pin in a retrograde way, and assisted for a period of 60 postoperative days. Radiographic examinations, histopathological and biomechanical analysis of the ulna were performed.The present paper demonstrated that there was not a significant consolidation measure between the groups with no BMP, however HAD + BMP presented more efficient results for DC in hens in the histopathological evaluation, leading to an osteoinductive response by cement and osteogenic by the protein.

Estudar a arquitetura genética de uma dada característica quantitativa significa descrever os fatores genéticos e ambientais que a afetam, bem como o valor dos efeitos genéticos de cada loco e suas interações. O presente trabalho teve por objetivo geral estudar a arquitetura genética de características quantitativas associadas ao desempenho e ao rendimento de carcaça de uma população experimental oriunda do cruzamento entre uma linhagem de postura (CC) e uma de corte (TT) genotipada para marcadores microssatélites que foram associados ao peso vivo aos 42 dias na população recíproca TCTC nos cromossomos 1, 3 e 4. Para tanto, foram propostos três objetivos específicos: 1) caracterizar genotipicamente as duas populações referências (TCTC e CTCT); 2) construir mapas de ligação para a população CTCT; 3) mapear QTLs associados ao desempenho e ao rendimento de carcaça na população CTCT, utilizando o Mapeamento por Intervalo Composto (CIM). Os resultados evidenciaram que as duas linhagens parentais (CC e TT) possibilitaram a criação de gerações recíprocas F1 com elevados valores do conteúdo de informação polimórfica e heterozigosidade observada, resultado do satisfatório número de alelos verificado. Isto implica que as populações recíprocas F2, derivadas de ambas as gerações F1, são apropriadas para mapear QTLs associados ao desempenho e ao rendimento de carcaça. Adicionalmente, os mapas de ligação da população CTCT são similares ao de sua população recíproca TCTC e ao Mapa Consenso da galinha doméstica. A estimação de intervalos de confiança para as distâncias entre locos permitiu melhor entendimento das diferenças obtidas tanto no tamanho dos cromossomos quanto na ordem dos locos. Finalmente, foram observadas vantagens com o uso do CIM nas estimativas de número de QTLs mapeados e em suas posições. As regiões onde os QTLs foram mapeados neste estudo corroboram algumas daquelas da população recíproca TCTC, mas por outro lado sugerem que outras regiões do genoma dos cromossomos 1, 3 e 4 podem controlar tais características. Foram definidas duas regiões ainda não descritas na literatura no cromossomo 4: uma associada ao ganho de peso (MCW0240- LEI0063) e outra ao consumo de ração (LEI0085-MCW0174) 35-41 dias. Os resultados deste estudo podem ser explorados através do mapeamento fino, buscas in silico por genes candidatos por posição e validação em populações comerciais, a fim de implementar a seleção assistida por marcadores em programas de melhoramento genético avícolas. / Understanding the genetic architecture means to describe the genetic and environment factors that affect a quantitative trait, together with the estimation of individual genetic effects and its interactions. The aim of this work was to understand the genetic architecture of quantitative traits associated with performance and carcass yield of a chicken reference population created from crosses between a layer line (CC) and a broiler line (TT) genotyped for microsatellite markers that were associated with body weight at 42 days in its reciprocal cross on chromosomes 1, 3 and 4. Three specific topics were presented: 1) to characterize genotypically two reference populations (TCTC and CTCT); 2) to construct linkage maps in the CTCT population and 3) to map QTL associated with performance and carcass yield in CTCT population, using Composite Interval Mapping (CIM). The results showed that the two parental lines (CC and TT) created reciprocal F1 generations with suitable polymorphic information content values and observed heterozygosity, as result of the satisfactory number of alleles. This implies that the reciprocal F2 populations, derived from both F1 generations, are appropriated to map QTL associated with performance and carcass yield. The linkage maps from CTCT population were similar to its reciprocal population and to the Chicken Consensus Linkage Map. Estimating confidence intervals for distances between loci allowed the elucidation of the causes for differences both on chromosome sizes and on order loci. Finally, there were advantages in using CIM, mainly on QTL number and location. The regions where QTLs were mapped in this study not only corroborated some results from TCTC reciprocal population, but also suggested that other genome regions on chromosomes 1, 3 and 4 may control such traits. On chromosome 4 two regions were defined that were not previously described in the literature: one associated with weight gain (MCW0240-LEI0063) and another one with feed intake (LEI0085-MCW0174) at 35- 41 days. The results of this study can be explored through fine mapping, searches in silico for candidate genes and by validation in commercial populations, in order to implement marker assisted selection in poultry breeding programs.

A partir de uma linha macho de corte e outra de postura, foi desenvolvida uma população experimental F2 com objetivo de mapear locos de características quantitativas (QTLs) para características de interesse comercial. Foi gerado um total de 2.063 animais F2 em 17 incubações que foram criados como frangos de corte até a 6ª semana de idade, quando foram avaliadas seis características de desempenho. As famílias utilizadas para o estudo, foram as que obtiveram maior número de marcadores microssatélites informativos em trabalhos anteriores envolvendo os cromossomos 1 a 5 com a mesma população. Vinte marcadores dos cromossomos 19, 23, 24, 26, 27 e 28 foram testados nos indivíduos parentais e F1 das famílias escolhidas para checar se eram ou não informativos. Após a genotipagem das 5 famílias escolhidas, foram construídos os mapas de ligação e realizada a análise de mapeamento de QTL por intervalo para cada cromossomo utilizando o método de regressão e o modelo genético F2. Dois modelos foram testados: um incluindo apenas o efeito aditivo do QTL e outro modelo que incluiu também o efeito de dominância. Caso fosse identificado QTL com nível de significância no mínimo sugestivo no genoma, os modelos foram confrontados para confirmar o efeito de dominância do QTL. Foram conduzidas também análises complementares com o intuito de detectar interação do QTL x sexo e QTL x família. Foram estimados a porcentagem da variância fenotípica e o intervalo de confiança para cada QTL. No cromossomo 26 foi mapeado QTL significativo a 5% no cromossomo para ganho de peso dos 35 aos 41 dias, e no cromossomo 27 foi identificado, para a característica peso vivo aos 35 dias um QTL sugestivo no genoma. Os QTL localizados nos cromossomo 26 e 27 foram localizados a 0.0 e 103.0 cM e explicaram 1,95 e 2,03% da variação fenotípica, respectivamente. / With the objective of mapping quantitative trait loci (QTLs) for economically valuable characteristics, an F2 chicken population was developed by crossing a broiler sire line and a layer dam line. A total of 2.063 F2 chickens from 17 incubations were reared as broilers and slaughtered at 6 week of age, when six performance traits were measured. Five families were chosen for this study based on previous work to determine the most informative families. Twenty markers from chromosomes 19, 23, 24, 26, 27 and 28 were tested in the parental and F1 chickens from the chosen families to select the informative markers. After genotyping parental, F1 and F2 chickens, the linkage maps were constructed and QTL Interval mapping analysis was conducted for each chromosome using regression methods and the F2 genetic model. Two different models were tested: one including only the additive effect of the QTL and another model that also included the dominance effect. If at least a genome-wide suggestive QTL was detected, they were compared through standard F tests to confirm the dominance effect of the QTL. Complementary analyses were conducted to investigate the existence of QTL x sex and QTL x family interactions. The percentage of the phenotypic variance explained by the QTL and the confidence intervals were estimated for each QTL. A 5% chromosome-wide significant QTL for weight gain from 35 to 41 d was mapped to chromosome 26 and a QTL that exceeded the genome-wide suggestive threshold for body weight at 35 d was mapped to chromosome 27. This QTL positioned at 103 cM explained 2.03% of the phenotypic variance of the trait and presented a confidence interval from 0 to 111 cM.

While adenovirus (Ad) vectors have been shown to elicit potent antigen-specific T cell responses, the kinetics and nature of antigen-specific mucosa! and systemic T-cell responses has rarely been examined, especially following mucosal administration of Ad-based vectors. In the present studies, the phenotypic and functional characterization of antigen-specific CD8+ T cell responses following intrarectal (i.r.) vaccination with an Ad vector expressing Gallus gallus ovalbumin (OVA) was conducted. The frequencies of OVA-specific CD8+ T cells was maximal at 2 weeks post-vaccination in all tissues examined and then declined, demonstrating normal expansion and contraction kinetics. CD8+ T cells induced in the course of immunization exhibited phenotypic characteristics of effector memory T cells including up-regulation of the cell surface molecules CD43, CD44 and a low level of expression of CD127 at both local and systemic sites. While the discordance between the number of tetramer-reactive and cytokine-producing OVA-specific CD8+ T cells was observed, CD8+ T cells appeared to be fully functional in vivo. Upon secondary antigen exposure, the CD8+ T cell population expanded dramatically, particularly at the mucosa! surfaces. In addition, the CD8+ T cell response generated in the course of i.r. priming protected mice from intravaginal (i. vag.) vaccinia virus one month after immunization, thus underscoring the importance of inducing a tissue-resident effector memory T cell subset for protection against pathogens at mucosal surfaces. In developing future vaccines for mucosal diseases, the induction of a tissue-resident effector memory T cell subset should be one of the immunization objectives. Lentiviral vectors represent an attractive mode of genetic vaccination. Most commonly used, vesicular stomatitis virus glycoprotein (VSVG)-pseudotyped lentiviral vectors do not efficiently infect epithelial cells from the apical side, and, therefore, are not suitable as mucosa! vaccines. In the present studies, Ebola Zaïre strain glycoprotein (EboZ)-pseudotyped lentiviral vectors, which have been previously used to deliver transgene to the lung epithelium, were delivered i.r. and evaluated as a mucosal booster vaccine. Rectal delivery of EboZ-pseudotyped lentiviral vectors expressing β-galactosidase (β-gal) had resulted in low, but detectable levels of β-gal expression 2 weeks after administration. When delivered on its own, EboZ-pseudotyped lentivirus did not prime detectable antigen-specific immune response. However, when delivered i.r. 30 days after i.r. Adβ-gal immunization, a significant enlargement (boost) of β-gal-specific CD8+ T cell responses, especially in the colonic lamina propria (LP), was observed as compared to the delivery of EboZ-pseudotyped vector encoding different transgenes or VSVG-pseudotyped lentivirus expressing β-gal. When these animals were i. vag. challenged with vaccinia virus expressing β-gal, a dramatic expansion of β-gal-specific CD8+ T cells, especially in the vaginal tract, was observed. In addition, this prime and boost strategy protected the mice from i. vag. vaccinia virus challenge. Therefore, i.r. Ad-based priming followed by i.r. EboZ-pseudotyped lentiviral boosting was an effective strategy for eliciting protective mucosal CD8+ T cell responses. / Thesis / Doctor of Philosophy (PhD)

The avian immune system is a complex system of defence mechanisms that protect bird hosts against threats from ubiquitous pathogens. According to the co-evolutionary models, variability in immune traits of hosts is the key component providing ability to adapt and enhance their defence mechanisms in presence of constant selective pathogen pressure. Domestic chicken (Gallus gallus f. domestica) is used as a model organism in avian biology and also is one of the most important food-producing animals, not only for their meat but also for the egg production. Unfortunately, in research usually only inbred chicken lines are used and modern poultry husbandry is tight with unilateral breeding towards highly productive breeds. Those approaches decrease intra-population polymorphism in chickens. However, especially in case of farm animals, searching and extending the pool of immune variability and enhancing pathogen resistance is crucial for sustaining healthy and biologically secure populations and their products. Morphologically highly distinct traditional chicken breeds, which have evolved for hundreds years under different selective pressures, may represent this desirable immunological variability. In my thesis I described variability in chosen immunological traits, haematological parameters and proteomic...

The avian immune system is a complex system of defence mechanisms that protect bird hosts against threats from ubiquitous pathogens. According to the co-evolutionary models, variability in immune traits of hosts is the key component providing ability to adapt and enhance their defence mechanisms in presence of constant selective pathogen pressure. Domestic chicken (Gallus gallus f. domestica) is used as a model organism in avian biology and also is one of the most important food-producing animals, not only for their meat but also for the egg production. Unfortunately, in research usually only inbred chicken lines are used and modern poultry husbandry is tight with unilateral breeding towards highly productive breeds. Those approaches decrease intra-population polymorphism in chickens. However, especially in case of farm animals, searching and extending the pool of immune variability and enhancing pathogen resistance is crucial for sustaining healthy and biologically secure populations and their products. Morphologically highly distinct traditional chicken breeds, which have evolved for hundreds years under different selective pressures, may represent this desirable immunological variability. In my thesis I described variability in chosen immunological traits, haematological parameters and proteomic...

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.