Thèses sur le sujet « Gene PARL »
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Semir, Frappart David de. « Reparación de mutaciones en el gent CFTR como estrategia de terapia génica para la fibrosis quística ». Doctoral thesis, Universitat Pompeu Fabra, 2005. http://hdl.handle.net/10803/7084.
Texte intégralDASILIO, A. « Utilidade filogenética de genes nucleares em comparação com gene mitocondrial para Phyllostomidae (Chiroptera) ». Universidade Federal do Espírito Santo, 2016. http://repositorio.ufes.br/handle/10/3861.
Texte intégralPhyllostomidae, da subordem Microchiroptera, é uma família com uma grande variedade morfológica e de hábitos alimentares, com mais gêneros do que qualquer outra família de morcegos. Porém um grande desafio tem sido a resolução de suas relações filogenéticas principalmente devido ao paralelismo evolutivo e convergência entre linhagens. Várias tentativas foram feitas para resgatar as relações dentro dessa família, a fim de reconstruir suas transições evolutivas e identificar as relações entre gêneros, desde estudos morfológicos a moleculares. Entretanto, estas pesquisas em sua maioria, tem usado principalmente o DNA mitocondrial, com pouco sucesso com marcadores nucleares. Estudos apresentando incongruências entre filogenias têm se expandido rapidamente, derivadas, principalmente, de dados morfológicos em face de análises moleculares, ou até mesmo entre as árvores baseadas em diferentes subconjuntos de seqüências moleculares. Diante deste cenário, este trabalho teve como objetivo fazer uma investigação filogenética de cinco genes (um mitocondrial e quatro nucleares) a fim de identificar marcadores nucleares que apresentassem os melhores resultados para Phyllostomidae. Isso ainda não havia sido reportado na literatura para filostomideos. Os genes selecionados para o estudo foram: dois éxons de genes nucleares recombination activating protein 2 (RAG2) e o gene for von Willebrand factor (VWF), dois íntrons Beta-Fibrinogênio (Fgb) e o B-spectrin non-erythrocytic 1 (SPTBN1), e um gene mitocondrial cytochrome oxidase subunit 1 (COI). A metodologia de obtenção das sequências nucleotídicas consistiu em extração do DNA total da célula, amplificação da região controle do DNA mitocondrial através da Reação em Cadeia da Polimerase, purificação do produto da PCR e sequenciamento. Sequências disponíveis no GenBank também foram utilizadas. Dentre os marcadores nucleares estudados os resultados das análises indicaram que o Beta-Fibrinogênio é o marcador nuclear mais promissor, estimulando futuros trabalhos moleculares com os morcegos filostomídeos utilizando esse gene. Palavras-chaves: Phyllostomidae, investigação filogenética, marcadores nucleares, DNA mitocondrial.
Wagner, Priscilla Koch. « Uma nova abordagem para identificação da provável origem de genes exclusivos de bactérias ». Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/100/100131/tde-24052018-175017/.
Texte intégralComparison of genomes, genes or even non-coding nucleotide sequences is an important task in which bioinformatics can be applied, since it allows the application of phylogenetic analyses. Phylogenetic analysis, in its turn, seeks to analyze the evolutionary relation of each species, considering its genetic characteristics. These processes and the techniques that implement them are based on nucleotide sequences sequenced and stores in databases of public genomes. With phylogenetic analysis it is also possible to identify possible origins of a gene. This task has a great importance, because it allows the identification of the origin of pathogenic genes, which may help to combat or prevent deseases. A potencial problem of these sequences is the possibility of having annotation errors (sequences marking as genes). These errors are little explored by researchers nowadays. Another unexplored topic is the phylogenetic analysis of exclusive genes, which are genes thaht manifest in only one species, considering a group of nearby species. The identification of exclusive genes of a species may serve to correctly identify, for example, a desease, in order to allow the use of a more especific and appropriate treatment. The importance of discovering phylogenies of exclusive genes and the difficulty of guaranteeing the consistency of genetic annotations motivated this work, whose objective was to implement tools to interpret data of genetic comparison, identifying annotation errors in exclusive genes and creating strategies to identify the origin of these genes.The origins of exclusive genes explored in this work involve the possibility of the exclusive genes have derived of other gene families of the organism itself, or, the exclusive genes differed a lot from the ancestral genes. Theses hypotheses, with the hypotesis of the existance of annotation errors, were explored in experiments using the developed tools. The experiments aimed to analyse the applicability of the developed strategy. Genomes of bacteria of the genus Xanthomonas were used, which contains a large group of bacteria that cause diseases in plants. The results show that there is a considerable amount of annotation errors on the genomes, proving the hypothesis that the inconsistency in genomic annotations has a great influence on the difficulty in identifying phylogenies (both exclusive and non-exclusive genes). The results also show that much of exclusive genes possibly originated from other gene families of the genome itself. Furthermore, these genes may have sufferedmodifications in relation to the ancestral genes, but still have certain similarities with nucleotide sequences that don\'t encode genes in other more distant species. Finally, the strategy developed proved useful on phylogenetic analysis of the studied bacteria, which is a strong indication that the same approach can be used for similar problems with other species of living beings
Melo, Vinicius André Morais Rocha. « Construção de ferramentas para estudo da possível interação entre interferon-beta e p53 ». Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-17082009-121304/.
Texte intégralFormation of tumors it must to combinations of factors. The p53 pathway has an essential role in proliferation control and apoptosis. The interferon-beta (IFNb) is important in modulation of the immunologic response, in the antitumoral effect and in the apoptotic impact in tumor cells. According to literature, IFNb activate the p53 transcription and components of IFN system effect its function to p53/p14arf pathway. In this project, a series of tools was constructed to explore interactions between p53 and IFNb. The first tool, a cellular lineage derivative of B16 with expression of p53 reduced by miRNA. We also construct plasmidial and adenoviral vectors carriers of cDNAs for eGFP, Luciferase, p53 or IFNb. The vectors are used to introduce these factors, alone or agreed, in the target cell. Even confirming the activity of p53 or IFNb alone, an additive effect of these factors combined was not observed with this type of assay. Future studies of the possible interactions between p53 and IFNb pathways will have the benefit of the tools constructed in this project.
Fernandes, Jussara Gonçalves. « Análise comparativa dos processos inflamatórios agudo e crônico no tecido subcutâneo e exsudato em camundongos selecionados para máxima ou mínima inflamação ». Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/42/42133/tde-30012013-092920/.
Texte intégralAIRmax and AIRmin mouse lines differ in terms of acute inflammatory response after Biogel injection. The distinct AIR in these lines is well established, however, differences in late or chronic inflammatory response to Biogel were not described yet. Thus, we decided to check if the genetic selection that modified the acute inflammatory response in these lines, also affected the development of a chronic inflammatory response. We found that AIRmax mice had higher cellular influx in the inflammatory exudate than AIRmin mice in both analyzed periods (48h and 30d) and that after 48 hours of Biogel injection, AIRmax mice showed higher cytokine levels in inflammatory exudates. This line also showed higher number of up regulated genes in AIRmax than in AIRmin mice involved with inflammatory response, immune response and signal transduction. Some acute inflammatory response genes also showed differences on day 30. Our results indicate that the genetic selection for acute inflammatory response may also have affected the chronic inflammatory response to Biogel.
Jaskowiak, Pablo Andretta. « Estudo de coeficientes de correlação para medidas de proximidade em dados de expressão gênica ». Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-05052011-143134/.
Texte intégralThe development of microarray technology made possible the expression level measurement of hundreds or even thousands of genes simultaneously for various experimental conditions. The huge amount of available data generated the need for computational methods that allow its analysis in an effcient and automated way. In many of the computational methods employed during gene expression data analysis the choice of a proximity measure is necessary. Among the proximity measures available, correlation coefficients have been widely employed because of their ability to capture similarity trends among the compared numeric sequences (genes or samples). The present work has as objective to compare different correlation measures for the three major tasks involved in the analysis of gene expression data: clustering, feature selection and classification. To this extent, in this dissertation an overview of gene expression data analysis and the different correlation measures considered for this comparison are presented. In the present work are also presented empirical results obtained from the comparison of correlation coefficients for gene clustering, sample clustering, gene selection for sample classification and sample classification
Araujo, Tânia Kawasaki de 1985. « Utilização da técnica de Open Array para investigação de genes associados a fendas labiopalatais em amostra da população brasileira ». [s.n.], 2015. http://repositorio.unicamp.br/jspui/handle/REPOSIP/313118.
Texte intégralTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas
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Resumo: A fenda de labiopalatal (FLP) isolada é o defeito craniofacial mais comum em humanos. O objetivo deste estudo foi avaliar associações entre 39 genes e a etiologia de FLP isolada em uma amostra da população brasileira. Este estudo de associação do tipo caso-controle foi desenhado com um poder estatístico de 81,29% por meio de regressão logística. O grupo de casos foi composto por 182 pacientes com FLP isolada registrados na Base Brasileira de Dados Clínicos e Familiais de Fendas Orofaciais Típicas. O grupo controle foi formado por 355 indivíduos saudáveis, sem história de fendas orais em três gerações. Toda a amostra foi genotipada por meio do sistema OpenArray®TaqManTM para 253 polimorfismos de nucleotídeo único (SNPs) em 39 genes, incluindo dois genes que, recentemente, haviam sido descritos por este grupo de pesquisa. A seleção de SNPs foi feita com o programa SNPbrowser 4.0 (Applied Biosystems) para verificar o número e a localização dos SNPs apropriados para explorar a associação de cada gene com FLP isolada. A análise de associação foi realizada por meio de regressão logística e regressão stepwise. Os resultados foram corrigidos para múltiplos testes (correção de Bonferroni). Vinte e quatro SNPs em 16 genes foram significativamente associados com a etiologia da FLP isolada, incluindo MSX1, SPRY1, MSX2, PRSS35, TFAP2A, SHH, VAX1, TBX10, WNT11, PAX9, BMP4, JAG2, AXIN2, DVL2, KIF7 e TCBE3. A análise de regressão stepwise revelou que 11 genes contribuiram em 15,5% do fenótipo de FLP isolada nessa amostra. Este é o primeiro estudo a associar os genes KIF7 e TCEB3 à FLP isolada
Abstract: Nonsyndromic cleft lip and palate (NSCLP) is the most common craniofacial birth defect. The aim of this study was to evaluate associations between 39 genes and the etiology of NSCLP in a Brazilian population. This case-control association study was designed with 81.29% statistical power according to logistic regression. The case group was composed of 182 patients with NSCLP enrolled in the Brazilian Database on Orofacial Clefts. The controls included 355 healthy individuals with no history of oral clefting in the past three generations. All samples were genotyped by TaqMan®OpenArrayTM system for 253 single nucleotide polymorphisms (SNPs) in 39 genes, including two that had recently been associated with this process. The SNPs selection was made by SNPbrowser 4.0 (Applied Biosystems) in order to establish the best SNPs to explor the association between each gene and NSCLP. The association analysis was performed using logistic regression and stepwise regression. The results were corrected for multiple testing (Bonferroni correction). Twenty-four SNPs in 16 genes were significantly associated with the etiology of NSCLP, including MSX1, SPRY1, MSX2, PRSS35, TFAP2A, SHH, VAX1, TBX10, WNT11, PAX9, BMP4, JAG2, AXIN2, DVL2, KIF7 and TCBE3. Stepwise regression analysis revealed that 11 genes contributed to 15.5% of the phenotype of NSCLP in the sample. This is the first study to associate KIF7 and TCEB3 with NSCLP
Doutorado
Ciencias Biomedicas
Doutora em Ciências Médicas
Pereira, Joana Filipa de Sousa. « Estudo do gene FOXE1 e identificação de novos genes de susceptibilidade para o cancro da tiróide familiar ». Master's thesis, Faculdade de Ciências e Tecnologia, 2012. http://hdl.handle.net/10362/9925.
Texte intégralAs formas familiares de carcinomas não-medulares da tiróide (FNMTC) representam 5% das neoplasias da tiróide. Foram já mapeados 8 loci de susceptibilidade para o FNMTC, no entanto, até à data, apenas o gene DICER1 foi identificado. O envolvimento de diferentes loci sugere a existência de heterogeneidade genética para o FNMTC, contudo, a sua base molecular, é essencialmente desconhecida. Os factores de transcrição NKX2-1, FOXE1, PAX8 e HHEX estão envolvidos na morfogénese e diferenciação da tiróide. Estudos recentes levaram à identificação de mutações germinais no gene NKX2-1 em famílas com FNMTC. No entanto, continua por esclarecer o papel destes factores de transcrição na etiologia do FNMTC. A nova tecnologia de sequenciação global do exoma (WES) tem facilitado a identificação de genes de susceptibilidade para diferentes doenças hereditárias. Este projecto teve como objectivos o estudo do papel do gene FOXE1 em FNMTC e a identificação de novos genes de susceptibilidade para esta doença, utilizando a WES. Desenvolveram-se estudos funcionais para a variante p.A248G do gene FOXE1, identificada numa família com FNMTC, usando como modelos células de tiróide normal (PCCL3) e uma linha celular de carcinoma papilar da tiróide (TPC-1). Nestes ensaios, observou-se que a variante p.A248G promovia a proliferação e migração celular, sugerindo que esta variante poderá contribuir para a tumorigénese na tiróide. Por WES, identificou-se uma nova variante (p.T22I) no gene C8orf48. Esta variante segregava com a doença na família. O gene C8orf48 interage com proteínas da via de sinalização WNT. Em estudos preliminares de expressão génica, identificaram-se alguns genes-alvo desta via (CCND1 e MYC) que apresentavam sobre-expressão no tumor da tiróide relativamente à tiróide normal no probando. Estudos funcionais poderão esclarecer o papel desta variante na tumorigénese. Neste trabalho, foram identificadas variantes genéticas, potencialmente patogénicas nos genes FOXE1 e C8orf48, que constituem a primeira evidência do seu envolvimento em FNMTC.
Carvalho, Anna Carolina Pereira Vieira de. « Construção e caracterização de um vírus Adeno-associado com expressão direcionada para células em divisão ». Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-18062010-125910/.
Texte intégralThe utilization of recombinant adeno-associated virus (AAVr) as a gene transfer vector in tumor cells is increasing. In this work, the promoter of the E2F-1 gene, active during cell division, was inserted in an AAVr vector and used to drive the expression of HSV-tk or luciferase and, simultaneously, eGFP with the intent of limiting viral expression to proliferating cells. Also, vectors with the constitutive CMV promoter were constructed to be used as controls. The E2F-1 promoter was not efficient in driving the expression of the transgenes in the HT1080 cell line, while the CMV promoter shows high level expression of the reporter and the therapeutic genes. The low efficiency of E2F promoter has not yet been explored, though this problem could be related to the intrinsic performance of this promoter, the biology of the vector AAV and cell-specific factors. However, the performance of the AAVr containing the CMV promoter creates the possibility of performing new gene transfer protocols for the treatment and visualization of tumor cells.
Leal, Dora Yovana Barrios. « História Demográfica e Estrutura de Populações para a Espécie Cactófila Drosophila meridionalis ». Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-12062013-150608/.
Texte intégralDrosophila meridionalis is an endemic species of South America, being widely distributed in the Atlantic Coast of Brazil. Aiming to develop a phylogeographic hypothesis for this species, sequences of mitochondrial COI and nuclear period genes were obtained. The diversity indexes, AMOVA, neutrality tests, Mismatch Distribution, Bayesan Skyline Plot and NCPA were calculated. We obtained three networks for the COI gene, denominated A (inland populations), B (south coast populations) and C (eastern and southeastern coast populations) and a single network obtained for the period gene, this network divides the population into two groups, being the first congruent with the network A of the COI gene and the second comprising the networks B and C of the COI gene. The AMOVA results, showed a high and significant structuring among inland and coastal populations, for both genes (ct=0,72 COI gene; ct=0,70 period gene), that can be explained by the presence of geographical barriers, such as Serra do Mar. Population expansion events and restricted gene flow with isolation by distance events were detected in coastal and inland populations respectively. The expansion of the area of occurrence of D. meridionalis probably was initiated with the populations of the coast of Rio Grande do Sul, towards the coast of Santa Catarina with subsequent long-distance colonization of the states of São Paulo, Rio de Janeiro and Bahia. Asynchronic migrations of individuals from coastal populations of São Paulo and Santa Catarina probably colonized the inland of São Paulo, and from these populations, a population expansion towards the south through the inland was initiated, colonizing the states of Paraná and Rio Grande do Sul. The bayesian analysis (MCCT) indicated that the time of the most recent common ancestor (TMRCA) for all haplotypes of D. meridionalis is from 81,700 years ago, a date that marks the separation of inland and coastal populations approximately at the end of the Pleistocene. Similar events have been suggested to explain the geographic distribution of species of the cluster D. buzzatii, occurring in sympatry largely with populations of D. meridionalis. This species, as the cluster D. buzzatii species, presented indicatives of demographic fluctuations, which can be associated with the expansion and contraction of the distribution of xerophytic vegetation, during the paleoclimatic fluctuations of the Pleistocene.
Kashiwabara, Andre Yoshiaki. « MYOP : um arcabouço para predição de genes ab initio\" ». Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/45/45134/tde-25112009-151237/.
Texte intégralThe demand for efficient approaches for the gene structure prediction has motivated the implementation of different programs. In this work, we have analyzed successful programs that apply the probabilistic approach. We have observed similarities between different implementations, the same mathematical framework called generalized hidden Markov chain (GHMM) is applied. One problem with these implementations is that they maintain fixed GHMM architectures that are hard-coded. Due to this problem and similarities between the programs, we have implemented the MYOP framework (Make Your Own Predictor) with the objective of providing a flexible environment that allows the rapid evaluation of each gene model. We have demonstrated the utility of this tool through the implementation and evaluation of 96 gene models in which each model has a set of states and each state has a duration distribution and a probabilistic model. We have shown that a sophisticated probabilisticmodel is not sufficient to obtain better predictor, showing the experimentation relevance and the importance of a system as MYOP.
Silva, Luiz Guilherme Soares da. « Modelo binário para expressão gênica em um embrião de Drosophila melanogaster ». Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/100/100132/tde-05092017-163540/.
Texte intégralThis dissertation analyzes the results of several transcription simulations using the binary model of externally regulated gene expression. The number of mRNA molecules and the state of the gene were considered as stochastic variables. In this model the gene may be in the active state (ON) or repressed state (OFF) and the change of gene state occurs at determined rates in each simulation for activation and for repression. The number of mRNA molecules is changed by the transcription of new molecules and by the degradation of existing molecules at determined rates. These simulations used the Gillespie algorithm for exact stochastic simulation of coupled chemical reactions was used
Saraiva, Katia Daniella da Cruz. « CaracterizaÃÃo, anÃlise filogenÃtica e perfil de expressÃo da famÃlia multigÃnica do fator de elongaÃÃo 1 alfa (EF1α) de soja [Glycine max (L.) MERR.] : detecÃÃo de genes normalizadores para qPCR ». Universidade Federal do CearÃ, 2013. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=11113.
Texte intégralO fator de elongaÃÃo 1alfa (EF1α) à responsÃvel pela ligaÃÃo do aminoacil-tRNA ao sÃtio A do ribossomo, atuando, assim, na fase de alongamento da sÃntese proteica. O EF1α em plantas à codificado por uma famÃlia multigÃnica com nÃmero de genes variÃvel entre espÃcies. O objetivo do presente trabalho foi caracterizar, analisar filogeneticamente e elucidar o perfil de expressÃo dos genes EF1α em soja durante o desenvolvimento, bem como selecionar o(s) gene(s) de referÃncia mais estÃveis para ensaios de qRT-PCR no desenvolvimento e condiÃÃes de estresse. AnÃlises in silico nos genomas de soja e de outras leguminosas disponÃveis em bancos de dados revelaram famÃlias gÃnicas de 3 a 6 membros com estrutura conservada de 2 Ãxons e 2 Ãntrons. Dentre as espÃcies analisadas (Glycine max, Cajanus cajan, Vigna unguiculata, Medicago truncatula e Phaseolus vulgaris) G. max foi a que apresentou o maior nÃmero de genes, classificados como EF1α 1a; 1b; 1c; 2a; 2b e 3 apÃs anÃlise filogenÃtica. A expressÃo dos genes EF1α foi estudada em diferentes tecidos (flores, vagens, sementes, cotilÃdones, folhas unifolioladas e trifolioladas, raÃzes, hipocÃtilos e epicÃtilos) durante o desenvolvimento da soja. A anÃlise de expressÃo por qPCR revelou que os genes EF1α sÃo funcionais, sendo expressos em todos os tecidos, contudo apresentam expressÃo diferencial dependente do tecido e do estÃdio de desenvolvimento. A expressÃo relativa entre os genes membros mostrou predomÃnio de expressÃo para 5 dos 6 genes analisados: EF1α 1a: sem predomÃnio de expressÃo; EF1α 1b: GerminaÃÃo e desenvolvimento do hipocÃtilo; EF1α 1c: Desenvolvimento da vagem; EF1α 2a: Desenvolvimento da vagem, folhas unifoliolada e trifoliolada; EF1α 2b: Desenvolvimento da vagem, folhas unifolioladas; EF1α 3: GerminaÃÃo, flores, raÃzes, fases iniciais do desenvolvimento do hipocÃtilo e epicÃtilo. Esses dados, juntamente com os de folhas e de raÃzes submetidas a condiÃÃes de estresse (PEG e AS) foram usados para avaliar a estabilidade de expressÃo dos diferentes genes EF1α de soja atravÃs dos programas GeNorm e NormFinder. Para as anÃlises durante o desenvolvimento, quatro genes de expressÃo estÃvel (UKN1, SKIP16, EF1β e MTP) foram tambÃm utilizados. Os genes EF1α foram mais estÃveis em cotilÃdones (EF1α 3 e EF1α 1c); epicÃtilos (EF1α 1b, EF1α 2b e EF1α 1a); hipocÃtilos (EF1α 1a e EF1β); vagens (EF1α 2a e EF1α 2b) e raÃzes (EF1α 2a e UKN1) e menos estÃveis em folhas trifolioladas/unifolioladas (UKN1 e SKIP16) e sementes em germinaÃÃo (EF1β e SKIP16). Em folhas sob condiÃÃes de estresse, anÃlises atravÃs do GeNorm revelaram que quatro genes (EF1α 2a >1b >2b >1a) apresentaram classificaÃÃo de estabilidade semelhante nos estresses por AS e PEG. Jà em raÃzes, distinto padrÃo de estabilidade foi encontrado: EF1α 2a > 1c >2b >1b > 1a >3 para PEG e EF1α 1c > 3 > 2a > 1a > 2b > 1b para AS. Tais resultados foram confirmados usando o programa NormFinder. A despeito das variaÃÃes de expressÃo gÃnica em diferentes tecidos em desenvolvimento e condiÃÃes de estresse, foram determinados genes EF1α que podem ser usados para normalizar ensaios de PCR em tempo real em soja e leguminosas (tribo Phaseoleae) vez que genes EF1α ortÃlogos foram identificados entre essas diferentes espÃcies.
The elongation factor 1alpha (EF1α) is responsible for binding of aminoacyl-tRNA to the A site of the ribosome, acting thus the elongation phase of protein synthesis. The EF1α in plants is encoded by a multigene family with variable number of genes among species. The aim of this study was to characterize, analyze phylogenetic and elucidate the expression profile of EF1α genes in soybean during development, as well as select (s) gene (s) of the most stable reference for qRT-PCR assays in the development and conditions stress. In silico analyses in the genomes of soybean and other leguminous plants available in databases revealed gene families 3-6 members with conserved structure of 2 exons and 2 introns. Among the analyzed species (Glycine max, Cajanus cajan, Vigna unguiculata, Phaseolus vulgaris and Medicago truncatula) G. max was the one with the largest number of genes classified as EF1α 1a, 1b, 1c, 2a, 2b and 3 after phylogenetic analysis. The EF1α gene expression was studied in different tissues (flowers, pods, seeds, cotyledons, trifoliate and unifolioladas leaves, roots, hypocotyls and epicotyls) during the development of soybean. Expression analyses by qPCR revealed that the EF1α genes are functional and expressed in all tissues, however exhibit differential expression dependent on the tissue and developmental stage. Relative expression between genes members showed predominance of expression for 5 of the 6 genes analyzed: EF1α 1a: no predominance of expression; EF1α 1b: Germination and development hypocotyl; EF1α 1c: pods development; EF1α 2a: pods development, unifoliate and trifoliate leaves; EF1α 2b: pods development, unifoliate leaves; EF1α 3: Germination, flowers, roots, early stages development (hypocotyl and epicotyl). These data, together with the leaves and roots subjected to stress conditions (PEG and AS) were used to assess the stability of expression of different EF1α genes soybean through the programs GeNorm and NormFinder. For the analyses during development, four stable genes (UKN1, SKIP16, EF1β and MTP) were also used. EF1α genes were more stable in cotyledons (EF1α 3 and EF1α 1c); epicotyls (EF1α 1b, 2b and 1a), hypocotyls (EF1α 1a, EF1β and EF1α 1c); pods (EF1α 2a and EF1α 2b) and roots (EF1α 2b and UKN1) and less stable in trifoliate/unifoliolate leaves (UKN1 and SKIP16) and germinating seeds (EF1β and SKIP16). In leaves under stress conditions, through GeNorm analyses revealed that four genes (EF1α 2a> 1b> 2b> 1a) showed similar stability in the classification of stress for AS and PEG. Already in roots, distinct pattern of stability was found: EF1α 2a> 1c> 2b> 1b> 1a> 3 for PEG and EF1α 1c> 3> 2a> 1a> 2b> 1b to AS. These results were confirmed using the program NormFinder. In spite of changes in gene expression in different tissues in development and stress conditions were determined EF1α genes that can be used to normalize the qPCR assays in soybean and others leguminous plants (Phaseoleae tribe) seeing that EF1α genes orthologous were identified between these different species.
Junior, Antonio Paulo Galdeano Damiance. « Desenvolvimento de modelos dinâmicos para a formação de clusters aplicados em dados biológicos ». Universidade de São Paulo, 2006. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-23012007-103117/.
Texte intégralWith the advent of microarray technology, a large amount of gene expression data is now available. Clustering is the computational technique usually employed to analyze and explore the data produced by microarrays. Due to the variety of information that can be extracted from the expression data, many clustering techniques with different approaches are needed. In the work proposed by (Zhao et. al. 2003a), the dynamical model for data clustering has several interesting features to the clustering task: the number of clusters does not need to be known, the multi-scale property, high parallelism, and it is flexible to use more complex rules while clustering the data. However, two desirable features for clustering techniques are not present: the ability to detect different clusters sizes and shapes, and a hierarchical representation of the clusters. This project presents three techniques, overcoming the restrictions of the dynamical model proposed by (Zhao et. al. 2003a). The first technique, called Model1, is more effective than the original model and was obtained simplifying it. The second technique, called Model2, is capable of detecting different clusters sizes and shapes. The third technique consists in a hierarchical algorithm that uses Model1 as a building block. The techniques here developed were used with biological data. Microarray image segmentation was performed and the St. Jude Leukemia gene expression data was analyzed and explored.
Jones, Matthew Leslie. « The subnuclear localisation of Notch responsive genes ». Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274909.
Texte intégralPitroski, Carlos Eduardo Ferreira. « Análise do gene mutyh em indivíduos em risco para síndrome da polipose associa ao gene mutyh ». reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2010. http://hdl.handle.net/10183/28342.
Texte intégralAraújo, Ana Paula Gonçalves de. « Polimorfismos no gene EGF : susceptibilidade para cancro na mulher ». Master's thesis, Universidade de Aveiro, 2008. http://hdl.handle.net/10773/827.
Texte intégralIntrodução: Os factores de crescimento desempenham um papel fundamental na regulação da proliferação celular, e o seu descontrolo é uma característica do desenvolvimento maligno. O gene EGF codifica um factor de crescimento que se liga ao receptor EGFR envolvido na activação das vias que promovem a proliferação, sobrevivência, migração e diferenciação celular, através da estimulação de uma cascata de cinases. Estudos recentes propõem que a variabilidade genética, como os SNPs, poderá desempenhar um papel significativo na predisposição para cancro. Objectivos: Neste estudo avaliou-se a correlação do polimorfismo do gene EGF, na posição 61 (A/G), e a susceptibilidade para cancro do ovário, mama e colo do útero. Material e Métodos: Para tal, procedeu-se à análise por PCR-RFLP, de 1442 amostras de DNA, 175 de indivíduos com carcinoma do ovário, 383 com caricinoma da mama, 384 com lesões cervicais e 500 mulheres sem doença oncológica. Resultados: Concluiu-se, neste estudo, que os indivíduos portadores do alelo G e com carcinoma do ovário tem menor risco de desenvolver esta neoplasia (OR=0,72; 95%CI: 0,55-0,94; p=0,012). Esta protecção também ocorre em mulheres com idade inferior a 53 anos (OR=0,63; 95%CI: 0,43-0,91; p=0,009), assim como para doença avançada (OR=0,63; 95%CI: 0,45-0,89; p=0,006). No tempo de aparecimento de doença, os portadores do genótipo GG apresentam este cancro mais tarde que os portadores do alelo AA (p=0.035). O mesmo efeito é observado no cancro da mama, observa-se menos risco para desenvolver a doença (OR=0,82; 95%CI: 0,08-1,00; p=0,012), assim como os portadores GG desenvolvem a doença mais tarde (p=0,041). As mulheres mais jovens, com cancro cervical em doença avançada e portadoras de G têm maior risco de desenvolver esta neoplasia (OR=3,17; 95%CI: 1,21-8,26; p=0,016). Discussão: Com base nestes resultados, pode inferir-se que a presença do alelo G poderá estar associada a um efeito protector para desenvolvimento de cancro do ovário e da mama. Estes carcinomas apresentam um aumento significativo de expressão de EGFR, e a protecção poderá ser explicada pelo facto dos portadores do alelo G terem maior produção de EGF, e de este estar envolvido na internalização e degradação do seu receptor e consequentemente ocorrer menor expressão de EGFR à superfície da célula. No carcinoma cervical um aumento do factor de crescimento poderá aumentar a sinalização das vias activadas por EGF por parte dos portadores G. ABSTRACT: Introduction: Growth factors perform an essential role in the cellular proliferation regulation and its miss control is a characteristic of malignant development. The EGF gene codifies a growth factor that binds to the EGF receptor involved in the activation of ways that promote the proliferation, survival, migration and cellular differentiation, through the stimulation of a kinase cascade. Recent studies propose that the genetic variability, as the SNPs, may perform a significant role in the cancer predisposition. This study had the objective of appraising the correlation of EGF gene A61G polymorphism and the susceptibility of ovarian, breast and cervical cancer. Material and methods: In this manner we proceeded to the analysis of 1442 DNA sample by PCR-RFLP, 175 people with ovarian cancer, 383 with breast cancer, 384 with cervical lesions and 500 women without cancer. Results: We concluded that G carriers with ovarian cancer had less risk of developing this neoplasia (OR=0,72; 95%CI: 0,55-0,94; p=0,012). This protection also occurs in women with ages below 53 years (OR=0,63; 95%CI: 0,43-0,91; p=0,009), as well advanced disease (OR=0,63; 95%CI: 0,45-0,89; p=0,006). In the time to onset disease analysis, GG genotype subjects present this cancer later than AA carriers (p=0.035). The same effect is observed in breast cancer with less risk to develop this disease (OR=0,82; 95%CI: 0,08-1,00; p=0,012) and the GG carriers develop this disease later (p=0,041). The younger women G carriers with advanced cervical cancer have more risk to develop this disease (OR=3,17; 95%CI: 1,21-8,26; p=0,016). Discussion: With support in these results, we can deduce that the presence of G carrier may be associated with the protection effect of ovarian and breast cancer development. These cancers show a significative increase of EGFR expression and this protection can be explained by the fact that G carrier subjects have a higher production of EGF and this one is involved in the internalization and degradation of its receptor and consequently occurring less EGFR expression at the cell surface. In cervical cancer an increase of this growth factor may increase the pathways activated to EGF in G carriers.
Bandeira, Flavia Miranda Gomes de Constantino. « Triagem familiar ampliada para o gene da hemoglobina S ». reponame:Repositório Institucional da FIOCRUZ, 2006. https://www.arca.fiocruz.br/handle/icict/3893.
Texte intégralObjetivou-se determinar a prevalência de síndromes falciformes em familiares selecionados a partir de casos índice, com particular interesse em determinar o número de afetados adicionais detectados pelo modelo de triagem familiar ampliado. Utilizou-se um estudo de corte transversal de base populacional, realizado em familiares dos casos-índice identificados pela triagem neonatal no Recife, região metropolitana do Recife e em algumas cidades do interior do estado de Pernambuco. Foram estudados os membros familiares dos casos-índice recrutados a partir da listagem fornecida pelo Programa de Triagem Neonatal de Pernambuco alocados em núcleos definidos como: 1) núcleo reduzido (NR): constituído de pai, mãe e irmãos; 2) núcleo de primeiro grau (N1): constituído de avós, tios e primos de primeiro grau; 3) núcleo de segundo grau (N2): filhos dos primos de primeiro grau; 4) núcleo ampliado (NA): NR+N1+N2 e 5) núcleo ampliado de primeiro grau (NA1): NR+N1. Foram coletadas de agosto de 2004 a junho de 2005, informações e amostras de sangue periférico de 463 membros familiares pertencentes a 21 casos-índice. A mediana de idade foi de 22 anos onde 81,5 por cento desconheciam o que era anemia falciforme. Destes, 90,5 por cento eram do Recife e região metropolitana. O gene HBB*S esteve presente em 114 indivíduos. A freqüência deste gene foi maior no NR (69 por cento), mas também elevada no N1 (22,8 por cento). De fato, o NA1 resultou na detecção de 69 portadores adicionais (cerca de 172 por cento de casos adicionais). Também ocorreu um incremento de 73 por cento na média comparando o NR com o N1. Esses resultados indicam que um número relevante de indivíduos portadores do gene HBB*S seria detectado com a ampliação do NR através da inclusão do N1. Observou-se que 53,3 por cento da população estudada, estava na faixa considerada reprodutiva e 80 por cento das pessoas que carregavam o gene HBB*S já tinham gerado filhos. Os resultados permitem as seguintes recomendações: 1) A triagem para hemoglobinopatias deve permanecer de maneira universal no estado de Pernambuco. 2) A triagem familiar ampliada, para identificação de portadores de síndrome falciforme deve ser estendida para os familiares até o primeiro grau. 3) É recomendável que ações educativas sobre as síndromes falciformes ocorram de forma sistemática em Pernambuco. 4) É necessário o envolvimento dos atores do sistema de atenção básica à saúde no tocante a multiplicação do conhecimento sobre estas síndromes.
Rego, Fernanda Orpinelli Ramos do. « Modelagem computacional de famílias de proteínas microbianas relevantes para produção de bioenergia ». Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-28082015-222248/.
Texte intégralHidden Markov Models (HMMs) are essential tools for automated annotation of protein sequences. For many years now protein family resources based on HMMs have been made available to the scientific community (e.g. TIGRfams). Much effort has also been devoted to the automated generation of protein family HMMs (e.g Panther). However, manually curated protein family HMMs remain the gold standard for use in genome annotation. In this context, this work had as main objectives the generation of appoximately 80 protein families based on HMMs. We follow a standard protocol, that was generated in this work, to create the HMMs. At first, we start from a protein with experimentally proven function, associated to a publication and that was manually annotated with new terms from Gene Ontology provided by MENGO¹ (Microbial ENergy Gene Ontology). The next steps consists of (1) definition of selection criteria to capture members of the family; (2) search for members via BLAST; (3) generation of multiple alignment (MUSCLE 3.7) and the HMM (HMMER 3.0); (4) result analysis and iteration of the process, using the preliminary HMM; (5) cutoff definition to the final HMM; (6) individual validation of the models using tests against NCBIs NR database. The main deliverables of this work are 74 HMMs manually curated available in the site project (mengofams.lbi.iq.usp.br) that allows browsing and download of all HMMs curated so far, a standard protocol manual curation of protein families, a list with proteins that need to be reviewed.
Santos, Rafael Miyashiro Nunes dos. « Substituição gênica ortotópica de porco para humano baseada em CRISPR/Cas9 e recombinases para xenotransplante ». Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/5/5168/tde-14112017-153947/.
Texte intégralHumanized pig models are very important for biomedical research, and drugs and treatment development. Not only it is a better model for diseases than smaller animals because of its closer physiology, anatomy, metabolism and life span, it also may provide unlimited organs for transplantation. In spite of all this advantages, inconsistent gene expression in transgenic animals make its generation and evaluation expensive, unpredictable and do not allow proper outcome comparison between different animals. In this report we describe a reproducible technique utilizing the endogenous promoter for generation of a clonal pattern gene replacement protocol (clonal gene transplant) without cell cloning, maintaining the normal gene expression and its regulation. This protocol is reproducible and applicable to more than one gene target, allowing fast generation of transgenic animals cell lines (as low as 14-20 days) and could become the new standard for transgenic large animal generation
Bassan, Meire Menezes. « Genes de referência de Diaphorina citri para estudos de expressão gênica quantitativa e seu controle por RNAi em laranja doce ». Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/11/11136/tde-24082017-155635/.
Texte intégralHLB has been one of the main diseases responsible for the economic losses faced in the citriculture worldwide. This disease is associated to three species of colonization bacteria restricted to the phloem of the plants, which are transmitted by the psyllid Diaphorina citri. Since there are no curative methos for the disease, management is based on preventive methods including vector insect control. Gene silencing by RNA interference (RNAi) has been presented as a new biotechnological tool in pest control, since it provides a efficient and especific gene-specie control. However, this technology depends on analyzes of gene expression with suitable and stable reference genes. Thus, this work aimed to select and validate the stability of the expression of six potential reference genes of D. citri under different experimental conditions and to evaluate the biology of this insect on sweet orange transgenic plants expressing dsRNA of DcV-ATPase-A gene aiming their control. In order to do this, it was evaluated: 1) the stability of six candidate reference genes: elongation factor 1 alpha (EF 1-α), actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein L7 (RPL7), ribosomal protein L17 (RPL17) e alpha tubulin (TUB), through different mathematical algorithms: Delta Ct, NormFinder, BestKeeper and Genorm in five developmental stages and two hosts (Citrus sinensis and Murraya paniculata). The final rank was obtained through the RefFinder and validated by the V-ATPase-A gene; 2) the survival of adult psyllids fed on transgenic plants; the biology of D. citri in transgenic plants expressing dsRNA of the DcV-ATPase-A gene; and the relative expression of this gene. According to our results, two reference genes are recommended when different hosts and different developmental stages are considered. For gene expression analysis, regardless the insect developmental stage, when using M. paniculata as a breeding host, it is recommended to use GAPDH and RPL7 genes, whereas for C. sinensis GAPDH and EF 1-α are indicated. The bioassays demonstrated the insect\'s internalization of the dsRNA / siRNA molecules produced by the transgenic plants and the potential for reducing the target gene expression by RNAi. Despite the absence of lethal phenotype in adult psyllids fed to transgenic plants, significant changes in duration, survival and longevity were observed for D. citri when it developed its biological cycle in plants that express dsRNA of the DcVAPTase-A gene.
Souza, Glaucia Mendes. « Estudo dos mecanismos envolvidos no controle por cAMP da expressão do gene para uma molécula de adesão em Dictyostelium discoideum ». Universidade de São Paulo, 1993. http://www.teses.usp.br/teses/disponiveis/46/46131/tde-18042012-111926/.
Texte intégralThe initial goal of the present work was the study of gene expression regulated by cAMP in Dictyostelium discoideum development. For this, several cDNA clones, from a Iibrary constructed using mRNA of cells stimulated with cAMP, were analyzed. Analysis of one of this clones showed that it corresponded to gp80, a cell adhesion molecule expressed during cell aggregation in early development. gp80 gene regulation was then studied. Low concentrations of cAMP induces gp80 mRNA expression. The induction seems to be via the cell surface cAMP receptor and by a mechanism that does not involve changes in intracellular cAMP. Interestingly, high concentrations of cAMP, which down-regulate the cell surface cAMP receptor, elicit destabilization of gp80 mRNA in agregation competent cells. The mechanism by which high concentrations of cAMP selectively destabilize the gp80 mRNA was investigated. This treatment which leads to down-regulation of the cAMP receptor was found to also cause an increase in calcium uptake. Given this observation, we sought a role for calcium as a second messenger in the degradation of the gp80 mRNA. Changes in the mRNA leveis were examined after treating cells with compounds known to alter the intracellular Ca2+ concentrations. The sum of the data suggest that it is the cAMP-induced influx of Ca2+ across the plasma membrane, as apposed to a cAMP-mediated release of Ca2+ from intracellular stores, that initiates gp80 mRNA degradation. Also, cell incubation with staurosporin partially prevents the action of cAMP, implicating a possible role of protein kinase C. Regulation by cAMP of the message stability during vegetative growth was also studied in cells which constitutively express the gp8ü cDNA. The results indicate that like aggregation competent cells, these cells are able to evoque destabilization of the mRNA in response to a raise in intracellular calcium concentration. However, they are unable to induce the mRNA degradation after cAMP treatment.
Edson, de Albuquerque Filho José. « JNOM : uma ferramenta para encontrar motifs ». Universidade Federal de Pernambuco, 2005. https://repositorio.ufpe.br/handle/123456789/2801.
Texte intégralA regulação gênica está intimamente ligada com a transcrição de proteínas, e esse mecanismo é muito importante para o desenvolvimento dos seres vivos, pois é através dele que os organismos conseguem sintetizar proteínas. Um interessante problema da biologia moderna é o entendimento de mecanismos da regulação da transcrição. Muitos aspectos dessa regulação envolvem fatores de transcrição (proteínas ligantes ao DNA). Esses fatores regulam a expressão gênica pela conexão em posições específicas de regiões do genoma (conjunto de genes de uma espécie) que podem estar próximas ou não, como veremos em maiores detalhes oportunamente. Os fatores de transcrição conectam-se a subseqüências especificas de DNA, os promotores, que podem, com dificuldade, ser determinados por análises biológicas. Esse alto grau de dificuldade motiva os cientistas a procurarem meios computacionais mais rápidos e eficientes para solucionar o problema da busca pelos sítios de ligação dos promotores. O crescente aumento da disponibilidade de seqüências completas de genoma motiva tentativas de entender e modelar o mecanismo regulatório através de análises computacionais. A identificação de sítios de ligação envolve duas etapas principais: aprender modelos de sítios de ligação e buscar sítios em novas seqüências. Parte do trabalho foi desenvolver uma ferramenta para auxiliar os cientistas na busca por essas regiões especiais, os motifs, no genoma. Como desenvolvemos essa ferramenta usando Java, combinamos o fonema inglês da letra "J" com o sufixo "nom" da palavra "genom" para compor o nome da ferramenta e a chamamos de Jnom. A primeira tarefa é aprender modelos de sítios de ligação em potencial em um dado genoma. Usam-se exemplos de sítios de ligação verificados biologicamente e tenta-se encontrar sítios similares em outras regiões promotoras. Em seguida, é necessário descobrir uma seqüência de motifs em uma coleção de longas seqüências que são supostamente ligadas pelo mesmo fator. Neste caso, um motif encontrado indica um possível fator desconhecido que regula o conjunto de genes. A natureza combinatória dos fatores de transcrição é o mecanismo pelo qual as células dos seres superiores (eucariotes) atuam para controlar a expressão de conjuntos inteiros de genes. A intenção deste trabalho é investigar essa natureza combinante e tentar utilizar esse fato para melhorar o desempenho em relação a ferramentas existentes. O principal objetivo dessa pesquisa é construir uma ferramenta capaz de considerar a ação combinada dos fatores de transcrição através da seqüência de genes para encontrar novos motifs a partir de alguns já conhecidos
Sequeira, Ana Filipa Pereira. « Development of a novel platform for high-throughput gene design and artificial gene synthesis to produce large libraries of recombinant venom peptides for drug discovery ». Doctoral thesis, Universidade de Lisboa, Faculdade de Medicina Veterinária, 2016. http://hdl.handle.net/10400.5/12265.
Texte intégralAnimal venoms are complex mixtures of biologically active molecules that, while presenting low immunogenicity, target with high selectivity and efficacy a variety of membrane receptors. It is believed that animal venoms comprise a natural library of more than 40 million different natural compounds that have been continuously fine-tuned during the evolutionary process to disturb cellular function. Within animal venoms, reticulated peptides are the most attractive class of molecules for drug discovery. However, the use of animal venoms to develop novel pharmacological compounds is still hampered by difficulties in obtaining these low molecular mass cysteine-rich polypeptides in sufficient amounts. Here, a high-throughput gene synthesis platform was developed to produce synthetic genes encoding venom peptides. The final goal of this project is the production of large libraries of recombinant venom peptides that can be screened for drug discovery. A robust and efficient Polymerase Chain Reaction (PCR) methodology was refined to assemble overlapping oligonucleotides into small artificial genes (< 500 bp) with high-fidelity. In addition, two bioinformatics tools were constructed to design multiple optimized genes (ATGenium) and overlapping oligonucleotides (NZYOligo designer), in order to allow automation of the high-throughput gene synthesis platform. The platform can assemble 96 synthetic genes encoding venom peptides simultaneously, with an error rate of 1.1 mutations per kb. To decrease the error rate associated with artificial gene synthesis, an error removal step using phage T7 endonuclease I was designed and integrated into the gene synthesis methodology. T7 endonuclease I was shown to be highly effective to specifically recognize and cleave DNA mismatches allowing a dramatically reduction of error frequency in large synthetic genes, from 3.45 to 0.43 errors per kb. Combining the knowledge acquired in the initial stages of the work, a comprehensive study was performed to investigate the influence of gene design, presence of fusion tags, cellular localization of expression, and usage of Tobacco Etch Virus (TEV) protease for tag removal, on the recombinant expression of disulfide-rich venom peptides in Escherichia coli. Codon usage dramatically affected the levels of recombinant expression in E. coli. In addition, a significant pressure in the usage of the two cysteine codons suggests that both need to be present at equivalent levels in genes designed de novo to ensure high levels of expression. This study also revealed that DsbC was the best fusion tag for recombinant expression of disulfide-rich peptides, in particular when expression of the fusion peptide was directed to the bacterial periplasm. TEV protease was highly effective for efficient tag removal and its recognition sites can tolerate all residues at its C-terminal, with exception of proline, confirming that no extra residues need to be incorporated at the N-terminus of recombinant venom peptides. This study revealed that E. coli is a convenient heterologous host for the expression of soluble and potentially functional venom peptides. Thus, this novel high-throughput gene synthesis platform was used to produce ~5,000 synthetic genes with a low error rate. This genetic library supported the production of the largest library of recombinant venom peptides constructed until now. The library contains 2736 animal venom peptides and it is presently being screened for the discovery of novel drug leads related to different diseases.
RESUMO - Desenvolvimento de uma nova plataforma de alta capacidade para desenhar e sintetizar genes artificiais, para a produção de péptidos venómicos recombinantes - Os venenos animais são misturas complexas de moléculas biologicamente activas que se ligam com elevada selectividade e eficácia a uma grande variedade de receptores de membrana. Embora apresentem baixa imunogenicidade, os venenos podem afectar a função celular actuando ao nível dos seus receptores. Actualmente, pensa-se que os venenos de animais constituam uma biblioteca natural de mais de 40 milhões de moléculas diferentes que têm sido continuamente aperfeiçoadas ao longo do processo evolutivo. Tendo em conta a composição dos venenos, os péptidos reticulados são a classe mais atractiva de moléculas com interesse farmacológico. No entanto, a utilização de venenos para o desenvolvimento de novos fármacos está limitada por dificuldades em obter estas moléculas em quantidades adequadas ao seu estudo. Neste trabalho desenvolveu-se uma plataforma de alta capacidade para a síntese de genes sintéticos codificadores de péptidos venómicos, com o objectivo de produzir bibliotecas de péptidos venómicos recombinantes que possam ser rastreadas para a descoberta de novos medicamentos. Com o objectivo de sintetizar genes pequenos (< 500 pares de bases) com elevada fidelidade e em simultâneo, desenvolveu-se uma metodologia de PCR (polymerase chain reaction) robusta e eficiente, que se baseia na extensão de oligonucleótidos sobrepostos. Para possibilitar a automatização da plataforma de síntese de genes, foram construídas duas ferramentas bioinformáticas para desenhar simultaneamente dezenas a milhares de genes optimizados para a expressão em Escherichia coli (ATGenium) e os respectivos oligonucleótios sobrepostos (NZYOligo designer). Esta plataforma foi optimizada para sintetizar em simultâneo 96 genes sintéticos, tendo-se obtido uma taxa de erro de 1.1 mutações por kb de DNA sintetizado. A fim de diminuir a taxa de erro associada à produção de genes sintéticos, desenvolveu-se um método para remoção de erros utilizando a enzima T7 endonuclease I. A enzima T7 endonuclease I mostrou-se muito eficaz no reconhecimento e clivagem de moléculas DNA que apresentam emparelhamentos incorrectos, reduzindo drasticamente a frequência de erros identificados em genes grandes, de 3.45 para 0.43 erros por kb de DNA sintetizado. Investigou-se também a influência do desenho dos genes, da presença de tags de fusão, da localização celular da expressão e da actividade da protease Tobacco Etch Virus (TEV) para a remoção eficiente de tags, na expressão de péptidos venómicos ricos em cisteínas em E. coli. A utilização de codões meticulosamente escolhidos afectou drasticamente os níveis de expressão em E. coli. Para além disso, os resultados mostram que existe uma pressão significativa no uso dos dois codões que codificam para o resíduo cisteína, o que sugere que ambos os codões têm de estar presentes, em níveis equivalentes, nos genes que foram desenhados e optimizados para garantir elevados níveis de expressão. Este trabalho indicou também que o tag de fusão DsbC foi o mais apropriado para a expressão eficiente de péptidos venómicos ricos em cisteínas, particularmente quando os péptidos recombinantes foram expressos no periplasma bacteriano. Confirmou-se que a protease TEV é eficaz na remoção de tags de fusão, podendo o seu local de reconhecimento conter quaisquer aminoácidos na extremidade C-terminal, com excepção da prolina. Desta forma, verificou-se não ser necessário incorporar qualquer aminoácido extra na extremidade N-terminal dos péptidos venómicos recombinantes. Reunindo todos os resultados, verificou-se que a E. coli é um hospedeiro adequado para a expressão, na forma solúvel, de péptidos venómicos potencialmente funcionais. Por último, foram produzidos, com uma taxa de erro reduzida, ~5000 genes sintéticos codificadores de péptidos venómicos utilizando a nova plataforma de elevada capacidade para a síntese de genes aqui desenvolvida. A nova biblioteca de genes sintéticos foi usada para produzir a maior biblioteca de péptidos venómicos recombinantes construída até agora, que inclui 2736 péptidos venómicos. Esta biblioteca recombinante está presentemente a ser rastreada com o objectivo de descobrir novas drogas com interesse para a saúde humana.
Diz, Maria Del Pilar Estevez. « Impacto do encaminhamento para ambulatório de câncer hereditário na qualidade de vida de pacientes portadores de câncer de mama ». Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/5/5155/tde-20082007-161259/.
Texte intégralHere we evaluated the impact of breast cancer hereditary cancer risk evaluation on the quality of life in a population of breast cancer patients, as measured by the EORTC questionnaires QLQ-C30 and QLQ-BR23. Of the 282 invited patients, 272 agree to participate and answered QLQ before and after the risk determination by Frank, Evans and BRCAPRO methods. High risk was defined as at least 10%. Overall 198 pts completed the study. In the 180 evaluable patients, median age was 53 (+11,5) years old and time since diagnosis was less than 36 months in 89. We did not detected significant differences in quality of life parameters after risk determination, except for negative body image and mastectomy/conservative surgery (p<0.001) There were 45 patients classified as high risk by Frank, 35 by the BRCAPRO and 21 by Evans, agreement being reached in 12. We conclude that pts wish to know about their hereditary breast cancer risk, and this do not cause necessarily more stress. Apart from that, there is a need for local methods of risk calculation.
Lima, Nathália Ferreira. « Métodos moleculares para detecção e quantificação de gametócitos de Plasmodium ». Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/42/42135/tde-23042013-104032/.
Texte intégralThe microscopic detection of gametocytes may underestimate their prevalence, leading to an inaccurate assessment of the potential for malaria transmission in receptive areas and a poor estimate of the proportion of infected individuals who are infectious. We aimed to standardize molecular methods for detection and quantification of gametocytes of Plasmodium falciparum and Plasmodium vivax. Here, we describe a qRT-PCR that targets transcripts of the mature gametocyte-specific pvs25 gene. We found mature gametocytes in 53 of 55 (96.4%) P. vivax infections diagnosed during an ongoing cohort study in a farming settlement located in the southern of Amazonas state. SYBR green qRT-PCR was more sensitive than a conventional RT-PCR that targets the same gene. Most (61.9%) gametocyte carriers were either asymptomatic or had subpatent parasitemias, and would have been missed by routine malaria control strategies. However, potentially undiagnosed gametocyte carriers usually had low-density infections and contributed up to 4% to the overall gametocyte burden in the community.
Ricci, Juliana Morena Bonita [UNESP]. « Caracterização do gene vasa em Rhamdia quelen para aplicações biotecnológicas ». Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/144037.
Texte intégralConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
Fundação para o Desenvolvimento da UNESP (FUNDUNESP)
O gene vasa codifica uma proteína que pertence a uma família de proteínas denominada DEAD (Asp-Glu-Ala-Asp) Box, constituída de RNA helicases ATP-dependente. Extremamente conservada entre os organismos, sua função está associada com o metabolismo do RNA. Na maioria das espécies investigadas, a expressão do vasa restringe-se a linhagem germinativa. Estudos realizados utilizando metodologias distintas (knockdown, knockout, mutação) para conhecer o papel do vasa, demonstraram que o vasa tem fundamental importância no desenvolvimento da linhagem germinativa dos invertebrados e vertebrados. Em nosso estudo, caracterizamos o cDNA do vasa de forma inédita em uma espécie nativa, R. quelen (Heptapteridae, Siluriformes). Análises comparativas da proteína foram realizadas, mostrando que a proteína é altamente conservada ao longo da evolução. Além disso, a expressão do Rqvasa (Rhamdia quelen vasa) por RT-PCR (transcrição reversa - reação em cadeia da polimerase) e qRT-PCR (PCR quantitativo em tempo real) em diferentes tecidos mostra que o mesmo é expresso somente nas gônadas. Os sítios de expressão do Rqvasa localizam-se exclusivamente nas células da linhagem germinativa. Análises por RT-PCR e por qRT-PCR durante o desenvolvimento embrionário de R. quelen demonstram que o Rqvasa é herdado maternalmente e sua expressão diminui gradativamente ao longo do desenvolvimento embrionário e larval. Através da hibridização in situ nos embriões e larvas, foi possível visualizar o processo migratório das células germinativas primordiais (CGPs). Desta forma, este trabalho caracteriza de forma inédita, o cDNA do Rqvasa, descrevendo sua expressão durante o desenvolvimento assim como o processo migratório das CGPs. Os resultados obtidos neste estudo servirão de base para utilizar o gene vasa em diferentes abordagens biotecnológicas, como por exemplo, esterilidade, transgenia (vasa
The vasa gene encodes a protein that belongs to protein family called DEAD (Asp-Glu-Ala-Asp) Box, which is constituted of ATP-dependent RNA helicases. This protein is extremely conserved among the organisms, and its role is associated with RNA metabolism. In the majority of the investigated species, vasa expression is restricted to the germline cells. Different methods (such as knockdown, knockout and mutation) to address vasa's role have demonstrated that vasa is crucial for germ cell development. In this study, we have characterized the full cDNA of vasa from a native species, R. quelen (Heptapteridae Siluriformes). Comparative analysis using the protein sequence has demonstrated that Vasa is highly conserved along the evolution. Moreover, we have evaluated through RT-PCR and qRT-PCR Rqvasa expression in different tissues, showing that vasa transcripts are exclusively expressed in the R. quelen gonads, specifically in the germinal cells RT-PCR and qRT-PCR analysis during embryonic and larval development have shown that Rqvasa is maternally inherited and its expression decreased during development. in situ hybridization techniques performed in whole embryos and larvae allowed to study the primordial germ cells (PGCs) migratory process towards the gonadal ridge. This work has characterized for the first time the full length cDNA of vasa, describing its expression patterns during R. quelen embryonic development as well as the PGCs migratory process in this species. Our results will contribute for the basic reproductive biology of this native species, and will support studies using vasa in different biotechnological studies, such as sterility, transgenesis (vasa
CNPq: 482946/2012-1
FAPESP: 2012/00423-6
FUNDUNESP: 447/2014
Ricci, Juliana Morena Bonita. « Caracterização do gene vasa em Rhamdia quelen para aplicações biotecnológicas / ». Jaboticabal, 2015. http://hdl.handle.net/11449/144037.
Texte intégralBanca: Elisabeth Criscuolo Urbinati
Banca: George Shigueki Yasui
Resumo: O gene vasa codifica uma proteína que pertence a uma família de proteínas denominada DEAD (Asp-Glu-Ala-Asp) Box, constituída de RNA helicases ATP-dependente. Extremamente conservada entre os organismos, sua função está associada com o metabolismo do RNA. Na maioria das espécies investigadas, a expressão do vasa restringe-se a linhagem germinativa. Estudos realizados utilizando metodologias distintas (knockdown, knockout, mutação) para conhecer o papel do vasa, demonstraram que o vasa tem fundamental importância no desenvolvimento da linhagem germinativa dos invertebrados e vertebrados. Em nosso estudo, caracterizamos o cDNA do vasa de forma inédita em uma espécie nativa, R. quelen (Heptapteridae, Siluriformes). Análises comparativas da proteína foram realizadas, mostrando que a proteína é altamente conservada ao longo da evolução. Além disso, a expressão do Rqvasa (Rhamdia quelen vasa) por RT-PCR (transcrição reversa - reação em cadeia da polimerase) e qRT-PCR (PCR quantitativo em tempo real) em diferentes tecidos mostra que o mesmo é expresso somente nas gônadas. Os sítios de expressão do Rqvasa localizam-se exclusivamente nas células da linhagem germinativa. Análises por RT-PCR e por qRT-PCR durante o desenvolvimento embrionário de R. quelen demonstram que o Rqvasa é herdado maternalmente e sua expressão diminui gradativamente ao longo do desenvolvimento embrionário e larval. Através da hibridização in situ nos embriões e larvas, foi possível visualizar o processo migratório das células germinativas primordiais (CGPs). Desta forma, este trabalho caracteriza de forma inédita, o cDNA do Rqvasa, descrevendo sua expressão durante o desenvolvimento assim como o processo migratório das CGPs. Os resultados obtidos neste estudo servirão de base para utilizar o gene vasa em diferentes abordagens biotecnológicas, como por exemplo, esterilidade, transgenia (vasa::egfp, como exemplo), transplante...
Abstract: The vasa gene encodes a protein that belongs to protein family called DEAD (Asp-Glu-Ala-Asp) Box, which is constituted of ATP-dependent RNA helicases. This protein is extremely conserved among the organisms, and its role is associated with RNA metabolism. In the majority of the investigated species, vasa expression is restricted to the germline cells. Different methods (such as knockdown, knockout and mutation) to address vasa's role have demonstrated that vasa is crucial for germ cell development. In this study, we have characterized the full cDNA of vasa from a native species, R. quelen (Heptapteridae Siluriformes). Comparative analysis using the protein sequence has demonstrated that Vasa is highly conserved along the evolution. Moreover, we have evaluated through RT-PCR and qRT-PCR Rqvasa expression in different tissues, showing that vasa transcripts are exclusively expressed in the R. quelen gonads, specifically in the germinal cells RT-PCR and qRT-PCR analysis during embryonic and larval development have shown that Rqvasa is maternally inherited and its expression decreased during development. in situ hybridization techniques performed in whole embryos and larvae allowed to study the primordial germ cells (PGCs) migratory process towards the gonadal ridge. This work has characterized for the first time the full length cDNA of vasa, describing its expression patterns during R. quelen embryonic development as well as the PGCs migratory process in this species. Our results will contribute for the basic reproductive biology of this native species, and will support studies using vasa in different biotechnological studies, such as sterility, transgenesis (vasa::egfp, for example) germ cell transplantation and others
Mestre
Coeli, de Barros Correia Melo Fárida. « Protocolo para avaliação da expressão gene ABL sob estresse radioativo ». Universidade Federal de Pernambuco, 2008. https://repositorio.ufpe.br/handle/123456789/9821.
Texte intégralAs crescentes aplicações das radiações ionizantes, associadas à evolução das técnicas de análises moleculares, têm despertado grande interesse para identificação de marcadores moleculares de irradiação ocupacional ou acidental. Alguns genes envolvidos na resposta molecular ao estresse radioativo foram identificados pela alteração de sua capacidade de expressão. Entretanto, os métodos comumente utilizados para avaliação da expressão gênica são laboriosos e de alto custo. Neste trabalho, o gene ABL foi utilizado como base no estabelecimento de um protocolo para avaliação da expressão gênica em linfócitos, após irradiação gama. Para tanto, foram testadas amostras de sangue periférico de indivíduos sadios após 3, 6 e 12 horas de irradiação com doses de 1 e 3 Gy a partir de uma fonte de Cobalto-60. A técnica de avaliação empregada foi a de Reação em Cadeia da Polimerase em Tempo Real, tendo o fluoróforo Sybr green como intercalante de DNA. Em todas as etapas, amostras não irradiadas foram empregadas como controle. O RNA foi extraído dos linfócitos totais e o cDNA, sintetizado pelo método de transcrição reversa. Com base no protocolo desenvolvido, foi possível identificar um aumento na expressão do gene ABL na dose de 1 Gy, após seis horas. Entretanto, não foram evidenciadas variações estatisticamente significantes dos níveis de expressão desse gene nas demais condições analisadas. O protocolo estabelecido nessa pesquisa mostrou-se de fácil reprodução e rápido. Os recursos empregados para avaliação de sua eficácia constataram a confiabilidade do método, sugerindo sua aplicação em análises tanto dos níveis de expressão do gene ABL, quanto em investigações de genes candidatos a biomarcadores moleculares de exposição à radiação ionizante
Coletta, Rocio Riatto Della. « Análise das repetições CA do gene IGF1, VNTR do gene da insulina e região promotora P4 do gene IGF2 em indivíduos nascidos pequenos para idade gestacional ». Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/5/5135/tde-29042008-144128/.
Texte intégralIntroduction: Polymorphisms in the promoter region of insulin (INS), IGF2 and IGF1 genes may decrease their expression during fetal life and afterward could be related to intra-uterine fetal growth retardation and greater risk of hypospadia development. In post-natal life, decreased expression of these genes can result in lack of stature recovery and in lower IGF1 serum levels in children, as well as in higher risk for type 2 diabetes mellitus and metabolic syndrome in adults. Objectives: The aims of the present study were: (1) to analyze the allelic and the genotypic frequency of the insulin (INS) gene variable number of tandem repeats (VNTR) and the IGF1 gene CA repeats; (2) to analyze the P4 promoter region of IGF2 gene (3) to test the contribution of INS VNTR, IGF1 gene CA repeats on insulin sensitivity and IGF1 serum levels in children born SGA with and without catch up, respectively. Patients: We studied 142 individuals born SGA with catch up (n = 66) and without catch up (n = 76) selected from three different centers (HCFMUSP, Santa Casa de Sao Paulo and HC-UFPR). The control group consisted of 297 children born appropriate for gestational age (AGA). Methods: Extraction of genomic DNA, PCR-amplification of the VNTR of insulin gene, CA repeats of IGF1 and IGF2 gene P4 promoter region; restriction analysis; Genescan software; automatic sequencing. Blood measurements of serum level of glucose, insulin and IGF1. Statistical analysis (Statistical Package for Social Sciences software). Results: Regarding birth parameters, the average of Z-height, Z-BMI (body mass index) and Z-height paternal and Z- EA (target height) were higher in children born SGA who had catch up. Interestingly, we observed that the Z-PC was higher in children born SGA without catch up. In addition, the Z-IGF1 serum levels were significantly higher in children who had catch up (p <0.05). The molecular analysis of IGF1 gene CA repeats and of INS gene VNTR locus did not show a statistically significant difference in the allelic and genotypic distribution of these polymorphisms between adequate for gestational age (AGA) and SGA groups nor between SGA with and without catch up. Similarly, we have not found an association of these polymorphisms with clinical or laboratory variables of this study. A novel polymorphism in the P4 promoter region of the IGF2 gene was identified. It was characterized by cytosine repeats (9-12) at position -1982 before transcription initiation site of exon 2 of IGF2 gene. Yet, we have identified a heterozygous substitution of cytosine for thymine at the nucleotide position 9 in the allele 11C in four children born SGA. This change was also absent in the control population. Quantization of IGF2 gene expression in two of these children did show loss of expression of this gene in patients carrying the variant 9C/T. Conclusions: We have not observed an association of the above described polymorphisms with pre and post natal growth, or with the occurrence of insulin resistance in individuals born SGA. IGF-1 levels did not seem to be associated with the polymorphisms either. A new variant in the P4 promoter region of IGF2 gene was identified, however preliminary studies showed no influence on intra-uterine growth.
Sasazaki, Mariana Yuri. « Infraestrutura computacional para avaliação da similaridade funcional composta entre microRNAs baseada em ontologias ». Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-02112014-133658/.
Texte intégralMicroRNAs (miRNAs) are small non-coding RNA that mainly negatively regulate gene expression by inhibiting translation of target RNAs. Increasing evidences show that such molecules play critical roles in many important biological processes. Since there are no terms of miRNAs annotations in Gene Ontology (GO), nor a database with microRNAs functional annotations, directly calculating the functional similarity between miRNAs does not have an estabilished pattern aproach. However, the existence of miRNAs target genes database, such as TarBase, and a miRNAs-disease associations database, such as HMDD, allow us to indirectly infer functional similarity of miRNAs through the analysis of their target genes in GO or between their related diseases in MeSH. Moreover, according to the structure of the ontology of miRNAs OMIT, a miRNA can also be annotated with other information, such as if it acts as an oncogene or a tumor suppressor, the organism that it belongs, the experiment in which it was found, its associations with diseases, target genes, proteins and pathological events. Thus, miRNAs similarity can be inferred based on the combination of a broad set of information contained in their annotations, indeed, we can use all available information defining the calculation of a composed functional similarity. In this study, we propose the creation and application of CFSim method applied to the OMIT using the diseases ontology, MeSH, and gene ontology, GO, to compute miRNAs similarity based on different information in their annotations. We validated our method by comparing with functional similarity inferred by miRNA families and the results showed that our method is efficient in sense that the functional similarity between miRNAs in the same family was greater compared to other miRNAs from distinct families. Furthermore, in comparison with existing methods of functional similarity in the literature until the present day, the CFSim showed better results. Finally, to make feasible the use of the proposed method, an environment was designed and implemented, containing the necessary infrastructure so that researchers can include data from new discoveries and see information about a particular miRNA, as well as calculate the similarity between two miRNAs, based in the proposed method.
Jesus, Marcelo Bispo de 1980. « Utilização de ferramentas nanotecnologicas para a indução de morte em celulas de cancer de prostata ». [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314163.
Texte intégralTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Mesmo após mais de meio século de pesquisas e desenvolvimento em quimioterapia, o câncer ainda é uma das doenças mais difíceis de serem tratadas. Dentre os tipos de câncer, o de próstata aparece em destaque por ser a forma mais incidente entre os homens. O pequeno progresso alcançado até os dias de hoje no tratamento desta doença nos levou a pesquisar duas estratégias para intervir na multiplicação de células de câncer de próstata. Na primeira, um sistema de liberação de fármacos (drug delivery) baseado em ciclodextrinas e destinado a melhorar a biodisponibilidade da riboflavina (vitamina capaz de induz apoptose em células tumorais) foi preparado, caracterizado e testado. A segunda estratégia consistiu no desenvolvimento de um sistema de transferência de genes (gene delivery) baseado em nanopartículas lipídicas sólidas, para futura transferência de genes supressores de tumor e, portanto, indutores da morte das células de câncer prostático. Na primeira parte foi realizada a caracterização físico-química de complexos de riboflavina com beta (b-CD) e hidroxipropil beta (HP-b-CD) ciclodextrinas, seguida de avaliação da toxicidade em células de câncer de próstata. A associação da riboflavina com as ciclodextrinas aumenta a solubilidade desta vitamina e melhora sua eficiência contra células de câncer de próstata. Entretanto, a interação molecular da riboflavina, tanto com b-CD quanto com HP-b-CD, mostrou-se não usual, como comprovado por ressonância magnética nuclear, pelos ensaios de Efeito Nuclear Overhauser. Na segunda parte, foram desenvolvidas nanopartículas lipídicas sólidas de ca. 100 nm, compostas de ácido esteárico, dioleil-propanoato de trimetilamônio e Pluronic F68; foi também estudada a influência da adição de dioleil-fosfatidiletanolamina a essas formulações. As nanopartículas se mostraram bastante estáveis quanto ao tamanho e potencial Zeta, durante o período (140 dias) estudado. Elas também foram capazes de proteger o material genético transportado contra a ação da enzima DNase e apresentaram eficiência de transfecção comparável à da Lipofectamina 2000®, um carreador comercial de uso consagrado para transfecção. Palavras chave: Próstata - Câncer; Riboflavina; Ciclodextrinas; Nanopartículas lipídicas sólidas; Técnicas de transferência de genes.
Abstract: Even after more than half a century of research and development in chemotherapy, cancer remains one of the most difficult diseases to treat. Among the cancer types, prostate adenocarcinome is the most incident in male. The insufficient advances attained so far in cancer treatment led us to explore two strategies designed to obstruct proliferation of prostate cancer cells. At the first, a drug delivery system based on cyclodextrins and aimed to improve the bioavailability of riboflavin (a vitamin able to induce apoptosis in tumor cells) was prepared, characterized and tested. The second strategy consisted in the development of a gene delivery system based on solid lipid nanoparticles for future transfer of tumor suppressor genes able to induce death of prostate cancer cells. The first part of this thesis comprises the physico-chemical characterization of beta (b-CD) and hydroxypropyl beta (HP-b-CD) cyclodextrins complexes with riboflavin, followed by evaluation of their toxicity against prostate cancer cells. Riboflavin complexation with cyclodextrins increased the solubility of this vitamin and its effectiveness against prostate cancer cells growth. However, the molecular interaction of riboflavin with either b-CD or HP-b-CD was unusual, as evidenced by nuclear magnetic resonance (Overhauser Nuclear Effect) experiments. In the second part solid lipid nanoparticles of ca. 100 nm and composed of stearic acid, 1,2-dioleoyl-3-trimethylammonium-propane and Pluronic F68 (with or without 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) were prepared. Stability (evaluated by size and Zeta potential of the nanoparticles) was quite good during a 140 days storage period. The nanoparticles were able to protect genetic material against DNase action and showed a transfection capacity comparable to that of Lipofectamine 2000®, a commercially available gene carrier. Keywords: Prostate - Cancer; Riboflavin; Cyclodextrins; Solid lipid nanoparticles; Gene transfer techniques.
Doutorado
Bioquimica
Doutor em Biologia Funcional e Molecular
Takahashi, Elizabete Keiko. « Transferência do gene atacina A para plantas de maracujá amarelo (Passiflora edulis Sims f. flavicarpa Deg.) por biobalística ». Universidade de São Paulo, 2002. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-03122002-083637/.
Texte intégralBrazil is the leading producer of the yellow passion fruit. However, the productivity is fairly low, about 10,000 t per hectare. Fruit yields vary with cultivars, climatic conditions, management and other factors, namely bacterial and virus díseases. Genetic transformation methodologies are modern alternatives to obtain plant resistance. The insectderived protein, attacin A acts as bacterícide, and it has been used to confer resistance to plant species. The objectives of the present study were (i) to obtain in vitro shoot regeneration, (ii) to test the efficiency of certain selective agents during the organogenesis process, (iií) to construct the cassette containing the attacin A gene, and (iv) to determine the physical and biological conditions for genetic transformation of passion fruit plants by using the biolistic approach. Regarding the ín vítro studies, three culture recipients were evaluated as well as different concentrations of benzylaminopurine (BA) and coconut water that suppiemented the basal medium. Phytagei and agar were aiso tested as solidifying agents. Cultures were evaluated with respect to leaf dises morphogenic responses. The attacín A gene was sequenced, and cioned to receive the CAMV 35S promoter with a duplicated enhancer sequence, and the 35S terminator. This vector was denoted pFFatacina. The cassette was cioned in pcambia 1300 and pcambia 2300 vectors that contain the hygromícin (hpt) and kanamycin (nptil) genes, respectively. Leaf discs, as well as internodal segments and hypocotyl-derived sections chosen to índuce calii, were used in the biolistic experiments. The uida gene expression was evaluated for testing bombardment parameters, namely the helium pressure (psi) and the distance from the stopping screen to the target tissue (cm). The organogenic response of the leaf discs did not differ when petri dishes, tubes or culture vesseis were used although the tubes (2,4 x 8,5 cm, 30 ml capacity) showed to be slightly better. The agar (0.6%)-solidifíed MS (Murashige & Skoog, Physíología Plantarum, 15, 1962) medium suppiemented with 0.5 mg/L BA and 5% (wlv) coconut water proved to be efficient to induce organogenesis. Shoots were obtained after 30 days. Internada[ and hypocotyl-derived segments produced 300 bud-like structures per explant. Scanning microscopy and histologícal anaiyses provided evidences that they were leaf structures, which last 50 days in 1/2 MS to evolve into shoots. Hygromicin at 5 mg/L proved to be proper as selective agent, inhibiting organogenesis in 60% of the explants. Kanamycin at 50 mg/L was also effective. Morphogenic calli up to 10 days old and 3 d-leaf discs showed high levels of transient uida gene expression under 80016.5 or 1000/9.5 helium pressureldistance from the stopping screen to the target tissue. Cotransformation experiments with pBI426 (8.7 kb) that contain the nptil gene and pFFatacina (5.25 kb) were carried on as well singre vector transformation tríals (pcatacina 1300). Stable transformation frequency of 0.85% was obtained. Transgene integration was confirmei by PCR for the attacin A gene. This is the first report on agronomicaily useful-gene transfer to yeilow passion fruit plants by biolistics.
Rosa, Daniel Dias. « Uma abordagem genômica para o entendimento do crescimento fastidioso de Leifsonia xyli subsp. xyli ». Universidade de São Paulo, 2006. http://www.teses.usp.br/teses/disponiveis/11/11135/tde-16112006-095127/.
Texte intégralSugarcane (Saccharum officinarum L.) is one of the most important tropical crops. Cultivated in more than 127 countries, it is of importance both for the social economy and culture of many regions of Brazil and of the world. Its productivity depends on diverse factors that are dealt with the intense interspecific hybridization aiming for more productive cultivars, that are resistant to diverse types of stress. Of these, stresses caused by microorganisms are the most relevant and among these the bacterium Leifsonia xyli subsp. xyli (Lxx), the causal agent of the ratoon stunting disease is one of the most important. The study of this patosystem, however, is very difficult, since Lxx is a fastidious bacterium. The availability of the complete genome sequence of Lxx made possible the understanding of the physiological causes of its fastidious behavior. Thus, the objectives of this work were to optimize the culture medium of Lxx by analyzing important pathways and to study gene expression when Lxx is cultivated in the presence and absence of methionine. Bioinformatic analyzes of the Lxx genome indicated that it is capable to use diverse sources of carbon, vitamins, metals, iron and amino acids. In fact Lxx was able to grow in the presence of mannose, fructose and galactose as the main sugar components of the medium, but not so efficiently as in glucose. It was also observed that the addition of the vitamins cobalamin, thiamin, biotin and the Nitsch´s vitamin complex resulted in a better Lxx growth. It was also verified that Lxx is capable to use iron citrate, iron sulphate and iron chloride as the main sources of iron, but less efficiently than when compared to hemin bovine chloride. With these results, it was verified that the addition of methionine (1 g/L) and of the vitamins D-biotin (0.01 g/L) and thiamine chloride (0.01 g/L) resulted in a faster growth of Lxx in vitro by as much as 30% on average compared to the standard medium. Gene expression analyses showed that the addition of methionine to the medium resulted in an alteration of expression levels of 114 genes, 95 of which were up regulated and 19 otherwise. This result indicated that Lxx needs an outside source of methionine and that it uses this amino acid a source of nitrogen. Also, it indicated that the improved growth in the presence of methionine is highly correlated with up regulation of genes of the central metabolism pathways.
Campedelli, Fabio Lemos. « POLIMORFISMO DO GENE eNOS G894T (Glu298Asp) EM PACIENTES SINTOMÁTICOS PARA ATEROSCLEROSE ». Pontifícia Universidade Católica de Goiás, 2016. http://tede2.pucgoias.edu.br:8080/handle/tede/3554.
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INTRODUCTION: Atherosclerotic disease (AD) with its cardiovascular complications is responsible for 17.5 million deaths a year, according to the World Health Organization (WHO). There is consensus that atherosclerosis involves multiple pathogenic processes initiated by endothelial dysfunction, with inflammation and vascular proliferation determining alterations in the matrix, with consequent formation of the atheromatous plaque and its clinical implications. Risk factors such as hypertension, diabetes mellitus, dyslipidemia and smoking are widely known. Currently genotyping, which is not directly related to these factors, is not accepted to estimate the risk of cardiovascular diseases, but strong evidence indicates several polymorphic genes as factors of risk and progression leading to complications of the disease. Among the genes involved, eNOS (endothelial nitric oxide synthase gene), which is responsible for the production of endothelial nitric oxide (NO, an important arterial vasodilator), when presented in polymorphic variation can determine production malfunction and predisposition to AD. OBJECTIVES: To analyze the G894T polymorphism of eNOS gene in groups of individuals diagnosed with atherosclerosis and in the control group. MATERIALS AND METHODS: 200 blood samples were collected from patients previously diagnosed with DA and 100 from the control group. The genotyping analysis for polymorphism of eNOS gene was determined by PCR. RESULTS: After analysis of polymorphism between the DA and control groups and association with variables such as gender, relation with smoking, smoking history and alcohol consumption, statistical difference were found in the distribution of the case and control groups (p = 0.0378) and in non-smoking patients (p = 0.0263). In the other associations no statistically significant difference was found. CONCLUSION: In the population studied, the frequency of the heterozygous genotype (GT) was much higher than in the other popualations (GG and TT) in both groups (case and control). The GG genotype showed greater susceptibility to AD. The association of GG genotype in nonsmokers also showed greater susceptibility. Gender, alcohol consumption, smoking and smoking history did not influence AD.
Campedelli FL. Polimorfismo do gene eNOS G894T (Glu298Asp) em pacientes sintomáticos para aterosclerose [dissertação]. Goiânia: Pontifícia Universidade Católica, PUC-GO; 2016. INTRODUÇÃO: A doença aterosclerótica (DA) com suas complicações cardiovasculares é responsável por 17,5 milhões de mortes por ano segundo a Organização Mundial de Saúde (OMS). É consenso que a aterosclerose envolve múltiplos processos patogênicos que se iniciam pela disfunção endotelial, com inflamação e proliferação vascular determinando alterações da matriz com consequente formação da placa ateromatosa e suas repercussões clínicas. Fatores de risco como a hipertensão arterial, diabetes mellitus, dislipidemias e tabagismo são amplamente conhecidos. Atualmente a genotipagem, não relacionada diretamente a estes fatores, não é aceita para estimativa de risco das doenças cardiovasculares, porém fortes evidências relacionam diversos genes polimórficos, como fator de risco e evolução para complicações da doença. Dentre os genes envolvidos o eNOS (gene da síntese de óxido nítrico endotelial), responsável pela produção de Óxido nítrico (NO), endotelial (importante vasodilatador arterial), quando se apresenta em variação polimórfica pode determinar mal funcionamento da produção e predispor a DA. OBJETIVOS: Analisar o polimorfismo G894T do gene eNOS nos grupos de indivíduos com diagnóstico de aterosclerose e no grupo controle. MATERIAIS E MÉTODOS: Foram coletados amostras de sangue periférico de 200 pacientes com DA previamente diagnosticados e 100 amostras de grupo controle. A análise de genotipagem para o polimorfismo do gene eNOS foi determinada por PCR. RESULTADOS: Após análise do polimorfismo entre os grupos com DA e grupo controle, e associação com as variáveis gênero, relação com hábito de fumar, carga tabágica e consumo de bebida alcóolica, foram encontrados diferença estatísticas na distribuição dos grupos caso e controle (p=0,0378) e nos pacientes não tabagistas (p=0,0263). Nas demais associações não houve diferença estatisticamente significativa. CONCLUSÃO: Na população estudada evidenciou a frequência do genótipo heterozigoto (GT) muito superior aos demais (GG e TT) em ambos os grupos (caso e controle). O genótipo GG demonstrou maior suscetibilidade à DA. A associação do genótipo GG em não tabagista também apresentou maior suscetibilidade. O gênero, o etilismo, o hábito de fumar e carga tabágica não influenciaram na DA.
Kashiwabara, André Yoshiaki. « MYOP/ToPS/SGEval : Um ambiente computacional para estudo sistemático de predição de genes ». Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/45/45134/tde-02042012-184145/.
Texte intégralThe challenge of correctly identify eukaryotic protein-coding genes in the genomic se- quences is an open problem. In this work, we implemented a plataform with the aim of improving the way that gene predictors are implemented and evaluated. ToPS (Toolkit of Probabilistic Models of Sequence) was the first object-oriented framework that provides tools for implementation, manipulation, and combination of probabilistic models that represent sequences of symbols. MYOP (Make Your Own Predictor) facilitates the construction of gene predictors. SGEval (Splicing Graph Evaluation) uses splicing graphs to compare dif- ferent annotations with alternative splicing events. We used our plataform to develop gene finders in eleven distinct genomes: A. thaliana, C. elegans, Z. mays, P. falciparum, D. me- lanogaster, D. rerio, M. musculus, R. norvegicus, O. sativa, G. max e H. sapiens. With this development, we established a protocol for implementing new gene predictors. In addi- tion, using our platform, we developed a pipeline to find genes in the 109 sugarcane BAC sequences produced by BIOEN (FAPESP Bioenergy Program).
Scuderi, Maria Cristina. « Identificazione molecolare di lattobacilli umani ed epidemiologia delle resistenze ». Thesis, Universita' degli Studi di Catania, 2011. http://hdl.handle.net/10761/306.
Texte intégral45 Lactobacillus strains isolated from human were identified by molecular tecniques (16S rDNA PCR-RFLP; multiplex PCR 16S-ITS-23S rDNA and its flancking region; multiplex PCR tuf gene ). In vitro activities were tested by broth microdiluition and agar diffusion against different antimicrobial classes (beta-lactams, macrolides, lincosamides, fluoroquinolones, glycopeptides and aminoglycosides).Genotypic study was performed to investigate quinolone resitance by PCR and sequencing QRDR (Quinolone Resistance Determining Region) of gyrA and parC genes.
Steemburgo, Thais. « Interação gene e nutriente em pacientes com diabete melito tipo 2 : aspectos relacionados às complicações crônicas do diabetes, síndrome metabólica e efeitos dos polimorfismos rs9939609 (A/T) e rs7204609 (CT) do gene do FTO ». reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2009. http://hdl.handle.net/10183/16853.
Texte intégralSeidenberger, Katia. « Construção e avaliação da ação de plasmídio contendo gene suicida timidina quinase e gene imunomodulador da interleucina 12 otimizada, visando terapia gênica para carcinoma medular de tireóide ». Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/5/5135/tde-11122007-131612/.
Texte intégralPresent treatments of advanced and metastatic medullary thyroid carcinoma (MTC) are unsatisfactory. Tissue-specific cancer gene therapy is a promising alternative approach. IL-12 gene is a good citokyne to be used in gene therapy because it appears to be the most effective immunomodulatory gene. Literature data shows synergism in the association of two antitumor methods: suicide gene thymidine kinase (HSV-tk) and interleukin genes; therefore, they should ideally be together in the vector. The evolved interleukin12, obtained by DNA shuffling, is believed to elicit more antitumoral immune response than the human IL-12. None of them has been tested in MTC, only the murine IL-12 has been employed in MTC gene therapy. To explore a more efficient multi-gene antitumor treatment, development and evaluation of a plasmid expressing both herpes simplex virus thymidine kinase type 1 (HSVtk) and evolved interleukin-12 (evIL-12) under the control of modified calcitonin promoter (TCP) were done in this study. TCP promoter is more specific and efficient than the natural calcitonin promoter CT/CGRP, and has already been used in several studies. To verify IL-12 biological activity, lymphocyte proliferation and dendritic cell stimulation after IL-12 were studied. TT cells (human MTC) were transfected by pTCPtkevIL-12 plasmid or by pTCPmIL-12 (plasmid containing murine IL-12 gene, under control of TCP promoter). Lymphocyte proliferation was analysed by flow cytometry, and Th1 response was assessed by IFN-? and IL-4 ELISA measurement. The phenothypic analysis of dendritic cells (DCs) by flow cytometry was based on the expression of the maturative surface markers CD80, CD83, CD86 and CD40. Also, plasmid pTCPtkevIL-12 ability to promote TT transfected cells apoptosis, through the suicide system HSV-tk/ganciclovir, was evaluated and confirmed. Both IL-12 elicited similar intense lymphocyte proliferation. Nevertheless, the main IL-12 function is not to stimulate lymphocyte proliferation but induce Th1 immune response, which is essential for efficient anti-tumour response. Both IL-12, showed great Th1 response; however fortunately, ev-IL12 was superior to mIL-12 in promoting T cell Th1 response. Flow cytometry analysis of DCs revealed significant higher expression of CD40 surface molecule after differentiated DCs were exposed to TT transfected cells, either with pTCPtkevIL-12 or pTCPmIL-12, supernatants. DCs stimulated with supernatants containing evIL-12 were 36.91% CD40+, whereas when stimulated by supernatants containing mIL-12 were 14.74% CD40+. The other maturative markers (CD80, CD83, CD86) remained with the same expression level. Moreover, TT pTCPtkevIL-12- transfected cells supernatants, showed a even higher ability of increasing CD40 expression in DCs after treatment with GCV. At least partially, this increase in dendritic cells CD40 expression could explain the synergism observed with the simultaneous expression of thymidine kinase and interleukin genes. Outstanding lymphocyte proliferation and dendritic cell stimulation were achieved by the evIL-12 secreted in the supernatants, confirming that this interleukin 12 is really very potent. The good results achieved by the present study justify further experiments with this therapeutic plasmid. It could be used intra-tumorally and to stimulate/mature dendritic cells. Vaccine with DCs stimulated by TT pTCPtkevIL-12-transfected cells after GCV treatment supernatants, due to higher CD40 expression, could be very suitable for the treatment of MTC metastasis. Several studies show better primary tumor and metastasis regression in the presence of high levels of CD40 expression.
Santos, Neto Antonio Alves dos. « UTILIZAÇÃO DE METODOLOGIAS PARA ANÁLISE COMPARATIVA DE SEQUÊNCIAS NUCLEOTÍDICAS DE UM GENE RELACIONADO AO CÂNCER DE PELE ». Universidade do Oeste Paulista, 2015. http://bdtd.unoeste.br:8080/tede/handle/tede/345.
Texte intégralThe p53 gene is considered one of the most intensively studied genes from the genomic point of view and is related to the most common types of skin cancers, which show a trend of increasing incidence in modern human populations. DNA sequences of this gene are available in genomic databases with public access on the Internet and provide useful information for a wide range of applications. This research aimed to employ methods of comparative analysis of nucleotide sequences for evaluating mutations in the p53 gene in different countries, and evaluate the applicability of bioinformatics tools available on the web environment. Investigations were carried out to verify the most frequent mutations in the p53 gene whose sequences are deposited in human genomic databases located in the United States (NCBI), Europe (EBI) and Japan (DDBJ). In the NCBI database we found 194 mutant sequences of the p53 gene, and six of them were described as coming from people with skin cancer. In EBI database 62 mutant sequences of the p53 gene were found, and 50 were from patients with skin cancer. In DDBJ database we found 4075 mutant sequences for the same gene, but not identified as coming from patients with cancer. The original sequence of the p53 gene was compared with the mutant sequences derived from patients with various types of skin cancers, through the CLUSTALW and MAFFT bioinformatics tools. Studies comparing the mutant sequences allowed to establish relationships among the most frequent mutations and that might be related to the disease in different countries. The results showed the feasibility of the proposed approach, and allowed the identification of common characteristics between the analyzed mutants. It was possible to identify the gene regions most sensitive to changes in nucleotide sequences in the p53 gene, which might be related to the origin of the pathology. It was also possible to identify that the mutations commonly occur in very close areas, both for the sequences of the NCBI database as to those collected from EBI database.
O gene p53 é considerado um dos genes mais intensamente estudados do ponto de vista genômico e está relacionado com os tipos mais comuns de cânceres de pele, os quais mostram uma tendência de aumento da incidência em populações humanas modernas. Sequencias de DNA deste gene estão disponíveis em bancos de dados genômicos com acesso público na internet e fornecem informações úteis para uma grande variedade de aplicações. Esta pesquisa teve como objetivo empregar métodos de análise comparativa das sequências de nucleotídeos para a avaliação de mutações no gene p53 em diferentes países, e avaliar a aplicabilidade das ferramentas de bioinformática disponíveis no ambiente web. As investigações foram realizadas a fim de verificar as mutações mais frequentes no gene p53 já depositadas em bancos de dados genômicos humanos localizados nos Estados Unidos (NCBI), Europa (EBI) e Japão (DDBJ). Na base de dados NCBI foram encontradas 194 sequencias mutantes para o referido gene, sendo que seis destas sequências eram descritas como provenientes de pessoas com câncer de pele. Na base de dados EBI foram encontradas 62 sequencias mutantes do gene p53 em humanos, sendo que 50 eram provenientes de pacientes com câncer de pele. Na base de dados DDBJ foram localizadas 4075 sequencias mutantes para o mesmo gene, mas não identificadas como provenientes de pacientes com câncer. A seqüência original do gene p53 foi comparada com as sequências mutantes oriundas de pacientes com diversos tipos de cânceres de pele, por meio das ferramentas de bioinformática CLUSTALW e MAFFT. Estudos comparando as sequências mutantes permitiram estabelecer relações entre as mutações mais freqüentes e que podem estar relacionados com a patologia nos diferentes países. Os resultados mostraram a viabilidade da abordagem proposta, e permitiram a identificação de características comuns entre os mutantes analisados. Foi possível identificar as regiões gênicas mais sensíveis às alterações nas sequências de nucleotídeos no gene p53, e que podem estar relacionados com a origem da patologia. Também foi possível identificar que as mutações comumente ocorrem em regiões bem próximas, tanto para as sequencias oriundas do banco de dados NCBI quanto para aquelas coletadas do banco de dados EBI.
Pignata, Luiz Fernando Martins. « Pipeline para Análise In Sílico de Dados de Expressão de miRNAs e mRNAs em Células de Mamíferos ». Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-14062012-132754/.
Texte intégralThe microRNAs are involved in the regulation of gene expression of the cell. The miRNA molecule binds to the messenger RNA and interrupts the gene expression by disrupting the translation. Through microarray data analysis, bioinformatics is a valuable aid for the identification of several genes that encode miRNAs in plants and animals, including mammals. It is also very useful for predicting structures. Data of miRNA and mRNA expression were obtained by the collaboration the Bioinformatics Laboratory and the Molecular Immunogenetics Laboratory of the Department of Genetics of the Faculty of Medicine of Ribeirão Preto - USP, coordinated by professors Silvana Giuliatti and Geraldo A. S. Passos, respectively. During the development and tests of the research, microarrays data (numerical values os the expression) were obtained from the comparison between the expression of miRNA and mRNA of the thymus of non obese diabetic mice with diabetes mellitus type 1, as well as from comparisons of their expression in other experiments. The present study is aimed at the development of a pipeline for in silico analysis of the data of miRNAs and mRNA gene expression obtained by microarray. Based on miRNAs and mRNA expression, it was possible to analyze several tools, develop and adjust scripts that allowed the sequential analysis of such data. The pipeline includes the quantification of gene expression data from microarray, the normalization of the data, the statistical analysis of differentially expressed sequences using Multi Experiment Viewer, the construction of networks of interaction of miRNA-mRNAs, and the search for targets of miRNAs based on such network using GenMir++. The pipeline was performed easily and allowed the correct analysis of the data, avoiding waste of time in bench analysis. From the results, new targets of miRNA were found using the pipeline and were verified further in bench analysis. The results were presented in the 55 th Brazilian Genetics Congress in the paper entitled \"MicroRNA-mRNA Network Controlling the Promiscuous Gene Expression in the Thymus of NOD (Non Obese Diabetic) Mice: Implications in the Emergence of Type 1 Diabetes Mellitus\".
Radaic, Allan 1986. « Desenvolvimento de nanopartículas lipídicas para o carreamento conjunto do gene para PTEN e mitoxantrona em células de câncer de mama e de próstata ». [s.n.], 2012. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314171.
Texte intégralDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: O câncer é a doença genética responsável pelo maior número de mortes em países desenvolvidos e a segunda maior causa mortis em países em desenvolvimento. Uma das principais formas de tratamento do câncer é a quimioterapia, que se utiliza de fármacos para induzir a morte em células cancerígenas, impedindo, assim, seu crescimento anormal. Para ultrapassar desvantagens das tratamentos atuais, novas terapias vêm sendo desenvolvidas. Dentre elas, a terapia gênica e o uso de sistemas de liberação de fármacos foram as abordagens escolhidas em nossa pesquisa. Carreadores Lipídicos Nanoestruturados (CLN) e Nanopartículas Lipídicas Sólidas (NLS) são alternativas interessantes para viabilizar tais terapias, por conseguirem entregar material genético de forma efetiva e segura de genes, fármacos e proteínas em células alvo. Portanto, esta dissertação teve por objetivos i) desenvolver e aperfeiçoar um novo método de produção de CLN e NLS: a extrusão de microemulsão e ii) produzir nanopartículas capazes de carrear genes (gene codificante para PTEN) e fármacos (mitoxantrona) concomitantemente em células de câncer. Os resultados demonstram que a extrusão de microemulsão é um método factível para a produção de tais partículas, sendo que 15 passagens pela membrana de 100 nm, 5 ºC acima da temperatura de fusão dos lipídios sólidos são os melhores parâmetros para otimização deste processo. As nanopartículas lipídicas produzidas apresentaram diâmetro médio em torno de 140 nm e foram estáveis por, pelo menos, 180 dias estocadas a 4 ºC. Além disso, CLN e NLS mostraram-se semelhantes quanto ao tamanho, potencial Zeta e polidispersão (PDI). Apesar de não apresentarem diferenças quanto a transição de fase, as nanopartículas lipídicas apresentaram uma ultraestrutura monolítica bastante distinta dos lipossomas, o que garantiu uma alta eficiência de encapsulamento para o fármaco mitoxantrona: de 81% em CLN e 64 % em NLS. Finalmente, o carreamento concomitante do fármaco mitoxantrona e do gene da PTEN diminuiu a viabilidade celular em linhagens de câncer de mama (MCF-7) e de próstata (PC3), de maneira mais eficiente que formulações lipossomais
Abstract: Cancer is the genetic disease responsible for major death causes in developed countries and it is the second leading cause of death in developing countries. One of the main forms of cancer treatment is chemotherapy, which uses drugs to induce death in neoplastic cells, thereby preventing their overgrowth. To overcome disadvantages of current treatments, new therapies have been developed. Among them, gene therapy and the use of drug delivery systems were the approaches used in our research. Nanostructured Lipid Carriers (NLC) and Solid Lipid Nanoparticles (SLN) are suitable carriers for such therapies since they can effectively and safely deliver genetic material, drugs and proteins in target cells. Therefore, this work was aimed i) to develop and optimize a new method of production of NLC and SLN: the microemulsion extrusion and ii) to produce nanoparticles capable of co-delivery genes (the coding gene for PTEN) and drugs (mitoxantrone) into cancer cells. The results demonstrate that microemulsion extrusion is a reliable method for the production of such particles, being 15 passages through 100 nm membrane, at 5 °C above the solid lipid melting temperature, are the best parameters for process optimization. The lipid nanoparticles showed average diameter of 140 nm and they were stable up to 180 days of storage at 4 °C. Moreover, NLC and SLN showed similar size, Zeta potential and polydispersity (PDI). While calorimetry did not reveal great differences among the formulations tested, transmission electron microscopy revealed a monolithic structure for lipid nanoparticles distinct from lipossomes, which allowed NLC and SLN to encapsulate 81 and 64 %, respectively, of mitoxantrone. Finally, concomitant entrapment of mitoxantrone and PTEN gene in lipid nanoparticles led to a decrease in the cell viability of breast (MCF-7) and prostate (PC3) cancer cells, more efficiently than liposomal formulations
Mestrado
Bioquimica
Mestre em Biologia Funcional e Molecular
Marques, Carolinne de Sales. « Associação de genes da resposta imune na hanseníase e episódios reacionais ». reponame:Repositório Institucional da FIOCRUZ, 2014. https://www.arca.fiocruz.br/handle/icict/13621.
Texte intégralFundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil
A hanseníase é uma doença infecciosa causada pelo Mycobacterium leprae, uma bactéria intracelular obrigatória. Estudos demonstram que a genética do hospedeiro pode influenciar no desfecho da doença em pelo menos em três etapas distintas: na hanseníase per se, no desenvolvimento das formas clínicas e nos episódios reacionais. Genes que participam da via principal de ativação da resposta imune inata a micobactérias tais como TRL1/2 e NOD2, foram apontados como associados à hanseníase em diferentes populações, alguns desses estudos avaliando os episódios reacionais como desfecho. Entretanto, o efeito dessas associações na população brasileira merece maior investigação. Assim o objetivo geral desse projeto foi estudar a associação dos genes TRL1 e NOD2 na susceptibilidade à hanseníase per se, e a associação de sete genes candidatos da resposta imune nos episódios reacionais. Inicialmente foram realizados estudos caso-controle e em famílias, conduzidos em quatro populações de diferentes regiões do Brasil, para verificar o efeito de SNPs do TLR1 na hanseníase. Os resultados mostraram a associação entre o TLR1 +743A>G (equivalente à troca N248S) e risco à hanseníase per se, o que foi confirmado em todas as populações estudadas (ORGG= 1,51, p<0,001). Em seguida, a correlação genótipo-fenótipo foi avaliada, e o alelo +743G foi relacionado à redução da razão TNF/IL10, bem como à alteração no perfil eletrostático protéico (diminuição da eletronegatividade) em estudos in silico Na segunda etapa do trabalho, foi desenvolvido um estudo multicêntrico incluindo cinco populações brasileiras de regiões distintas, onde foram avaliados genes candidatos à associação com a hanseníase, escolhidos com base no primeiro estudo de associação do genoma completo conduzido em chineses. Dentre os 36 marcadores avaliados, os SNPs rs8057341 no gene NOD2 e rs4942254 no locus CCDC-LACC1 exibiram efeito protetor à doença, e a análise combinada confirma a associação com proteção na população brasileira (ORAA= 0,49, p<0,001; ORCC = 0,72, p = 0,003, respectivamente). Por fim, investigamos a associação dos genes TNF/LTA, IFNG, IL10, TLR1, NOD2 e IL6 com os episódios reacionais ou subtipos (tipo 1 e tipo 2) em uma amostra de pacientes do Rio de Janeiro. Como resultado, observamos a associação do gene IL6 com reação, indicando que os genótipos rs2069840-GG e rs2069845-AG conferem proteção (OR= 0.14, p= 0.001) e risco (OR= 1.78, p = 0.01), respectivamente, ao desfecho reação per se. Os resultados do presente estudo confirmam a associação dos genes TLR1 e NOD2 na hanseníase per se, bem como do gene IL6 nas reações hansênicas, indicando-os como possíveis marcadores de susceptibilidade a esses desfechos na população brasileira
Leprosy is an infectiou s disease caused by Mycobacterium leprae , an obligatory intracellular bacterium. Studies have shown that genes are able to influence the disease outcome in at least three distinct steps: leprosy per se, clinical forms development, and leprosy reactions. Ge nes in the major pathway of innate immune response against mycobacteria such as TRL1/2 and NOD2 , have been pinpointed as associated with leprosy in different populations , some studies including leprosy reaction as outcome . However, the effect of such assoc iations in Brazilian population deserves further investigation. Therefore, the aim of this project was to study the association of TRL1 and NOD2 genes in susceptibility to leprosy per se and also the association of seven immune response candidate genes in leprosy reactions. First, case - control and family - based studies were performed in four populations from different regions of Brazil, to investigate the effect of TLR1 SNPs in leprosy. The results indicated an association between +743A>G (amino acid exchang e N248S) and leprosy risk, which was confirmed in all populations used (OR GG = 1.51, p<0.001) . In addition, we evaluated the genotype - phenotype correlation, and found the +743 G allele related to lower TNF/IL10 ratio, and also modifying the electrostatic pr ofile (reducing the electronegativity) at TLR1 protein by in silico approach . In the second step of our work, we performed a multicentric study including five Brazilian populations, to evaluate the association of candidate genes with leprosy. These genes w ere selected from the first genome - wide association study in leprosy, performed in Chinese. Among the 36 markers evaluated , both rs8057341 at NOD2 gene and rs4942254 at CCDC122 - LACC1 gene showed protector effect to leprosy, and the combined analysis confir med the association with protection in Brazilians (OR AA = 0.49, p<0.001; OR CC = 0.72, p = 0.003, respectively). Finally, we investigated the association between TNF/LTA , IFNG , IL10 , TLR1 , NOD2 and IL6 genes and leprosy reacti ons or subtypes (type 1 and type 2), using a sample of patients from Rio de Janeiro. As result, we observed the association between IL6 gene and reaction, indicating a protective (OR= 0.14, p= 0.001) and risk (OR= 1.78, p = 0.01) effect of rs2069840 - GG and rs2069845 - AG genotypes, respectively. The results of our study confirm the association of TLR1 and NOD2 genes with leprosy per se , as well as the IL6 gene with leprosy reactions, indicating them as potential markers of susceptibility to these outcomes in Brazilians
Pinho, Raquel de Mello e. « Uso do silenciamento gênico mediado por RNA de interferência e de TAL effector nucleases para aumento de eventos gene targeting em células de cão ». Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/10/10132/tde-13012015-102643/.
Texte intégralThe insertion of exogenous DNA into a host genome is achieved primarily through the use of DNA repair pathways such as Non-Homologous End Joining (NHEJ) and the Homologous Recombination (HR). The integration by NHEJ has a random feature and is much more common than HR insertions, which are more likely to produce gene targeting events . TAL effector nucleases (TALENs) and RNA interference (RNAi) can be used to increase the rate of specific integration and thus improving the efficiency of gene editing. In this work, we used short interference RNA (siRNA)-mediated gene silencing for transient inhibition of genes ATF7IP (implicated in histone methylation), EP300 (acetyltransferase) and Ku70 (essential to NHEJ) and a pair of TALENs RNAm complementary to canine muscle dystrophin (DMD) gene. MDCK I Canine Cells were transfected by lipofectamine 2000 (Invitrogen) with 320 pmol of siRNAs for ATF7IP and EP300; and 64 pmol of siRNA for Ku70 in different groups. After 40 hours cells were transfected with 15 μg of a vector derived from pEGFP- N1 (Clontech) containing two regions homologous to the canine DMD gene (left arm length: 873 bp and right arm length: 1370 bp) and 10 μg of TALEN mRNA. The cell selection was achieved with DMEM high glucose with 600μg/ml G418 for 14-16 days. The colonies collected through biopsies were analyzed by polymerase chain reaction and gene sequencing. Three pairs of primers were used; an endogenous control (GAPDH) , an internal control of the insert (Neo qPCR) and a primer set to confirm the occurrence of homologous recombination events (DMD3). .Groups showed great variation in cell death rate and consequently in the number of colonies: ATF7IP+Vector had highest number of colonies (648c) and the group EP300+Ku70+Vetor+TALENs the lowest one (1c) The highest rate of homologous recombination was in ATF7IP +Ku70+Vetor+TALENs group that had 40% of the neomycin positives cells confirmed as gene targeting events, a considerable increase in the recombination rate compared to the 3.1% in the control group transfected only with the template vector. That shows that the combined use of siRNAs and TALENs was a success for increasing directed gene editing events.
Kano, Flora Satiko. « Anaplasma marginale : análise da variabilidade do gene msp1 a e avaliação imunogênica da vacina de DNA contendo genes para MSP1a, MSP1b e MSP5 em camundongos BALB/c ». Universidade Estadual de Londrina. Centro de Ciências Agrárias. Programa de Pós-Graduação em Ciência Animal, 2007. http://www.bibliotecadigital.uel.br/document/?code=vtls000123331.
Texte intégralAnaplasma marginale is an important tick-transmitted rickettsial pathogen of cattle that invades and multiplies within erythrocytes, causing severe hemolytic anemia during acute infection. Immunization with purified outer membrane proteins (OMP) induces protection against acute A. marginale disease. Of 21 OMP described six major surface proteins (MSPs 1a, 1b, 2-5) have been well-characterized. The complex MSP1 (MSP1a and 1b) is an adhesin for bovine erythrocyte, and MSP1a vary in size and sequence due to the number of tandem 28-29-amino acid repeats. DNA vaccine against anaplasmosis has been investigated using the msp1a and msp1? genes, and the results related cellular and humoral response in mice and cattle. Immunization with DNA plasmids encoding antigens of interest represents a novel and promising method in vaccine research and development. Multiepitope DNA vaccine is a new experience to increase immunogenicity and protection for vaccinated animal as compared in single epitope. The objectives of this study were to analyze the variability of the msp1a gene of A. marginale strains from Parana State, evaluate the capacity of the recombinant plasmids to express MSP1a, MSP1b, and MSP5 in eukaryotic cells, and evaluate the immunogenicity of BALB/c mice immunized with these DNA vaccines encoding MSPs of A. marginale PR1 strain individually or in association. The analysis of the msp1a gene identified the presence of six, five and three tandem repeats in PR1, PR2 PR3, respectively; however, the region of MSP1a responsible for immunogenicity was conserved. The plasmids pcDNA-msp1?, pcDNA-msp1? and pcDNA-msp5, which encode the MSPs genes under the control of cytomegalovirus enhancer/promoter and intron A, were constructed, multiplied in TOP10 E. coli and purified. Expression of MSP1a, MSP1b, and MSP5 in vitro was performed into Vero cells using lipofectamine 2000, following Indirect Immunofluorescen Assay (IFA) using monoclonal antibodies. Seven experimental groups of mice were immunized to evaluate the production of whole IgG and to determinate IgG1 and IgG2a isotype: G1-100 ml PBS; G2-100 mg empty vector; G3-100 mg A. marginale initial bodies + Freund´s adjuvant; G4-100 mg pcDNA-msp1a; G5-100 mg pcDNA-msp1b; G6-100 mg pcDNA-msp5; and G7-pool of recombinant plasmids (33 mg for each). Three weeks after the last immunization, mice were sacrified to evaluate spleen cells proliferation. Vero cells transfected with recombinants plasmids reacted with specific monoclonal antibodies, demonstrating the expression of msp genes. Specific IgG against MSP1a and MSP5 were detected in either by ELISA and Western blot. The groups that received pcDNA-msp1a and pcDNA-msp5 exhibited predominance for IgG2a production and splenocytes proliferation, suggesting that these recombinant plasmids are good candidates for elicited T helper 1 immune response. The association of three recombinant plasmids (pcDNA-msp1a, pcDNA-msp1b and pcDNA-msp5) used in the immunization of mice induced high antibodies response by ELISA and reacted with all recombinant proteins (rMSP1a, rMSP1b, and rMSP5) of A. marginale by Western blot. Also, the combination of plasmids provide strong lymphoproliferation (SI = 12,2), whereas the genes to MSP1a provide significant splenocytes (SI = 2,6) and the genes to MSP1b and MSP5 did not provide significant proliferation (SI<2). The results showed no suppression when the recombinant plasmids were taken in association, and demonstrated that they can generate significant T-cell lymphocyte. Thus, the immunization in association of recombinant plasmids encoding MSPs can be an effective strategy for immunoprofilaxy of anaplasmosis.
Fagundes, Naiara Simarro. « Diferentes estratégias do uso de sorgo para frangos de corte : desempenho e saúde intestinal ». Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/11/11139/tde-01082016-153147/.
Texte intégralThe aim of this study was to evaluate performance, intestinal health and metabolizability of diets in broilers fed different corn- or sorghum (ground or whole)- based diets, continuously or with abrupt change between the diets. Exp. 1 - Change in the type of grain: C100% (corn-based diet); S100% (sorghum-based diet); C:S50% (50% corn and 50% sorghum-based diet); PC-S (corn-based diet in pre-starter phase and sorghum-based diet in other phases); PS-C (sorghum-based diet in pre-starter phase and corn-based diet in other phases). Exp. 2 - Change in the form of sorghum grain: Gs100% (ground sorghum-based diet); Ws100% (whole sorghum-based diet); PGs-Ws (ground sorghum-based diet in pre-starter phase and whole sorghum-based diet in other phases); PWs-Gs (whole sorghum-based diet in pre-starter phase and ground sorghum-based diet in other phases). Experiments were conducted in a randomized block design for to evaluate performance and jejunal epithelium (r=8), intestinal microbiota (r=4) and metabolizabilty of diets (r=10). The changes between corn and sorghum did not affect performance, jejunal epithelium or metabolizability of the diets, but influenced the genera Clostridium, Weissella, Bacillus and Alkaliphilus in the small intestine, and Lactobacillus and Desulfotomaculum in the caecum. Whole sorghum resulted in decreased performance at seven days of age. At 40 days, Gs100% and PGs-Ws showed similar performance, PWs-Gs showed lower weight gain and the best feed conversion rate, and Ws100% showed the worst performance. Ws100% and PGs-Ws resulted in the biggest gizzard relative weight and the highest diet metabolizability values, as well as the lowest level of Clostridium and highest level of Actinomycetales and Bacillales in the small intestine. Ws100% showed lower level of Alkaliphilus and Enterococcus than Gs100% in the caecum. The best strategy to use sorghum in broilers diets is replacing 100% of corn for ground sorghum since the first day followed by change to whole sorghum, because this diet did not affect performance or jejunal epithelium, improved diet metabolizability values, and reduced Clostridium in the small intestine of broilers.
Johansson, Ann-Sofi. « RhoGTPase Signaling in Cell Polarity and Gene Regulation ». Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6698.
Texte intégralArruda, Andrelisse. « Utilização do promotor do gene PGK1 de Pichia pastoris para expressão heteróloga ». reponame:Repositório Institucional da UnB, 2008. http://repositorio.unb.br/handle/10482/2599.
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A levedura metilotrófica Pichia pastoris tem sido utilizada com sucesso para a expressão de várias proteínas heterólogas sendo que diversos vetores já foram desenvolvidos para este sistema. Os principais vetores de expressão de P. pastoris são baseados no promotor do gene AOX1 que codifica a enzima álcool oxidase 1. Alguns estudos têm sido realizados para o uso de promotores alternativos uma vez que o sistema AOX1 apresenta algumas desvantagens. Em nosso laboratório foi isolado e caracterizado o promotor do gene PGK1 de P. pastoris (PPGK1), um promotor forte e constitutivo, que representa uma alternativa promissora para a construção de novos vetores. O objetivo deste estudo foi determinar a região promotora mínima do PPGK1 por meio de deleções controladas utilizando o gene da α-amilase de Bacillus subtilis como gene repórter. Quatro deleções foram obtidas sendo que a menor (PPGKΔ3), com ~400 pb, ainda manteve atividade promotora. Foi demonstrado que esta seqüência é capaz de dirigir a integração de um vetor no genoma de P. pastoris e 51% dos clones transformantes tiveram mais de uma cópia integrada. O uso deste promotor propiciou a expressão heteróloga de α-amilase em altos níveis (250 U.mL-1). Também foram construídos vetores para expressão intracelular baseados no promotor PGK que, todavia, ainda necessitam ser aprimorados para uso em P. pastoris. _______________________________________________________________________________ ABSTRACT
The methylotrophic yeast Pichia pastoris has been successfully used for the expression of heterologous proteins and several different expression vectors have been developed for this system. The main expression vectors for P. pastoris are based on the alcohol oxidase 1 gene promoter, AOX1. Some studies have been carried out aiming at the use of alternative promoters once the AOX1 system shows some disadvantages. Our laboratory has isolated and characterized the P. pastoris promoter from the PGK1 gene (PPGK1), a strong and constitutive promoter, which represents a promising alternative for the construction of new vectors. The aim of this study was to determine the minimal promoter sequences from PPGK1 through controlled deletions using the α-amylase gene from Bacillus subtilis as a reporter gene. Four deletions were obtained and the smallest (PPGK Δ3) with ~ 400 bp, still maintained promoter activity. We have demonstrated that this sequence was able to direct vector integration into the P. pastoris genome and 51% of the transformants showed more than one copy integrated. The use of this promoter allowed high level expression of α-amylase (250 UmL-1). Also, vectors for intracellular expression were based on the PGK promoter were also constructed which however still need to be improved for use in P. pastoris.
Fontoura, Carla Adriane Ramos Segatto. « UM MÉTODO MULTIESTATÍSTICO PARA IDENTIFICAÇÃO DE VIAS GENÉTICAS DIFERENCIALMENTE EXPRESSAS ». Universidade Federal de Santa Maria, 2016. http://repositorio.ufsm.br/handle/1/3937.
Texte intégralThe determination of the causes and origins of a given disease is a complex undertaking, considering that there is a large number of genes engaged that interact with each other (Watson, 2006). Bioinformatics experts working in the search for a perfect integration between biology and information, in order to understand the likely factors that trigger certain diseases (Pevzner, 2000). To achieve this, the revolutionary methodology of Microarrays (LOCKHART et al., 1996) based on the gene expression of patients, it has been widely used to simultaneously measuring changes and regulation of the genes of the genome under certain biological conditions, resulting in a list of genes that may be considered interesting from a biological point of view for a particular disease. In this thesis, we present a multi-statistic method to detect differentially expressed genetic pathways in DNA microarray data. Many statistical methods of analysis are based on the use of a single statistical test. It is believed that the use of multiple tests decreases the number of false positive discoveries. Our method can be applied to transcriptome data to investigate which pathways have changes in expression when subjected to some type of disturbance. The method determines the activity of pathways evaluated, and verifies if the changes found are statistically significant through the bootstrap, Fisher exact and Wilcoxon tests. Implemented in R language and available for download from the Comprehensive R Archive Network (CRAN) as a package called PATHChange, our method showed consistency in its results with those predicted in the literature when tested for microarray of cancer and pre-cancer colon public data. The PATHChange method offers an alternative type of analysis of differentially expressed genes pathways for researchers seeking to determine phenotypes of diseases such as cancer.
A determinação das causas e origens de uma determinada doença é uma tarefa complexa, considerando que existe um grande número de genes comprometidos que interagem entre si (WATSON, 2006). Especialistas em Bioinformática trabalham na busca de uma perfeita integração entre a biologia e a informação, com o intuito de compreender os prováveis fatores que desencadeiam determinadas doenças (PEVZNER, 2000). Para tal, a metodologia revolucionária de Microarranjos (LOCKHART et al., 1996), baseada na expressão gênica de pacientes, tem sido amplamente utilizada para medir simultaneamente as mudanças e regulação dos genes do genoma sob certas condições biológicas, resultando em uma lista de genes que podem ser considerados interessantes do ponto de vista biológico para uma determinada doença. Na presente tese, nós apresentamos um método multiestatístico destinado à detectar vias genéticas diferencialmente expressas em dados de microarranjos de DNA. Grande parte dos métodos de análise estatística são baseados no uso de apenas um teste estatístico. Acredita-se que associar métodos estatísticos baseados em testes diferentes diminui o número de falsos positivos. O método que nós desenvolvemos determina a atividade das vias avaliadas, e verifica se as alterações encontradas são estatisticamente significativas através dos testes de bootstrap, exato de Fisher e Wilcoxon. Este método pode ser aplicado à dados de transcriptoma para investigar quais vias apresentam mudanças na expressão de seus genes quando submetidos à algum tipo de perturbação. Implementado em linguagem R e disponibilizado para download no CRAN (do inglês, Comprehensive R Archive Network) como um pacote denominado PATHChange, nosso método demonstrou consistência entre os seus resultados com os previstos na literatura quando testado para dados públicos de microarranjos de câncer e pré-câncer de cólon. O método do PATHChange oferece um tipo alternativo de análise de vias de genes diferencialmente expressas para os pesquisadores que buscam apurar fenótipos de doenças, tais como o câncer.
Ruiz, Jorge Luis Maria. « Caracterização de uma nanopartícula lipídica semelhante à LDL (LDE) como vetor para RNA de interferência ». Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/5/5167/tde-14062011-154226/.
Texte intégralNanoparticles are considered promising vectors for efficient and safe delivery of nucleic acids to specific types of cell or tissue, providing an alternative to viral vectors for gene therapy. However, most of these systems cannot target and deliver oligonucleotides to specific cells in vivo. The use of nanoemulsion functionally resemble low density emulsion could solve this problem, once particle is capable of direct the molecules transport to the cell through internalization in LDL receptors. Here, we describe a lipid system similar to low density lipoprotein, LDE, capable of targeting and release small interfering RNA (siRNA) to tumor cells in vitro and in vivo in a cell model that expresses multidrug resistance (sarcoma uterine cell line; MES-SA/Dx5). Were also studied the characteristics of uptake of the complex LDE-siRNA, as well as the downregulation of mdr-1 gene. The results suggest that LDE is stable and bind with high affinity to siRNAs allowing them to enter tumor cells, with cytoplasmic localization enhanced. In conclusion, LDE, binds to siRNA through LDL receptors, and promotes mdr-1 silenciament by RNAi in MES-sa/Dx5 cells, increasing their sensitivity to chemotherapeutics agents