Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano
Autor(a) principal: | |
---|---|
Data de Publicação: | 2016 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | Repositório Institucional da UFSCAR |
Texto Completo: | https://repositorio.ufscar.br/handle/ufscar/7537 |
Resumo: | Knowledge about horizontal gene transfer has been proposed even before the determination of the molecular structure of DNA. It has been experimentally shown that micro-homologies rich in adenine and cytosine mediates the integration of Trypanosoma cruzi’s kDNA minicircle, in the vertebrate genome. After human genome sequencing, the genome characterization of different organisms has been one of the main driving forces of science, providing a quantity of biological data for modern biomedical research, unprecedented in the history of science. However, even though traditional DNA mapping algorithms are highly accurate, they operate at a much lower rate than that needed for the next generation sequencers to accumulate new data. This great asymmetry between data generation and analysis capability requires the rapid evolution of mapping and reading algorithms so that this large volume of information can be worked through targeted searches. Thus, this work proposes an efficient, fast and easy way to search and locate multiple signatures of indicators that allow exogenous kDNA integration in the human genome, by creating a set of scripts for in silico analysis adapted to large files sequences. Three scripts based in R language were developed: to permute the elements (nucleic acids or amino acids codes); for search, grouping and plotting matches in genome; and for counting total matches and chromosomal window. All adenine and cytosine signatures were properly identified in the human genome, but no point more susceptible to T. cruzi kDNA integration was identified. With the obtained data, a genetic map was created, listing all matchings in each cytogenetic band, but it was not possible to identify which chromosome was more prone to mutations, since the bigger the chromosome is, the higher the quantity of matches are. |
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Santana, Jhonne Pedro PedottLeonardecz, Eduardohttp://lattes.cnpq.br/5987629981784287Borra, Ricardo Carneirohttp://lattes.cnpq.br/5655362515357840http://lattes.cnpq.br/70583669017636320b658af5-8176-4057-80e1-ece34febb84b2016-09-27T19:57:40Z2016-09-27T19:57:40Z2016-03-23SANTANA, Jhonne Pedro Pedott. Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano. 2016. Dissertação (Mestrado em Genética Evolutiva e Biologia Molecular) – Universidade Federal de São Carlos, São Carlos, 2016. Disponível em: https://repositorio.ufscar.br/handle/ufscar/7537.https://repositorio.ufscar.br/handle/ufscar/7537Knowledge about horizontal gene transfer has been proposed even before the determination of the molecular structure of DNA. It has been experimentally shown that micro-homologies rich in adenine and cytosine mediates the integration of Trypanosoma cruzi’s kDNA minicircle, in the vertebrate genome. After human genome sequencing, the genome characterization of different organisms has been one of the main driving forces of science, providing a quantity of biological data for modern biomedical research, unprecedented in the history of science. However, even though traditional DNA mapping algorithms are highly accurate, they operate at a much lower rate than that needed for the next generation sequencers to accumulate new data. This great asymmetry between data generation and analysis capability requires the rapid evolution of mapping and reading algorithms so that this large volume of information can be worked through targeted searches. Thus, this work proposes an efficient, fast and easy way to search and locate multiple signatures of indicators that allow exogenous kDNA integration in the human genome, by creating a set of scripts for in silico analysis adapted to large files sequences. Three scripts based in R language were developed: to permute the elements (nucleic acids or amino acids codes); for search, grouping and plotting matches in genome; and for counting total matches and chromosomal window. All adenine and cytosine signatures were properly identified in the human genome, but no point more susceptible to T. cruzi kDNA integration was identified. With the obtained data, a genetic map was created, listing all matchings in each cytogenetic band, but it was not possible to identify which chromosome was more prone to mutations, since the bigger the chromosome is, the higher the quantity of matches are.Com o sequenciamento do genoma humano e tantas outras espécies, abre-se agora uma nova janela de oportunidades analíticas. Podemos pensar em fazer buscas orientadas dentro dessa massa enorme de dados publicados em bancos de dados biológicos. Tendo isso em foco, buscamos estruturar uma forma automatizada de busca dentro do genoma humano, pela qual pudéssemos inferir sobre os sítios mais prováveis de integração de DNA exógeno. Para isso utilizamos como modelo os trabalhos que indicam que a doença de Chagas é produzida pela introgressão do kDNA de Trypanosoma cruzi no genoma hospedeiro, por meio de herança genética horizontal. Já foi demonstrado experimentalmente que micro-homologias ricas em adenina e citosina medeiam as integrações de minicírculos de kDNA do T. cruzi, no genoma de vertebrados. Deste modo, o presente trabalho propõe uma maneira eficiente, fácil e rápida para a busca e localização de múltiplas assinaturas dos sinalizadores que propiciam a introgressão do kDNA exógeno no genoma humano, através da criação de um conjunto de scripts para análises in silico, adaptados a grandes arquivos de sequências. Foram desenvolvidos três scripts, baseados na linguagem R: para permutação de elementos (ácidos nucleicos ou aminoácidos); para busca, agrupamento e plotagem das correspondências em genoma; e para contagem total de correspondências e contagem por janela cromossômica. Todas as assinaturas compostas por adenina e citosina (motivos CA’s) foram devidamente identificadas no genoma humano, porém não foi identificado nenhum ponto mais suscetível à integração do kDNA de T. cruzi. Com os dados obtidos, um mapa genético foi criado, listando as correspondências em cada banda citogenética, porém não foi possível identificar qual cromossomo possui maior propensão à mutações, já que quanto maior o cromossomo, maior é a quantidade de correspondências presentes.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)porUniversidade Federal de São CarlosCâmpus São CarlosPrograma de Pós-Graduação em Genética Evolutiva e Biologia Molecular - PPGGEvUFSCarTransferência Horizontal de GenesAnálise BioinformáticaGenoma HumanoDoença de ChagasTrypanosoma cruzikDNAHorizontal Gene TransferBioinformatics AnalysisHuman GenomeChagas DiseaseTrypanosoma cruzikDNACIENCIAS BIOLOGICASLocalização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humanoLOCALIZATION OF POTENTIAL REGIONS FOR INTEGRATION OF Trypanosoma cruzi KDNA IN THE HUMAN GENOMEinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisOnline6006001c8bb01a-83d1-493d-9277-2e2560e8cafeinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFSCARinstname:Universidade Federal de São Carlos (UFSCAR)instacron:UFSCARORIGINALDissJPPS.pdfDissJPPS.pdfapplication/pdf2939420https://repositorio.ufscar.br/bitstream/ufscar/7537/1/DissJPPS.pdf44366c4d259a65ba75e54d36b01b8483MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81957https://repositorio.ufscar.br/bitstream/ufscar/7537/2/license.txtae0398b6f8b235e40ad82cba6c50031dMD52TEXTDissJPPS.pdf.txtDissJPPS.pdf.txtExtracted texttext/plain114795https://repositorio.ufscar.br/bitstream/ufscar/7537/3/DissJPPS.pdf.txt11cf35d04674d1a0428ad03a3633cec0MD53THUMBNAILDissJPPS.pdf.jpgDissJPPS.pdf.jpgIM Thumbnailimage/jpeg7516https://repositorio.ufscar.br/bitstream/ufscar/7537/4/DissJPPS.pdf.jpgfd655280314afa755bcaa2bf5cfe259dMD54ufscar/75372023-09-18 18:30:51.798oai:repositorio.ufscar.br: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Repositório InstitucionalPUBhttps://repositorio.ufscar.br/oai/requestopendoar:43222023-09-18T18:30:51Repositório Institucional da UFSCAR - Universidade Federal de São Carlos (UFSCAR)false |
dc.title.por.fl_str_mv |
Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano |
dc.title.alternative.eng.fl_str_mv |
LOCALIZATION OF POTENTIAL REGIONS FOR INTEGRATION OF Trypanosoma cruzi KDNA IN THE HUMAN GENOME |
title |
Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano |
spellingShingle |
Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano Santana, Jhonne Pedro Pedott Transferência Horizontal de Genes Análise Bioinformática Genoma Humano Doença de Chagas Trypanosoma cruzi kDNA Horizontal Gene Transfer Bioinformatics Analysis Human Genome Chagas Disease Trypanosoma cruzi kDNA CIENCIAS BIOLOGICAS |
title_short |
Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano |
title_full |
Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano |
title_fullStr |
Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano |
title_full_unstemmed |
Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano |
title_sort |
Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano |
author |
Santana, Jhonne Pedro Pedott |
author_facet |
Santana, Jhonne Pedro Pedott |
author_role |
author |
dc.contributor.authorlattes.por.fl_str_mv |
http://lattes.cnpq.br/7058366901763632 |
dc.contributor.author.fl_str_mv |
Santana, Jhonne Pedro Pedott |
dc.contributor.advisor1.fl_str_mv |
Leonardecz, Eduardo |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/5987629981784287 |
dc.contributor.advisor-co1.fl_str_mv |
Borra, Ricardo Carneiro |
dc.contributor.advisor-co1Lattes.fl_str_mv |
http://lattes.cnpq.br/5655362515357840 |
dc.contributor.authorID.fl_str_mv |
0b658af5-8176-4057-80e1-ece34febb84b |
contributor_str_mv |
Leonardecz, Eduardo Borra, Ricardo Carneiro |
dc.subject.por.fl_str_mv |
Transferência Horizontal de Genes Análise Bioinformática Genoma Humano Doença de Chagas Trypanosoma cruzi kDNA |
topic |
Transferência Horizontal de Genes Análise Bioinformática Genoma Humano Doença de Chagas Trypanosoma cruzi kDNA Horizontal Gene Transfer Bioinformatics Analysis Human Genome Chagas Disease Trypanosoma cruzi kDNA CIENCIAS BIOLOGICAS |
dc.subject.eng.fl_str_mv |
Horizontal Gene Transfer Bioinformatics Analysis Human Genome Chagas Disease Trypanosoma cruzi kDNA |
dc.subject.cnpq.fl_str_mv |
CIENCIAS BIOLOGICAS |
description |
Knowledge about horizontal gene transfer has been proposed even before the determination of the molecular structure of DNA. It has been experimentally shown that micro-homologies rich in adenine and cytosine mediates the integration of Trypanosoma cruzi’s kDNA minicircle, in the vertebrate genome. After human genome sequencing, the genome characterization of different organisms has been one of the main driving forces of science, providing a quantity of biological data for modern biomedical research, unprecedented in the history of science. However, even though traditional DNA mapping algorithms are highly accurate, they operate at a much lower rate than that needed for the next generation sequencers to accumulate new data. This great asymmetry between data generation and analysis capability requires the rapid evolution of mapping and reading algorithms so that this large volume of information can be worked through targeted searches. Thus, this work proposes an efficient, fast and easy way to search and locate multiple signatures of indicators that allow exogenous kDNA integration in the human genome, by creating a set of scripts for in silico analysis adapted to large files sequences. Three scripts based in R language were developed: to permute the elements (nucleic acids or amino acids codes); for search, grouping and plotting matches in genome; and for counting total matches and chromosomal window. All adenine and cytosine signatures were properly identified in the human genome, but no point more susceptible to T. cruzi kDNA integration was identified. With the obtained data, a genetic map was created, listing all matchings in each cytogenetic band, but it was not possible to identify which chromosome was more prone to mutations, since the bigger the chromosome is, the higher the quantity of matches are. |
publishDate |
2016 |
dc.date.accessioned.fl_str_mv |
2016-09-27T19:57:40Z |
dc.date.available.fl_str_mv |
2016-09-27T19:57:40Z |
dc.date.issued.fl_str_mv |
2016-03-23 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
SANTANA, Jhonne Pedro Pedott. Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano. 2016. Dissertação (Mestrado em Genética Evolutiva e Biologia Molecular) – Universidade Federal de São Carlos, São Carlos, 2016. Disponível em: https://repositorio.ufscar.br/handle/ufscar/7537. |
dc.identifier.uri.fl_str_mv |
https://repositorio.ufscar.br/handle/ufscar/7537 |
identifier_str_mv |
SANTANA, Jhonne Pedro Pedott. Localização de regiões potenciais para integração do kDNA de Trypanosoma cruzi no genoma humano. 2016. Dissertação (Mestrado em Genética Evolutiva e Biologia Molecular) – Universidade Federal de São Carlos, São Carlos, 2016. Disponível em: https://repositorio.ufscar.br/handle/ufscar/7537. |
url |
https://repositorio.ufscar.br/handle/ufscar/7537 |
dc.language.iso.fl_str_mv |
por |
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por |
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600 600 |
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1c8bb01a-83d1-493d-9277-2e2560e8cafe |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Universidade Federal de São Carlos Câmpus São Carlos |
dc.publisher.program.fl_str_mv |
Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular - PPGGEv |
dc.publisher.initials.fl_str_mv |
UFSCar |
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Universidade Federal de São Carlos Câmpus São Carlos |
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