Gene target discovery with network analysis in Toxoplasma gondii

Autores
Alonso, Andrés Mariano; Corvi, Maria Martha; Diambra, Luis Anibal
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Infectious diseases are of great relevance for global health, but needed drugs and vaccines have not been developed yet or are not efective in many cases. In fact, traditional scientifc approaches with intense focus on individual genes or proteins have not been successful in providing new treatments. Hence, innovations in technology and computational methods provide new tools to further understand complex biological systems such as pathogen biology. In this paper, we apply a gene regulatory network approach to analyze transcriptomic data of the parasite Toxoplasma gondii. By means of an optimization procedure, the phenotypic transitions between the stages associated with the life cycle of T. gondii were embedded into the dynamics of a gene regulatory network. Thus, through this methodology we were able to reconstruct a gene regulatory network able to emulate the life cycle of the pathogen. The community network analysis has revealed that nodes of the network can be organized in seven communities which allow us to assign putative functions to 338 previously uncharacterized genes, 25 of which are predicted as new pathogenic factors. Furthermore, we identifed a small gene circuit that drives a series of phenotypic transitions that characterize the life cycle of this pathogen. These new fndings can contribute to the understanding of parasite pathogenesis.
Fil: Alonso, Andrés Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Fil: Corvi, Maria Martha. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Diambra, Luis Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Materia
TOXOPLASMA GONDII
GENE REGULATION
NETWORK ANALYSIS
ANTIGENS
GENE REGULATION
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/112038
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/112038
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Gene target discovery with network analysis in Toxoplasma gondiiAlonso, Andrés MarianoCorvi, Maria MarthaDiambra, Luis AnibalTOXOPLASMA GONDIIGENE REGULATIONNETWORK ANALYSISANTIGENSGENE REGULATIONhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Infectious diseases are of great relevance for global health, but needed drugs and vaccines have not been developed yet or are not efective in many cases. In fact, traditional scientifc approaches with intense focus on individual genes or proteins have not been successful in providing new treatments. Hence, innovations in technology and computational methods provide new tools to further understand complex biological systems such as pathogen biology. In this paper, we apply a gene regulatory network approach to analyze transcriptomic data of the parasite Toxoplasma gondii. By means of an optimization procedure, the phenotypic transitions between the stages associated with the life cycle of T. gondii were embedded into the dynamics of a gene regulatory network. Thus, through this methodology we were able to reconstruct a gene regulatory network able to emulate the life cycle of the pathogen. The community network analysis has revealed that nodes of the network can be organized in seven communities which allow us to assign putative functions to 338 previously uncharacterized genes, 25 of which are predicted as new pathogenic factors. Furthermore, we identifed a small gene circuit that drives a series of phenotypic transitions that characterize the life cycle of this pathogen. These new fndings can contribute to the understanding of parasite pathogenesis.Fil: Alonso, Andrés Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaFil: Corvi, Maria Martha. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Diambra, Luis Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; ArgentinaNature Publishing Group2019-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/112038Alonso, Andrés Mariano; Corvi, Maria Martha; Diambra, Luis Anibal; Gene target discovery with network analysis in Toxoplasma gondii; Nature Publishing Group; Scientific Reports; 9; 646; 1-2019; 1-142045-2322CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41598-018-36671-yinfo:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-018-36671-yinfo:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/10.1101/397398v1info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:45:26Zoai:ri.conicet.gov.ar:11336/112038instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:45:27.176CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Gene target discovery with network analysis in Toxoplasma gondii
title Gene target discovery with network analysis in Toxoplasma gondii
spellingShingle Gene target discovery with network analysis in Toxoplasma gondii
Alonso, Andrés Mariano
TOXOPLASMA GONDII
GENE REGULATION
NETWORK ANALYSIS
ANTIGENS
GENE REGULATION
title_short Gene target discovery with network analysis in Toxoplasma gondii
title_full Gene target discovery with network analysis in Toxoplasma gondii
title_fullStr Gene target discovery with network analysis in Toxoplasma gondii
title_full_unstemmed Gene target discovery with network analysis in Toxoplasma gondii
title_sort Gene target discovery with network analysis in Toxoplasma gondii
dc.creator.none.fl_str_mv Alonso, Andrés Mariano
Corvi, Maria Martha
Diambra, Luis Anibal
author Alonso, Andrés Mariano
author_facet Alonso, Andrés Mariano
Corvi, Maria Martha
Diambra, Luis Anibal
author_role author
author2 Corvi, Maria Martha
Diambra, Luis Anibal
author2_role author
author
dc.subject.none.fl_str_mv TOXOPLASMA GONDII
GENE REGULATION
NETWORK ANALYSIS
ANTIGENS
GENE REGULATION
topic TOXOPLASMA GONDII
GENE REGULATION
NETWORK ANALYSIS
ANTIGENS
GENE REGULATION
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Infectious diseases are of great relevance for global health, but needed drugs and vaccines have not been developed yet or are not efective in many cases. In fact, traditional scientifc approaches with intense focus on individual genes or proteins have not been successful in providing new treatments. Hence, innovations in technology and computational methods provide new tools to further understand complex biological systems such as pathogen biology. In this paper, we apply a gene regulatory network approach to analyze transcriptomic data of the parasite Toxoplasma gondii. By means of an optimization procedure, the phenotypic transitions between the stages associated with the life cycle of T. gondii were embedded into the dynamics of a gene regulatory network. Thus, through this methodology we were able to reconstruct a gene regulatory network able to emulate the life cycle of the pathogen. The community network analysis has revealed that nodes of the network can be organized in seven communities which allow us to assign putative functions to 338 previously uncharacterized genes, 25 of which are predicted as new pathogenic factors. Furthermore, we identifed a small gene circuit that drives a series of phenotypic transitions that characterize the life cycle of this pathogen. These new fndings can contribute to the understanding of parasite pathogenesis.
Fil: Alonso, Andrés Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
Fil: Corvi, Maria Martha. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina
Fil: Diambra, Luis Anibal. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de La Plata. Centro Regional de Estudios Genómicos; Argentina
description Infectious diseases are of great relevance for global health, but needed drugs and vaccines have not been developed yet or are not efective in many cases. In fact, traditional scientifc approaches with intense focus on individual genes or proteins have not been successful in providing new treatments. Hence, innovations in technology and computational methods provide new tools to further understand complex biological systems such as pathogen biology. In this paper, we apply a gene regulatory network approach to analyze transcriptomic data of the parasite Toxoplasma gondii. By means of an optimization procedure, the phenotypic transitions between the stages associated with the life cycle of T. gondii were embedded into the dynamics of a gene regulatory network. Thus, through this methodology we were able to reconstruct a gene regulatory network able to emulate the life cycle of the pathogen. The community network analysis has revealed that nodes of the network can be organized in seven communities which allow us to assign putative functions to 338 previously uncharacterized genes, 25 of which are predicted as new pathogenic factors. Furthermore, we identifed a small gene circuit that drives a series of phenotypic transitions that characterize the life cycle of this pathogen. These new fndings can contribute to the understanding of parasite pathogenesis.
publishDate 2019
dc.date.none.fl_str_mv 2019-01
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/112038
Alonso, Andrés Mariano; Corvi, Maria Martha; Diambra, Luis Anibal; Gene target discovery with network analysis in Toxoplasma gondii; Nature Publishing Group; Scientific Reports; 9; 646; 1-2019; 1-14
2045-2322
CONICET Digital
CONICET
url http://hdl.handle.net/11336/112038
identifier_str_mv Alonso, Andrés Mariano; Corvi, Maria Martha; Diambra, Luis Anibal; Gene target discovery with network analysis in Toxoplasma gondii; Nature Publishing Group; Scientific Reports; 9; 646; 1-2019; 1-14
2045-2322
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/s41598-018-36671-y
info:eu-repo/semantics/altIdentifier/doi/10.1038/s41598-018-36671-y
info:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/10.1101/397398v1
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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