Computational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystems

Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia plant phyllosphere microorgani...

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Autores:
Díaz Riaño, Jorge Iván
Tipo de recurso:
Fecha de publicación:
2018
Institución:
Universidad de los Andes
Repositorio:
Séneca: repositorio Uniandes
Idioma:
eng
OAI Identifier:
oai:repositorio.uniandes.edu.co:1992/34599
Acceso en línea:
http://hdl.handle.net/1992/34599
Palabra clave:
Radiación ultravioleta - Investigaciones
Deinococcus swuensis - Investigaciones
Deinococcus swuensis - Efecto de la radiación ultravioleta
Espeletia - Investigaciones
Biología
Rights
openAccess
License
http://creativecommons.org/licenses/by-nc-sa/4.0/
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dc.title.es_CO.fl_str_mv Computational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystems
title Computational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystems
spellingShingle Computational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystems
Radiación ultravioleta - Investigaciones
Deinococcus swuensis - Investigaciones
Deinococcus swuensis - Efecto de la radiación ultravioleta
Espeletia - Investigaciones
Biología
title_short Computational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystems
title_full Computational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystems
title_fullStr Computational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystems
title_full_unstemmed Computational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystems
title_sort Computational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystems
dc.creator.fl_str_mv Díaz Riaño, Jorge Iván
dc.contributor.advisor.none.fl_str_mv Reyes Muñoz, Alejandro
Zambrano Eder, María Mercedes
dc.contributor.author.none.fl_str_mv Díaz Riaño, Jorge Iván
dc.contributor.jury.none.fl_str_mv Duitama Castellanos, Jorge Alexander
Chica Pratesi, Claudia
dc.subject.keyword.es_CO.fl_str_mv Radiación ultravioleta - Investigaciones
Deinococcus swuensis - Investigaciones
Deinococcus swuensis - Efecto de la radiación ultravioleta
Espeletia - Investigaciones
topic Radiación ultravioleta - Investigaciones
Deinococcus swuensis - Investigaciones
Deinococcus swuensis - Efecto de la radiación ultravioleta
Espeletia - Investigaciones
Biología
dc.subject.themes.none.fl_str_mv Biología
description Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of D. swuensis showed high survival rate of 60% after UVR treatment at 800 J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400 J/m2 of UVR (whit survival rate >95%). Differentially expressed genes were identified, using a D. swuensis sequenced reference strain, with the R-Bioconductor package NOISeq and compared with other reported resistance strategies for bacteria. Few genes were identified as being overexpressed and these included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also found to be differentially expressed, some of which have been previously implicated in the response to stress conditions. Domain prediction for some unannotated hypothetical proteins is also proposed. Elucidating UVR resistance strategies is crucial to develop and implement novel strategies against resistant bacteria and gain knowledge about their adaptation capacity to extreme environmental conditions.
publishDate 2018
dc.date.issued.none.fl_str_mv 2018
dc.date.accessioned.none.fl_str_mv 2020-06-10T09:13:45Z
dc.date.available.none.fl_str_mv 2020-06-10T09:13:45Z
dc.type.spa.fl_str_mv Trabajo de grado - Maestría
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dc.identifier.uri.none.fl_str_mv http://hdl.handle.net/1992/34599
dc.identifier.pdf.none.fl_str_mv u808101.pdf
dc.identifier.instname.spa.fl_str_mv instname:Universidad de los Andes
dc.identifier.reponame.spa.fl_str_mv reponame:Repositorio Institucional Séneca
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identifier_str_mv u808101.pdf
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dc.language.iso.es_CO.fl_str_mv eng
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dc.publisher.program.es_CO.fl_str_mv Maestría en Biología Computacional
dc.publisher.faculty.es_CO.fl_str_mv Facultad de Ciencias
dc.publisher.department.es_CO.fl_str_mv Departamento de Biología
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spelling Al consultar y hacer uso de este recurso, está aceptando las condiciones de uso establecidas por los autores.http://creativecommons.org/licenses/by-nc-sa/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Reyes Muñoz, Alejandro9e4d3f3f-d194-4692-aa8b-4497c83504ba400Zambrano Eder, María Mercedes2864709d-4964-4d01-81c6-f52f482c82d0500Díaz Riaño, Jorge Iváne3217240-7527-4243-b7dc-90807569415b500Duitama Castellanos, Jorge AlexanderChica Pratesi, Claudia2020-06-10T09:13:45Z2020-06-10T09:13:45Z2018http://hdl.handle.net/1992/34599u808101.pdfinstname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/Ultraviolet radiation (UVR) is widely known as deleterious for many organisms since it can cause damage to biomolecules either directly or indirectly via formation of reactive oxygen species. The goal of this study was to analyze the capacity of high-mountain Espeletia plant phyllosphere microorganisms to survive UVR and to identify genes related to resistance strategies. A strain of D. swuensis showed high survival rate of 60% after UVR treatment at 800 J/m2 and was used for differential expression analysis using RNA-seq after exposing cells to 400 J/m2 of UVR (whit survival rate >95%). Differentially expressed genes were identified, using a D. swuensis sequenced reference strain, with the R-Bioconductor package NOISeq and compared with other reported resistance strategies for bacteria. Few genes were identified as being overexpressed and these included transcriptional regulators and genes involved in protection against damage by UVR. Non-coding (nc)RNAs were also found to be differentially expressed, some of which have been previously implicated in the response to stress conditions. Domain prediction for some unannotated hypothetical proteins is also proposed. Elucidating UVR resistance strategies is crucial to develop and implement novel strategies against resistant bacteria and gain knowledge about their adaptation capacity to extreme environmental conditions.La radiación ultravioleta (UVR) es ampliamente conocida como un factor deletéreo para muchos organismos, esta puede causar daños atacando directamente las biomoléculas o generando la formación indirecta de especies reactivas de oxígeno. El objetivo de este estudio fue analizar la capacidad de supervivencia a UVR de los microorganismos asociados a la filósfera de Espeletia. Una cepa de D. swuensis mostró una tasa de supervivencia de 60% posterior al tratamiento por UVR a 800 J/m2 y fue usada para el análisis de expresión diferencial a través de RNA-seq sobre células expuestas a de UVR 400 J/m2 (con una tasa de supervivencia >95%). Los genes diferencialmente expresados fueron identificados usando como referencia una cepa secuenciada de D. swuensis con el paquete para R-Biocondutor NOISeq y comparándolo con estrategias de resistencia reportadas para bacteria. Se identificaron pocos genes diferencialmente expresados, estos incluyeron reguladores transcripcionaes y genes responsables de la protección contra daño por UVR. Algunos ARNs no codificantes (ncARNs) tuvieron expresión diferencial y han sido relacionados con la respuesta a condiciones de estrés. La predicción de dominios funcionales para algunas proteínas hipotéticas también es sugerida. Dilucidar las estrategias de resistencia a UVR es crucial para desarrollar e implementar nuevas aproximaciones contra las bacterias resistentes mejorando el conocimiento acerca de su capacidad de adaptación a condiciones ambientales extremas.Magíster en Biología ComputacionalMaestría48 hojasapplication/pdfengUniandesMaestría en Biología ComputacionalFacultad de CienciasDepartamento de Biologíainstname:Universidad de los Andesreponame:Repositorio Institucional SénecaComputational search of UV radiation resistance strategies in Deinococcus swuensis, isolated from paramo ecosystemsTrabajo de grado - Maestríainfo:eu-repo/semantics/masterThesishttp://purl.org/coar/version/c_970fb48d4fbd8a85Texthttp://purl.org/redcol/resource_type/TMRadiación ultravioleta - InvestigacionesDeinococcus swuensis - InvestigacionesDeinococcus swuensis - Efecto de la radiación ultravioletaEspeletia - InvestigacionesBiologíaPublicationORIGINALu808101.pdfapplication/pdf2758483https://repositorio.uniandes.edu.co/bitstreams/d6b42a98-c499-4724-bac1-f3e280a6d4a2/download5fa26ec21163cead59cb164dd6cbeffcMD51TEXTu808101.pdf.txtu808101.pdf.txtExtracted texttext/plain93436https://repositorio.uniandes.edu.co/bitstreams/b21892a0-d65d-4930-aafb-ef60cfd35fb7/download055bb3a329d1c2413c5c053691889e44MD54THUMBNAILu808101.pdf.jpgu808101.pdf.jpgIM Thumbnailimage/jpeg26180https://repositorio.uniandes.edu.co/bitstreams/77e23330-10fb-45c9-bf0d-e71b5cf374b6/download7142099415b13b1f0f8380cfa33a486fMD551992/34599oai:repositorio.uniandes.edu.co:1992/345992023-10-10 19:23:59.762http://creativecommons.org/licenses/by-nc-sa/4.0/open.accesshttps://repositorio.uniandes.edu.coRepositorio institucional Sénecaadminrepositorio@uniandes.edu.co

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