Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments

1 documento

Autores:: Zambrano, María Mercedes
Baena, Sandra
Venegas de Balzer, Ivonne
Alvarez , Diana
Torres, Esperanza
Chacón, María Isabel
López, Camilo
Nemogá, Gabriel
Vélez, Patricia
Moreno, Pedro A.
Chacón , María Isabel
López, Camilo
Nemogá , Gabriel
Vélez, Patricia
Moreno, Pedro A.
Restrepo, Silvia
Alvarez , Luis Miguel
Barraza, Fernando
González, Janneth

Tipo de recurso:: Investigation report

Fecha de publicación:: 2010

Institución:: Ministerio de Ciencia, Tecnología e Innovación

Repositorio:: Repositorio Minciencias

Idioma:: spa

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dc.title.spa.fl_str_mv	Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments
title	Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments
spellingShingle	Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments Desarrollo de software Investigación y desarrollo Proyectos de investigación Bioinformática
title_short	Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments
title_full	Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments
title_fullStr	Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments
title_full_unstemmed	Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments
title_sort	Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments
dc.creator.fl_str_mv	Zambrano, María Mercedes Baena, Sandra Venegas de Balzer, Ivonne Alvarez , Diana Torres, Esperanza Chacón, María Isabel López, Camilo Nemogá, Gabriel Vélez, Patricia Moreno, Pedro A. Chacón , María Isabel López, Camilo Nemogá , Gabriel Vélez, Patricia Moreno, Pedro A. Restrepo, Silvia Alvarez , Luis Miguel Barraza, Fernando González, Janneth
dc.contributor.author.none.fl_str_mv	Zambrano, María Mercedes Baena, Sandra Venegas de Balzer, Ivonne Alvarez , Diana Torres, Esperanza Chacón, María Isabel López, Camilo Nemogá, Gabriel Vélez, Patricia Moreno, Pedro A. Chacón , María Isabel López, Camilo Nemogá , Gabriel Vélez, Patricia Moreno, Pedro A. Restrepo, Silvia Alvarez , Luis Miguel Barraza, Fernando González, Janneth
dc.subject.lemb.none.fl_str_mv	Desarrollo de software Investigación y desarrollo Proyectos de investigación
topic	Desarrollo de software Investigación y desarrollo Proyectos de investigación Bioinformática
dc.subject.proposal.spa.fl_str_mv	Bioinformática
description	1 documento
publishDate	2010
dc.date.issued.none.fl_str_mv	2010-02
dc.date.accessioned.none.fl_str_mv	2024-01-05T17:20:52Z
dc.date.available.none.fl_str_mv	2024-01-05T17:20:52Z
dc.type.none.fl_str_mv	Informe de investigación
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dc.identifier.uri.none.fl_str_mv	https://repositorio.minciencias.gov.co/handle/20.500.14143/50187
url	https://repositorio.minciencias.gov.co/handle/20.500.14143/50187
dc.language.iso.none.fl_str_mv	spa
language	spa
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dc.rights.accessrights.none.fl_str_mv	info:eu-repo/semantics/openAccess
dc.rights.creativecommons.none.fl_str_mv	Atribución 4.0 Internacional (CC BY 4.0)
rights_invalid_str_mv	https://creativecommons.org/licenses/by/4.0/ Atribución 4.0 Internacional (CC BY 4.0) http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv	openAccess
dc.format.extent.none.fl_str_mv	39 p.
dc.format.mimetype.none.fl_str_mv	application/pdf
dc.publisher.none.fl_str_mv	Corporación Corpogen Pontificia Universidad Javeriana Universidad Naciona l de Colombia Universidad del Cauca Universidad del Valle Universidad de Caldas ParqueSoft
dc.publisher.place.none.fl_str_mv	Bogotá
publisher.none.fl_str_mv	Corporación Corpogen Pontificia Universidad Javeriana Universidad Naciona l de Colombia Universidad del Cauca Universidad del Valle Universidad de Caldas ParqueSoft
institution	Ministerio de Ciencia, Tecnología e Innovación
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spelling	Zambrano, María MercedesBaena, SandraVenegas de Balzer, IvonneAlvarez , DianaTorres, EsperanzaChacón, María IsabelLópez, CamiloNemogá, GabrielVélez, PatriciaMoreno, Pedro A.Chacón , María IsabelLópez, CamiloNemogá , GabrielVélez, PatriciaMoreno, Pedro A.Restrepo, SilviaAlvarez , Luis MiguelBarraza, FernandoGonzález, Janneth2024-01-05T17:20:52Z2024-01-05T17:20:52Z2010-02https://repositorio.minciencias.gov.co/handle/20.500.14143/501871 documentoThe present report summarizes work carried out during t he first t wo years ( Phase 1) . During this ti me we have worked on building the capacity to carry ou t studies in both genomics and bioinformatics by exploring new ecosystems by bioprospecting of themicrobial diversity present in the Nevados National Natural Park (Nevados NNP) . We have currently stud ied the diversity present in different habitats , such as soils and thermal springs, and have moved towards t he construction of libraries and a nalysis of the metagenome itself. The screens of our libraries for cellulases and lipases have thus far identified 2 clones for each of the screens . Screens of all clones available are still being carried out . In addition , new libraries are being constructed both in new vectors and using DNA from enriched cultures. These studies are being complemente d by the isolation and analysis of culture collections of different microbes present in these hab itats . The bioinformatics work has focused on the development and t esting of pipelines for analysis of sequence data and of microbial diversity. Mining in formation from the metagenome has been specifically emphasized during the last months, both because it provides valuable biological information and because it allows u s to test different approaches and tools for data analys is and for comparative work. Fu t ure work w ill focus on the use and development of additional tools and strateg ies for analysis of metagenomic and genomic data . In addition , laboratory work will also move towards identification of potentially useful compounds . Throughout the project we have also worked continually in aspects that are extremely relevant to diversity and bioprospecting in Colombia. This wo r k covers aspects such as intellectual property rights, competitive intell igence and analysi s of the current regimen on access to genetic resources.39 p.application/pdfspaCorporación CorpogenPontificia Universidad JaverianaUniversidad Naciona l de ColombiaUniversidad del CaucaUniversidad del ValleUniversidad de CaldasParqueSoftBogotáhttps://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessAtribución 4.0 Internacional (CC BY 4.0)http://purl.org/coar/access_right/c_abf2Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environmentsInforme de investigaciónhttp://purl.org/coar/resource_type/c_18wshttp://purl.org/coar/resource_type/c_18ghhttp://purl.org/coar/resource_type/c_93fcTextinfo:eu-repo/semantics/reporthttp://purl.org/redcol/resource_type/INFhttp://purl.org/coar/version/c_970fb48d4fbd8a85Desarrollo de softwareInvestigación y desarrolloProyectos de investigaciónBioinformáticaEstudiantes, Profesores, Comunidad científica colombiana, etc.Altschul, S. F., et al. (1990). "Basic local alignment search tool." J Mol Biol215(3): 403- 1 O.Ashby, M. N., et al. (2007). "Serial analysis of rRNA genes and the unexpected do mi nance of rare members of microbial communities." Appl Enviran Microbio!73(14): 4532-42.Baker, G. C., et al. (2003). "Review and re-analysis of domain-specific 16S primers." J Microbio! Methods 55(3) : 541-55.Bierman, M. , et al. (1992) . "Piasmid cloning vectors for the conjuga! transfer of DNA from Escherichia coli to Streptomyces spp." Gene 116(1 ): 43-9.Brodie, E. L. , et al. (2007). "Urban aerosols harbar divers e and dynamic bacteria! populations." Proc Natl Acad Sci U S A 104(1): 299-304.Chan, O. C., et al. (2005). "Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment." Enviran Microbio!7(8): 1139-49.Day, J. M. & J. Dóbereiner (1976). "Physiological aspects of N2-fixation by a Spirillumfrom Digitaria roots" Soil Biol Biochem 8(1 ): 45-50.Delgado, L. F. (2009). Diversidad microbiana en ambientes extremos del Parque Nacional Natural Los Nevados: una aproximación basada en el sistema de secuenciación 454. Ciencias Biológicas. Bogotá, Universidad de los Andes.Biology/Microbiology.DeSantis, T. Z., et al. (2007). "High-density universal 16S rRNA microarray analysisreveals broader diversity than typical clone library when sampling theenvironment." Microb Ecol 53(3): 371-83.DeSantis, T. Z., et al. (2003). "Comprehensive aligned sequence construction forautomated design of effective probes (CASCADE-P) using 16S rDNA." Bioinformatics 19(12): 1461-8.DeSantis, T. Z. , et al. (2006) . "Greengenes, a chimera-checked 16S rRNA gene data base and workbench compatible with ARB." Appl Enviran Microbio! 72(7):5069-72.Edgar, R. C. (2004). "MUSCLE: multiple sequence alignment with high accuracy and high throughput." Nucleic Acids Res 32(5): 1792-7.Gebix (2009). Second Progress Report- Colciencias. Bogotá, Colombian Center for Genomics and Bioinformatics of Extreme Environments.Goloboff, P., et al. (2000). TNT (Tree analysis using New Technology) (BETA). Tucumán, Argentina.Guevara, C. & M. M. Zambrano (2006). "Sugarcane cellulose utilization by a defined microbial consortium." FEMS Microbio! Lett 255(1 ): 52-8.Guindan, S. & O. Gascuel (2003). "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood." Syst Biol 52(5): 696-704.Gupta, N., et al. (2002). "Simplified para-nitrophenyl palmitate assay for lipases and esterases." Anal Biochem 311 (1 ): 98-9.Henne, A. , et al. (2000) . "Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli." Appl. Enviran. Microbio!. 66(7): 3113-6.Hull, D., et al. (2006). "Taverna: a tool for building and running workflows of services." Nucleic Acids Res 34(Web Server issue): W729-32.Huse, S. M., et al. (2007). "Accuracy and quality of massively parallel DNA pyrosequencing." Genome Biol 8(7): R143.Kasana, R. C., et al. (2008). "A rapid and easy method for the detection of microbial cellulases on agar plates using grams iodine." Curr Microbio! 57(5): 503-7.Konstantinidis, K. T. , et al. (2009). "Comparative metagenomic analysis of a microbial community residing ata depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre." Appl Enviran Microbio! 75(16): 5345-55.Koonin, E. V. (2009). "Darwinian evolution in the light of genomics." Nucleic Acids Res 37(4): 1011-34.Kouker, G. & K. E. Jaeger (1987). "Specific and sensitive plate assay for bacteria! lipases." Appl Enviran Microbio! 53(1) : 211-3.Krause, L. , et al. (2008). "Phylogenetic classification of short environmental DNA fragments." Nucleic Acids Res 36(7): 2230-9.Larkin, M. A., et al. (2007). "Ciustal W and Clustal X version 2.0." Bioinformatics 23(21 ): 2947-8.Lozupone, C., et al. (2006). "UniFrac--an on line tool for comparing microbial community diversity in a phylogenetic context." BMC Bioinformatics 7: 371 .Meyer, F., et al. (2008). "The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes." BMC Bioinformatics 9: 386.Mitra, S., et al. (2009). "Visual and statistical comparison of metagenomes." Bioinformatics 25(15): 1849-55.Nawrocki, E. P. , et al. (2009). "Infernal 1.0: inference of RNA alignments." Bioinformatics 25(10) : 1335-7.Ranjan, R. , et al. (2005). "lsolation of novel lipolytic genes from uncultured bacteria of pond water." Biochem Biophys Res Commun 335(1) : 57-65.Rusch, D. B., et al. (2007). "The Sorcerer 11 Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific." PLoS Biol 5(3): e77.Schloss, P. D. & J. Handelsman (2005). "lntroducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness." 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"Environmental microarray analyses of Antarctic soi l microbial communities ." ISME J 3(3) : 340-51 .Yokouchi , H., et al. (2006) . "Whole-metagenome amplification of a microbial commun ity associated with scleractinian cora l by multiple displacement amplification using phi29 polymerase ." Enviran Microbio! 8(7) : 1155-63 .657039219990Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments015-2007Departamento Administrativo de Ciencia, Tecnología e Innovación [CO] ColcienciasPublicationORIGINAL6570-392-19990.pdf6570-392-19990.pdfapplication/pdf24667105https://repositorio.minciencias.gov.co/bitstreams/a368c927-0224-4c5a-b574-bf489fea06d6/downloade45fed401cb3809d26fd688ca15d0436MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-815543https://repositorio.minciencias.gov.co/bitstreams/b3666654-f099-4368-80fc-b95e6ab5e030/download73a5432e0b76442b22b026844140d683MD5220.500.14143/50187oai:repositorio.minciencias.gov.co:20.500.14143/501872024-01-05 17:20:54.59https://creativecommons.org/licenses/by/4.0/restrictedhttps://repositorio.minciencias.gov.coRepositorio Institucional de Mincienciascendoc@minciencias.gov.co

Establishment of a metagenomics and bioinfo rmatics platform for the characterization and exploration of genetic resources from ext reme environments

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