Nuclease-assisted suppression of human DNA background in sepsis.

Sepsis is a severe medical condition characterized by a systemic inflammatory response of the body caused by pathogenic microorganisms in the bloodstream. Blood or plasma is typically used for diagnosis, both containing large amount of human DNA, greatly exceeding the DNA of microbial origin. In ord...

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Autores principales:	Yajing Song, Christian G Giske, Patrik Gille-Johnson, Olof Emanuelsson, Joakim Lundeberg, Peter Gyarmati
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b97666bb816e491d9ab13c4c26ffd78a
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spelling	oai:doaj.org-article:b97666bb816e491d9ab13c4c26ffd78a2021-11-25T06:06:40ZNuclease-assisted suppression of human DNA background in sepsis.1932-620310.1371/journal.pone.0103610https://doaj.org/article/b97666bb816e491d9ab13c4c26ffd78a2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25076135/?tool=EBIhttps://doaj.org/toc/1932-6203Sepsis is a severe medical condition characterized by a systemic inflammatory response of the body caused by pathogenic microorganisms in the bloodstream. Blood or plasma is typically used for diagnosis, both containing large amount of human DNA, greatly exceeding the DNA of microbial origin. In order to enrich bacterial DNA, we applied the C0t effect to reduce human DNA background: a model system was set up with human and Escherichia coli (E. coli) DNA to mimic the conditions of bloodstream infections; and this system was adapted to plasma and blood samples from septic patients. As a consequence of the C0t effect, abundant DNA hybridizes faster than rare DNA. Following denaturation and re-hybridization, the amount of abundant DNA can be decreased with the application of double strand specific nucleases, leaving the non-hybridized rare DNA intact. Our experiments show that human DNA concentration can be reduced approximately 100,000-fold without affecting the E. coli DNA concentration in a model system with similarly sized amplicons. With clinical samples, the human DNA background was decreased 100-fold, as bacterial genomes are approximately 1,000-fold smaller compared to the human genome. According to our results, background suppression can be a valuable tool to enrich rare DNA in clinical samples where a high amount of background DNA can be found.Yajing SongChristian G GiskePatrik Gille-JohnsonOlof EmanuelssonJoakim LundebergPeter GyarmatiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 7, p e103610 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yajing Song Christian G Giske Patrik Gille-Johnson Olof Emanuelsson Joakim Lundeberg Peter Gyarmati Nuclease-assisted suppression of human DNA background in sepsis.
description	Sepsis is a severe medical condition characterized by a systemic inflammatory response of the body caused by pathogenic microorganisms in the bloodstream. Blood or plasma is typically used for diagnosis, both containing large amount of human DNA, greatly exceeding the DNA of microbial origin. In order to enrich bacterial DNA, we applied the C0t effect to reduce human DNA background: a model system was set up with human and Escherichia coli (E. coli) DNA to mimic the conditions of bloodstream infections; and this system was adapted to plasma and blood samples from septic patients. As a consequence of the C0t effect, abundant DNA hybridizes faster than rare DNA. Following denaturation and re-hybridization, the amount of abundant DNA can be decreased with the application of double strand specific nucleases, leaving the non-hybridized rare DNA intact. Our experiments show that human DNA concentration can be reduced approximately 100,000-fold without affecting the E. coli DNA concentration in a model system with similarly sized amplicons. With clinical samples, the human DNA background was decreased 100-fold, as bacterial genomes are approximately 1,000-fold smaller compared to the human genome. According to our results, background suppression can be a valuable tool to enrich rare DNA in clinical samples where a high amount of background DNA can be found.
format	article
author	Yajing Song Christian G Giske Patrik Gille-Johnson Olof Emanuelsson Joakim Lundeberg Peter Gyarmati
author_facet	Yajing Song Christian G Giske Patrik Gille-Johnson Olof Emanuelsson Joakim Lundeberg Peter Gyarmati
author_sort	Yajing Song
title	Nuclease-assisted suppression of human DNA background in sepsis.
title_short	Nuclease-assisted suppression of human DNA background in sepsis.
title_full	Nuclease-assisted suppression of human DNA background in sepsis.
title_fullStr	Nuclease-assisted suppression of human DNA background in sepsis.
title_full_unstemmed	Nuclease-assisted suppression of human DNA background in sepsis.
title_sort	nuclease-assisted suppression of human dna background in sepsis.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/b97666bb816e491d9ab13c4c26ffd78a
work_keys_str_mv	AT yajingsong nucleaseassistedsuppressionofhumandnabackgroundinsepsis AT christianggiske nucleaseassistedsuppressionofhumandnabackgroundinsepsis AT patrikgillejohnson nucleaseassistedsuppressionofhumandnabackgroundinsepsis AT olofemanuelsson nucleaseassistedsuppressionofhumandnabackgroundinsepsis AT joakimlundeberg nucleaseassistedsuppressionofhumandnabackgroundinsepsis AT petergyarmati nucleaseassistedsuppressionofhumandnabackgroundinsepsis
_version_	1718414186349854720

Nuclease-assisted suppression of human DNA background in sepsis.

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