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Joseph Jacobson. Jakimo, Noah Massachusetts Institute of Technology. Department of Architecture. Program in Media Arts and Sciences. Program in Media Arts and Sciences (Massachusetts Institute of Technology) 2015-09-17T19:00:31Z 2015-09-17T19:00:31Z 2015 2015 http://hdl.handle.net/1721.1/98625 920474963 Thesis: S.M., Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2015. Cataloged from PDF version of thesis. Includes bibliographical references (pages 40-41). Technologies for long-term recording of cellular pathway activation are constrained by the difficultly to constantly monitor transient signaling events and expression of target genes. To overcome these limitations we designed a recording tool that uses the transcriptional output of a signaling pathway as the input for an engineered genome encoded memory. The mechanism of recording leverages the programmable nature of the bacterial immune system that consists of Clustered Regularly Interspaced Short Palindromic Repeat Sequences (CRISPR), which can recognize and cleave viral DNA using an RNA-guided directed endonuclease. Cuts left by the endonuclease are repaired by an error-prone DNA damage repair mechanism, namely non-homologous end joining (NHEJ), likely to leave mutations at the cut sites. Defining the cut site with pathway-dependent transcription of guide RNA, this genomic region is sequenced to measure pathway activation by the amount of accumulated mutations. To demonstrate a system to monitor cancer metabolism, guide RNA is expressed in mammalian cell culture with a NF-kappaB promoter. To demonstrate a system that can monitor sugar intake in an environment like the gut, guide RNA is expressed in bacteria with an arabinose promoter. by Noah Jakimo. S.M. 41 pages eng Massachusetts Institute of Technology M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 Architecture. Program in Media Arts and Sciences. Genomic nucleic acid memory storage with directed endonucleases Thesis application/pdf false Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="4ac32854-e91d-4c85-ad59-7791de678d8c"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Genomic nucleic acid memory storage with directed endonucleases</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2015</PublicationDate> <Authors> <Author> <DisplayName>Jakimo, Noah</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Architecture. Program in Media Arts and Sciences.</Keyword> <Abstract>Technologies for long-term recording of cellular pathway activation are constrained by the difficultly to constantly monitor transient signaling events and expression of target genes. To overcome these limitations we designed a recording tool that uses the transcriptional output of a signaling pathway as the input for an engineered genome encoded memory. The mechanism of recording leverages the programmable nature of the bacterial immune system that consists of Clustered Regularly Interspaced Short Palindromic Repeat Sequences (CRISPR), which can recognize and cleave viral DNA using an RNA-guided directed endonuclease. Cuts left by the endonuclease are repaired by an error-prone DNA damage repair mechanism, namely non-homologous end joining (NHEJ), likely to leave mutations at the cut sites. Defining the cut site with pathway-dependent transcription of guide RNA, this genomic region is sequenced to measure pathway activation by the amount of accumulated mutations. To demonstrate a system to monitor cancer metabolism, guide RNA is expressed in mammalian cell culture with a NF-kappaB promoter. To demonstrate a system that can monitor sugar intake in an environment like the gut, guide RNA is expressed in bacteria with an arabinose promoter.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>