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25755, "username": "flefevre", "name": "François LE FEVRE", "links": { "alternate": { "href": "https://www.zotero.org/flefevre", "type": "text/html" } } }, "lastModifiedByUser": { "id": 34691, "username": "dbikard", "name": "David Bikard", "links": { "alternate": { "href": "https://www.zotero.org/dbikard", "type": "text/html" } } }, "creatorSummary": "Marliere", "parsedDate": "2009-12", "numChildren": 0 }, "data": { "key": "HITDJGSA", "version": 9460, "itemType": "journalArticle", "title": "The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world", "creators": [ { "creatorType": "author", "firstName": "Philippe", "lastName": "Marliere" } ], "abstractNote": "Biotechnology has empirically established that it is easier to construct and evaluate variant genes and proteins than to account for the emergence and function of wild-type macromolecules. Systematizing this constructive approach, synthetic biology now promises to infer and assemble entirely novel genomes, cells and ecosystems. It is argued here that the theoretical and computational tools needed for this endeavor are missing altogether. However, such tools may not be required for diversifying organisms at the basic level of their chemical constitution by adding, substituting or removing elements and molecular components through directed evolution under selection. 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We have constructed a genetically encoded edge detection algorithm that programs an isogenic community of E. coli to sense an image of light, communicate to identify the light-dark edges, and visually present the result of the computation. The algorithm is implemented using multiple genetic circuits. An engineered light sensor enables cells to distinguish between light and dark regions. In the dark, cells produce a diffusible chemical signal that diffuses into light regions. Genetic logic gates are used so that only cells that sense light and the diffusible signal produce a positive output. A mathematical model constructed from first principles and parameterized with experimental measurements of the component circuits predicts the performance of the complete program. Quantitatively accurate models will facilitate the engineering of more complex biological behaviors and inform bottom-up studies of natural genetic regulatory networks.", "publicationTitle": "Cell", "publisher": "", "place": "", "date": "Juin 26, 2009", "volume": "137", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "1272-1281", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.cell.2009.04.048", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/B6WSN-4WM10D8-M/2/7ed3bdec022f64afc6c44f8adc21e8ef", "accessDate": "2009-07-31T11:52:41Z", "PMID": "", "PMCID": "", "ISSN": "0092-8674", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "ScienceDirect", "callNumber": "0131", "rights": "", "extra": "00346", "tags": [ { "tag": "CHEMBIO", "type": 1 }, { "tag": "SYSBIO", "type": 1 } ], "collections": [ "NMVRDWK7" ], "relations": {}, "dateAdded": "2009-08-04T18:00:05Z", "dateModified": "2017-08-06T12:09:44Z" } }, { "key": "JX982V43", "version": 9447, "library": { "type": "group", "id": 899, "name": "synthetic biology", "links": { "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/899/items/JX982V43", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology/items/JX982V43", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25755, "username": "flefevre", "name": "François LE FEVRE", "links": { "alternate": { "href": "https://www.zotero.org/flefevre", "type": "text/html" } } }, "lastModifiedByUser": { "id": 165918, "username": "leszek3", "name": "Lech Trzeciak", "links": { "alternate": { "href": "https://www.zotero.org/leszek3", "type": "text/html" } } }, "creatorSummary": "Nagel", "parsedDate": "1974", "numChildren": 0 }, "data": { "key": "JX982V43", "version": 9447, "itemType": "document", "title": "What is it like to be a bat", "creators": [ { "creatorType": "author", "firstName": "Thomas", "lastName": "Nagel" } ], "abstractNote": "", "type": "", "date": "1974", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "http://organizations.utep.edu/Portals/1475/nagel_bat.pdf", "accessDate": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "5180", "rights": "", "extra": "07088", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-10-19T10:03:45Z", "dateModified": "2017-08-06T12:09:43Z" } }, { "key": "JNTVZQHV", "version": 9447, "library": { "type": "group", "id": 899, "name": "synthetic biology", "links": { "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/899/items/JNTVZQHV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology/items/JNTVZQHV", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25755, "username": "flefevre", "name": "François LE FEVRE", "links": { "alternate": { "href": "https://www.zotero.org/flefevre", "type": "text/html" } } }, "lastModifiedByUser": { "id": 165918, "username": "leszek3", "name": "Lech Trzeciak", "links": { "alternate": { "href": "https://www.zotero.org/leszek3", "type": "text/html" } } }, "creatorSummary": "Gardner et al.", "parsedDate": "2000-01-20", "numChildren": 0 }, "data": { "key": "JNTVZQHV", "version": 9447, "itemType": "journalArticle", "title": "Construction of a genetic toggle switch in Escherichia coli", "creators": [ { "creatorType": "author", "firstName": "Timothy S.", "lastName": "Gardner" }, { "creatorType": "author", "firstName": "Charles R.", "lastName": "Cantor" }, { "creatorType": "author", "firstName": "James J.", "lastName": "Collins" } ], "abstractNote": "", "publicationTitle": "Nature", "publisher": "", "place": "", "date": "January 20, 2000", "volume": "403", "issue": "6767", "section": "", "partNumber": "", "partTitle": "", "pages": "339-342", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nature", "DOI": "10.1038/35002131", "citationKey": "", "url": "http://dx.doi.org/10.1038/35002131", "accessDate": "2009-10-19T09:24:32Z", "PMID": "", "PMCID": "", "ISSN": "0028-0836", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Nature", "callNumber": "2016", "rights": "", "extra": "03365", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-10-19T09:24:32Z", "dateModified": "2017-08-06T12:09:42Z" } }, { "key": "JEZKI376", "version": 9447, "library": { "type": "group", "id": 899, "name": "synthetic biology", "links": { "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/899/items/JEZKI376", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology/items/JEZKI376", "type": "text/html" } }, "meta": { "createdByUser": { "id": 34691, "username": "dbikard", "name": "David Bikard", "links": { "alternate": { "href": "https://www.zotero.org/dbikard", "type": "text/html" } } }, "lastModifiedByUser": { "id": 165918, "username": "leszek3", "name": "Lech Trzeciak", "links": { "alternate": { "href": "https://www.zotero.org/leszek3", "type": "text/html" } } }, "creatorSummary": "Ellis et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "JEZKI376", "version": 9447, "itemType": "journalArticle", "title": "Diversity-based, model-guided construction of synthetic gene networks with predicted functions", "creators": [ { "creatorType": "author", "firstName": "Tom", "lastName": "Ellis" }, { "creatorType": "author", "firstName": "Xiao", "lastName": "Wang" }, { "creatorType": "author", "firstName": "James J", "lastName": "Collins" } ], "abstractNote": "", "publicationTitle": "Nat Biotech", "publisher": "", "place": "", "date": "Mai 2009", "volume": "27", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "465-471", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Biotech", "DOI": "10.1038/nbt.1536", "citationKey": "", "url": "http://dx.doi.org/10.1038/nbt.1536", "accessDate": "2009-08-04T17:56:03Z", "PMID": "", "PMCID": "", "ISSN": "1087-0156", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Nature", "callNumber": "0181", "rights": "", "extra": "00397", "tags": [], "collections": [ "NMVRDWK7" ], "relations": {}, "dateAdded": "2009-08-04T17:59:06Z", "dateModified": "2017-08-06T12:09:41Z" } }, { "key": "HAWPU7VF", "version": 9447, "library": { "type": "group", "id": 899, "name": "synthetic biology", "links": { "alternate": { "href": 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"", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "1999", "publisher": "Presses universitaires de France", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "", "ISBN": "2-13-049992-9 978-2-13-049992-3", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Books", "callNumber": "0107", "rights": "", "extra": "00159", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-10-18T13:36:30Z", "dateModified": "2017-08-06T12:09:40Z" } }, { "key": "GHK3ZQBE", "version": 9447, "library": { "type": "group", "id": 899, "name": "synthetic biology", "links": { "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/899/items/GHK3ZQBE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology/items/GHK3ZQBE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 34691, "username": "dbikard", "name": "David Bikard", "links": { "alternate": { "href": "https://www.zotero.org/dbikard", "type": "text/html" } } }, "lastModifiedByUser": { "id": 165918, "username": "leszek3", "name": "Lech Trzeciak", "links": { "alternate": { "href": "https://www.zotero.org/leszek3", "type": "text/html" } } }, "creatorSummary": "Sohka et al.", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "GHK3ZQBE", "version": 9447, "itemType": "journalArticle", "title": "An externally tunable bacterial band-pass filter", "creators": [ { "creatorType": "author", "firstName": "Takayuki", "lastName": "Sohka" }, { "creatorType": "author", "firstName": "Richard A.", "lastName": "Heins" }, { "creatorType": "author", "firstName": "Ryan M.", "lastName": "Phelan" }, { "creatorType": "author", "firstName": "Jennifer M.", "lastName": "Greisler" }, { "creatorType": "author", "firstName": "Craig A.", "lastName": "Townsend" }, { "creatorType": "author", "firstName": "Marc", "lastName": "Ostermeier" } ], "abstractNote": "The current paradigm for tuning synthetic biological systems is through re-engineering system components. Biological systems designed with the inherent ability to be tuned by external stimuli will be more versatile. We engineered cells to behave as an externally tunable band-pass filter for enzyme activity and small molecules. The band's location can be positioned within a range of 4 orders of magnitude simply by the addition of compounds to the growth medium. Inclusion in the genetic network of an enzyme-substrate pair that functions as an attenuator is a generalizable strategy that enables this tunability. The genetic circuit enabled bacteria growth to be patterned in response to chemical gradients in nonintuitive ways and facilitated the isolation of engineered allosteric enzymes. The application of this strategy to other biological systems will increase their utility for biotechnological applications and their usefulness as a tool for gaining insight into nature's underlying design principles.", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "Juin 23, 2009", "volume": "106", "issue": "25", "section": "", "partNumber": "", "partTitle": "", "pages": "10135-10140", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1073/pnas.0901246106", "citationKey": "", "url": "http://www.pnas.org/content/106/25/10135.abstract", "accessDate": "2009-07-31T12:11:21Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Highwire 2.0", "callNumber": "0049", "rights": "", "extra": "00122", "tags": [], "collections": [ "NMVRDWK7" ], "relations": {}, "dateAdded": "2009-08-04T18:00:20Z", "dateModified": "2017-08-06T12:09:39Z" } }, { "key": "GAB67TIK", "version": 9447, "library": { "type": "group", "id": 899, "name": "synthetic biology", "links": { "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/899/items/GAB67TIK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology/items/GAB67TIK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25755, "username": "flefevre", "name": "François LE FEVRE", "links": { "alternate": { "href": "https://www.zotero.org/flefevre", "type": "text/html" } } }, "lastModifiedByUser": { "id": 165918, "username": "leszek3", "name": "Lech Trzeciak", "links": { "alternate": { "href": "https://www.zotero.org/leszek3", "type": "text/html" } } }, "creatorSummary": "Arendt", "parsedDate": "1992", "numChildren": 1 }, "data": { "key": "GAB67TIK", "version": 9447, "itemType": "book", "title": "Eichmann in Jerusalem", "creators": [ { "creatorType": "author", "firstName": "Hannah", "lastName": "Arendt" } ], "abstractNote": "", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "1992", "publisher": "Penguin Classics", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "", "ISBN": "0-14-018765-0 978-0-14-018765-6", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Books", "callNumber": "0000", "rights": "", "extra": "08949", "tags": [], "collections": [], "relations": {}, "dateAdded": "2009-10-18T13:07:35Z", "dateModified": "2017-08-06T12:09:38Z" } }, { "key": "F79EZ8TH", "version": 9460, "library": { "type": "group", "id": 899, "name": "synthetic biology", "links": { "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/899/items/F79EZ8TH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/synthetic_biology/items/F79EZ8TH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 25755, "username": "flefevre", "name": "François LE FEVRE", "links": { "alternate": { "href": "https://www.zotero.org/flefevre", "type": "text/html" } } }, "lastModifiedByUser": { "id": 34691, "username": "dbikard", "name": "David Bikard", "links": { "alternate": { "href": "https://www.zotero.org/dbikard", "type": "text/html" } } }, "creatorSummary": "Endy", "parsedDate": "2005-11-24", "numChildren": 0 }, "data": { "key": "F79EZ8TH", "version": 9460, "itemType": "journalArticle", "title": "Foundations for engineering biology", "creators": [ { "creatorType": "author", "firstName": "Drew", "lastName": "Endy" } ], "abstractNote": "Engineered biological systems have been used to manipulate information, construct materials, process chemicals, produce energy, provide food, and help maintain or enhance human health and our environment. 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