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His provocative vision of the future will change the way we think about viruses, and perhaps remove a potential threat to humanity’s survival.“An astonishingly lucid book on an important topic. 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"lastName": "Rojas" } ], "abstractNote": "", "publicationTitle": "Current Biology", "publisher": "", "place": "", "date": "2015-11-02", "volume": "25", "issue": "21", "section": "", "partNumber": "", "partTitle": "", "pages": "R1026-R1028", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Current Biology", "DOI": "10.1016/j.cub.2015.06.044", "citationKey": "", "url": "https://www.cell.com/current-biology/abstract/S0960-9822(15)00738-1", "accessDate": "2020-02-06T05:00:41Z", "PMID": "", "PMCID": "", "ISSN": "0960-9822", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "www.cell.com", "callNumber": "", "rights": "", "extra": "PMID: 26528739", "tags": [], "collections": [ "4CN95UHH" ], "relations": {}, "dateAdded": "2020-02-06T05:00:41Z", "dateModified": "2020-02-06T05:00:41Z" } }, { "key": "ZCBJNLBR", "version": 896, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { 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A.", "lastName": "O'Connell" }, { "creatorType": "author", "firstName": "Harold H.", "lastName": "Zakon" }, { "creatorType": "author", "firstName": "David C.", "lastName": "Cannatella" } ], "abstractNote": "Abstract. Complex phenotypes typically have a correspondingly multifaceted genetic component. However, the genotype–phenotype association between chemical defe", "publicationTitle": "Molecular Biology and Evolution", "publisher": "", "place": "", "date": "2016/04/01", "volume": "33", "issue": "4", "section": "", "partNumber": "", "partTitle": "", "pages": "1068-1080", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Mol Biol Evol", "DOI": "10.1093/molbev/msv350", "citationKey": "", "url": "https://academic.oup.com/mbe/article/33/4/1068/2579744", "accessDate": "2020-02-06T05:00:31Z", "PMID": "", "PMCID": "", "ISSN": "0737-4038", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "academic.oup.com", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "4CN95UHH" ], "relations": {}, "dateAdded": "2020-02-06T05:00:31Z", "dateModified": "2020-02-06T05:00:31Z" } }, { "key": "48AAL9KG", "version": 896, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/48AAL9KG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/48AAL9KG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": "https://www.zotero.org/karnesky", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "48AAL9KG", "version": 896, "itemType": "webpage", "title": "Why don’t poisonous animals poison themselves? - Rebecca D. Tarvin", "creators": [], "abstractNote": "Thousands of animal species use toxic chemicals to defend themselves from predators. Snakes have blood clotting compounds in their fangs, the bombardier beetle has corrosive liquid in its abdomen and jellyfish have venomous, harpoon-like structures in their tentacles. But how do these animals survive their own poisons? Rebecca D. Tarvin details the strategies that protect animals from themselves.", "websiteTitle": "TED-Ed", "websiteType": "", "date": "", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "https://ed.ted.com/lessons/why-don-t-poisonous-animals-poison-themselves-rebecca-d-tarvin", "accessDate": "2020-02-06T05:00:29Z", "shortTitle": "Why don’t poisonous animals poison themselves?", "language": "en", "rights": "", "extra": "", "tags": [], "collections": [ "4CN95UHH" ], "relations": {}, "dateAdded": "2020-02-06T05:00:29Z", "dateModified": "2020-02-06T05:00:29Z" } }, { "key": "UWUZVIAA", "version": 896, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/UWUZVIAA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/UWUZVIAA", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/469383/items/3XTI2WBH", "type": "application/json" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": "https://www.zotero.org/karnesky", "type": "text/html" } } } }, "data": { "key": "UWUZVIAA", "version": 896, "parentItem": "3XTI2WBH", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2020-02-06T05:00:26Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/28935799", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2020-02-06T05:00:26Z", "dateModified": "2020-02-06T05:00:26Z" } }, { "key": "3XTI2WBH", "version": 896, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/3XTI2WBH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/3XTI2WBH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": "https://www.zotero.org/karnesky", "type": "text/html" } } }, "creatorSummary": "Tarvin et al.", "parsedDate": "2017-09-22", "numChildren": 1 }, "data": { "key": "3XTI2WBH", "version": 896, "itemType": "journalArticle", "title": "Interacting amino acid replacements allow poison frogs to evolve epibatidine resistance", "creators": [ { "creatorType": "author", "firstName": "Rebecca D.", "lastName": "Tarvin" }, { "creatorType": "author", "firstName": "Cecilia M.", "lastName": "Borghese" }, { "creatorType": "author", "firstName": "Wiebke", "lastName": "Sachs" }, { "creatorType": "author", "firstName": "Juan C.", "lastName": "Santos" }, { "creatorType": "author", "firstName": "Ying", "lastName": "Lu" }, { "creatorType": "author", "firstName": "Lauren A.", "lastName": "O’Connell" }, { "creatorType": "author", "firstName": "David C.", "lastName": "Cannatella" }, { "creatorType": "author", "firstName": "R. Adron", "lastName": "Harris" }, { "creatorType": "author", "firstName": "Harold H.", "lastName": "Zakon" } ], "abstractNote": "Poison frogs resist their own chemical defense\nPoison frogs produce a neurotoxin that protects them from predation. The frogs, however, run the risk of intoxicating themselves. Studying the frog neurotoxin epibatidine, which binds to acetylcholine receptors, Tarvin et al. found a single amino acid substitution. The substitution changes the configuration of the acetylcholine receptor, so that it decreases its sensitivity to the toxin. But acetylcholine signaling is essential for normal life. Expressing frog receptors in human cells revealed that different amino acid substitutions have occurred in different lineages that allow the frog to resist its own toxins while still letting target neurotransmitters function effectively.\nScience, this issue p. 1261\nAnimals that wield toxins face self-intoxication. Poison frogs have a diverse arsenal of defensive alkaloids that target the nervous system. Among them is epibatidine, a nicotinic acetylcholine receptor (nAChR) agonist that is lethal at microgram doses. Epibatidine shares a highly conserved binding site with acetylcholine, making it difficult to evolve resistance yet maintain nAChR function. Electrophysiological assays of human and frog nAChR revealed that one amino acid replacement, which evolved three times in poison frogs, decreased epibatidine sensitivity but at a cost of acetylcholine sensitivity. However, receptor functionality was rescued by additional amino acid replacements that differed among poison frog lineages. Our results demonstrate how resistance to agonist toxins can evolve and that such genetic changes propel organisms toward an adaptive peak of chemical defense.\nPoison frogs have evolved mutations in nicotinic acetylcholine receptor genes that confer toxin resistance.\nPoison frogs have evolved mutations in nicotinic acetylcholine receptor genes that confer toxin resistance.", "publicationTitle": "Science", "publisher": "", "place": "", "date": "2017/09/22", "volume": "357", "issue": "6357", "section": "", "partNumber": "", "partTitle": "", "pages": "1261-1266", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1126/science.aan5061", "citationKey": "", "url": "https://science.sciencemag.org/content/357/6357/1261", "accessDate": "2020-02-06T05:00:25Z", "PMID": "", "PMCID": "", "ISSN": "0036-8075, 1095-9203", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "science.sciencemag.org", "callNumber": "", "rights": "Copyright © 2017, American Association for the Advancement of Science. http://www.sciencemag.org/about/science-licenses-journal-article-reuseThis is an article distributed under the terms of the Science Journals Default License.", "extra": "PMID: 28935799", "tags": [], "collections": [ "4CN95UHH" ], "relations": {}, "dateAdded": "2020-02-06T05:00:25Z", "dateModified": "2020-02-06T05:00:25Z" } }, { "key": "HW6MIHGN", "version": 894, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/HW6MIHGN", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/HW6MIHGN", "type": "text/html" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": 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"tag": "West Oakland (Calif.) -- History", "type": 1 } ], "collections": [ "XFQ8KPL4" ], "relations": {}, "dateAdded": "2020-01-22T17:09:31Z", "dateModified": "2020-01-22T17:09:31Z" } }, { "key": "RQE8LRAA", "version": 893, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/RQE8LRAA", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/RQE8LRAA", "type": "text/html" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": "https://www.zotero.org/karnesky", "type": "text/html" } } }, "creatorSummary": "Bloomfield et al.", "parsedDate": "1986", "numChildren": 0 }, "data": { "key": "RQE8LRAA", "version": 893, "itemType": "book", "title": "Oakland Cultural Heritage Survey", "creators": [ { "creatorType": "editor", "firstName": "Anne", "lastName": "Bloomfield" }, { "creatorType": "editor", "firstName": "Betty", "lastName": "Marvin" }, { "creatorType": "editor", "firstName": "Melinda Young", "lastName": "Frye" }, { "creatorType": "editor", "firstName": "", "lastName": "Oakland Cultural Heritage Survey" } ], "abstractNote": "Oakland Cutlural Heritage Survey documents architecturally and historically important resources throughout Oakland", "series": "Oakland cultural heritage survey", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "1986", "publisher": "City of Oakland", "place": "Oakland", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "", "ISBN": "", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "oaklandlibrary.org", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Adams Point (Oakland, Calif.)", "type": 1 }, { "tag": "Architecture", "type": 1 }, { "tag": "Buildings", "type": 1 }, { "tag": "Buildings, structures, etc", "type": 1 }, { "tag": "California Oakland", "type": 1 }, { "tag": "California Oakland Buildings", "type": 1 }, { "tag": "Commerical buildings", "type": 1 }, { "tag": "Conservation and restoration", "type": 1 }, { "tag": "Handbooks, manuals, etc", "type": 1 }, { "tag": "Historic buildings", "type": 1 }, { "tag": "Lake Merritt neighborhood (Oakland, Calif.)", "type": 1 }, { "tag": "Lakeside Park (Oakland, Calif.)", "type": 1 }, { "tag": "Municipal buildings", "type": 1 }, { "tag": "Parks", "type": 1 }, { "tag": "Public libraries", "type": 1 }, { "tag": "Public schools", "type": 1 } ], "collections": [ "XFQ8KPL4" ], "relations": {}, "dateAdded": "2020-01-22T17:09:02Z", "dateModified": "2020-01-22T17:09:02Z" } }, { "key": "ZEZTAVTH", "version": 892, "library": { "type": "group", "id": 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{}, "dateAdded": "2020-01-22T17:04:40Z", "dateModified": "2020-01-22T17:04:40Z" } }, { "key": "CMMTGWG8", "version": 892, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/CMMTGWG8", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/CMMTGWG8", "type": "text/html" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": "https://www.zotero.org/karnesky", "type": "text/html" } } }, "creatorSummary": "Vale", "parsedDate": "2018-11-20", "numChildren": 1 }, "data": { "key": "CMMTGWG8", "version": 892, "itemType": "book", "title": "After the Projects: Public Housing Redevelopment and the Governance of the Poorest Americans", "creators": [ { "creatorType": "author", "firstName": "Lawrence J.", "lastName": "Vale" } ], "abstractNote": "America is in the midst of a rental housing affordability crisis. More than a quarter of those that rent their homes spend more than half of their income for housing, even as city leaders across the United States have been busily dismantling the nation's urban public housing projects. In After the Projects, Lawrence Vale investigates the deeply-rooted spatial politics of public housing development and redevelopment at a time when lower-income Americans face a desperate struggle to find affordable rental housing in many cities. Drawing on more than 200 interviews with public housing residents, real estate developers, and community leaders, Vale analyzes the different ways in which four major American cities implemented the federal government's HOPE VI program for public housing transformation, while also providing a national picture of this program. Some cities attempted to minimize the presence of the poorest residents in their new mixed-income communities, but other cities tried to serve as many low-income households as possible. Through examining the social, political, and economic forces that underlie housing displacement, Vale develops the novel concept of governance constellations. He shows how the stars align differently in each city, depending on community pressures that have evolved in response to each city's past struggles with urban renewal. This allows disparate key players to gain prominence when implementing HOPE VI redevelopment. A much-needed comparative approach to the existing research on public housing, After the Projects shines a light on the broad variety of attitudes towards public housing redevelopment in American cities and identifies ways to achieve more equitable processes and outcomes for low-income Americans.", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2018-11-20", "publisher": "Oxford University Press", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "505", "ISBN": "978-0-19-062434-7", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "After the Projects", "language": "en", "libraryCatalog": "Google Books", "callNumber": "", "rights": "", "extra": "Google-Books-ID: rwJ6DwAAQBAJ", "tags": [ { "tag": "Political Science / American Government / State", "type": 1 }, { "tag": "Political Science / Public Policy / General", "type": 1 }, { "tag": "Social Science / Sociology / General", "type": 1 } ], "collections": [ "XFQ8KPL4" ], "relations": {}, "dateAdded": "2020-01-22T17:04:40Z", "dateModified": "2020-01-22T17:04:40Z" } }, { "key": "BJNQQFKQ", "version": 891, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/BJNQQFKQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/BJNQQFKQ", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/469383/items/WFKXAI5Q", "type": "application/json" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": "https://www.zotero.org/karnesky", "type": "text/html" } } } }, "data": { "key": "BJNQQFKQ", "version": 891, "parentItem": "WFKXAI5Q", "itemType": "attachment", "linkMode": "linked_url", "title": "Google Books Link", "accessDate": "2020-01-22T17:04:16Z", "url": "https://books.google.com/books?id=dC6OBAAAQBAJ", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2020-01-22T17:04:16Z", "dateModified": "2020-01-22T17:04:16Z" } }, { "key": "WFKXAI5Q", "version": 891, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/WFKXAI5Q", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/WFKXAI5Q", "type": "text/html" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": "https://www.zotero.org/karnesky", "type": "text/html" } } }, "creatorSummary": "Gutman", "parsedDate": "2014-09-19", "numChildren": 1 }, "data": { "key": "WFKXAI5Q", "version": 891, "itemType": "book", "title": "A City for Children: Women, Architecture, and the Charitable Landscapes of Oakland, 1850-1950", "creators": [ { "creatorType": "author", "firstName": "Marta", "lastName": "Gutman" } ], "abstractNote": "American cities are constantly being built and rebuilt, resulting in ever-changing skylines and neighborhoods. While the dynamic urban landscapes of New York, Boston, and Chicago have been widely studied, there is much to be gleaned from west coast cities, especially in California, where the migration boom at the end of the nineteenth century permanently changed the urban fabric of these newly diverse, plural metropolises. In A City for Children, Marta Gutman focuses on the use and adaptive reuse of everyday buildings in Oakland, California, to make the city a better place for children. She introduces us to the women who were determined to mitigate the burdens placed on working-class families by an indifferent industrial capitalist economy. Often without the financial means to build from scratch, women did not tend to conceive of urban land as a blank slate to be wiped clean for development. Instead, Gutman shows how, over and over, women turned private houses in Oakland into orphanages, kindergartens, settlement houses, and day care centers, and in the process built the charitable landscape—a network of places that was critical for the betterment of children, families, and public life. The industrial landscape of Oakland, riddled with the effects of social inequalities and racial prejudices, is not a neutral backdrop in Gutman’s story but an active player. Spanning one hundred years of history, A City for Children provides a compelling model for building urban institutions and demonstrates that children, women, charity, and incremental construction, renovations, alterations, additions, and repurposed structures are central to the understanding of modern cities.", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2014-09-19", "publisher": "University of Chicago Press", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "numPages": "479", "ISBN": "978-0-226-31128-9", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "A City for Children", "language": "en", "libraryCatalog": "Google Books", "callNumber": "", "rights": "", "extra": "Google-Books-ID: dC6OBAAAQBAJ", "tags": [ { "tag": "Architecture / History / Modern (late 19th Century to 1945)", "type": 1 }, { "tag": "History / General", "type": 1 }, { "tag": "History / United States / 19th Century", "type": 1 }, { "tag": "History / United States / 20th Century", "type": 1 }, { "tag": "History / United States / State & Local / West (AK, CA, CO, HI, ID, MT, NV, UT, WY)", "type": 1 }, { "tag": "Political Science / Public Policy / Social Services & Welfare", "type": 1 }, { "tag": "Social Science / Sociology / Urban", "type": 1 }, { "tag": "Social Science / Women's Studies", "type": 1 } ], "collections": [ "XFQ8KPL4" ], "relations": {}, "dateAdded": "2020-01-22T17:04:16Z", "dateModified": "2020-01-22T17:04:16Z" } }, { "key": "H28R4QE3", "version": 890, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/H28R4QE3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/H28R4QE3", "type": "text/html" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": "https://www.zotero.org/karnesky", "type": "text/html" } } }, "creatorSummary": "Costello and Martin", "parsedDate": "2019-03-01", "numChildren": 0 }, "data": { "key": "H28R4QE3", "version": 890, "itemType": "journalArticle", "title": "How to Hallucinate Functional Proteins", "creators": [ { "creatorType": "author", "firstName": "Zak", "lastName": "Costello" }, { "creatorType": "author", "firstName": "Hector Garcia", "lastName": "Martin" } ], "abstractNote": "Here we present a novel approach to protein design and phenotypic inference using a generative model for protein sequences. BioSeqVAE, a variational autoencoder variant, can hallucinate syntactically valid protein sequences that are likely to fold and function. BioSeqVAE is trained on the entire known protein sequence space and learns to generate valid examples of protein sequences in an unsupervised manner. The model is validated by showing that its latent feature space is useful and that it accurately reconstructs sequences. Its usefulness is demonstrated with a selection of relevant downstream design tasks. This work is intended to serve as a computational first step towards a general purpose structure free protein design tool.", "publicationTitle": "arXiv:1903.00458 [q-bio]", "publisher": "", "place": "", "date": "2019-03-01", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://arxiv.org/abs/1903.00458", "accessDate": "2020-01-22T17:00:53Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "arXiv.org", "callNumber": "", "rights": "", "extra": "arXiv: 1903.00458", "tags": [ { "tag": "Quantitative Biology - Quantitative Methods", "type": 1 } ], "collections": [ "DZHBY7PQ" ], "relations": {}, "dateAdded": "2020-01-22T17:00:53Z", "dateModified": "2020-01-22T17:00:53Z" } }, { "key": "D2HV7GRN", "version": 890, "library": { "type": "group", "id": 469383, "name": "Nerd Nite East Bay", "links": { "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/469383/items/D2HV7GRN", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/nerd_nite_east_bay/items/D2HV7GRN", "type": "text/html" } }, "meta": { "createdByUser": { "id": 24202, "username": "karnesky", "name": "Richard Karnesky", "links": { "alternate": { "href": "https://www.zotero.org/karnesky", "type": "text/html" } } }, "creatorSummary": "Alonso-Gutierrez et al.", "parsedDate": "2015-03-01", "numChildren": 0 }, "data": { "key": "D2HV7GRN", "version": 890, "itemType": "journalArticle", "title": "Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering", "creators": [ { "creatorType": "author", "firstName": "Jorge", "lastName": "Alonso-Gutierrez" }, { "creatorType": "author", "firstName": "Eun-Mi", "lastName": "Kim" }, { "creatorType": "author", "firstName": "Tanveer S.", "lastName": "Batth" }, { "creatorType": "author", "firstName": "Nathan", "lastName": "Cho" }, { "creatorType": "author", "firstName": "Qijun", "lastName": "Hu" }, { "creatorType": "author", "firstName": "Leanne Jade G.", "lastName": "Chan" }, { "creatorType": "author", "firstName": "Christopher J.", "lastName": "Petzold" }, { "creatorType": "author", "firstName": "Nathan J.", "lastName": "Hillson" }, { "creatorType": "author", "firstName": "Paul D.", "lastName": "Adams" }, { "creatorType": "author", "firstName": "Jay D.", "lastName": "Keasling" }, { "creatorType": "author", "firstName": "Hector", "lastName": "Garcia Martin" }, { "creatorType": "author", "firstName": "Taek Soon", "lastName": "Lee" } ], "abstractNote": "Targeted proteomics is a convenient method determining enzyme expression levels, but a quantitative analysis of these proteomic data has not been fully explored yet. Here, we present and demonstrate a computational tool (principal component analysis of proteomics, PCAP) that uses quantitative targeted proteomics data to guide metabolic engineering and achieve higher production of target molecules from heterologous pathways. The method is based on the application of principal component analysis to a collection of proteomics and target molecule production data to pinpoint specific enzymes that need to have their expression level adjusted to maximize production. We illustrated the method on the heterologous mevalonate pathway in Escherichia coli that produces a wide range of isoprenoids and requires balanced pathway gene expression for high yields and titers. PCAP-guided engineering resulted in over a 40% improvement in the production of two valuable terpenes. PCAP could potentially be productively applied to other heterologous pathways as well.", "publicationTitle": "Metabolic Engineering", "publisher": "", "place": "", "date": "March 1, 2015", "volume": "28", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "123-133", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Metabolic Engineering", "DOI": "10.1016/j.ymben.2014.11.011", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S109671761400161X", "accessDate": "2020-01-22T17:00:49Z", "PMID": "", "PMCID": "", "ISSN": "1096-7176", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Heterologous pathway", "type": 1 }, { "tag": "Metabolic engineering", "type": 1 }, { "tag": "Mevalonate pathway", "type": 1 }, { "tag": "Principal component analysis (PCA)", "type": 1 }, { "tag": "Targeted proteomics", "type": 1 } ], "collections": [ "DZHBY7PQ" ], "relations": {}, "dateAdded": "2020-01-22T17:00:49Z", "dateModified": "2020-01-22T17:00:49Z" } } ]