[ { "key": "BQLLPZJI", "version": 80, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/BQLLPZJI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/BQLLPZJI", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/132531/items/W3IIM96J", "type": "application/json" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "BQLLPZJI", "version": 80, "parentItem": "W3IIM96J", "itemType": "attachment", "linkMode": "imported_url", "title": "Full Text PDF", "accessDate": "2023-02-26T12:46:46Z", "url": "http://www.cell.com/article/S2405471223000273/pdf", "note": "", "contentType": "application/pdf", "charset": "", "filename": "Segrè et al. - 2023 - What do you most want to understand about how coll.pdf", "md5": "23ff9ad1cee8a11847750d4990f2f614", "mtime": 1677415605960, "tags": [], "relations": {}, "dateAdded": "2023-02-26T12:46:46Z", "dateModified": "2023-02-26T12:46:46Z" } }, { "key": "SFHMSP6W", "version": 71, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/SFHMSP6W", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/SFHMSP6W", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/132531/items/W3IIM96J", "type": "application/json" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } } }, "data": { "key": "SFHMSP6W", "version": 71, "parentItem": "W3IIM96J", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2023-02-26T12:46:43Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/36796334", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2023-02-26T12:46:43Z", "dateModified": "2023-02-26T12:46:43Z" } }, { "key": "W3IIM96J", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/W3IIM96J", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/W3IIM96J", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Segrè et al.", "parsedDate": "2023-02-15", "numChildren": 2 }, "data": { "key": "W3IIM96J", "version": 81, "itemType": "journalArticle", "title": "What do you most want to understand about how collective features emerge in microbial communities?", "creators": [ { "creatorType": "author", "firstName": "Daniel", "lastName": "Segrè" }, { "creatorType": "author", "firstName": "Sara", "lastName": "Mitri" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" }, { "creatorType": "author", "firstName": "Gürol M.", "lastName": "Süel" }, { "creatorType": "author", "firstName": "Itzhak", "lastName": "Mizrahi" }, { "creatorType": "author", "firstName": "Libusha", "lastName": "Kelly" }, { "creatorType": "author", "firstName": "María", "lastName": "Rebolleda-Gómez" }, { "creatorType": "author", "firstName": "Christoph", "lastName": "Ratzke" }, { "creatorType": "author", "firstName": "C. Brandon", "lastName": "Ogbunugafor" }, { "creatorType": "author", "firstName": "Julia A.", "lastName": "Schwartzman" }, { "creatorType": "author", "firstName": "Sergey", "lastName": "Kryazhimskiy" }, { "creatorType": "author", "firstName": "Gabriel E.", "lastName": "Leventhal" }, { "creatorType": "author", "firstName": "Christian", "lastName": "Kost" }, { "creatorType": "author", "firstName": "Thomas", "lastName": "Bell" } ], "abstractNote": "", "publicationTitle": "Cell Systems", "publisher": "Elsevier", "place": "", "date": "2023-02-15", "volume": "14", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "91-97", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "cels", "DOI": "10.1016/j.cels.2023.01.001", "citationKey": "", "url": "https://www.cell.com/cell-systems/abstract/S2405-4712(23)00027-3", "accessDate": "2023-02-26T12:46:42Z", "PMID": "36796334", "PMCID": "", "ISSN": "2405-4712", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "www.cell.com", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-02-26T12:46:42Z", "dateModified": "2023-02-26T12:46:42Z" } }, { "key": "67RLEUAT", "version": 70, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/67RLEUAT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/67RLEUAT", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/132531/items/XDBD9YLQ", "type": "application/json" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } } }, "data": { "key": "67RLEUAT", "version": 70, "parentItem": "XDBD9YLQ", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2023-02-21T07:18:43Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/36794804", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2023-02-21T07:18:43Z", "dateModified": "2023-02-21T07:18:43Z" } }, { "key": "XDBD9YLQ", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/XDBD9YLQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/XDBD9YLQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Kurt et al.", "parsedDate": "2023", "numChildren": 1 }, "data": { "key": "XDBD9YLQ", "version": 81, "itemType": "journalArticle", "title": "Co-cultivation is a powerful approach to produce a robust functionally designed synthetic consortium as a live biotherapeutic product (LBP)", "creators": [ { "creatorType": "author", "firstName": "Fabienne", "lastName": "Kurt" }, { "creatorType": "author", "firstName": "Gabriel E.", "lastName": "Leventhal" }, { "creatorType": "author", "firstName": "Marianne Rebecca", "lastName": "Spalinger" }, { "creatorType": "author", "firstName": "Laura", "lastName": "Anthamatten" }, { "creatorType": "author", "firstName": "Philipp", "lastName": "Rogalla von Bieberstein" }, { "creatorType": "author", "firstName": "Carmen", "lastName": "Menzi" }, { "creatorType": "author", "firstName": "Markus", "lastName": "Reichlin" }, { "creatorType": "author", "firstName": "Marco", "lastName": "Meola" }, { "creatorType": "author", "firstName": "Florian", "lastName": "Rosenthal" }, { "creatorType": "author", "firstName": "Gerhard", "lastName": "Rogler" }, { "creatorType": "author", "firstName": "Christophe", "lastName": "Lacroix" }, { "creatorType": "author", "firstName": "Tomas", "lastName": "de Wouters" } ], "abstractNote": "The success of fecal microbiota transplants (FMT) has provided the necessary proof-of-concept for microbiome therapeutics. Yet, feces-based therapies have many associated risks and uncertainties, and hence defined microbial consortia that modify the microbiome in a targeted manner have emerged as a promising safer alternative to FMT. The development of such live biotherapeutic products has important challenges, including the selection of appropriate strains and the controlled production of the consortia at scale. Here, we report on an ecology- and biotechnology-based approach to microbial consortium construction that overcomes these issues. We selected nine strains that form a consortium to emulate the central metabolic pathways of carbohydrate fermentation in the healthy human gut microbiota. Continuous co-culturing of the bacteria produces a stable and reproducible consortium whose growth and metabolic activity are distinct from an equivalent mix of individually cultured strains. Further, we showed that our function-based consortium is as effective as FMT in counteracting dysbiosis in a dextran sodium sulfate mouse model of acute colitis, while an equivalent mix of strains failed to match FMT. Finally, we showed robustness and general applicability of our approach by designing and producing additional stable consortia of controlled composition. We propose that combining a bottom-up functional design with continuous co-cultivation is a powerful strategy to produce robust functionally designed synthetic consortia for therapeutic use.", "publicationTitle": "Gut Microbes", "publisher": "", "place": "", "date": "2023", "volume": "15", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "2177486", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Gut Microbes", "DOI": "10.1080/19490976.2023.2177486", "citationKey": "", "url": "", "accessDate": "", "PMID": "36794804", "PMCID": "", "ISSN": "1949-0984", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Animals", "type": 1 }, { "tag": "Colitis", "type": 1 }, { "tag": "Fecal Microbiota Transplantation", "type": 1 }, { "tag": "Feces", "type": 1 }, { "tag": "Gastrointestinal Microbiome", "type": 1 }, { "tag": "Humans", "type": 1 }, { "tag": "Mice", "type": 1 }, { "tag": "Microbiome therapeutics", "type": 1 }, { "tag": "Microbiota", "type": 1 }, { "tag": "anaerobic carbohydrate metabolism", "type": 1 }, { "tag": "consortium design", "type": 1 }, { "tag": "continuous co-cultivation", "type": 1 }, { "tag": "division of labor", "type": 1 }, { "tag": "live biotherapeutic products (LBP)", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2023-02-21T07:18:42Z", "dateModified": "2023-02-21T07:18:42Z" } }, { "key": "UMURYWK5", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/UMURYWK5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/UMURYWK5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Xie and Shou", "parsedDate": "2021-11-23", "numChildren": 0 }, "data": { "key": "UMURYWK5", "version": 81, "itemType": "journalArticle", "title": "Steering ecological-evolutionary dynamics to improve artificial selection of microbial communities", "creators": [ { "creatorType": "author", "firstName": "Li", "lastName": "Xie" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" } ], "abstractNote": "Microbial communities often perform important functions that depend on inter-species interactions. To improve community function via artificial selection, one can repeatedly grow many communities to allow mutations to arise, and “reproduce” the highest-functioning communities by partitioning each into multiple offspring communities for the next cycle. Since improvement is often unimpressive in experiments, we study how to design effective selection strategies in silico. Specifically, we simulate community selection to improve a function that requires two species. With a “community function landscape”, we visualize how community function depends on species and genotype compositions. Due to ecological interactions that promote species coexistence, the evolutionary trajectory of communities is restricted to a path on the landscape. This restriction can generate counter-intuitive evolutionary dynamics, prevent the attainment of maximal function, and importantly, hinder selection by trapping communities in locations of low community function heritability. We devise experimentally-implementable manipulations to shift the path to higher heritability, which speeds up community function improvement even when landscapes are high dimensional or unknown. Video walkthroughs: https://go.nature.com/3GWwS6j; https://online.kitp.ucsb.edu/online/ecoevo21/shou2/.", "publicationTitle": "Nature Communications", "publisher": "Nature Publishing Group", "place": "", "date": "2021-11-23", "volume": "12", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "6799", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Commun", "DOI": "10.1038/s41467-021-26647-4", "citationKey": "", "url": "https://www.nature.com/articles/s41467-021-26647-4", "accessDate": "2023-02-08T09:34:28Z", "PMID": "", "PMCID": "", "ISSN": "2041-1723", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.nature.com", "callNumber": "", "rights": "2021 The Author(s)", "extra": "Number: 1", "tags": [ { "tag": "Evolutionary ecology", "type": 1 }, { "tag": "Evolutionary theory", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2023-02-08T09:34:28Z", "dateModified": "2023-02-08T09:34:28Z" } }, { "key": "W4RC94VF", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/W4RC94VF", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/W4RC94VF", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Hart et al.", "parsedDate": "2019-02-22", "numChildren": 0 }, "data": { "key": "W4RC94VF", "version": 81, "itemType": "journalArticle", "title": "Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells", "creators": [ { "creatorType": "author", "firstName": "Samuel F. M.", "lastName": "Hart" }, { "creatorType": "author", "firstName": "Hanbing", "lastName": "Mi" }, { "creatorType": "author", "firstName": "Robin", "lastName": "Green" }, { "creatorType": "author", "firstName": "Li", "lastName": "Xie" }, { "creatorType": "author", "firstName": "Jose Mario Bello", "lastName": "Pineda" }, { "creatorType": "author", "firstName": "Babak", "lastName": "Momeni" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" } ], "abstractNote": "Quantitative modeling is useful for predicting behaviors of a system and for rationally constructing or modifying the system. The predictive power of a model relies on accurate quantification of model parameters. Here, we illustrate challenges in parameter quantification and offer means to overcome these challenges, using a case example in which we quantitatively predict the growth rate of a cooperative community. Specifically, the community consists of two Saccharomyces cerevisiae strains, each engineered to release a metabolite required and consumed by its partner. The initial model, employing parameters measured in batch monocultures with zero or excess metabolite, failed to quantitatively predict experimental results. To resolve the model–experiment discrepancy, we chemically identified the correct exchanged metabolites, but this did not improve model performance. We then remeasured strain phenotypes in chemostats mimicking the metabolite-limited community environments, while mitigating or incorporating effects of rapid evolution. Almost all phenotypes we measured, including death rate, metabolite release rate, and the amount of metabolite consumed per cell birth, varied significantly with the metabolite environment. Once we used parameters measured in a range of community-like chemostat environments, prediction quantitatively agreed with experimental results. In summary, using a simplified community, we uncovered and devised means to resolve modeling challenges that are likely general to living systems.", "publicationTitle": "PLOS Biology", "publisher": "Public Library of Science", "place": "", "date": "Feb 22, 2019", "volume": "17", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "e3000135", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLOS Biology", "DOI": "10.1371/journal.pbio.3000135", "citationKey": "", "url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000135", "accessDate": "2023-02-06T09:38:19Z", "PMID": "", "PMCID": "", "ISSN": "1545-7885", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "PLoS Journals", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Adenine", "type": 1 }, { "tag": "Cell metabolism", "type": 1 }, { "tag": "Cloning", "type": 1 }, { "tag": "Death rates", "type": 1 }, { "tag": "Flow cytometry", "type": 1 }, { "tag": "Glucose", "type": 1 }, { "tag": "Lysine", "type": 1 }, { "tag": "Metabolites", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2023-02-06T09:38:19Z", "dateModified": "2023-02-06T09:38:19Z" } }, { "key": "F2H8H68V", "version": 59, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/F2H8H68V", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/F2H8H68V", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Hart et al.", "parsedDate": "2019-03-01", "numChildren": 0 }, "data": { "key": "F2H8H68V", "version": 59, "itemType": "journalArticle", "title": "High-throughput quantification of microbial birth and death dynamics using fluorescence microscopy", "creators": [ { "creatorType": "author", "firstName": "Samuel F. M.", "lastName": "Hart" }, { "creatorType": "author", "firstName": "David", "lastName": "Skelding" }, { "creatorType": "author", "firstName": "Adam J.", "lastName": "Waite" }, { "creatorType": "author", "firstName": "Justin C.", "lastName": "Burton" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" } ], "abstractNote": "Microbes live in dynamic environments where nutrient concentrations fluctuate. Quantifying fitness in terms of birth rate and death rate in a wide range of environments is critical for understanding microbial evolution and ecology.", "publicationTitle": "Quantitative Biology", "publisher": "", "place": "", "date": "2019-03-01", "volume": "7", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "69-81", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Quantitative Biology", "DOI": "10.1007/s40484-018-0160-7", "citationKey": "", "url": "https://doi.org/10.1007/s40484-018-0160-7", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2095-4697", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": { "owl:sameAs": "http://zotero.org/groups/149203/items/GR484YEP" }, "dateAdded": "2022-09-20T18:37:32Z", "dateModified": "2022-09-20T18:37:32Z" } }, { "key": "EAVB7FZY", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/EAVB7FZY", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/EAVB7FZY", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Niehaus et al.", "parsedDate": "2019", "numChildren": 1 }, "data": { "key": "EAVB7FZY", "version": 81, "itemType": "journalArticle", "title": "Microbial coexistence through chemical-mediated interactions", "creators": [ { "creatorType": "author", "firstName": "Lori", "lastName": "Niehaus" }, { "creatorType": "author", "firstName": "Ian", "lastName": "Boland" }, { "creatorType": "author", "firstName": "Minghao", "lastName": "Liu" }, { "creatorType": "author", "firstName": "Kevin", "lastName": "Chen" }, { "creatorType": "author", "firstName": "David", "lastName": "Fu" }, { "creatorType": "author", "firstName": "Catherine", "lastName": "Henckel" }, { "creatorType": "author", "firstName": "Kaitlin", "lastName": "Chaung" }, { "creatorType": "author", "firstName": "Suyen Espinoza", "lastName": "Miranda" }, { "creatorType": "author", "firstName": "Samantha", "lastName": "Dyckman" }, { "creatorType": "author", "firstName": "Matthew", "lastName": "Crum" }, { "creatorType": "author", "firstName": "Sandra", "lastName": "Dedrick" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" }, { "creatorType": "author", "firstName": "Babak", "lastName": "Momeni" } ], "abstractNote": "Many microbial functions happen within communities of interacting species. Explaining how species with disparate growth rates can coexist is important for applications such as manipulating host-associated microbiota or engineering industrial communities. Here, we ask how microbes interacting through their chemical environment can achieve coexistence in a continuous growth setup (similar to an industrial bioreactor or gut microbiota) where external resources are being supplied. We formulate and experimentally constrain a model in which mediators of interactions (e.g. metabolites or waste-products) are explicitly incorporated. Our model highlights facilitation and self-restraint as interactions that contribute to coexistence, consistent with our intuition. When interactions are strong, we observe that coexistence is determined primarily by the topology of facilitation and inhibition influences not their strengths. Importantly, we show that consumption or degradation of chemical mediators moderates interaction strengths and promotes coexistence. Our results offer insights into how to build or restructure microbial communities of interest.", "publicationTitle": "Nature Communications", "publisher": "", "place": "", "date": "05 03, 2019", "volume": "10", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "2052", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Commun", "DOI": "10.1038/s41467-019-10062-x", "citationKey": "", "url": "", "accessDate": "", "PMID": "31053707", "PMCID": "PMC6499789", "ISSN": "2041-1723", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Brevibacillus", "type": 1 }, { "tag": "Escherichia coli", "type": 1 }, { "tag": "Microbial Interactions", "type": 1 }, { "tag": "Microbiota", "type": 1 }, { "tag": "Models, Biological", "type": 1 }, { "tag": "Staphylococcus", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2019-07-22T17:30:44Z", "dateModified": "2019-07-22T17:30:44Z" } }, { "key": "W39QWN2S", "version": 56, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/W39QWN2S", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/W39QWN2S", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/132531/items/EAVB7FZY", "type": "application/json" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } } }, "data": { "key": "W39QWN2S", "version": 56, "parentItem": "EAVB7FZY", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2019-07-22T17:30:44Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/31053707", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2019-07-22T17:30:44Z", "dateModified": "2019-07-22T17:30:44Z" } }, { "key": "D2ZRKF8T", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/D2ZRKF8T", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/D2ZRKF8T", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Xie et al.", "parsedDate": "2019-06-25", "numChildren": 0 }, "data": { "key": "D2ZRKF8T", "version": 81, "itemType": "journalArticle", "title": "Simulations reveal challenges to artificial community selection and possible strategies for success", "creators": [ { "creatorType": "author", "firstName": "Li", "lastName": "Xie" }, { "creatorType": "author", "firstName": "Alex E.", "lastName": "Yuan" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" } ], "abstractNote": "Multispecies microbial communities often display \"community functions\" arising from interactions of member species. Interactions are often difficult to decipher, making it challenging to design communities with desired functions. Alternatively, similar to artificial selection for individuals in agriculture and industry, one could repeatedly choose communities with the highest community functions to reproduce by randomly partitioning each into multiple \"Newborn\" communities for the next cycle. However, previous efforts in selecting complex communities have generated mixed outcomes that are difficult to interpret. To understand how to effectively enact community selection, we simulated community selection to improve a community function that requires 2 species and imposes a fitness cost on one or both species. Our simulations predict that improvement could be easily stalled unless various aspects of selection were carefully considered. These aspects include promoting species coexistence, suppressing noncontributors, choosing additional communities besides the highest functioning ones to reproduce, and reducing stochastic fluctuations in the biomass of each member species in Newborn communities. These considerations can be addressed experimentally. When executed effectively, community selection is predicted to improve costly community function, and may even force species to evolve slow growth to achieve species coexistence. Our conclusions hold under various alternative model assumptions and are therefore applicable to a variety of communities.", "publicationTitle": "PLoS biology", "publisher": "", "place": "", "date": "Jun 25, 2019", "volume": "17", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "e3000295", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS Biol.", "DOI": "10.1371/journal.pbio.3000295", "citationKey": "", "url": "", "accessDate": "", "PMID": "31237866", "PMCID": "", "ISSN": "1545-7885", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2019-07-22T17:28:52Z", "dateModified": "2019-07-22T17:28:52Z" } }, { "key": "3TE2FMJ3", "version": 52, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/3TE2FMJ3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/3TE2FMJ3", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Hart et al.", "parsedDate": "2019-06-04", "numChildren": 0 }, "data": { "key": "3TE2FMJ3", "version": 52, "itemType": "journalArticle", "title": "Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community", "creators": [ { "creatorType": "author", "firstName": "Samuel Frederick Mock", "lastName": "Hart" }, { "creatorType": "author", "firstName": "Jose Mario Bello", "lastName": "Pineda" }, { "creatorType": "author", "firstName": "Chi-Chun", "lastName": "Chen" }, { "creatorType": "author", "firstName": "Robin", "lastName": "Green" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" }, { "creatorType": "editor", "firstName": "Kevin J", "lastName": "Verstrepen" }, { "creatorType": "editor", "firstName": "Diethard", "lastName": "Tautz" }, { "creatorType": "editor", "firstName": "Antoine", "lastName": "Frenoy" } ], "abstractNote": "Mutualisms can be promoted by pleiotropic win-win mutations which directly benefit self (self-serving) and partner (partner-serving). Intuitively, partner-serving phenotype could be quantified as an individual’s benefit supply rate to partners. Here, we demonstrate the inadequacy of this thinking, and propose an alternative. Specifically, we evolved well-mixed mutualistic communities where two engineered yeast strains exchanged essential metabolites lysine and hypoxanthine. Among cells that consumed lysine and released hypoxanthine, a chromosome duplication mutation seemed win-win: it improved cell’s affinity for lysine (self-serving), and increased hypoxanthine release rate per cell (partner-serving). However, increased release rate was due to increased cell size accompanied by increased lysine utilization per birth. Consequently, total hypoxanthine release rate per lysine utilization (defined as ‘exchange ratio’) remained unchanged. Indeed, this mutation did not increase the steady state growth rate of partner, and is thus solely self-serving during long-term growth. By extension, reduced benefit production rate by an individual may not imply cheating.", "publicationTitle": "eLife", "publisher": "", "place": "", "date": "June 4, 2019", "volume": "8", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "e44812", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.7554/eLife.44812", "citationKey": "", "url": "https://doi.org/10.7554/eLife.44812", "accessDate": "2019-06-10T23:46:07Z", "PMID": "", "PMCID": "", "ISSN": "2050-084X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "eLife", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "benefit", "type": 1 }, { "tag": "cost", "type": 1 }, { "tag": "evolution", "type": 1 }, { "tag": "mutualism", "type": 1 }, { "tag": "partner-serving", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2019-06-10T23:46:07Z", "dateModified": "2019-06-10T23:46:07Z" } }, { "key": "KSX8ZSZU", "version": 51, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/KSX8ZSZU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/KSX8ZSZU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 775968, "username": "aricc", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aricc", "type": "text/html" } } }, "lastModifiedByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Momeni et al.", "parsedDate": "2013-11-12", "numChildren": 0 }, "data": { "key": "KSX8ZSZU", "version": 51, "itemType": "journalArticle", "title": "Spatial self-organization favors heterotypic cooperation over cheating", "creators": [ { "creatorType": "author", "firstName": "Babak", "lastName": "Momeni" }, { "creatorType": "author", "firstName": "Adam James", "lastName": "Waite" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" } ], "abstractNote": "Cooperation between individuals of the same species, and also between different species, is known to be important in evolution. Large fish, for example, rely on small cleaner fish to remove parasites, while the small fish benefit from the nutrients in these parasites. However, cooperation can be undermined by other individuals or species who “cheat” by taking advantage of those who cooperate, without providing any benefits in return. For example, some cleaner fish cheat by biting off healthy tissue from their host, in addition to parasites.\n\nGenetically-related individuals who cooperate by sharing identical benefits can combat cheaters by giving preferential treatment to their relatives (a process known as kin discrimination) or by staying close to the relatives to form clusters (kin fidelity). However, two genetically-unrelated populations that mutually cooperate by sharing different benefits cannot employ these methods to overcome cheaters. Instead they rely on either partner choice or partner fidelity feedback.\n\nPartner choice – the approach adopted by cleaner fish and their hosts – relies on one population recognizing a signal from the other population and responding accordingly: for example, large fish observe cleaner fish and approach those that cooperate with their current host and avoid those that cheat. Partner fidelity feedback, on the other hand, relies on repeated interactions between the two populations providing an advantage in terms of evolutionary fitness to both: for example, organelles called mitochondria and chloroplasts live inside cells, helping the cells to harvest energy and providing energy for themselves and the host cells in the process. In some cases – such as the cooperation between figs and fig wasps, or between certain plants and the bacteria that fix nitrogen in their roots – researchers cannot agree if the populations are relying on partner choice or partner fidelity feedback.\n\nNow Momeni et al. have used a combination of experiments on yeast and mathematical modeling to explore partner fidelity feedback in greater detail. They started by using genetic engineering techniques to produce two species of yeast that mutually cooperate, each providing a metabolite that is essential to the other, but are not able to recognize each other: this means that these populations cannot rely on partner choice to combat cheaters. Momeni et al. then observed how these two species interacted with each other and a third species of yeast that cheated by consuming one of the metabolites without releasing any metabolite of its own . \n\nMomeni et al. found that as long as there was space for the yeast cells to grow into, the two species that cooperated self-organized into mixed clusters, with the cheating species being excluded from these clusters. The self-organization was driven by a positive feedback loop involving the two species that cooperated, with each species helping to increase the fitness of the other. The results of Momeni et al. demonstrate that it is possible for two genetically unrelated populations to cooperate and combat cheaters without the use of partner choice.\n\nDOI: [http://dx.doi.org/10.7554/eLife.00960.002][1]\n\n [1]: /lookup/doi/10.7554/eLife.00960.002", "publicationTitle": "eLife", "publisher": "", "place": "", "date": "11/12/2013", "volume": "2", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "00960", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.7554/eLife.00960", "citationKey": "", "url": "http://elife.elifesciences.org/content/2/e00960", "accessDate": "2013-11-15T04:07:40Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "elife.elifesciences.org", "callNumber": "", "rights": "Copyright © 2013, Momeni et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.", "extra": "", "tags": [ { "tag": "S. cerevisiae", "type": 1 }, { "tag": "community ecology", "type": 1 }, { "tag": "cooperation", "type": 1 }, { "tag": "mutualism", "type": 1 }, { "tag": "pattern formation", "type": 1 }, { "tag": "self-organization", "type": 1 }, { "tag": "spatial structure", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-11-15T04:08:11Z", "dateModified": "2019-01-05T22:28:34Z" } }, { "key": "QIC5PS4N", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/QIC5PS4N", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/QIC5PS4N", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Kang et al.", "parsedDate": "2014", "numChildren": 1 }, "data": { "key": "QIC5PS4N", "version": 81, "itemType": "journalArticle", "title": "Simulating microbial community patterning using Biocellion", "creators": [ { "creatorType": "author", "firstName": "Seunghwa", "lastName": "Kang" }, { "creatorType": "author", "firstName": "Simon", "lastName": "Kahan" }, { "creatorType": "author", "firstName": "Babak", "lastName": "Momeni" } ], "abstractNote": "Mathematical modeling and computer simulation are important tools for understanding complex interactions between cells and their biotic and abiotic environment: similarities and differences between modeled and observed behavior provide the basis for hypothesis formation. Momeni et al. (Elife 2:e00230, 2013) investigated pattern formation in communities of yeast strains engaging in different types of ecological interactions, comparing the predictions of mathematical modeling, and simulation to actual patterns observed in wet-lab experiments. However, simulations of millions of cells in a three-dimensional community are extremely time consuming. One simulation run in MATLAB may take a week or longer, inhibiting exploration of the vast space of parameter combinations and assumptions. Improving the speed, scale, and accuracy of such simulations facilitates hypothesis formation and expedites discovery. Biocellion is a high-performance software framework for accelerating discrete agent-based simulation of biological systems with millions to trillions of cells. Simulations of comparable scale and accuracy to those taking a week of computer time using MATLAB require just hours using Biocellion on a multicore workstation. Biocellion further accelerates large scale, high resolution simulations using cluster computers by partitioning the work to run on multiple compute nodes. Biocellion targets computational biologists who have mathematical modeling backgrounds and basic C++ programming skills. This chapter describes the necessary steps to adapt the original Momeni et al.'s model to the Biocellion framework as a case study.", "publicationTitle": "Methods in Molecular Biology (Clifton, N.J.)", "publisher": "", "place": "", "date": "2014", "volume": "1151", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "233-253", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Methods Mol. Biol.", "DOI": "10.1007/978-1-4939-0554-6_16", "citationKey": "", "url": "", "accessDate": "", "PMID": "24838890", "PMCID": "", "ISSN": "1940-6029", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Computer Simulation", "type": 1 }, { "tag": "Microbial Consortia", "type": 1 }, { "tag": "Microbial Interactions", "type": 1 }, { "tag": "Models, Biological", "type": 1 }, { "tag": "Software", "type": 1 }, { "tag": "Yeasts", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2015-01-28T01:56:55Z", "dateModified": "2015-01-28T01:56:55Z" } }, { "key": "HTGDZIIR", "version": 45, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/HTGDZIIR", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/HTGDZIIR", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/132531/items/QIC5PS4N", "type": "application/json" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } } }, "data": { "key": "HTGDZIIR", "version": 45, "parentItem": "QIC5PS4N", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2015-01-28T01:56:55Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/24838890", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-01-28T01:56:55Z", "dateModified": "2015-01-28T01:56:55Z" } }, { "key": "PZZRNKT4", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/PZZRNKT4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/PZZRNKT4", "type": "text/html" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Waite and Shou", "parsedDate": "2014", "numChildren": 1 }, "data": { "key": "PZZRNKT4", "version": 81, "itemType": "journalArticle", "title": "Constructing synthetic microbial communities to explore the ecology and evolution of symbiosis", "creators": [ { "creatorType": "author", "firstName": "Adam James", "lastName": "Waite" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" } ], "abstractNote": "Synthetically engineered microbial communities based on model organisms provide a simplified model of their naturally occurring counterparts while still retaining essential features of living organisms. The degree of control afforded by this approach has been critical in understanding how similar types of natural communities might have persisted and evolved. Here, we first discuss important considerations when designing a synthetically engineered system. Then, we describe the steps required to create a two-partner cooperative system based on the yeast Saccharomyces cerevisiae.", "publicationTitle": "Methods in Molecular Biology (Clifton, N.J.)", "publisher": "", "place": "", "date": "2014", "volume": "1151", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "27-38", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Methods Mol. Biol.", "DOI": "10.1007/978-1-4939-0554-6_2", "citationKey": "", "url": "", "accessDate": "", "PMID": "24838876", "PMCID": "", "ISSN": "1940-6029", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "eng", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Biological Evolution", "type": 1 }, { "tag": "Ecosystem", "type": 1 }, { "tag": "Genetic Engineering", "type": 1 }, { "tag": "Saccharomyces cerevisiae", "type": 1 }, { "tag": "Symbiosis", "type": 1 }, { "tag": "synthetic biology", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2015-01-18T06:35:21Z", "dateModified": "2015-01-18T06:35:21Z" } }, { "key": "EIDXFMD3", "version": 44, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/EIDXFMD3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/EIDXFMD3", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/132531/items/PZZRNKT4", "type": "application/json" } }, "meta": { "createdByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } } }, "data": { "key": "EIDXFMD3", "version": 44, "parentItem": "PZZRNKT4", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed entry", "accessDate": "2015-01-18T06:35:21Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/24838876", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2015-01-18T06:35:21Z", "dateModified": "2015-01-18T06:35:21Z" } }, { "key": "KZTQNNME", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/KZTQNNME", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/KZTQNNME", "type": "text/html" } }, "meta": { "createdByUser": { "id": 775968, "username": "aricc", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aricc", "type": "text/html" } } }, "lastModifiedByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Shou et al.", "parsedDate": "2002", "numChildren": 1 }, "data": { "key": "KZTQNNME", "version": 81, "itemType": "journalArticle", "title": "Cdc5 influences phosphorylation of Net1 and disassembly of the RENT complex", "creators": [ { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" }, { "creatorType": "author", "firstName": "Ramzi", "lastName": "Azzam" }, { "creatorType": "author", "firstName": "Susan L", "lastName": "Chen" }, { "creatorType": "author", "firstName": "Michael J", "lastName": "Huddleston" }, { "creatorType": "author", "firstName": "Christopher", "lastName": "Baskerville" }, { "creatorType": "author", "firstName": "Harry", "lastName": "Charbonneau" }, { "creatorType": "author", "firstName": "Roland S", "lastName": "Annan" }, { "creatorType": "author", "firstName": "Steve A", "lastName": "Carr" }, { "creatorType": "author", "firstName": "Raymond J", "lastName": "Deshaies" } ], "abstractNote": "BACKGROUND\n\nIn S. cerevisiae, the mitotic exit network (MEN) proteins, including the Polo-like protein kinase Cdc5 and the protein phosphatase Cdc14, are required for exit from mitosis. In pre-anaphase cells, Cdc14 is sequestered to the nucleolus by Net1 as a part of the RENT complex. When cells are primed to exit mitosis, the RENT complex is disassembled and Cdc14 is released from the nucleolus.\n\n\nRESULTS\n\nHere, we show that Cdc5 is necessary to free nucleolar Cdc14 in late mitosis, that elevated Cdc5 activity provokes ectopic release of Cdc14 in pre-anaphase cells, and that the phosphorylation state of Net1 is regulated by Cdc5 during anaphase. Furthermore, recombinant Cdc5 and Xenopus Polo-like kinase can disassemble the RENT complex in vitro by phosphorylating Net1 and thereby reducing its affinity for Cdc14. Surprisingly, although RENT complexes containing Net1 mutants (Net1(7m) and Net1(19m') lacking sites phosphorylated by Cdc5 in vitro are refractory to disassembly by Polo-like kinases in vitro, net1(7m) and net1(19m') cells grow normally and exhibit only minor defects in releasing Cdc14 during anaphase. However, net1(19m') cells exhibit a synergistic growth defect when combined with mutations in CDC5 or DBF2 (another MEN gene).\n\n\nCONCLUSIONS\n\nWe propose that although Cdc5 potentially disassembles RENT by directly phosphorylating Net1, Cdc5 mediates exit from mitosis primarily by phosphorylating other targets. Our study suggests that Cdc5/Polo is unusually promiscuous and highlights the need to validate Cdc5/Polo in vitro phosphorylation sites by direct in vivo mapping experiments.", "publicationTitle": "BMC molecular biology", "publisher": "", "place": "", "date": "2002", "volume": "3", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "3", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "BMC Mol. Biol.", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "11960554", "PMCID": "", "ISSN": "1471-2199", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2012-12-18T00:25:13Z", "dateModified": "2013-01-03T21:54:34Z" } }, { "key": "54R8CTQS", "version": 9, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/54R8CTQS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/54R8CTQS", "type": "text/html" } }, "meta": { "createdByUser": { "id": 775968, "username": "aricc", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aricc", "type": "text/html" } } }, "creatorSummary": "Momeni and Shou", "parsedDate": "2012", "numChildren": 1 }, "data": { "key": "54R8CTQS", "version": 9, "itemType": "webpage", "title": "Cryosectioning Yeast Communities for Examining Fluorescence Patterns... | JoVE Video", "creators": [ { "creatorType": "author", "firstName": "Babak", "lastName": "Momeni" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" } ], "abstractNote": "We present a protocol for freezing and cryosectioning yeast communities to observe internal patterns of fluorescent cells. The method relies on methanol-fixing and OCT-embedding to preserve the spatial distribution of cells without inactivating fluorescent proteins within a community....", "websiteTitle": "", "websiteType": "", "date": "2012", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "http://www.jove.com/video/50101/cryosectioning-yeast-communities-for-examining-fluorescence-patterns", "accessDate": "2012-12-18T00:21:57Z", "shortTitle": "", "language": "", "rights": "", "extra": "", "tags": [ { "tag": "Clinical Laboratory Techniques", "type": 1 }, { "tag": "Cytological Techniques", "type": 1 }, { "tag": "Investigative Techniques", "type": 1 }, { "tag": "Life Sciences (General)", "type": 1 }, { "tag": "Microbiology", "type": 1 }, { "tag": "Saccharomyces cerevisiae", "type": 1 }, { "tag": "Yeasts", "type": 1 }, { "tag": "[cryosectioning", "type": 1 }, { "tag": "community interactions ]", "type": 1 }, { "tag": "cryotome", "type": 1 }, { "tag": "fixing", "type": 1 }, { "tag": "microbial community", "type": 1 }, { "tag": "scientific video journal", "type": 1 }, { "tag": "sectioning", "type": 1 }, { "tag": "yeast colonies", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2012-12-18T00:21:57Z", "dateModified": "2012-12-18T00:46:19Z" } }, { "key": "QACK83DK", "version": 81, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/QACK83DK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/QACK83DK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 775968, "username": "aricc", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aricc", "type": "text/html" } } }, "lastModifiedByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Momeni et al.", "parsedDate": "2011", "numChildren": 4 }, "data": { "key": "QACK83DK", "version": 81, "itemType": "journalArticle", "title": "Using artificial systems to explore the ecology and evolution of symbioses", "creators": [ { "creatorType": "author", "firstName": "Babak", "lastName": "Momeni" }, { "creatorType": "author", "firstName": "Chi-Chun", "lastName": "Chen" }, { "creatorType": "author", "firstName": "Kristina L", "lastName": "Hillesland" }, { "creatorType": "author", "firstName": "Adam", "lastName": "Waite" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" } ], "abstractNote": "The web of life is weaved from diverse symbiotic interactions between species. Symbioses vary from antagonistic interactions such as competition and predation to beneficial interactions such as mutualism. What are the bases for the origin and persistence of symbiosis? What affects the ecology and evolution of symbioses? How do symbiotic interactions generate ecological patterns? How do symbiotic partners evolve and coevolve? Many of these questions are difficult to address in natural systems. Artificial systems, from abstract to living, have been constructed to capture essential features of natural symbioses and to address these key questions. With reduced complexity and increased controllability, artificial systems can serve as useful models for natural systems. We review how artificial systems have contributed to our understanding of symbioses.", "publicationTitle": "Cellular and molecular life sciences: CMLS", "publisher": "", "place": "", "date": "2011", "volume": "68", "issue": "8", "section": "", "partNumber": "", "partTitle": "", "pages": "1353-1368", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cell. Mol. Life Sci.", "DOI": "10.1007/s00018-011-0649-y", "citationKey": "", "url": "", "accessDate": "", "PMID": "21424911", "PMCID": "", "ISSN": "1420-9071", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Biological Evolution", "type": 1 }, { "tag": "Biomedical and Life Sciences", "type": 1 }, { "tag": "Ecology", "type": 1 }, { "tag": "Ecosystem", "type": 1 }, { "tag": "Models, Theoretical", "type": 1 }, { "tag": "Symbiosis", "type": 1 } ], "collections": [], "relations": { "dc:replaces": "http://zotero.org/groups/132531/items/ZMNFM6WA" }, "dateAdded": "2012-12-17T20:49:30Z", "dateModified": "2012-12-18T00:37:40Z" } }, { "key": "X9FSR6PG", "version": 1, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/X9FSR6PG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/X9FSR6PG", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/132531/items/QACK83DK", "type": "application/json" } }, "meta": { "createdByUser": { "id": 775968, "username": "aricc", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aricc", "type": "text/html" } } } }, "data": { "key": "X9FSR6PG", "version": 1, "parentItem": "QACK83DK", "itemType": "attachment", "linkMode": "linked_url", "title": "PubMed Link", "accessDate": "2012-12-18T00:22:47Z", "url": "http://www.ncbi.nlm.nih.gov/pubmed/21424911", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2012-12-18T00:22:47Z", "dateModified": "2012-12-18T00:37:40Z" } }, { "key": "X7TWKEBK", "version": 3, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/X7TWKEBK", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/X7TWKEBK", "type": "text/html" } }, "meta": { "createdByUser": { "id": 775968, "username": "aricc", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aricc", "type": "text/html" } } }, "creatorSummary": "Shou et al.", "parsedDate": "2007", "numChildren": 0 }, "data": { "key": "X7TWKEBK", "version": 3, "itemType": "journalArticle", "title": "Synthetic cooperation in engineered yeast populations", "creators": [ { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" }, { "creatorType": "author", "firstName": "Sri", "lastName": "Ram" }, { "creatorType": "author", "firstName": "Jose M. G.", "lastName": "Vilar" } ], "abstractNote": "Cooperative interactions are key to diverse biological phenomena ranging from multicellularity to mutualism. Such diversity makes the ability to create and control cooperation desirable for potential applications in areas as varied as agriculture, pollutant treatment, and medicine. Here we show that persistent cooperation can be engineered by introducing a small set of genetic modifications into previously noninteracting cell populations. Specifically, we report the construction of a synthetic obligatory cooperative system, termed CoSMO (cooperation that is synthetic and mutually obligatory), which consists of a pair of nonmating yeast strains, each supplying an essential metabolite to the other strain. The behavior of the two strains in isolation, however, revealed unintended constraints that restrict cooperation, such as asymmetry in starvation tolerance and delays in nutrient release until near cell death. However, the joint system is shown mathematically and experimentally to be viable over a wide range of initial conditions, with oscillating population ratio settling to a value predicted by nutrient supply and consumption. Unexpectedly, even in the absence of explicitly engineered mechanisms to stabilize cooperation, the cooperative system can consistently develop increased ability to survive reductions in population density. Extending synthetic biology from the design of genetic circuits to the engineering of ecological interactions, CoSMO provides a quantitative system for linking processes at the cellular level to the collective behavior at the system level, as well as a genetically tractable system for studying the evolution of cooperation.", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "2007", "volume": "104", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "1877-1882", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PNAS", "DOI": "10.1073/pnas.0610575104", "citationKey": "", "url": "http://www.pnas.org/content/104/6/1877", "accessDate": "2012-10-23T03:06:26Z", "PMID": "", "PMCID": "", "ISSN": "0027-8424, 1091-6490", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.pnas.org", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Ecology", "type": 1 }, { "tag": "Models, Genetic", "type": 1 }, { "tag": "Organisms, Genetically Modified", "type": 1 }, { "tag": "Saccharomyces cerevisiae", "type": 1 }, { "tag": "Symbiosis", "type": 1 }, { "tag": "mathematical modeling", "type": 1 }, { "tag": "mutualism", "type": 1 }, { "tag": "obligate cooperation", "type": 1 }, { "tag": "quantitative biology", "type": 1 }, { "tag": "synthetic ecology", "type": 1 } ], "collections": [], "relations": { "dc:replaces": "http://zotero.org/groups/132531/items/7PIPGVB8" }, "dateAdded": "2012-12-17T20:49:30Z", "dateModified": "2012-12-18T00:37:30Z" } }, { "key": "XFTAA5CD", "version": 2, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/XFTAA5CD", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/XFTAA5CD", "type": "text/html" } }, "meta": { "createdByUser": { "id": 775968, "username": "aricc", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aricc", "type": "text/html" } } }, "creatorSummary": "Waite and Shou", "parsedDate": "2012", "numChildren": 0 }, "data": { "key": "XFTAA5CD", "version": 2, "itemType": "journalArticle", "title": "Adaptation to a new environment allows cooperators to purge cheaters stochastically", "creators": [ { "creatorType": "author", "firstName": "Adam James", "lastName": "Waite" }, { "creatorType": "author", "firstName": "Wenying", "lastName": "Shou" } ], "abstractNote": "Cooperation via production of common goods is found in diverse life forms ranging from viruses to social animals. However, natural selection predicts a “tragedy of the commons”: Cheaters, benefiting from without producing costly common goods, are more fit than cooperators and should destroy cooperation. In an attempt to discover novel mechanisms of cheater control, we eliminated known ones using a yeast cooperator–cheater system engineered to supply or exploit essential nutrients. Surprisingly, although less fit than cheaters, cooperators quickly dominated a fraction of cocultures. Cooperators isolated from these cocultures were superior to the cheater isolates they had been cocultured with, even though these cheaters were superior to ancestral cooperators. Resequencing and phenotypic analyses revealed that evolved cooperators and cheaters all harbored mutations adaptive to the nutrient-limited cooperative environment, allowing growth at a much lower concentration of nutrient than their ancestors. Even after the initial round of adaptation, evolved cooperators still stochastically dominated cheaters derived from them. We propose the “adaptive race” model: If during adaptation to an environment, the fitness gain of cooperators exceeds that of cheaters by at least the fitness cost of cooperation, the tragedy of the commons can be averted. Although cooperators and cheaters sample from the same pool of adaptive mutations, this symmetry is soon broken: The best cooperators purge cheaters and continue to grow, whereas the best cheaters cause rapid self-extinction. We speculate that adaptation to changing environments may contribute to the persistence of cooperative systems before the appearance of more sophisticated mechanisms of cheater control.", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "2012", "volume": "109", "issue": "47", "section": "", "partNumber": "", "partTitle": "", "pages": "19079-19086", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Proceedings of the National Academy of Sciences", "DOI": "10.1073/pnas.1210190109", "citationKey": "", "url": "http://www.pnas.org/content/109/47/19079.abstract", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "evolution of cooperation and cheating", "type": 1 }, { "tag": "experimental evolution", "type": 1 }, { "tag": "genetic hitchhiking", "type": 1 }, { "tag": "synthetic biology", "type": 1 } ], "collections": [], "relations": { "dc:replaces": "http://zotero.org/groups/132531/items/A4SHKEPH" }, "dateAdded": "2012-12-17T20:49:30Z", "dateModified": "2012-12-18T00:37:10Z" } }, { "key": "6CWWCEQV", "version": 82, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/6CWWCEQV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/6CWWCEQV", "type": "text/html" } }, "meta": { "createdByUser": { "id": 775968, "username": "aricc", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aricc", "type": "text/html" } } }, "lastModifiedByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Traverso et al.", "parsedDate": "2001", "numChildren": 1 }, "data": { "key": "6CWWCEQV", "version": 82, "itemType": "journalArticle", "title": "Characterization of the Net1 cell cycle-dependent regulator of the Cdc14 phosphatase from budding yeast", "creators": [ { "creatorType": "author", "firstName": "E E", "lastName": "Traverso" }, { "creatorType": "author", "firstName": "C", "lastName": "Baskerville" }, { "creatorType": "author", "firstName": "Y", "lastName": "Liu" }, { "creatorType": "author", "firstName": "W", "lastName": "Shou" }, { "creatorType": "author", "firstName": "P", "lastName": "James" }, { "creatorType": "author", "firstName": "R J", "lastName": "Deshaies" }, { "creatorType": "author", "firstName": "H", "lastName": "Charbonneau" } ], "abstractNote": "In the budding yeast Saccharomyces cerevisiae, the multifunctional protein Net1 is implicated in regulating the cell cycle function of the Cdc14 protein phosphatase. Genetic and cell biological data suggest that during interphase and early mitosis Net1 holds Cdc14 within the nucleolus where its activity is suppressed. Upon its transient release from Net1 at late anaphase, active Cdc14 promotes exit from mitosis by dephosphorylating targets in the nucleus and cytoplasm. In this paper we present evidence supporting the proposed role of Net1 in regulating Cdc14 and exit from mitosis. We show that the NH(2)-terminal fragment Net1(1-600) directly binds Cdc14 in vitro and is a highly specific competitive inhibitor of its activity (K(i) = 3 nm) with five different substrates including the physiologic targets Swi5 and Sic1. An analysis of truncation mutants indicates that the Cdc14 binding site is located within a segment of Net1 containing residues 1-341. We propose that Net1 inhibits by occluding the active site of Cdc14 because it acts as a competitive inhibitor, binds to a site located within the catalytic domain (residues 1-374), binds with reduced affinity to a Cdc14 C283S mutant in which an active site Cys is replaced, and is displaced by tungstate, a transition state analog known to bind in the catalytic site of protein-tyrosine phosphatases.", "publicationTitle": "The Journal of biological chemistry", "publisher": "", "place": "", "date": "2001", "volume": "276", "issue": "24", "section": "", "partNumber": "", "partTitle": "", "pages": "21924-21931", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Biol. Chem.", "DOI": "10.1074/jbc.M011689200", "citationKey": "", "url": "", "accessDate": "", "PMID": "11274204", "PMCID": "", "ISSN": "0021-9258", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Binding Sites", "type": 1 }, { "tag": "Cell Cycle", "type": 1 }, { "tag": "Cell Cycle Proteins", "type": 1 }, { "tag": "Enzyme Inhibitors", "type": 1 }, { "tag": "Kinetics", "type": 1 }, { "tag": "Mitosis", "type": 1 }, { "tag": "Nuclear Proteins", "type": 1 }, { "tag": "Peptide Fragments", "type": 1 }, { "tag": "Phosphoprotein Phosphatases", "type": 1 }, { "tag": "Protein Tyrosine Phosphatases", "type": 1 }, { "tag": "Recombinant Proteins", "type": 1 }, { "tag": "Saccharomyces cerevisiae", "type": 1 }, { "tag": "Saccharomyces cerevisiae Proteins", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2012-12-18T00:26:04Z", "dateModified": "2012-12-18T00:36:29Z" } }, { "key": "9U4IAHKQ", "version": 82, "library": { "type": "group", "id": 132531, "name": "ShouLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/shoulab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/132531/items/9U4IAHKQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/shoulab/items/9U4IAHKQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 775968, "username": "aricc", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/aricc", "type": "text/html" } } }, "lastModifiedByUser": { "id": 265588, "username": "wenying.shou", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/wenying.shou", "type": "text/html" } } }, "creatorSummary": "Straight et al.", "parsedDate": "1999", "numChildren": 1 }, "data": { "key": "9U4IAHKQ", "version": 82, "itemType": "journalArticle", "title": "Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity", "creators": [ { "creatorType": "author", "firstName": "A F", "lastName": "Straight" }, { "creatorType": "author", "firstName": "W", "lastName": "Shou" }, { "creatorType": "author", "firstName": "G J", "lastName": "Dowd" }, { "creatorType": "author", "firstName": "C W", "lastName": "Turck" }, { "creatorType": "author", "firstName": "R J", "lastName": "Deshaies" }, { "creatorType": "author", "firstName": "A D", "lastName": "Johnson" }, { "creatorType": "author", "firstName": "D", "lastName": "Moazed" } ], "abstractNote": "The Sir2 protein mediates gene silencing and repression of recombination at the rDNA repeats in budding yeast. Here we show that Sir2 executes these functions as a component of a nucleolar complex designated RENT (regulator of nucleolar silencing and telophase exit). Net1, a core subunit of this complex, preferentially cross-links to the rDNA repeats, but not to silent DNA regions near telomeres or to active genes, and tethers the RENT complex to rDNA. Net1 is furthermore required for rDNA silencing and nucleolar integrity. During interphase, Net1 and Sir2 colocalize to a subdomain within the nucleous, but at the end of mitosis a fraction of Sir2 leaves the nucleolus and disperses as foci throughout the nucleus, suggesting that the structure of rDNA silent chromatin changes during the cell cycle. Our findings suggest that a protein complex shown to regulate exit from mitosis is also involved in gene silencing.", "publicationTitle": "Cell", "publisher": "", "place": "", "date": "1999", "volume": "97", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "245-256", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cell", "DOI": "", "citationKey": "", "url": "", "accessDate": "", "PMID": "10219245", "PMCID": "", "ISSN": "0092-8674", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "NCBI PubMed", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "Base Sequence", "type": 1 }, { "tag": "Cell Nucleolus", "type": 1 }, { "tag": "DNA Primers", "type": 1 }, { "tag": "DNA, Fungal", "type": 1 }, { "tag": "DNA, Ribosomal", "type": 1 }, { "tag": "DNA-Binding Proteins", "type": 1 }, { "tag": "Fluorescent Antibody Technique", "type": 1 }, { "tag": "Fungal Proteins", "type": 1 }, { "tag": "Histone Deacetylases", "type": 1 }, { "tag": "Macromolecular Substances", "type": 1 }, { "tag": "Mitosis", "type": 1 }, { "tag": "Nuclear Proteins", "type": 1 }, { "tag": "Recombination, Genetic", "type": 1 }, { "tag": "Saccharomyces cerevisiae", "type": 1 }, { "tag": "Silent Information Regulator Proteins, Saccharomyces cerevisiae", "type": 1 }, { "tag": "Sirtuin 2", "type": 1 }, { "tag": "Sirtuins", "type": 1 }, { "tag": "Trans-Activators", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2012-12-18T00:26:51Z", "dateModified": "2012-12-18T00:36:26Z" } } ]