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"links": { "self": { "href": "https://api.zotero.org/groups/458761/items/BGHFR3HM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bionumlab/items/BGHFR3HM", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/458761/items/NCQ68DZU", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1829470, "username": "jibe jeybee", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/jibe_jeybee", "type": "text/html" } } } }, "data": { "key": "BGHFR3HM", "version": 13, "parentItem": "NCQ68DZU", "itemType": "attachment", "linkMode": "linked_url", "title": "Full Text PDF", "accessDate": "2016-02-23T16:08:09Z", "url": "http://nar.oxfordjournals.org/content/42/5/2879.full.pdf", "note": "", "contentType": "application/pdf", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-02-23T16:08:09Z", "dateModified": "2016-02-23T16:08:09Z" } }, { "key": "NCQ68DZU", "version": 13, "library": { "type": "group", "id": 458761, "name": "BioNumLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/bionumlab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/458761/items/NCQ68DZU", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bionumlab/items/NCQ68DZU", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1829470, "username": "jibe jeybee", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/jibe_jeybee", "type": "text/html" } } }, "creatorSummary": "Goncearenco et al.", "parsedDate": "2014-03-01", "numChildren": 3 }, "data": { "key": "NCQ68DZU", "version": 13, "itemType": "journalArticle", "title": "Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins", "creators": [ { "creatorType": "author", "firstName": "Alexander", "lastName": "Goncearenco" }, { "creatorType": "author", "firstName": "Bin-Guang", "lastName": "Ma" }, { "creatorType": "author", "firstName": "Igor N.", "lastName": "Berezovsky" } ], "abstractNote": "DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.", "publicationTitle": "Nucleic Acids Research", "publisher": "", "place": "", "date": "03/01/2014", "volume": "42", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "2879-2892", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nucl. Acids Res.", "DOI": "10.1093/nar/gkt1336", "citationKey": "", "url": "http://nar.oxfordjournals.org/content/42/5/2879", "accessDate": "2016-02-23T16:08:09Z", "PMID": "", "PMCID": "", "ISSN": "0305-1048, 1362-4962", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "nar.oxfordjournals.org", "callNumber": "", "rights": "", "extra": "PMID: 24371267", "tags": [ { "tag": "GC content" }, { "tag": "Physics" }, { "tag": "evolution" } ], "collections": [ "CTWJU7NE" ], "relations": {}, "dateAdded": "2016-02-23T16:08:09Z", "dateModified": "2016-02-23T16:08:09Z" } }, { "key": "KM865RQS", "version": 13, "library": { "type": "group", "id": 458761, "name": "BioNumLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/bionumlab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/458761/items/KM865RQS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bionumlab/items/KM865RQS", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1829470, "username": "jibe jeybee", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/jibe_jeybee", "type": "text/html" } } }, "creatorSummary": "Šmarda et al.", "parsedDate": "2014-09-30", "numChildren": 3 }, "data": { "key": "KM865RQS", "version": 13, "itemType": "journalArticle", "title": "Ecological and evolutionary significance of genomic GC content diversity in monocots", "creators": [ { "creatorType": "author", "firstName": "Petr", "lastName": "Šmarda" }, { "creatorType": "author", "firstName": "Petr", "lastName": "Bureš" }, { "creatorType": "author", "firstName": "Lucie", "lastName": "Horová" }, { "creatorType": "author", "firstName": "Ilia J.", "lastName": "Leitch" }, { "creatorType": "author", "firstName": "Ladislav", "lastName": "Mucina" }, { "creatorType": "author", "firstName": "Ettore", "lastName": "Pacini" }, { "creatorType": "author", "firstName": "Lubomír", "lastName": "Tichý" }, { "creatorType": "author", "firstName": "Vít", "lastName": "Grulich" }, { "creatorType": "author", "firstName": "Olga", "lastName": "Rotreklová" } ], "abstractNote": "Genomic DNA base composition (GC content) is predicted to significantly affect genome functioning and species ecology. Although several hypotheses have been put forward to address the biological impact of GC content variation in microbial and vertebrate organisms, the biological significance of GC content diversity in plants remains unclear because of a lack of sufficiently robust genomic data. Using flow cytometry, we report genomic GC contents for 239 species representing 70 of 78 monocot families and compare them with genomic characters, a suite of life history traits and climatic niche data using phylogeny-based statistics. GC content of monocots varied between 33.6% and 48.9%, with several groups exceeding the GC content known for any other vascular plant group, highlighting their unusual genome architecture and organization. GC content showed a quadratic relationship with genome size, with the decreases in GC content in larger genomes possibly being a consequence of the higher biochemical costs of GC base synthesis. Dramatic decreases in GC content were observed in species with holocentric chromosomes, whereas increased GC content was documented in species able to grow in seasonally cold and/or dry climates, possibly indicating an advantage of GC-rich DNA during cell freezing and desiccation. We also show that genomic adaptations associated with changing GC content might have played a significant role in the evolution of the Earth’s contemporary biota, such as the rise of grass-dominated biomes during the mid-Tertiary. One of the major selective advantages of GC-rich DNA is hypothesized to be facilitating more complex gene regulation.", "publicationTitle": "Proceedings of the National Academy of Sciences", "publisher": "", "place": "", "date": "09/30/2014", "volume": "111", "issue": "39", "section": "", "partNumber": "", "partTitle": "", "pages": "E4096-E4102", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PNAS", "DOI": "10.1073/pnas.1321152111", "citationKey": "", "url": "http://www.pnas.org/content/111/39/E4096", "accessDate": "2016-02-23T16:07:13Z", "PMID": "", "PMCID": "", "ISSN": "0027-8424, 1091-6490", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.pnas.org", "callNumber": "", "rights": "", "extra": "PMID: 25225383", "tags": [ { "tag": "GC content" }, { "tag": "Poaceae", "type": 1 }, { "tag": "evolution" }, { "tag": "genome size evolution", "type": 1 }, { "tag": "geographical stratification", "type": 1 }, { "tag": "phylogenetic regression", "type": 1 }, { "tag": "plant genome", "type": 1 } ], "collections": [ "CTWJU7NE" ], "relations": {}, "dateAdded": "2016-02-23T16:07:13Z", "dateModified": "2016-02-23T16:07:13Z" } }, { "key": "GNNKEEMG", "version": 12, "library": { "type": "group", "id": 458761, "name": "BioNumLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/bionumlab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/458761/items/GNNKEEMG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bionumlab/items/GNNKEEMG", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/458761/items/KM865RQS", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1829470, "username": "jibe jeybee", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/jibe_jeybee", "type": "text/html" } } } }, "data": { "key": "GNNKEEMG", "version": 12, "parentItem": "KM865RQS", "itemType": 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"application/json" } }, "meta": { "createdByUser": { "id": 1829470, "username": "jibe jeybee", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/jibe_jeybee", "type": "text/html" } } } }, "data": { "key": "9J8VIFRR", "version": 12, "parentItem": "KM865RQS", "itemType": "attachment", "linkMode": "linked_url", "title": "Snapshot", "accessDate": "2016-02-23T16:07:13Z", "url": "http://www.pnas.org/content/111/39/E4096.full", "note": "", "contentType": "text/html", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-02-23T16:07:13Z", "dateModified": "2016-02-23T16:07:13Z" } }, { "key": "C443ZJ6W", "version": 10, "library": { "type": "group", "id": 458761, "name": "BioNumLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/bionumlab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/458761/items/C443ZJ6W", "type": "application/json" }, "alternate": { "href": 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stacking intereaction stabilize DNA, more than GC content

", "tags": [], "relations": {}, "dateAdded": "2016-02-23T16:03:12Z", "dateModified": "2016-02-23T16:03:34Z" } }, { "key": "SPBBTCTG", "version": 11, "library": { "type": "group", "id": 458761, "name": "BioNumLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/bionumlab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/458761/items/SPBBTCTG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bionumlab/items/SPBBTCTG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1829470, "username": "jibe jeybee", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/jibe_jeybee", "type": "text/html" } } }, "creatorSummary": "Yakovchuk et al.", "parsedDate": "2006-01-01", "numChildren": 4 }, "data": { "key": "SPBBTCTG", "version": 11, "itemType": "journalArticle", "title": "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix", "creators": [ { "creatorType": "author", "firstName": "Peter", "lastName": "Yakovchuk" }, { "creatorType": "author", "firstName": "Ekaterina", "lastName": "Protozanova" }, { "creatorType": "author", "firstName": "Maxim D.", "lastName": "Frank-Kamenetskii" } ], "abstractNote": "Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the first time, DNA stacking parameters are obtained directly (without extrapolation) for temperatures from below room temperature to close to melting temperature. We also obtain DNA stacking parameters for different salt concentrations ranging from 15 to 100 mM Na+. From stacking parameters of individual contacts, we calculate base-stacking contribution to the stability of A•T- and G•C-containing DNA polymers. We find that temperature and salt dependences of the stacking term fully determine the temperature and the salt dependence of DNA stability parameters. For all temperatures and salt concentrations employed in present study, base-stacking is the main stabilizing factor in the DNA double helix. A•T pairing is always destabilizing and G•C pairing contributes almost no stabilization. Base-stacking interaction dominates not only in the duplex overall stability but also significantly contributes into the dependence of the duplex stability on its sequence.", "publicationTitle": "Nucleic Acids Research", "publisher": "", "place": "", "date": "01/01/2006", "volume": "34", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "564-574", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nucl. Acids Res.", "DOI": "10.1093/nar/gkj454", "citationKey": "", "url": "http://nar.oxfordjournals.org/content/34/2/564", "accessDate": "2016-02-23T16:03:09Z", "PMID": "", "PMCID": "", "ISSN": "0305-1048, 1362-4962", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "nar.oxfordjournals.org", "callNumber": "", "rights": "", "extra": "PMID: 16449200", "tags": [ { "tag": "GC content" }, { "tag": "nucleic acid" }, { "tag": "stacking" } ], "collections": [ "CTWJU7NE" ], "relations": {}, "dateAdded": "2016-02-23T16:03:09Z", "dateModified": "2016-02-23T16:03:09Z" } }, { "key": "QRRGWDTH", "version": 10, "library": { "type": "group", "id": 458761, "name": "BioNumLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/bionumlab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/458761/items/QRRGWDTH", "type": "application/json" }, "alternate": { "href": 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"dateModified": "2016-02-23T16:03:09Z" } }, { "key": "3E67P6I3", "version": 9, "library": { "type": "group", "id": 458761, "name": "BioNumLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/bionumlab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/458761/items/3E67P6I3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bionumlab/items/3E67P6I3", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/458761/items/34AHZUQQ", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1829470, "username": "jibe jeybee", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/jibe_jeybee", "type": "text/html" } } } }, "data": { "key": "3E67P6I3", "version": 9, "parentItem": "34AHZUQQ", "itemType": "attachment", "linkMode": "linked_url", "title": "ACS Full Text PDF w/ Links", "accessDate": "2016-02-23T15:55:35Z", "url": "http://pubs.acs.org/doi/pdfplus/10.1021/acs.jpcb.5b06970", "note": "", "contentType": "application/pdf", "charset": "", "tags": [], "relations": {}, "dateAdded": "2016-02-23T15:55:35Z", "dateModified": "2016-02-23T15:55:35Z" } }, { "key": "34AHZUQQ", "version": 9, "library": { "type": "group", "id": 458761, "name": "BioNumLab", "links": { "alternate": { "href": "https://www.zotero.org/groups/bionumlab", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/458761/items/34AHZUQQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/bionumlab/items/34AHZUQQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1829470, "username": "jibe jeybee", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/jibe_jeybee", "type": "text/html" } } }, "creatorSummary": "Gu et al.", "parsedDate": "2015-10-22", "numChildren": 2 }, "data": { "key": "34AHZUQQ", "version": 9, "itemType": "journalArticle", "title": "Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix", "creators": [ { "creatorType": "author", "firstName": "Xiaobo", "lastName": "Gu" }, { "creatorType": "author", "firstName": "Blaine H. M.", "lastName": "Mooers" }, { "creatorType": "author", "firstName": "Leonard M.", "lastName": "Thomas" }, { "creatorType": "author", "firstName": "Joshua", "lastName": "Malone" }, { "creatorType": "author", "firstName": "Steven", "lastName": "Harris" }, { "creatorType": "author", "firstName": "Susan J.", "lastName": "Schroeder" } ], "abstractNote": "Consecutive G·U base pairs inside RNA helices can be destabilizing, while those at the ends of helices are thermodynamically stabilizing. To determine if this paradox could be explained by differences in base stacking, we determined the high-resolution (1.32 Å) crystal structure of (5?-GGUGGCUGUU-3?)2 and studied three sequences with four consecutive terminal G·U pairs by NMR spectroscopy. In the crystal structure of (5?-GGUGGCUGUU-3?)2, the helix is overwound but retains the overall features of A-form RNA. The penultimate base steps at each end of the helix have high base overlap and contribute to the unexpectedly favorable energetic contribution for the 5?-GU-3?/3?-UG-5? motif in this helix position. The balance of base stacking and helical twist contributes to the positional dependence of G·U pair stabilities. The energetic stabilities and similarity to A-form RNA helices suggest that consecutive G·U pairs would be recognized by RNA helix binding proteins, such as Dicer and Ago. Thus, these results will aid future searches for target sites of small RNAs in gene regulation.", "publicationTitle": "The Journal of Physical Chemistry B", "publisher": "", "place": "", "date": "October 22, 2015", "volume": "119", "issue": "42", "section": "", "partNumber": "", "partTitle": "", "pages": "13252-13261", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Phys. Chem. 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