[ { "key": "T4E246UT", "version": 3, "library": { "type": "group", "id": 64415, "name": "Microbiology MOOC", "links": { "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/64415/items/T4E246UT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc/items/T4E246UT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 697597, "username": "bioram", "name": "Robert Maxwell", "links": { "alternate": { "href": "https://www.zotero.org/bioram", "type": "text/html" } } }, "creatorSummary": "Keeling and Burki", "parsedDate": "2019-08-19", "numChildren": 0 }, "data": { "key": "T4E246UT", "version": 3, "itemType": "journalArticle", "title": "Progress towards the Tree of Eukaryotes", "creators": [ { "creatorType": "author", "firstName": "Patrick J.", "lastName": "Keeling" }, { "creatorType": "author", "firstName": "Fabien", "lastName": "Burki" } ], "abstractNote": "Developing a detailed understanding of how all known forms of life are related to one another in the tree of life has been a major preoccupation of biology since the idea of tree-like evolution first took hold. Since most life is microbial, our intuitive use of morphological comparisons to infer relatedness only goes so far, and molecular sequence data, most recently from genomes and transcriptomes, has been the primary means to infer these relationships. For prokaryotes this presented new challenges, since the degree of horizontal gene transfer led some to question the tree-like depiction of evolution altogether. Most eukaryotes are also microbial, but in contrast to prokaryotic life, the application of large-scale molecular data to the tree of eukaryotes has largely been a constructive process, leading to a small number of very diverse lineages, or ‘supergroups’. The tree is not completely resolved, and contentious problems remain, but many well-established supergroups now encompass much more diversity than the traditional kingdoms. Some of the most exciting recent developments come from the discovery of branches in the tree that we previously had no inkling even existed, many of which are of great ecological or evolutionary interest. These new branches highlight the need for more exploration, by high-throughput molecular surveys, but also more traditional means of observations and cultivation.", "publicationTitle": "Current Biology", "publisher": "", "place": "", "date": "2019-08-19", "volume": "29", "issue": "16", "section": "", "partNumber": "", "partTitle": "", "pages": "R808-R817", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Current Biology", "DOI": "10.1016/j.cub.2019.07.031", "citationKey": "", "url": "https://www.sciencedirect.com/science/article/pii/S0960982219308760", "accessDate": "2023-07-06T16:53:46Z", "PMID": "", "PMCID": "", "ISSN": "0960-9822", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-07-06T16:53:46Z", "dateModified": "2023-07-06T16:53:46Z" } }, { "key": "8RMAMS32", "version": 2, "library": { "type": "group", "id": 64415, "name": "Microbiology MOOC", "links": { "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/64415/items/8RMAMS32", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc/items/8RMAMS32", "type": "text/html" } }, "meta": { "createdByUser": { "id": 697597, "username": "bioram", "name": "Robert Maxwell", "links": { "alternate": { "href": "https://www.zotero.org/bioram", "type": "text/html" } } }, "creatorSummary": "Hug et al.", "parsedDate": "2016-04-11", "numChildren": 0 }, "data": { "key": "8RMAMS32", "version": 2, "itemType": "journalArticle", "title": "A new view of the tree of life", "creators": [ { "creatorType": "author", "firstName": "Laura A.", "lastName": "Hug" }, { "creatorType": "author", "firstName": "Brett J.", "lastName": "Baker" }, { "creatorType": "author", "firstName": "Karthik", "lastName": "Anantharaman" }, { "creatorType": "author", "firstName": "Christopher T.", "lastName": "Brown" }, { "creatorType": "author", "firstName": "Alexander J.", "lastName": "Probst" }, { "creatorType": "author", "firstName": "Cindy J.", "lastName": "Castelle" }, { "creatorType": "author", "firstName": "Cristina N.", "lastName": "Butterfield" }, { "creatorType": "author", "firstName": "Alex W.", "lastName": "Hernsdorf" }, { "creatorType": "author", "firstName": "Yuki", "lastName": "Amano" }, { "creatorType": "author", "firstName": "Kotaro", "lastName": "Ise" }, { "creatorType": "author", "firstName": "Yohey", "lastName": "Suzuki" }, { "creatorType": "author", "firstName": "Natasha", "lastName": "Dudek" }, { "creatorType": "author", "firstName": "David A.", "lastName": "Relman" }, { "creatorType": "author", "firstName": "Kari M.", "lastName": "Finstad" }, { "creatorType": "author", "firstName": "Ronald", "lastName": "Amundson" }, { "creatorType": "author", "firstName": "Brian C.", "lastName": "Thomas" }, { "creatorType": "author", "firstName": "Jillian F.", "lastName": "Banfield" } ], "abstractNote": "The tree of life is one of the most important organizing principles in biology1. Gene surveys suggest the existence of an enormous number of branches2, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships3–5 or on the known, well-classified diversity of life with an emphasis on eukaryotes6. These approaches overlook the dramatic change in our understanding of life's diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts7,8. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.", "publicationTitle": "Nature Microbiology", "publisher": "", "place": "", "date": "2016-04-11", "volume": "1", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "1-6", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat Microbiol", "DOI": "10.1038/nmicrobiol.2016.48", "citationKey": "", "url": "https://www.nature.com/articles/nmicrobiol201648", "accessDate": "2023-07-06T16:41:42Z", "PMID": "", "PMCID": "", "ISSN": "2058-5276", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "www.nature.com", "callNumber": "", "rights": "2016 Macmillan Publishers Limited", "extra": "Number: 5\nPublisher: Nature Publishing Group", "tags": [ { "tag": "Environmental microbiology", "type": 1 }, { "tag": "Phylogenetics", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2023-07-06T16:41:42Z", "dateModified": "2023-07-06T16:41:42Z" } }, { "key": "9JP3LVMG", "version": 2, "library": { "type": "group", "id": 64415, "name": "Microbiology MOOC", "links": { "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/64415/items/9JP3LVMG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc/items/9JP3LVMG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 697597, "username": "bioram", "name": "Robert Maxwell", "links": { "alternate": { "href": "https://www.zotero.org/bioram", "type": "text/html" } } }, "creatorSummary": "Blais and Archibald", "parsedDate": "2021-04-12", "numChildren": 0 }, "data": { "key": "9JP3LVMG", "version": 2, "itemType": "journalArticle", "title": "The past, present and future of the tree of life", "creators": [ { "creatorType": "author", "firstName": "Cédric", "lastName": "Blais" }, { "creatorType": "author", "firstName": "John M.", "lastName": "Archibald" } ], "abstractNote": "The advent of comparative genomics in the late 1990s led to the discovery of extensive lateral gene transfer in prokaryotes. The resulting debate over whether life as a whole is best represented as a tree or a network has since given way to a general consensus in which trees and networks co-exist rather than stand in opposition. Embracing this consensus allows us to move beyond the question of which is true or false. The future of the tree of life debate lies in asking what trees and networks can, and should, do for science.", "publicationTitle": "Current Biology", "publisher": "", "place": "", "date": "2021-04-12", "volume": "31", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "R314-R321", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Current Biology", "DOI": "10.1016/j.cub.2021.02.052", "citationKey": "", "url": "https://www.sciencedirect.com/science/article/pii/S0960982221002967", "accessDate": "2023-07-06T16:39:13Z", "PMID": "", "PMCID": "", "ISSN": "0960-9822", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "ScienceDirect", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2023-07-06T16:39:27Z", "dateModified": "2023-07-06T16:39:27Z" } }, { "key": "S39B8IPB", "version": 1, "library": { "type": "group", "id": 64415, "name": "Microbiology MOOC", "links": { "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/64415/items/S39B8IPB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc/items/S39B8IPB", "type": "text/html" } }, "meta": { "createdByUser": { "id": 697597, "username": "bioram", "name": "Robert Maxwell", "links": { "alternate": { "href": "https://www.zotero.org/bioram", "type": "text/html" } } }, "creatorSummary": "Isalan et al.", "parsedDate": "2008-04-17", "numChildren": 0 }, "data": { "key": "S39B8IPB", "version": 1, "itemType": "journalArticle", "title": "Evolvability and hierarchy in rewired bacterial gene networks", "creators": [ { "creatorType": "author", "firstName": "Mark", "lastName": "Isalan" }, { "creatorType": "author", "firstName": "Caroline", "lastName": "Lemerle" }, { "creatorType": "author", "firstName": "Konstantinos", "lastName": "Michalodimitrakis" }, { "creatorType": "author", "firstName": "Carsten", "lastName": "Horn" }, { "creatorType": "author", "firstName": "Pedro", "lastName": "Beltrao" }, { "creatorType": "author", "firstName": "Emanuele", "lastName": "Raineri" }, { "creatorType": "author", "firstName": "Mireia", "lastName": "Garriga-Canut" }, { "creatorType": "author", "firstName": "Luis", "lastName": "Serrano" } ], "abstractNote": "", "publicationTitle": "Nature", "publisher": "", "place": "", "date": "April 17, 2008", "volume": "452", "issue": "7189", "section": "", "partNumber": "", "partTitle": "", "pages": "840-845", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nature", "DOI": "10.1038/nature06847", "citationKey": "", "url": "http://dx.doi.org/10.1038/nature06847", "accessDate": "2012-02-01T14:55:59Z", "PMID": "", "PMCID": "", "ISSN": "0028-0836", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Nature", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2012-02-01T14:56:03Z", "dateModified": "2012-02-01T14:56:03Z" } }, { "key": "8EMT22CV", "version": 1, "library": { "type": "group", "id": 64415, "name": "Microbiology MOOC", "links": { "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/64415/items/8EMT22CV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc/items/8EMT22CV", "type": "text/html" } }, "meta": { "createdByUser": { "id": 697597, "username": "bioram", "name": "Robert Maxwell", "links": { "alternate": { "href": "https://www.zotero.org/bioram", "type": "text/html" } } }, "creatorSummary": "Redfield", "parsedDate": "1988-05-01", "numChildren": 0 }, "data": { "key": "8EMT22CV", "version": 1, "itemType": "journalArticle", "title": "Evolution of Bacterial Transformation: Is Sex With Dead Cells Ever Better Than No Sex at All?", "creators": [ { "creatorType": "author", "firstName": "R. J.", "lastName": "Redfield" } ], "abstractNote": "", "publicationTitle": "Genetics", "publisher": "", "place": "", "date": "May 01 , 1988", "volume": "119", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "213 -221", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.genetics.org/content/119/1/213.abstract", "accessDate": "2012-02-01T14:52:49Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Evolution of Bacterial Transformation", "language": "", "libraryCatalog": "Highwire 2.0", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2012-02-01T14:52:54Z", "dateModified": "2012-02-01T14:52:54Z" } }, { "key": "IZVCWV3S", "version": 1, "library": { "type": "group", "id": 64415, "name": "Microbiology MOOC", "links": { "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/64415/items/IZVCWV3S", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc/items/IZVCWV3S", "type": "text/html" } }, "meta": { "createdByUser": { "id": 697597, "username": "bioram", "name": "Robert Maxwell", "links": { "alternate": { "href": "https://www.zotero.org/bioram", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "IZVCWV3S", "version": 1, "itemType": "webpage", "title": "Genetics - Medical Microbiology - NCBI Bookshelf", "creators": [], "abstractNote": "", "websiteTitle": "", "websiteType": "", "date": "", "publisher": "", "place": "", "DOI": "", "citationKey": "", "url": "http://www.ncbi.nlm.nih.gov/books/NBK7908/#A468", "accessDate": "2012-02-01T14:49:25Z", "shortTitle": "", "language": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2012-02-01T14:49:40Z", "dateModified": "2012-02-01T14:49:40Z" } }, { "key": "PX3778GQ", "version": 1, "library": { "type": "group", "id": 64415, "name": "Microbiology MOOC", "links": { "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/64415/items/PX3778GQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/microbiology_mooc/items/PX3778GQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 697597, "username": "bioram", "name": "Robert Maxwell", "links": { "alternate": { "href": "https://www.zotero.org/bioram", "type": "text/html" } } }, "creatorSummary": "Casadesús and Low", "parsedDate": "2006-09", "numChildren": 0 }, "data": { "key": "PX3778GQ", "version": 1, "itemType": "journalArticle", "title": "Epigenetic Gene Regulation in the Bacterial World", "creators": [ { "creatorType": "author", "firstName": "Josep", "lastName": "Casadesús" }, { "creatorType": "author", "firstName": "David", "lastName": "Low" } ], "abstractNote": "Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.", "publicationTitle": "Microbiology and Molecular Biology Reviews", "publisher": "", "place": "", "date": "September 2006", "volume": "70", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "830 -856", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1128/MMBR.00016-06", "citationKey": "", "url": "http://mmbr.asm.org/content/70/3/830.abstract", "accessDate": "2012-01-30T15:32:01Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Highwire 2.0", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [], "relations": {}, "dateAdded": "2012-01-31T18:19:11Z", "dateModified": "2012-01-31T18:19:11Z" } } ]