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Search for a 'Tree of Life' in the thicket of the phylogenetic forest. 在系统发育森林的丛林中寻找“生命之树”。
Journal of Biology Pub Date : 2009-01-01 Epub Date: 2009-07-13 DOI: 10.1186/jbiol159
Pere Puigbò, Yuri I Wolf, Eugene V Koonin
{"title":"Search for a 'Tree of Life' in the thicket of the phylogenetic forest.","authors":"Pere Puigbò,&nbsp;Yuri I Wolf,&nbsp;Eugene V Koonin","doi":"10.1186/jbiol159","DOIUrl":"https://doi.org/10.1186/jbiol159","url":null,"abstract":"<p><strong>Background: </strong>Comparative genomics has revealed extensive horizontal gene transfer among prokaryotes, a development that is often considered to undermine the 'tree of life' concept. However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'.</p><p><strong>Results: </strong>A comprehensive comparative analysis of a 'forest' of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus, the nearly universal trees might reflect a significant central tendency, although they cannot represent the forest completely. However, topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla, suggesting that early phases of evolution could be non-tree-like (Biological Big Bang). Simulations of evolution under compressed cladogenesis or Biological Big Bang yielded a better fit to the observed dependence between tree inconsistency and phylogenetic depth for the compressed cladogenesis model.</p><p><strong>Conclusions: </strong>Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 6","pages":"59"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28374983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 261
Fish 'n' TRIMs. 鱼和TRIMs。
Journal of Biology Pub Date : 2009-01-01 Epub Date: 2009-05-29 DOI: 10.1186/jbiol150
Louis Du Pasquier
{"title":"Fish 'n' TRIMs.","authors":"Louis Du Pasquier","doi":"10.1186/jbiol150","DOIUrl":"https://doi.org/10.1186/jbiol150","url":null,"abstract":"<p><p>A novel diversified multigene family of tripartite-motif (TRIM) intracellular receptors with putative antiviral activity has been identified in teleost fish and published in BMC Biology. The history of these receptors involves ancient linkage to paralogs of the major histocompatibility complex, and the family has invertebrate precursors.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 5","pages":"50"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol150","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28237207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Exploiting the promiscuity of imatinib. 利用伊马替尼的滥交性。
Journal of Biology Pub Date : 2009-01-01 Epub Date: 2009-04-15 DOI: 10.1186/jbiol134
Shun J Lee, Jean Y J Wang
{"title":"Exploiting the promiscuity of imatinib.","authors":"Shun J Lee,&nbsp;Jean Y J Wang","doi":"10.1186/jbiol134","DOIUrl":"https://doi.org/10.1186/jbiol134","url":null,"abstract":"<p><p>The protein kinase inhibitor imatinib, also known as Gleevec, has been a notable success in treating chronic myelogenous leukemia. A recent paper in BMC Structural Biology reports a 1.75 A crystal structure of imatinib bound to the oxidoreductase NQO2 and reveals insights into the binding specificity and the off-target effects of the inhibitor.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 3","pages":"30"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol134","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28168490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 38
The bacterial pathogen Listeria monocytogenes: an emerging model in prokaryotic transcriptomics. 细菌病原体单核增生李斯特菌:原核生物转录组学中的一个新兴模型。
Journal of Biology Pub Date : 2009-01-01 Epub Date: 2009-12-30 DOI: 10.1186/jbiol202
Pascale Cossart, Cristel Archambaud
{"title":"The bacterial pathogen Listeria monocytogenes: an emerging model in prokaryotic transcriptomics.","authors":"Pascale Cossart,&nbsp;Cristel Archambaud","doi":"10.1186/jbiol202","DOIUrl":"https://doi.org/10.1186/jbiol202","url":null,"abstract":"<p><p>A major challenge in bacterial pathogenesis is understanding the molecular basis of the switch from saprophytism to virulence. Following a recent whole-genome transcriptomic analysis using tiling arrays, an article published in BMC Genomics reports the first use of RNA-seq in Listeria monocytogenes in order to identify genes controlled by sigma B, a transcriptional regulator with a critical role in virulence.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 12","pages":"107"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol202","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28629411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 25
Limb regeneration revisited. 重新审视肢体再生。
Journal of Biology Pub Date : 2009-01-01 Epub Date: 2009-01-13 DOI: 10.1186/jbiol105
Jessica L Whited, Clifford J Tabin
{"title":"Limb regeneration revisited.","authors":"Jessica L Whited,&nbsp;Clifford J Tabin","doi":"10.1186/jbiol105","DOIUrl":"https://doi.org/10.1186/jbiol105","url":null,"abstract":"<p><p>The investigation of vertebrate limb regeneration, a favorite topic of early developmental biologists, is enjoying a renaissance thanks to recently developed molecular and genetic tools, as indicated in recent papers in BMC Biology and BMC Developmental Biology. Classical experiments provide a rich context for interpreting modern functional studies.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 1","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27957130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 34
Mayr, mathematics and the study of evolution. 迈尔，数学和进化研究。
Journal of Biology Pub Date : 2009-01-01 Epub Date: 2009-02-23 DOI: 10.1186/jbiol117
James F Crow
{"title":"Mayr, mathematics and the study of evolution.","authors":"James F Crow","doi":"10.1186/jbiol117","DOIUrl":"https://doi.org/10.1186/jbiol117","url":null,"abstract":"<p><p>In 1959 Ernst Mayr challenged the relevance of mathematical models to evolutionary studies and was answered by JBS Haldane in a witty and convincing essay. Fifty years on, I conclude that the importance of mathematics has in fact increased and will continue to do so.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 2","pages":"13"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28048335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Liaison amid disorder: non-native interactions may underpin long-range coupling in proteins. 无序中的联系:非原生相互作用可能支持蛋白质的远程偶联。
Journal of Biology Pub Date : 2009-01-01 Epub Date: 2009-03-13 DOI: 10.1186/jbiol126
Hue Sun Chan, Zhuqing Zhang
{"title":"Liaison amid disorder: non-native interactions may underpin long-range coupling in proteins.","authors":"Hue Sun Chan,&nbsp;Zhuqing Zhang","doi":"10.1186/jbiol126","DOIUrl":"https://doi.org/10.1186/jbiol126","url":null,"abstract":"<p><p>A lattice-model study of double-mutant cycles published in BMC Structural Biology underscores how interactions in non-native conformations can lead to thermodynamic coupling between distant residues in globular proteins, adding to recent advances in delineating the often crucial roles played by disordered conformational ensembles in protein behavior.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 3","pages":"27"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol126","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28092154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Dysregulating the regulators. 对监管者的监管失灵。
Journal of Biology Pub Date : 2009-01-01 Epub Date: 2009-08-27 DOI: 10.1186/jbiol175
Miranda Robertson
{"title":"Dysregulating the regulators.","authors":"Miranda Robertson","doi":"10.1186/jbiol175","DOIUrl":"https://doi.org/10.1186/jbiol175","url":null,"abstract":"","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 7","pages":"60"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol175","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28454402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
The nature of cell-cycle checkpoints: facts and fallacies. 细胞周期检查点的本质:事实与谬误。
Journal of Biology Pub Date : 2009-01-01 DOI: 10.1186/jbiol195
Alexey Khodjakov, Conly L Rieder
{"title":"The nature of cell-cycle checkpoints: facts and fallacies.","authors":"Alexey Khodjakov,&nbsp;Conly L Rieder","doi":"10.1186/jbiol195","DOIUrl":"https://doi.org/10.1186/jbiol195","url":null,"abstract":"<p><p>The concept of checkpoint controls revolutionized our understanding of the cell cycle. Here we revisit the defining features of checkpoints and argue that failure to properly appreciate the concept is leading to misinterpretation of experimental results. We illustrate, using the mitotic checkpoint, problems that can arise from a failure to respect strict definitions and precise terminology.</p>","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 10","pages":"88"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol195","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28521757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 63
What we still don't know about AIDS. 我们对艾滋病还不了解的。
Journal of Biology Pub Date : 2009-01-01 DOI: 10.1186/jbiol200
Miranda Robertson
{"title":"What we still don't know about AIDS.","authors":"Miranda Robertson","doi":"10.1186/jbiol200","DOIUrl":"https://doi.org/10.1186/jbiol200","url":null,"abstract":"","PeriodicalId":15075,"journal":{"name":"Journal of Biology","volume":"8 10","pages":"87"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/jbiol200","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28587619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
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