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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”。
Pub Date : 2009-01-01 Epub Date: 2009-07-13 DOI: 10.1186/jbiol159
Pere Puigbò, Yuri I Wolf, Eugene V Koonin

Background: 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'.

Results: 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.

Conclusions: 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.

背景:比较基因组学揭示了原核生物之间广泛的水平基因转移,这一发展通常被认为破坏了“生命之树”的概念。然而,在系统发育的“生命森林”中仍然存在统计中心趋势的可能性仍然存在。结果:对6,901棵原核基因系统发育树的“森林”进行了全面的比较分析,发现了一致的系统发育信号,特别是在102棵几乎通用的树中,尽管拓扑结构高度不一致,可能是由于水平基因转移。横向转移似乎是随机分布的,并没有掩盖中心趋势。几乎普遍的树在拓扑结构上与许多其他树相似。因此,几乎普遍的树木可能反映了一个重要的集中趋势,尽管它们不能完全代表森林。然而,拓扑一致性主要出现在较浅的树深,而在古细菌和细菌门的辐射水平上突然下降,这表明进化的早期阶段可能不是树状的(生物大爆炸)。在压缩枝状发育或生物大爆炸下的进化模拟更符合压缩枝状发育模型中观察到的树不一致性与系统发育深度之间的相关性。结论:水平基因转移在原核生物中普遍存在,很少有基因树是完全一致的,使得原来的生命树概念过时。在古生菌和细菌的整个进化过程中,一个最可能代表垂直遗传的中心趋势是显而易见的,尽管压缩枝发生使主要古生菌和细菌枝之间关系的明确解决变得复杂。
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引用次数: 261
Fish 'n' TRIMs. 鱼和TRIMs。
Pub Date : 2009-01-01 Epub Date: 2009-05-29 DOI: 10.1186/jbiol150
Louis Du Pasquier

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.

在硬骨鱼中发现了一个新的具有抗病毒活性的tripartite-motif (TRIM)细胞内受体的多元化多基因家族,并发表在BMC Biology上。这些受体的历史涉及到与主要组织相容性复合体的类似物的古老联系,并且该家族有无脊椎动物的前身。
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引用次数: 11
Exploiting the promiscuity of imatinib. 利用伊马替尼的滥交性。
Pub Date : 2009-01-01 Epub Date: 2009-04-15 DOI: 10.1186/jbiol134
Shun J Lee, Jean Y J Wang

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.

蛋白激酶抑制剂伊马替尼,也被称为格列卫,在治疗慢性骨髓性白血病方面取得了显著的成功。最近发表在《BMC Structural Biology》上的一篇论文报道了伊马替尼与氧化还原酶NQO2结合的1.75 A晶体结构,并揭示了这种抑制剂的结合特异性和脱靶效应。
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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。
Pub Date : 2009-01-01 Epub Date: 2009-12-30 DOI: 10.1186/jbiol202
Pascale Cossart, Cristel Archambaud

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.

细菌发病机制的一个主要挑战是了解从腐生到毒力转换的分子基础。在最近的一项全基因组转录组分析之后,BMC Genomics发表的一篇文章报道了首次在单核增生李斯特菌中使用RNA-seq来鉴定由sigma B控制的基因,sigma B是一种在毒力中起关键作用的转录调节因子。
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引用次数: 25
Limb regeneration revisited. 重新审视肢体再生。
Pub Date : 2009-01-01 Epub Date: 2009-01-13 DOI: 10.1186/jbiol105
Jessica L Whited, Clifford J Tabin

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.

脊椎动物肢体再生的研究是早期发育生物学家最喜欢的话题,最近在BMC Biology和BMC developmental Biology上发表的论文表明,由于最近开发的分子和遗传工具,脊椎动物肢体再生的研究正在复兴。经典实验为解释现代功能研究提供了丰富的背景。
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引用次数: 34
Mayr, mathematics and the study of evolution. 迈尔,数学和进化研究。
Pub Date : 2009-01-01 Epub Date: 2009-02-23 DOI: 10.1186/jbiol117
James F Crow

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.

1959年,恩斯特·迈尔质疑数学模型与进化研究的相关性,JBS霍尔丹在一篇诙谐而令人信服的文章中回答了这一问题。50年过去了,我得出的结论是,数学的重要性实际上已经增加,并将继续增加。
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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。
Pub Date : 2009-01-01 Epub Date: 2009-03-13 DOI: 10.1186/jbiol126
Hue Sun Chan, Zhuqing Zhang

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.

发表在《BMC结构生物学》上的一项关于双突变周期的晶格模型研究强调了非天然构象中的相互作用如何导致球状蛋白中远端残基之间的热力学耦合,增加了最近在描述无序构象集成在蛋白质行为中所起的关键作用方面的进展。
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引用次数: 6
Dysregulating the regulators. 对监管者的监管失灵。
Pub Date : 2009-01-01 Epub Date: 2009-08-27 DOI: 10.1186/jbiol175
Miranda Robertson
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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。
Pub Date : 2009-01-01 DOI: 10.1186/jbiol195
Alexey Khodjakov, Conly L Rieder

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.

检查点控制的概念彻底改变了我们对细胞周期的理解。在这里,我们重新审视检查点的定义特征,并认为未能正确理解这一概念会导致对实验结果的误解。我们使用有丝分裂检查点来说明由于不遵守严格的定义和精确的术语而产生的问题。
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引用次数: 63
What we still don't know about AIDS. 我们对艾滋病还不了解的。
Pub Date : 2009-01-01 DOI: 10.1186/jbiol200
Miranda Robertson
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引用次数: 3
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