利用实验进化和全基因组测序对遗传系统进行分析。
Analysis of genetic systems using experimental evolution and whole-genome sequencing.
作者信息
Hegreness Matthew, Kishony Roy
机构信息
Department of Systems Biology, Harvard Medical School, Longwood Avenue, Boston, MA 02115, USA.
出版信息
Genome Biol. 2007;8(1):201. doi: 10.1186/gb-2007-8-1-201.
Abstract
The application of whole-genome sequencing to the study of microbial evolution promises to reveal the complex functional networks of mutations that underlie adaptation. A recent study of parallel evolution in populations of Escherichia coli shows how adaptation involves both functional changes to specific proteins as well as global changes in regulation.
摘要
将全基因组测序应用于微生物进化研究，有望揭示构成适应性基础的复杂突变功能网络。最近一项对大肠杆菌群体平行进化的研究表明，适应性如何涉及特定蛋白质的功能变化以及调控方面的全局变化。
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本文引用的文献
1
Analysis of one million base pairs of Neanderthal DNA.对一百万个碱基对的尼安德特人DNA进行分析。
Nature. 2006 Nov 16;444(7117):330-6. doi: 10.1038/nature05336.
2
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.对大肠杆菌进行比较基因组测序能够在实验室时间尺度上观察细菌的进化。
Nat Genet. 2006 Dec;38(12):1406-12. doi: 10.1038/ng1906. Epub 2006 Nov 5.
3
High-resolution mutation mapping reveals parallel experimental evolution in yeast.高分辨率突变图谱揭示了酵母中的平行实验进化。
PLoS Biol. 2006 Jul;4(8):e256. doi: 10.1371/journal.pbio.0040256.
4
Tests of parallel molecular evolution in a long-term experiment with Escherichia coli.在大肠杆菌的长期实验中对平行分子进化的测试。
Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9107-12. doi: 10.1073/pnas.0602917103. Epub 2006 Jun 2.
5
Evolution of an obligate social cheater to a superior cooperator.一个专性社会欺骗者向卓越合作者的演化。
Nature. 2006 May 18;441(7091):310-4. doi: 10.1038/nature04677.
6
Sociobiology: the Phoenix effect.社会生物学：凤凰效应。
Nature. 2006 May 18;441(7091):291-2. doi: 10.1038/441291a.
7
Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor.进化的细菌合作者及其作弊祖先中的全面突变鉴定。
Proc Natl Acad Sci U S A. 2006 May 23;103(21):8107-12. doi: 10.1073/pnas.0510740103. Epub 2006 May 17.
8
Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli.大肠杆菌长期实验进化过程中全局蛋白质谱的平行变化。
Genetics. 2006 Aug;173(4):1851-69. doi: 10.1534/genetics.105.049619. Epub 2006 May 15.
9
Functional classification of drugs by properties of their pairwise interactions.根据药物两两相互作用的性质对药物进行功能分类。
Nat Genet. 2006 Apr;38(4):489-94. doi: 10.1038/ng1755. Epub 2006 Mar 19.
10
An equivalence principle for the incorporation of favorable mutations in asexual populations.无性群体中有利突变整合的等效原理。
Science. 2006 Mar 17;311(5767):1615-7. doi: 10.1126/science.1122469.
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