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Critical Reviews in Biochemistry and Molecular Biology Volume 42, 2007 - Issue 4
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Research Article

Adaptive Amplification

P. J. Hastings Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
Pages 271-283 | Published online: 10 Oct 2008

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Rodrigo S. Galhardo, P. J. Hastings & Susan M. Rosenberg. (2007) Mutation as a Stress Response and the Regulation of Evolvability. Critical Reviews in Biochemistry and Molecular Biology 42:5, pages 399-435.
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Articles from other publishers (44)

Shefali Banerjee, Cathy Smith, Adam P Geballe, Stefan Rothenburg, Jacob O Kitzman & Greg Brennan. (2022) Gene amplification acts as a molecular foothold to facilitate cross-species adaptation and evasion of multiple antiviral pathways. Virus Evolution 8:2.
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Patrick T West, Rachael B Chanin & Ami S Bhatt. (2022) From genome structure to function: insights into structural variation in microbiology. Current Opinion in Microbiology 69, pages 102192.
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Patricia Adu‐Yeboah, Jenna M Malone, Gurjeet Gill & Christopher Preston. (2021) Stability of EPSPS gene copy number in Hordeum glaucum Steud (barley grass) in the presence and absence of glyphosate selection . Pest Management Science 77:7, pages 3080-3087.
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Holly A. Martin, Amanda A. Kidman, Jillian Socea, Carmen Vallin, Mario Pedraza-Reyes & Eduardo A. Robleto. (2020) The Bacillus Subtilis K-State Promotes Stationary-Phase Mutagenesis via Oxidative Damage. Genes 11:2, pages 190.
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Asiya Gusa & Sue Jinks-Robertson. (2019) Mitotic Recombination and Adaptive Genomic Changes in Human Pathogenic Fungi. Genes 10:11, pages 901.
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T. Chang, J. W. Rosch, Z. Gu, H. Hakim, C. Hewitt, A. Gaur, G. Wu & R. T. Hayden. (2018) Whole-Genome Characterization of Bacillus cereus Associated with Specific Disease Manifestations. Infection and Immunity 86:2.
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Miriam Dormeyer, Anastasia L. L?bke, Peter M?ller, Sabine Lentes, Daniel R. Reu?, Andrea Th?rmer, J?rg St?lke, Rolf Daniel, Sabine Brantl & Fabian M. Commichau. (2017) Hierarchical mutational events compensate for glutamate auxotrophy of a B acillus subtilis gltC mutant . Environmental Microbiology Reports 9:3, pages 279-289.
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Tanvir-Ul-Hassan Dar & Reiaz-Ul RehmanTanvir-Ul-Hassan Dar & Reiaz-Ul Rehman. 2017. Polyploidy: Recent Trends and Future Perspectives. Polyploidy: Recent Trends and Future Perspectives 89 99 .
Martha Gómez-Marroquín, Holly Martin, Amber Pepper, Mary Girard, Amanda Kidman, Carmen Vallin, Ronald Yasbin, Mario Pedraza-Reyes & Eduardo Robleto. (2016) Stationary-Phase Mutagenesis in Stressed Bacillus subtilis Cells Operates by Mfd-Dependent Mutagenic Pathways. Genes 7:7, pages 33.
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Predrag Šustar & Zdenka Brzović. 2016. Evolutionary Biology. Evolutionary Biology 273 287 .
Emanuele Rigato & Giuseppe Fusco. (2016) Enhancing effect of phenotype mutational robustness on adaptation in Escherichia coli . Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 326:1, pages 31-37.
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Greg Brennan, Jacob O. Kitzman, Jay Shendure & Adam P. Geballe. (2015) Experimental Evolution Identifies Vaccinia Virus Mutations in A24R and A35R That Antagonize the Protein Kinase R Pathway and Accompany Collapse of an Extragenic Gene Amplification. Journal of Virology 89:19, pages 9986-9997.
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Janet L. Gibson, Mary-Jane Lombardo, Ildiko Aponyi, Diana Vera Cruz, Mellanie P. Ray & Susan M. Rosenberg. (2015) Atypical Role for PhoU in Mutagenic Break Repair under Stress in Escherichia coli. PLOS ONE 10:5, pages e0123315.
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Carmel Mothersill, Dawn Austin, Cristian Fernandez-Palomo, Colin Seymour, Niall Auchinachie & Brian Austin. (2014) Rescue of fish exposed to a lethal dose of pathogen, by signals from sublethally exposed survivors. FEMS Microbiology Letters 362:5.
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Thomas Ferenci & Ram Maharjan. (2015) Mutational heterogeneity: A key ingredient of bet-hedging and evolutionary divergence?. BioEssays 37:2, pages 123-130.
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Wannasiri Wannarat, Shiori Motoyama, Kenta Masuda, Fujio Kawamura & Takashi Inaoka. (2014) Tetracycline tolerance mediated by gene amplification in Bacillus subtilis. Microbiology 160:11, pages 2474-2480.
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Hallie Wimberly, Chandan Shee, P. C. Thornton, Priya Sivaramakrishnan, Susan M. Rosenberg & P. J. Hastings. (2013) R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli. Nature Communications 4:1.
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Todd A. Gaines, Alice A. Wright, William T. Molin, Lothar Lorentz, Chance W. Riggins, Patrick J. Tranel, Roland Beffa, Philip Westra & Stephen B. Powles. (2013) Identification of Genetic Elements Associated with EPSPS Gene Amplification. PLoS ONE 8:6, pages e65819.
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Eduardo Robleto, Holly A. Martin, Carmen Vallin, Mario Pedraza-Reyes & Ronald Yasbin. 2013. Stress-Induced Mutagenesis. Stress-Induced Mutagenesis 41 57 .
Chandan Shee, P. J. Hastings & Susan M. Rosenberg. 2013. Stress-Induced Mutagenesis. Stress-Induced Mutagenesis 21 39 .
Fyodor A. Kondrashov. (2012) Gene duplication as a mechanism of genomic adaptation to a changing environment. Proceedings of the Royal Society B: Biological Sciences 279:1749, pages 5048-5057.
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Long N Truong, Shashikant Patil, Sherry S Martin, Jay F LeBlanc, Anil Nanda, Mary L Nordberg & Marie E Beckner. (2012) Rapid Detection of high-level oncogene amplifications in ultrasonic surgical aspirations of brain tumors. Diagnostic Pathology 7:1.
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Ben Ryall, Gustavo Eydallin & Thomas Ferenci. (2012) Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition. Microbiology and Molecular Biology Reviews 76:3, pages 597-625.
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J.M. Moore, Hallie Wimberly, P.C. Thornton, Susan M. Rosenberg & P.J. Hastings. (2012) Gross chromosomal rearrangement mediated by DNA replication in stressed cells: evidence from Escherichia coli. Annals of the New York Academy of Sciences 1267:1, pages 103-109.
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E. W. L. Chow, C. A. Morrow, J. T. Djordjevic, I. A. Wood & J. A. Fraser. (2012) Microevolution of Cryptococcus neoformans Driven by Massive Tandem Gene Amplification. Molecular Biology and Evolution 29:8, pages 1987-2000.
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Mariève Desjardins, Laurie A. Graham, Peter L. Davies & Garth L. Fletcher. (2012) Antifreeze protein gene amplification facilitated niche exploitation and speciation in wolffish. FEBS Journal 279:12, pages 2215-2230.
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R. JAYARAMAN. (2011) Hypermutation and stress adaptation in bacteria. Journal of Genetics 90:2, pages 383-391.
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Dan I. Andersson, Diarmaid Hughes & John R. Roth. (2011) The Origin of Mutants under Selection: Interactions of Mutation, Growth, and Selection. EcoSal Plus 4:2.
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Holly Anne Martin, Mario Pedraza-Reyes, Ronald E. Yasbin & Eduardo A. Robleto. (2011) Transcriptional De-Repression and Mfd Are Mutagenic in Stressed <i>Bacillus subtilis </i>Cells. Journal of Molecular Microbiology and Biotechnology 21:1-2, pages 45-58.
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Satoko Iida, Atsushi Kobiyama, Takehiko Ogata & Akio Murakami. (2010) Differential DNA Rearrangements of Plastid Genes, psbA and psbD, in Two Species of the Dinoflagellate Alexandrium. Plant and Cell Physiology 51:11, pages 1869-1877.
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Fyodor A. Kondrashov. 2010. Evolution after Gene Duplication. Evolution after Gene Duplication 57 76 .
Dan I. Andersson, Sanna Koskiniemi & Diarmaid Hughes. (2010) Biological roles of translesion synthesis DNA polymerases in eubacteria. Molecular Microbiology 77:3, pages 540-548.
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Alexandre Maréchal & Normand Brisson. (2010) Recombination and the maintenance of plant organelle genome stability. New Phytologist 186:2, pages 299-317.
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Elisa Närvä, Reija Autio, Nelly Rahkonen, Lingjia Kong, Neil Harrison, Danny Kitsberg, Lodovica Borghese, Joseph Itskovitz-Eldor, Omid Rasool, Petr Dvorak, Outi Hovatta, Timo Otonkoski, Timo Tuuri, Wei Cui, Oliver Brüstle, Duncan Baker, Edna Maltby, Harry D Moore, Nissim Benvenisty, Peter W Andrews, Olli Yli-Harja & Riitta Lahesmaa. (2010) High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nature Biotechnology 28:4, pages 371-377.
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Boris U. Stambuk, Barbara Dunn, Sergio L. AlvesJrJr, Eduarda H. Duval & Gavin Sherlock. (2009) Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis. Genome Research 19:12, pages 2271-2278.
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R. Jayaraman. (2009) Mutators and hypermutability in bacteria: the Escherichia coli paradigm. Journal of Genetics 88:3, pages 379-391.
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Zoran Minic. (2009) Organisms of deep sea hydrothermal vents as a source for studying adaptation and evolution. Symbiosis 47:3, pages 121-132.
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Alexandre Maréchal, Jean-Sébastien Parent, Félix Véronneau-Lafortune, Alexandre Joyeux, B. Franz Lang & Normand Brisson. (2009) Whirly proteins maintain plastid genome stability in Arabidopsis . Proceedings of the National Academy of Sciences 106:34, pages 14693-14698.
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Svetlana A. Yatsenko, Ellen K. Brundage, Erin K. Roney, Sau Wai Cheung, A. Craig Chinault & James R. Lupski. (2009) Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Human Molecular Genetics 18:11, pages 1924-1936.
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Rodrigo S Galhardo, Robert Do, Masami Yamada, Errol C Friedberg, P J Hastings, Takehiko Nohmi & Susan M Rosenberg. (2009) DinB Upregulation Is the Sole Role of the SOS Response in Stress-Induced Mutagenesis in Escherichia coli . Genetics 182:1, pages 55-68.
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P. J. Hastings, Grzegorz Ira & James R. Lupski. (2009) A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation. PLoS Genetics 5:1, pages e1000327.
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Olivier Humbert & Nina R. Salama. (2008) The Helicobacter pylori HpyAXII restriction?modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components. Nucleic Acids Research 36:21, pages 6893-6906.
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Caleb Gonzalez, Lilach Hadany, Rebecca G. Ponder, Mellanie Price, P. J. Hastings & Susan M. Rosenberg. (2008) Mutability and Importance of a Hypermutable Cell Subpopulation that Produces Stress-Induced Mutants in Escherichia coli. PLoS Genetics 4:10, pages e1000208.
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Sophie Karrenberg & Alex Widmer. (2008) Ecologically relevant genetic variation from a non-Arabidopsis perspective. Current Opinion in Plant Biology 11:2, pages 156-162.
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