Measuring competitive fitness in dynamic environments

Journal of Physical Chemistry B

Volumn 117, Issue 42, 2013, Pages 13175-13181

  Razinkov, Ivan A ^a   Baumgartner, Bridget L ^a   Bennett, Matthew R ^b   Tsimring, Lev S ^c,d   Hasty, Jeff ^a,c,d,e  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b RICE UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d University of California San Diego   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; COMPUTATION THEORY; STOCHASTIC SYSTEMS; YEAST;

COMPETITIVE FITNESS; DYNAMIC ENVIRONMENTS; ENVIRONMENTAL FLUCTUATIONS; EXPERIMENTAL PLATFORM; GROWTH ADVANTAGES; LABORATORY ENVIRONMENT; NATURAL SELECTION; PHENOTYPIC DIFFERENCES;

HEALTH;

CARBON; GAL1 PROTEIN, S CEREVISIAE; GALACTOKINASE; GALACTOSE; GLUCOSE; MESSENGER RNA; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; GENETICS; GENOTYPE; METABOLISM; MICROFLUIDIC ANALYSIS; MUTATION; SACCHAROMYCES CEREVISIAE;

CARBON; GALACTOKINASE; GALACTOSE; GENOTYPE; GLUCOSE; MICROFLUIDIC ANALYTICAL TECHNIQUES; MODELS, MOLECULAR; MUTATION; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84886678203     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp403162v     Document Type: Article

References (34)

1. Darwin, C. On the Origins of Species by Means of Natural Selection; Murray: London, 1859.
2. Bennett, M. R.; Hasty, J. Microfluidic Devices for Measuring Gene Network Dynamics in Single Cells Nat. Rev. Genet. 2009, 10, 628-638
3. Balagaddé, F. K.; You, L.; Hansen, C. L.; Arnold, F. H.; Quake, S. R. Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat Science 2005, 309, 137-140
4. Balaban, N. Q.; Merrin, J.; Chait, R.; Kowalik, L.; Leibler, S. Bacterial Persistence as a Phenotypic Switch Science 2004, 305, 1622-1625
5. Gottschamel, J.; Richter, L.; Mak, A.; Jungreuthmayer, C.; Birnbaumer, G.; Milnera, M.; Bruckl, H.; Ertl, P. Development of a Disposable Microfluidic Biochip for Multiparameter Cell Population Measurements Anal. Chem. 2009, 81, 8503-8512
6. Ferry, M. S.; Razinkov, I. A. Microfluidics for Synthetic Biology: From Design to Execution Methods Enzymol. 2011, 497, 295-372
7. Bennett, M. R.; Pang, W. L.; Ostroff, N. A.; Baumgartner, B. L.; Nayak, S.; Tsimring, L. S.; Hasty, J. Metabolic Gene Regulation in a Dynamically Changing Environment Nature 2008, 454, 1119-1122
8. Lohr, D.; Venkov, P.; Zlatanova, J. Transcriptional Regulation in the Yeast GAL Gene Family: A Complex Genetic Network FASEB J. 1995, 9, 777-787
9. Johnston, G.; Singer, R.; Sharrow, S.; Slater, M. Cell Division in the Yeast Saccharomyces cerevisiae Growing at Different Rates J. Gen. Microbiol. 1980, 118, 479-484
10. Scheffler, I. E.; de la Cruz, B. J.; Prieto, S. Control of mRNA Turnover as a Mechanism of Glucose Repression in Saccharomyces cerevisiae Int. J. Biochem. Cell Biol. 1998, 30, 1175-1193
11. Andrade, R. P.; Kötter, P.; Entian, K.-D.; Casal, M. Multiple Transcripts Regulate Glucose-Triggered mRNA Decay of the Lactate Transporter JEN1from Saccharomyces cerevisiae Biochem. Biophys. Res. Commun. 2005, 332, 254-262
12. Baumgartner, B. L.; Bennett, M. R.; Ferry, M.; Johnson, T. L.; Tsimring, L. S.; Hasty, J. Antagonistic Gene Transcripts Regulate Adaptation to New Growth Environments Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 21087-21092
13. Zhang, Z.; Boccazzi, P.; Choi, H.-G.; Perozziello, G.; Sinskey, A. J.; Jensen, K. F. Microchemostat-Microbial Continous Culture in a Polymer-Based, Instrumented Microbioreactor Lab Chip 2006, 6, 906-913
14. Brickner, D. G.; Cajigas, I.; Fondufe-Mittendorf, Y.; Ahmed, S.; Lee, P.-C.; Widom, J.; Brickner, J. H. H2A.Z-Mediated Localization of Genes at the Nuclear Periphery Confers Epigenetic Memory of Previous Transcriptional State PLoS Biol. 2007, 5, 704-716
15. Levy, S. F.; Ziv, N.; Siegal, M. L. Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress Protectant PLoS Biol. 2012, 10, e1001325
16. Veening, J.-W.; Stewart, E. J.; Berngruber, T. W.; Taddei, F.; Kuipers, O. P.; Hamoen, L. W. Bet-Hedging and Epigenetic Inheritance in Bacterial Cell Development Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 4393-4398
17. Beaumont, H. J.; Gallie, J.; Kost, C.; Ferguson, G. C.; Rainey, P. B. Experimental Evolution of Bet Hedging Nature 2009, 462, 90-93
18. Nevozhay, D.; Adams, R.; Van Itallie, E.; Bennett, M. R.; Balazsi, G. Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit PLoS Comput. Biol. 2012, 8, e1002480
19. Zacharioudakis, I.; Gligoris, T.; Tzamarias, D. A Yeast Catabolic Enzyme Controls Transcriptional Memory Curr. Biol. 2007, 17, 2041-2046
20. Fisher, R. The Theory of Natural Selection; Oxford University Press: London, 1930.
21. Giaever, G.; Chu, A. M.; Ni, L.; Connelly, C.; Riles, L.; Veronneau, S.; Dow, S.; Lucau-Danila, A.; Anderson, K.; Andre, B. Functional Profiling of the Saccharomyces cerevisiae Genome Nature 2002, 418, 387-391
22. Steinmetz, L. M.; Sinha, H.; Richards, D. R.; Spiegelman, J. I.; Oefner, P. J.; McCusker, J. H.; Davis, R. W. Dissecting the Architecture of a Quantitative Trait Locus in Yeast Nature 2002, 416, 326-330
23. Deutschbauer, A. M.; Jaramillo, D. F.; Proctor, M.; Kumm, J.; Hillenmeyer, M. E.; Davis, R. W.; Nislow, C.; Giaever, G. Mechanisms of Haploinsufficiency Revealed by Genome-Wide Profiling in Yeast Genetics 2005, 169, 1915-1925
24. Sliwa, P.; Korona, R. Loss of Dispensable Genes is Not Adaptive in Yeast Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 17670-17674
25. Breslow, D. K.; Cameron, D. M.; Collins, S. R.; Schuldiner, M.; Stewart-Ornstein, J.; Newman, H. W.; Braun, S.; Madhani, H. D.; Krogan, N. J.; Weissman, J. S. A Comprehensive Strategy Enabling High-Resolution Functional Analysis of the Yeast Genome Nat. Methods 2008, 5, 711-718
26. Jasnos, L.; Tomala, K.; Paczesniak, D.; Korona, R. Interactions Between Stressful Environment and Gene Deletions Alleviate the Expected Average Loss of Fitness in Yeast Genetics 2008, 178, 2105-2111
27. Thatcher, J.; Shaw, J. M.; Dickinson, W. Marginal Fitness Contributions of Nonessential Genes in Yeast Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 253-257
28. Bell, G. Experimental Genomics of Fitness in Yeast Proc. R. Soc. B 2010, 277, 1459-1467
29. Brown, J. A.; Sherlock, G.; Myers, C. L.; Burrows, N. M.; Deng, C.; Wu, H. I.; Mc- Cann, K. E.; Troyanskaya, O. G.; Brown, J. M. Global Analysis of Gene Function in Yeast by Quantitative Phenotypic Profiling Mol. Syst. Biol. 2006, 2, 1-9
30. Parsons, A. B.; Lopez, A.; Givoni, I. E.; Williams, D. E.; Gray, C. A.; Porter, J.; Chua, G.; Sopko, R.; Brost, R. L.; Ho, C.-H. Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast Cell 2006, 126, 611-625
31. Williams, P. D.; Hastings, A. Paradoxical Persistence Through Mixed-System Dynamics: Towards a Unified Perspective of Reversal Behaviours in Evolutionary Ecology Proc. R. Soc. B 2011, 278, 1281-1290
32. Wolf, D. M.; Vazirani, V. V.; Arkin, A. P. Diversity in Times of Adversity: Probabilistic Strategies in Microbial Survival Games J. Theor. Biol. 2005, 234, 227-253
33. Acar, M.; Mettetal, J. T.; van Oudenaarden, A. Stochastic Switching as a Survival Strategy in Fluctuating Environments Nat. Genet. 2008, 40, 471-475
34. Kussell, E.; Leibler, S. Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments Science 2005, 309, 2075-2078