Project 5: Evolvability and robustness in simple synthetic modules (Elowitz) (#31-32) We studied the role of noise in natural and man-made bacterial transcriptional networks. Our original aim of exploring the evolvability of these modules led us to methods to analyze them more precisely, by asking how noise affects their operation: 1) We performed a study of the cis-regulatory logic in prokaryotic promoters, based on a combinatorial promoter library composed of modular sequence elements. This study identified a number of heuristic rules for programming and modulating the combinatorial logic behavior of prokaryotic promoters. 2) We analyzed transient differentiation system that leads to competence in B. subtilis. To understand the operation of this excitable switch, we varied promoter strengths, circuit architecture, and stochastic fluctuations (noise). We identified the independent tuning of differentiation frequency and duration as a design principle, and showed that noise (fluctuations) is actually required for cellular differentiation37.
| Westerman, Erica L; VanKuren, Nicholas W; Massardo, Darli et al. (2018) Aristaless Controls Butterfly Wing Color Variation Used in Mimicry and Mate Choice. Curr Biol 28:3469-3474.e4 |
| Bonham, Kevin S; Wolfe, Benjamin E; Dutton, Rachel J (2017) Extensive horizontal gene transfer in cheese-associated bacteria. Elife 6: |
| Tamari, Zvi; Yona, Avihu H; Pilpel, Yitzhak et al. (2016) Rapid evolutionary adaptation to growth on an 'unfamiliar' carbon source. BMC Genomics 17:674 |
| Kim, Wook; Levy, Stuart B; Foster, Kevin R (2016) Rapid radiation in bacteria leads to a division of labour. Nat Commun 7:10508 |
| Muller, Nicolas; Piel, Matthieu; Calvez, Vincent et al. (2016) A Predictive Model for Yeast Cell Polarization in Pheromone Gradients. PLoS Comput Biol 12:e1004795 |
| Wahl, Mary E; Murray, Andrew W (2016) Multicellularity makes somatic differentiation evolutionarily stable. Proc Natl Acad Sci U S A 113:8362-7 |
| Hormoz, Sahand; Singer, Zakary S; Linton, James M et al. (2016) Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements. Cell Syst 3:419-433.e8 |
| Renn, Suzy C P; O'Rourke, Cynthia F; Aubin-Horth, Nadia et al. (2016) Dissecting the Transcriptional Patterns of Social Dominance across Teleosts. Integr Comp Biol 56:1250-1265 |
| Kastman, Erik K; Kamelamela, Noelani; Norville, Josh W et al. (2016) Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species. MBio 7: |
| Lavrentovich, Maxim O; Wahl, Mary E; Nelson, David R et al. (2016) Spatially Constrained Growth Enhances Conversional Meltdown. Biophys J 110:2800-2808 |
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