Mathematics Colloquia and Seminars

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All organisms live in complex, dynamic environments that expose them to fluctuations along many physical, chemical, and biological dimensions. One path to dominate their particular niche lies in evolving processes that facilitate rapid adaptation to environmental variations and protection against deleterious mutations. Our knowledge, however, of the dynamics and interplay between the various behaviors is limited. Even less is known about the underlying gene regulatory and biochemical networks that give rise to this rich phenotypic repertoire, despite their significance to microbial physiology. In this talk, I will present our computational and experimental work on studying the emergence of complex traits and their underlying mechanisms. First, I will present our microbial "virtual ecology" simulator, a simulation framework where <\it in silico> organisms compete, mutate, and evolve in dynamic spatio-temporal environments. The simulator employs abstract models of cellular (transcription, translation, cell death, etc.) and evolutionary (mutation, selection, horizontal gene transfer, etc.) phenomena, that allows us to test evolutionary hypotheses and generate testable predictions. Then, I will describe our ongoing experiments on <\it E. coli> evolution under various stresses (Acidic, Osmolarity, Butanol, and hydrogen peroxide stress). I will discuss the results we gathered for the first 1000 generations during evolution, where we clearly observe trade-offs in competition assays and growth curves. Further characterization by sequencing and transcriptional profiling of individual mutant clones, elucidate the genetic basis of these trade-offs and allow us to reconstruct the underlying biological network.