Document Type


Publication Date

December 2012

Publication Title

Journal of Biological Engineering








Adaptive evolution, hidden Markov Model, Visualizing evolution in real time, Population history


Chemical Engineering | Engineering


BackgroundEvolutionary dynamics of microbial organisms can now be visualized using the Visualizing Evolution in Real Time (VERT) system, in which several isogenic strains expressing different fluorescent proteins compete during adaptive evolution and are tracked using fluorescent cell sorting to construct a population history over time. Mutations conferring enhanced growth rates can be detected by observing changes in the fluorescent population proportions.ResultsUsing data obtained from several VERT experiments, we construct a hidden Markov-derived model to detect these adaptive events in VERT experiments without external intervention beyond initial training. Analysis of annotated data revealed that the model achieves consensus with human annotation for 85-93% of the data points when detecting adaptive events. A method to determine the optimal time point to isolate adaptive mutants is also introduced.ConclusionsThe developed model offers a new way to monitor adaptive evolution experiments without the need for external intervention, thereby simplifying adaptive evolution efforts relying on population tracking. Future efforts to construct a fully automated system to isolate adaptive mutants may find the algorithm a useful tool.


SJSU users: Use the following link to login and access the article via SJSU databases.This article was published in the Journal of Biological Engineering volume 6, 2012, and can also be found online here.Copyright © 2012, The Authors

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