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Computational Identification Of Adaptive Mutants Using The Vert System, James Winkler, Katy Kao
Computational Identification Of Adaptive Mutants Using The Vert System, James Winkler, Katy Kao
Faculty Publications
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 …
Visualizing Evolution In Real-Time Method For Strain Engineering, Luis Reyes, James Winkler, Katy Kao
Visualizing Evolution In Real-Time Method For Strain Engineering, Luis Reyes, James Winkler, Katy Kao
Faculty Publications
The adaptive landscape for an industrially relevant phenotype is determined by the effects of the genetic determinants on the fitness of the microbial system. Identifying the underlying adaptive landscape for a particular phenotype of interest will greatly enhance our abilities to engineer more robust microbial strains. Visualizing evolution in real-time (VERT) is a recently developed method based on in vitro adaptive evolution that facilitates the identification of fitter mutants throughout the course of evolution. Combined with high-throughput genomic tools, VERT can greatly enhance the mapping of adaptive landscapes of industrially relevant phenotypes in microbial systems, thereby expanding our knowledge on …