On my research as a PhD candidate I am interested in study experimentally how altered bacterial strains with reduced fitness re-alter their genomes to regain fitness. Using this approach I intend to gain insight into the underlying problems and the mechanisms that can lead to its solution.

Recombinant colonies at CSHL

Project I: Amelioration of plasmid cost
In one of my projects, I study the mechanisms by which Escherichia coli can reduce the cost of plasmid carriage. The horizontal transfer of plasmids and other pieces of foreign DNA into naïve bacteria may impose a fitness cost that must be reduced by genetic changes. This type of evolutionary change is very relevant in medical microbiology where the acquisition of plasmid is associated with antibiotic resistance, and in biotechnology, where the introduction of expression vectors may disturb the physiological balance of the engineered strain.

Project II: Significance of location and orientation of highly expressed genes

In other project, I investigate the organization of the bacterial chromosome, which is often highly skewed. The current hypothesis is that genomic-scale organization reflects selection pressure for maximum growth rate, by increasing the relative copy number of highly transcribed genes and minimizing the frequency of clashes between DNA and RNA polymerases. For each case, I experimentally test the basis of the fitness cost and ask whether, how, and how rapidly, an altered strain could genetically adapt to the acquire changes in genome content and/or structure.

Betül Kacar during her visit to Uppsala

Project III: Fitness consequences of ancestral and homologous EF-Tu variants

Icomplexity-figure-1n collaboration with Dr. Betül Kaçar I dove into exploring the limitations of adaptation of alien genes to a host genome. In this project, homologs from several species and phylogenetically inferred old genes of EF-Tu are introduced in a modern organism to study how the ancient protein behavior and sequence has changed through time and through the different evolutionary pathways. This work is based on previous research by Dr. Kaçar, who developed an experimental system that merges the fields of sequence reconstruction and experimental evolution.
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