Gene Expression

Regulation of gene expression coupled to cell growth and division in bacterial adaptation processes

The idea of the project is to understand gene expression and the cell cycle. Initially it was thought that bacterial DNA replication was determined by the size of the cell and this value was constant but recent studies have questioned this thinking and we seek to understand the mechanisms behind the initiation process of DNA replication. We investigate DNA replication by estimating DnaA-ATP protein activity of E.coli. However, the link between DnaA-ATP and constant initiation mass theory is unknown. Based on the previous results using wild type strain, an oscillating behavior of the DnaA-ATP protein within the cell cycle was observed. The DnaA-ATP has positive and negative autoregulation, by binding to its own promoter activating the gene expression when it is at low concentration and repressing the expression at high concentrations. However, the DnaA-ATP behavior is also controlled by other mechanisms, such as the protein SeqA, which is responsible for inhibiting the DnaA-ATP gene expression after the beginning of DNA replication. For this during the rotation I developed an pipeline to analyze image data using SuperSegger and Omnipose (Pipeline Documentation), a library to process this data, called Bacteria (Bacteria Documentation Site) and also the 3D modeling designs to fix the plate with PDMS to the centrifuge and distribute the bacteria in all channels of the microfluidic device (3D models fodler).