Over the course of this summer, I invested a full month of research into attempting to verify the identity of the reporter plasmid – and I failed to do so. In fact, I showed rather conclusively that the plasmid was not, in fact, the backbone that we had been led to believe it was. Interestingly, we also learned several other things about the plasmid, including that it does confer Kanamycin resistance upon E. coli, that it contains at least one cut site for a restriction enzyme that was anticipated in the original plasmid, and that it has a length probably several times longer than what was anticipated.
As a quick reminder, my project is working to create a tool that can eventually be used to correlate transcription and translation within a cell (whether the number of mRNA transcripts correlate directly to the eventual concentration of protein output). I intended to use a reporter plasmid to track the concentration of protein, while thinking about other tools to tackle the other side of the problem – identifying the concentration/number of transcripts.
Despite originally planning to work with X. laevis embryos this summer, my research took a new turn when the summer actually started. Now I am working towards a completely different goal: instead of looking at embryonic development and life, I’m looking at phages, which are viruses that can kill bacteria. Specifically, our lab is interested in the regulatory regions of these phages’ genomes, and understanding how that regulation can be strong or weak relative to its eventual output as proteins.
One of the most interesting questions in development is how cell fate can be determined. While it is widely understood that genetic material is passed down through DNA and controls the possible states of any given cell, the idea of patterning a whole organism is far more complicated to pass down, especially when every organism starts out as a single cell. Nerve cells in particular must create and maintain a pH gradient (a gradient of hydrogen ions) across their cell membrane. That is, they must have a different concentration of H+ ions inside the cell and outside the cell in order to allow them to properly carry out their function as neurons. The relationship between pH and cell fate acquisition has been recognized since the early 1940s, when Holtfreter et al. showed that low –acidic – pH in gastrula stage embryos induces neural development in cells. More recently, Sater et al. have argued that neural induction is correlated with a slight rise – alkalinization –in intracellular pH in Xenopus laevis, the African clawed frog.