Bryan Hernandez
Bio
- I am currently a UROP in the Endy Lab working with Jason Kelly.
- MIT Class of 2009; Majoring in Mathematics and Biological Engineering.
Projects
Sortostat
- We are currently using strain MC4100 E.Coli capable of expressing CFP and YFP (Cyan Fluorescent Protein and Yellow Fluorescent Protein, contained on plasmid pSB1A2 ) as these are easily distinguished between visually thereby aiding in our descriminitive assortment without relying on chemical selection. In this way, it is less likely for cells to avoid being sorted by a genetic mutation as one might expect using an antibiotic.
- Chemostat Theory
- Sortostat/Experiments
- Sortostat/Growth Tests
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Project Goals
- Debug a microfluidic chemostat (Sortostat) to improve the time-varying specific selection of cell populations.
- Currently troubleshooting problems: i) Cell Death after 3-4 days (presumably due to oxygen depletion,) and ii) Inaccurate cell counts due to poor image processing.
- Evaluate the response of populations of E.Coli cells containing engineered genetic circuits (http://parts.mit.edu) to particular selective pressures using the Sortostat.
Evolutionary stability project
It is known that mutations are more likely to occur with higher cell division rates. Everytime a cell divides it runs the risk of making a mistake in the replication process and creating a mutant cell. Evolution is largely in debt to this phenomonon; without mutants an organism's genome would be nearly static. However, beneficial this might be to the survival of a species, it poses a problem for our genetically engineered cells. If a cell divides and mutates in the process it could "break" our engineered genetic device. The cell will likely go on living, however, it will cease to perform its intended function. This is an unfortunate reality of biological engineering, and, as such, we must learn the characteristics of our devices and their liklihoods of "breaking."
In order to obtain a quantitative measure of how "fast" our devices break we will first need a controlled environment. By using a chemostat we can control the rate at which cells divide enabling us to calculate the number of cell divisions that have occured over some time. Note that number of divisions is but one variable that can be used to characterize the longevity of a device. One might imagine testing other variables such as temperature or cell cycle position for example, both of which likely have an effect on the "breaking rate."
Detecting when a cell's device has broken can be a challenge in it of itself; however, this challenge becomes much easier with the correct choice of device. We are using a device such that it's success is fatal to the cell under certain conditions, however, when the device breaks the cell lives and will grow. This is known as a counter-selectable marker and allows us to ultimately find out the rate at which our device breaks.
Once a mutation rate is established, we can talk quantitatively about device longevity under prespecified conditions. We also, and more importantly, have a valid control in which to compare methods of prolonging a devices life which go beyond that of the counter-selectable marker. Our aim is to show that by remapping the cell's codon space we will be increasing the device's life.
