My name is Azeem. I am a junior concentrating in biomedical engineering.
I currently work in the Morgan lab on a device called an Living Cell Array. My part in the project involves engineering DNA to become responsive to various transcription factors.
So...this is what I have done so far: Week 1: This week I held a workshop in basic molecular biology techniques. We covered a restriction digest, running a gel, excising DNA from a gel, and an ethanol precipitation. Three people attended the workshop I ran. Also, I have been familiarizing myself with the registry and thinking of how we can best create our bacterial maze.
Week 2: In order to make the bacterial maze we need two knockout strains. In particular, we need a double knockout of these two genes: motB and EnvZ histidine kinase. I have contacted Penn State and they have agreed to send us both the motB part (with RBS) and the motB KO. This is great news. There is a general frustration here with the fact that all the available parts are not necessarily on the plates.
Week 3: How do we make a double KO? I have no idea. We talked to a microbiologist and found out that it would be a summer long project. Great. OK Ok so a new idea. One evening I decided to meet with Annie at B & H and we decided we would attempt to fully understand the cell circuits from another team. We looked at Penn State and looked up all the parts they used, found out why they used them and began to understand their applications. We started to understand the use of IPTG, LacI, cI and AHL as extremely important molecules in cell-cell signalling and intracellular networks in iGem. That night I worked out the rest of the circuit for Annie's new idea - Bacterial freeze tag. I presented the idea at journal club on Friday.
Week 4 The bacterial freeze tag is now completely worked out. All the parts are labeled and the logic is beautiful. We are starting to grow up parts. We have divided in teams to grow parts for various sections of the project. My section is Dr. Unfreeze. It unfreezes the cell in response to AI-1 by creating cI, which will invert the circuit of Mr. Freeze. I have also added two parts to the wiki. The AHL sender and Mr. Freeze. Now it looks really pretty. There is sort of a problem with the fact that in designing the circuit everyone needs to agree as to the specific parts (for example: the strength of the RBS, whether we need a terminator or not, whether we need an LVA degradation tag) I have seen problems in these components and have voiced them. However, this is a problem because people have already grown up a certain part and don't really want to change that part since there is vested time in it. I think we need to have a meeting to address these issues next week for sure.
I am also a little skeptical about certain components of Mr. Freeze. I would like to work with Peter or Brendan to try to simplify this circuit.