Team Notebook: Format will be changed!!!

Week 1

The team started the project June 17, 2013, the immediate week following finals week. The team spent the first two weeks deciding on an iGEM project. The first week consists of a high level discussion about different areas of interest.

Day 1, June 17

Each team member prepared 5 ideas, and the team selected the top five ideas. These ideas include a biosensor for common parasites in water, a biosensor for UV damage, a bacteria that fights cavity, bacteria to produce diesel from food oil, and a composite biosensor that incorporates several biosensors.

Day 2, June 18

Each member focused on one idea. The goal for the day was to determine a possible mechanism. The goal for the day was to determine the feasibility of the idea. The team also considered several new ideas such as MSG detection, urine detection, and biofertilizer.

Day 3, June 19

This day was a continuation of the previous day. Emphasis today was to research previous iGEM teams for inspiration and possible mechanisms and biobricks.

Day 4, June 20

We tried to find one more idea that will be feasible. After meeting with advisors, we tried to focus more on the mechanistic details rather than a high level discussion of the project idea. We also took an inventory of the lab space and began sending out sponsorship emails.

Day 5, June 21

After deciding most of the ideas we have come up with are far from feasible, we focused again on previous iGEM teams, hoping to build on a previous team's work. Each team member was tasked with coming up with a new idea for the next week.

Week 2

The team began working on some lab work such as making different solutions that will be necessary for the rest of the summer. The team also made competent cells and tried to test competency by transforming them. The week ended with much frustration due to a lack of progress in brainstorming and lab work.

Day 6, June 24

The team decided on roles to improve efficiency and team organization. The team made SOB solution and obtained Top 10 cells from Dr. Leonard (one of our advisors). The team also talked quorum sensing of bacteria as a possible mechanism to detect parasites in water.

Day 7, June 25

The team discovered that UV sensing is already done several times by different iGEM teams. The idea may lack novelty. To improve on the biofuel idea, different starting materials are considered, hoping to increase the financial sensibility by decreasing the value of the starting materials.

Day 8, June 26

Today, the team focused primarily on oral health and tried to come up with several ways to attack biofilm formation in the mouth. The ideas that were discussed include engineering V. Parvula to upregulate lactic acid metabolism, introducing the CovR pathway to disrupt biofilm formation, and using the L-Arginine pathway to produce ammonia. The team also created CCMB solution.

Day 9, June 27

The team learned out to make plates (created 40) using CB antibiotic. The team continued to talk about the three ideas, trying to discover anything that will make the project feasible. The primary hurtle is the mechanism to import lactic acid from outside the cell.

Day 10, June 28

The transformation failed, and no cells grew on the plates. The professors pointed out that the upregulation of lactic acid uptake would disrupt the redox balance within the cell, causing the key enzyme lactate dehydrogenase to work in reverse. However, the team has decided that the project for the summer will involve oral health.

Week 3

As the team goes into the holiday weekend, very few things are working properly and frustration grew!

Day 11, July 1

The team redid the transformation experiment again. This time, all glassware was washed to make sure they are free of detergent. The team prepared for the meeting with professors by trying to flesh out the idea as much as possible.

Day 12, July 2

The cells did not grow once again. The team divided lab space in preparation of the next phase of the project where each member will have more independence. The team is focusing on pH sensor since that appears to be the common mechanism in all of the ideas that were brought up. To add an extra layer of complexity, the team will incorporate the idea of a "dual promoter" into the design.

Day 13, July 3

The team redid the transformation once again. Most of the materials used is store bought to eliminate any possible errors. Prior to leaving for the break, the team is brainstorming on a list of possible mechanisms for the pH sensor.

Day 14, July 4

The team came in just to check for the results of the transformation. Yet again, no cells grew.

Day 15, July 5

July 4th weekend holiday! No meetings.

Week 4

SUMMARY HERE. Someone needs to help me do the summaries for these two weeks!!

Day 16, July 8

Week 5