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Notebook

September 28th, 2011 - Had the first call-out meeting for iGEM.

October 5th, 2011 - Formed plans for attending the 2011 American Collegiate Regional Jamboree.

October 9th and 10th - Volunteered at the 2011 collegiate jamboree, gathered brainstorming ideas for project.

November 9th, 2011 - Met after a temporary hiatus, discussed brainstorming ideas such as cancer detector and amyloid fibrils.

November 16th - Assigned research groups to study the two projects.

November 23th - Came together to discuss the research papers, and assigned research summaries.

November 30th - We shared our research summaries, and decided that both projects were a little above what we would be able to do this year with iGEM. So it was

back to the drawing board to find projects.

December 14th - Some students shared project ideas, such as the problem of galactosemia and the detection of tuberculosis in fish. We told everyone to look

up research papers about these projects.

January 4th - After Christmas break, we shared the knowledge that we gained from the research we did. We decided that we could do both projects, and have two

groups within our team. One would detect the GALT enzyme in blood for galactosemics, and one would detect mycolic acid in aquariums for fish

tuberculosis.

January 11th - Our galactosemia group found a promoter called Gal1, which we could use to detect GALT in blood. This will help galactosemics monitor the

seriousness of their galactosemia. Our tuberculosis group found a promoter called mmaA2. This promoter detects mycolic acid, which is a defense

mechanism on the cell membrane of tuberculosis.

January 18th - Today we decided the vectors that we would use for our systems. Our galactosemic group is going to use yeast because the Gal genes are in yeast.

The tuberculosis group is going to use E.Coli, because it will survive better in an aquatic environment.

February 1st - We looked at reporters, and how we want to indicate with our promoters. As much as we want to do something complicated and impressive, we decided

on simple fluorescent proteins due to their ease and availability.

February 8th - Our galactosemic group contacted the author of one of the papers that they read, Dr. Fridovich-Keil of Emory University. She informed us that the Gal

promoters would not let us detect GALT, so that did not bode well for our project. But she also informed us that one thing clinicians need is a way to

detect galatose in the blood, since current blood sugar tests detect all types of sugar, not just galactose. We decided to change our project to that, and

still use the same Gal genes. We asked her if she could send us the promoter Gal1/10, so we would not have to extract it ourselves.

February 15th - In this meeting we practiced our presentation for the Chamber of Commerce meeting. We finished the presentation and ran through it a few times.

February 22nd - We looked at the procedures for part extraction and restriction enzymes, and went over them to know what to do when we started lab work.

February 29th - We created a list of materials we needed to buy, such as labcoats, rubber gloves, Restriction Enzymes, Phusion Polymerase, CaCl2, NDNTP, Ligase,

Exonuclease, Agarose, YPD, Yeast, and E. Coli. Hopefully we can get donation money from the Kiwanis Club presentation in a few days.

March 7th - Today we talked some of our newer members through the extraction procedures, and how primers work to extract parts from a plasmid.

March 12th - We went over the presentation to the Greenfield Area Kiwanis Club. We found out that one of the members of the club donated 2,000 dollars to fund our

project this year, and another individual donated 200 dollars!

March 21th - We recieved our promoters from Dr. Fridovich-Keil and researched the exact sequence of the Gal1/10 promoter so that we can make primers. We made

the 40 base pair primers and ordered them so we can extract the promoter from the plasmid.

April 3rd - Today we went over the activity that we are going to do with the 5th graders. They will put three strips of paper together and tape them together. The three

strips of paper represent a promoter,a translational unit, and a selective marker. The tape represents a sticky end created by restriction enzyme sites.

Through this activity, the kids will learn all about synthetic biology and will have fun doing it.

April 4th - Today we re-suspended the plasmids that Dr. Fridovich-Keil sent us. We spun the tubes in the centrifuge to make a pellet, then we dried out the excess

liquid. After that, we added 100uL of TE buffer to re-suspend it.

April 11th - We were supposed to get our primers today, but they did not arrive yet. We poured gel electrophoresis plates instead, to prep for tomorrow's lab. We put 2

grams of the agarose into 200 mL of distilled water, boiled it, poured the gels, and then let them set. Hopefully we will get our primers and we can extract

our gal1/10 promoter out of the plasmid that Dr. Fridovich-Keil sent us.

April 16th - Today we finally received our primers, which we then re-suspended in distilled water.

April 17th - Today we started extracting the promoter from the plasmid. We used a PCR machine to run the extraction. After the extraction was completed, we ran the

resulting DNA on a gel. Sadly, the DNA streaked across the gel and we could not get an accurate reading.

April 18th - We attempted to redo the gel electrophoresis that failed yesterday with the DNA that was still left over from the extraction. Once we finished it, we could not

see any visible bands in the gel. We used the last of the DNA, so we will have to redo the extraction procedure.

April 25th - We re-did the PCR extraction and then used the DNA in a gel. We unfortunately made the gel too dense and thick, so the DNA did not travel through it. We

used all of our DNA in this gel, so we will have to redo the extraction procedure once again. We do not have enough primer DNA or plasmid DNA to do

another extraction, so we will have to ask Dr. Fridovich-Keil for more plasmid DNA and order more primers.

April 30th - We talked to Dr. Fridovich-Keil, and she told us that we could use what little plasmid DNA we had left and insert it into an E.coli sample, which would then

be purified using a selection marker. Then we would have an infinite supply of the plasmid. We knew that you could do this, we just didn't think about

attempting it. We don't have amoxicillin for the selection marker though, so we will have to order that.

May 21st - We hosted a last school meeting to discuss our summer schedule. Our instructors are going to be at Purdue for the first week of June, so that's when we

will work on our poster and presentation.

May 29th - We met at Mason's house and started brainstorming about our presentation. We looked at the college presentations and posters from last year, and got

some good ideas. We set up the outline for our presentation and started making the slide graphics in Photoshop.

May 30th - We got together at Mason's house again and worked on the poster. We got a good design for it and started working on the text and graphics.

May 31st - We met at the school today and continued to work on the poster and presentation. The presentation is completely outlined and the presenters have started

their own specific parts.

June 4th - We continued to work on the poster and presentation.

June 6th - We once again worked on the presentation and poster, and updated the wiki.