User:Hetmann/Notebook/2006-6-12

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Official Start Day

Day Overview
The first official day of Harvard iGEM 2006 started with a morning meeting with all of the student participants and most of the faculty. We were asked to share ideas for projects for this summer and a team name. I envisioned an overarching project goal that would alleviate the effects of global warming, but I was not sure how to approach this. (note: Fortunately, this idea was linked to both carbon sequestration and alternate fuel sources, good & intriguing areas of research. Unfortunately, this idea never really found a toehold and quietly departed from our discussion and consciousness - but, as a great character in an old movie once stated, "hasta la vista...baby")

After eating sandwiches for lunch, we went to lab room 5088 and performed some introductory lab exercises. The teaching fellows paired more lab-savvy team members with less experienced students, savvy? I teamed up with the venerable Jeff Lau (Guild Wars Factons & Half-Life player extraordinaire). We practiced pipetting for the nanostructure experiment, learned how to create agarose gels, learned the purpose of BioBricks, and analyzed the mechanism by which BioBricks works. The agarose gels that we made were not utilized, but were instead placed in a refrigerator (as punishment).

We were instructed how to transform BioBricks for an experiment; the design was to ligate a BioBrick promoter to a luciferase BioBrick to create a BioBrick'd construct. We already knew that this final construct containing the promoter and the luciferase works and has been tested, and as a control we also included this BioBrick in our experiment. In summary, this first day was designed to elicit ideas for the summer and get lab experience, invaluable for everyone but especially to those who had never been in biology lab before.

First Monday Morning Meeting

 * Discussion of potential topics, a potential team name.
 * Team name suggestion from Perry: Transformers
 * 6/12 Brainstorming page

Advisors: George Church, Pam Silver, Alain Viel, Radhika Nagpal; Teaching Fellows: Chris Douchette, Shawn Douglas(, Nick Stroustrup ?)

Nanostructure Folding
Followed Shawn's Protocol to fold nanostructures.

Reactions were mixed and placed into tubes which were labeled as follows:


 * HH JL
 * oligonucleotides + scaffold (the products that are designed to combine)
 * HH JL -o
 * negative control with water instead of oligonucleotides
 * HH JL -s
 * negative control with water instead of scaffolds

These DNA nanostructure folding interactions were then incubated.

Agarose Gel
The agarose gels were poured utilizing the following protocol (with some changes).

Notes:


 * 1 g Ultrapure agarose w/ 100 mL 1X TBE (Tris/Borate/EDTA) was used; these were 1% agarose gels.
 * The flask was heated for 30 seconds in order to unscrew the cap and let gas escape, and then reheated for 30 seconds.
 * 3 μL EtBr (Ethidium Bromide) was pipetted into the flask.
 * The mixture was poured into gel frame and left alone for over 20 minutes (which is all it needs to harden), and since the gels were not used, they were placed in the refrigerator.

Transformation
Transformed the following BioBrick plasmids into OneShot Top10 competent cells (Invitrogen).


 * R0010
 * Jeff and I labeled these tubes as HH JL R0
 * E0241
 * Jeff and I labeled these tubes as HH JL E0
 * E7104
 * Jeff and I labeled these tubes as HH JL E7

Notes about the transformation:
 * E7104 is R0010 + E0241


 * 1 μL of each BioBrick was added to eppendorf tubes containing 30 μL of competent cells.
 * The competent cells were left on ice for 20 minutes, not 30 minutes.
 * 200 μL SOC was added to each tube.
 * The entire medium was pipetted and spread onto a labeled carbenicillin plates. (note: are the plates carbomycin?)
 * The plates were incubated agar-side up @ $$37^o$$C overnight.

Project Research
As part of the project planning process, we were instructed to find one project from past iGEM teams to present. I selected Davidson College's presentation from iGEM 2005 to present tomorrow.