IGEM:University of Chicago/2009/Meeting Notes

Meeting Notes

Friday, August 14

• So it's been awhile since we posted our meeting notes up here. Regardless, here's the schedule for what we're going to do next week (August 17-21)

• Rob will keep on working on making Superfolder GFP-Kan/His longtine constructs for eventual transformation in S. cerevisiae. This means miniprepping the colonies that grew up from last week's transformation, checking the plasmids with restriction digests, PCR-ing the constructs and transforming into yeast. Hopefully a brighter GFP will mean a better biosensor.

• Annie and Brandon will be redoing the GFP/OD fluorescence assay on the paraoxon biosensor constructs on Tuesday and Wednesday. Since Brandon has to leave early, these should be finished before 2:30 (which means induction by 11am, which means cultures must be started by 9). Analysis and compilation of data as well.

• Nora will be working on PCR-ing out the pnp/paraoxon degradation genes, and putting them under a constitutive expression vector. Will also work on making this vector biobrick standardized, and work on reconstructing the Longtine constructs to be biobrick standardized. All degradation enzymes will be (hopefully) be both vector and genome incorporated.

• Tony is still working on the website, and will be helping out in lab after Wednesday (once his classes let up).

• Miscellaneous:

Can we get surface display to work?
Permeable yeast? Ie how can we make a "bag of enzymes."

June 23, 2009

• Training schedule for this week

• Schedule for the rest of this week. Please note papers to read. Also, I may not be able to come in on Sunday so you guys will have to plan something out for then. All papers are accessible on the iGEM wiki brainstorming page. See you all tomorrow!

-Nora

Tuesday, June 23

• 9:00-9:30, C-shop: Discuss Longtine paper.
• 9:30-11, C-shop: Design primers, send in to Satoe
• 11-12, BSLC: pick-up keys, discuss PCR cycle design
• 12-12:30: Lunch!
• 12:30--End of day, BSLC: Review of lab basics, submit primers at the end of the day. Order paraoxon.
• DNA purification
• Agarose gel
• Streak out E. coli strains with Longtine plasmids
• Discuss enzyme digests

• We'll probably end early again today (around 4), but those who want to can stick around to help finish the Abbott Fund application.

• Paper to read for Wednesday: Takayama, et al (see wiki).

Wednesday, June 24

• 8:45 (Nora): Start 5mL cultures of Longtine strain
• 9-3:30: Rob, Damon and myself will be in lab. Lets use this time to figuring out what equipment we'll need for OPH/biosensor activity/cell surface display assays and tracking it down. We can also set up small cultures of the Longtine plasmids for purification at the end of the day.
• 3:30-4:00, BSLC: Discuss Takayama, et al paper.
• 4:00-5:30: Purification of Longtine plasmids, run gel

• Papers to read for Thursday: Colby et al and Boder et al. These are pretty similar papers so it shouldn't be too bad to do both.

Thursday, June 25

• 9-9:30, C-shop: Discuss Colby and Boder papers

-The rest of the day will depend on whether or not the primers come in. If they do, we'll start off with setting up our PCR reaction (as this usually takes 2-4 hours). If they haven't come in by the morning, we can do a practice restriction digest on the Longtine constructs. If we're able to do PCR we can finish up by transforming our yeast strain with the modified Longtine plasmids and streak on plates.

• Paper to read for Friday: Mulbry, et al. Basically the first real overview of OPH. Nice background information.

Friday, June 26 --Morning: Again, this is contingent on when the primers come in. Rob, Damon and I may just set up the PCR in the morning and we can do the transformations in the afternoon.

• 3:30-4: Discuss papers
• 4-5:30 Again, we might find ourselves either doing PCR, yeast transformations, or practice digests. It all depends on when our primers come in.

Saturday/Sunday:

• Pending

May 10, 2009

• A few notes on tutorials

1. Doing these tutorials gets harder the longer you put it off. Please keep up with the assignments, as they are cumulative. If you were not here, send me the answers to the quiz along with a screen shot.
2. We figured out how to use ApE to design primers for plasmid construction. Again, this is a much easier tutorial if you've done the previous assignments (esp. "Basic Oligo Design)

• Experimental design

Groups for next week are as follows. If you don't see your name, and want to be a part of experimental design, let me know. I put these groups together more or less randomly, so if you want to switch up, again, let me know :)

1. Damon, Annie, Ahad
2. Brandon, Rob, Andy
3. Juli, Amy, Alonso

• For next week groups will either
  • a) come up with a comprehensive questions they want to discuss with the group or
  • b) an idea for an experiment. Powerpoints are encouraged--a projector will be made available.

• Damon: Pizza bringer (once again). Sweet.

May 3, 2009

• Board positions

1. Treasurer: Brandon Lee
2. Social Chair: Damon Wang
3. Webmaster: Pending

• A number of you expressed interest in helping out with these positions, however I think we'll keep it down to one person each for now.

• Money: The BSCD has promised us some form of money, but hasn't yet specified the amount. Good news for those of you staying over the summer, although it will probably be enough to only pay one of you. Katen scholarships have been submitted

• Tutorials: Complete "Special case." Write down answers to the quiz at the end and be prepared to discuss them at meeting. I'll be going around and asking you questions one-by-one, so BE SURE TO ACTUALLY DO THE TUTORIAL. Like I've said before, it really doesn't take that long.

• Experiment: We're going ahead with the bioremediation project. Please go to the wiki, read through the papers, and come up with either 1) a question you have OR 2) an idea for an experiment. We'll split into small groups on Sunday, and each group will be responsible for presenting an experiment the following week. Fun, yes?

• PS. Meeting is 6:15, GCIS. IF YOU WANT TO BRING A SNACK let me know. Refunds will be had.

April 26, 2009

• First off, thanks for coming! Lets keep having everyone come to every meeting.
• Proposals: Go over the papers Brandon/Ahad and I post on the brainstorming page. Become familiar with the projects so we can come to a decision next meeting. More papers will be posted as we start experimental design.
• Tutorials: Finish the basic Oligo tutorial, and (if you haven't already) complete "Installing ApE".

• Positions: We need the following positions filled. Notice we've reduced the number from last week--with more time over the summer, I think we should be able to handle everything if its less split up.If you raised your hand when I mentioned them in meeting, please email me and I'll write you down. More than one person can be in each position.

1. Webmaster: Take care of the wiki and blog. Make sure everything looks nice and clean, and keep all information up-to-date.
2. Social Chair/Event coordinator: Plan out events, seminars, etc. Make sure all advertising works out.
3. Treasurer: Keep track of funds, grants sent out, fellowships, etc. This will also mean keeping in contact with our RSO adviser since all our funds are currently in an ORCSA account.

• Also, if you haven't given it to me already, send me your STUDENT ID so we can code your card to let you into GCIS.
• Food: All snack-bringers will be refunded for $20 dollars or less. Damon will be our snack-bringer next week. Yay Damon!
• See you next week! (6:15PM GCIS)

April 19, 2009

• Everybody must come to meetings.
• Change of time: 6:15PM (same place)
• Read Overview of cloning and Introduction to Biobricks. We'll go over the techniques mention during next meeting.

• Split up work. Email Nora if you are interested in one of the following positions:
  • Event coordinator: Be in charge of planning, executing Synthetic Biology events during the year
  • Public relations director: Organize advertising for Synthetic Biology events and increase the visibility of iGEM on campus. Communicate with media.
  • Treasurer: Keep track of our funds, from corporate sponsors to RSO money.
  • Corporate relations manager: Maintain communication with corporate sponsors and follow progress of grants and donations. Will work closely with treasurer.
  • Internet communications director: Keep up the wiki and website. Maintain blog.

• Not enough people attended today's meeting to thoroughly discuss project decision. Everybody must come next week to finalize project and begin experimental design.

• Logo/Slogans: If anyone wants to design our logo and/or self-deprecating slogans for our iGEM t-shirt email your ideas to the list-host. Otherwise we'll pay someone, which is completely unnecessary.

April 16, 2009

• We took individual pictures. Next meeting (Sunday, 5:15pm, GCIS)we'll take the rest of team member photos as well as a group photo.

• User accounts
  • Open WetWare: Apply for an Open Wetware account at How to Join It's super easy and you can always use it as a professional homepage :)
  • iGEM account: iGEM wiki Even if you're not staying full-time for the summer, we can credit you for any part time work easily, and you'll have a ready-made account if you chose to do iGEM next summer.

• HOMEWORK. We'll go over the first Berkeley tutorial on Sunday. Please let me know if you have any questions. As a reminder, you can access the tutorial/quiz here Complete "Installing Ape."

• Project decision. We'll also go over powerpoints on Sunday so be prepared if you had a project proposal. Check out the brainstorming page
• Our meeting is still this coming Sunday, April 19 at 5:15 in GCIS. I haven't received any word about your cards being activated, so I'll be in the front room to let you in.

April 5, 2009

• Ideas for Events
  • iGEM study break in October or this quarter?
  • Triple Helix
  • Guest lecture event
  • Movie series
  • Career fair
  • Vagina-monologue like "Tales of a Pre-med"
  • Band+Admission
• Funding
  • Women's board
  • Dean
  • Alumni
  • Companies: Cold-calling (this week)
• Sponsorship levels

1. Bronze Sponsor $1000+
2. Silver $5000+
3. Gold $10,000+

• Those interested in calling up companies: Rob, Annie, Amy, Nora
  • Nora will send out a schedule
  • Tomorrow, 2:30 PM Nora's apartment
• Weekly Tutorials (Berkeley JC Anderson Lab)
• Will send out assignments every Sunday night
• Project decision by meeting third meeting