Team:UIUC-Illinois/Notebook/MeetingNotes

From 2012.igem.org

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Monday, 6/11/12
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-  Divya, Washington characterization – transformed the petrobrick into the K 12 plasmid. The petrobrick uses ADC and ADR to make biofuel.
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-  Angela and Anthony can’t make it to high school jamboree
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-  Asha, human practices – high school jamboree is overnight on Friday, June 29 and all day on Jun 30th. Let me know ASAP if you can’t go. Also, for the GMO video we are now researching transgenic plants
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-  Bob, webmaster – is open to suggestions about progress on the wiki, need content and progress on the projects so that companies can see our progress, primers/structures/data etc should be sent to Bob so that it can be included in the wiki (it doesn’t have to be fancy), will look into putting a pretzi presentation on our wiki so that we can have an interactive flowchart element
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-  Adi, corporate – will have the elevator pitch done in time to present it at Friday’s advisor’s meeting, sent an email with supplies to Gold Biotech
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-  Cara, PHAT – transformed, emailed Parts registry and said that the parts will be shipped by the end of the week (we can expect them around next week)
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-  Uros – transformed split GFP (with Asha), has a rough draft of an RNA scaffold (will get put in the dropbox), got a program to work and is experimenting with placement of the PUF binding site, it’s looking to be 123 base pairs so it’s possible to synthesize it, is still looking to contact the Pam Silver author and RNA contacts on campus, will also further look into the crystal structure of binding PUF, hope to have a final draft of the RNA for Friday
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-  Angela – this is a busy week for many advisors so simply go to their offices and chat with them, Courtney is leaving in a few weeks so if we need to order anything let’s try to do that now, will teach Isiah how to do an order form, will be taking a leave starting on Friday to take care of her mother in Taiwan.
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Tuesday, 6/12/12
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- Bob, webmaster - Adi has added a basic pretzi to the wiki, google issues when searching for our wiki (need to get rid of old pages)
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- Divya, publicity - has created a logo and sent it to Bob, worked on blog
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- Washington characterization - cells grew, they aren’t being fed sugar so a control group of the petrobrick without sugar (so now alkanes), will talk to Jin about media and GCSM analysis
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- Cara, PHAT - grew 2 cultures of each strain of BM3 for glycerol stock and miniprepping tomorrow, got Falcon tubes from MMG
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- Uros, RNA scaffold - got a haircut, talked to Todd and got PUF binding sites, it seems that a good plan would be to sythesize it and put it in a plasmid. IGT has a 500 base pair synthesizing deal for $100. Todd will be giving us one of the plasmids, we already have the other one. The duet has 2 promoters so it can have 2 genes. One of the promoters will be used for the split GFP. In the future we will need 2 duets. One will encode the plasmid and then there is room for one other gene. That means we can get up to 3 genes for picetannol production.
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- Asha - worked on human practices stuff, got 3 boex for the -80. One box has the electrocompetent cells, and the other boxes are for PUF/PHAT as needed. Also inoculated both split GFPs and J04500.
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- Angela, PUF - we do have the plasmid with the testing part (PUF binding site and control), but are waiting on primers for the PUF gene so  we can subclone it. Transform the 2 plasmids into BL21 tomorrow for testing. AFter the completion of this control, we will do as many PUF constructs as possible as a backup plan for the scaffolding.
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Monday, 6/18/12
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- Adi, corporate - contacted IDT and VWR, tried to contact Fisher. Need to send Courtney a list of things to buy and also forward the email that was sent to Gold Biotech. Will upload a corporate folder to Dropbox. This will help us create a list of companies and their statuses on funding.
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- Elevator pitch: (this will be in video form later... also, team/company name is IllinoisSynth, product is IVOPC - in vivo o.. picetannol cascade). Edit info about team. Elaborate on obesity epidemic facts. Take out part about standardized tool kit, because that is no longer our product. Can discuss our process though, how we moved from the toolkit to a concrete application. Otherwise good! See the full text on the iGEM facebook page. Depending on how much work actually gets done, this pitch will change slightly.
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- Bob, webmaster - just updated the notebook section. Needed to put the actual iGEM logo, upright and at the top of the page, how does everyone like the format? What is the length of our scaffold? How many genes are on it? (Plan, Uros: 2 duet plasmids. One space will be for the scaffold itself. Cara: we can go either tyrosine -> resveratrol, p-cumaric acid-> picetannol. Both of these steps are 3 enzymes. But to go straight from tyrsoine -> picetannol is 6 enzymes... which is too many).
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- Asha/Anthony, PUF - 3rd PCR failure, there are primer dimers with only the lightest bands at the 700 bp mark. Potential problems with primer concentration. Will redo those calculations at 8:30 tomorrow.
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- Isiah/Divya, Washington characterization - Isiah will be working in the morning, Divya will be working in the afternoon. Running a gel for the petrobrick right now. Will make media tomorrow. Still several days away from needing the 
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- Cara, PHAT - need to get resveratrol/picetannol (will order and will get reimbursed), need a concentration in which to bathe the cells to produce picetannol (will start with in vitro concentration from the paper), performed TLC in lab today and feels confident to move forward with it for resveratrol → picetannol converstion. The orgo lab professor is willing to help and donate supplies. Parts from the registry have not yet been received, should have come in today and will check again tomorrow (the part is the 2 ligated genes from yeast).
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- Uros - RNA sequence has gotten final approval from Todd and Courtney, the ordering is dependent on IDT funds, emailed Melissa about it but she’s out for the week, Adi emailed IDT about it. Will not submit the sequence until we know that we have money. Tomorrow will transform cells with both GFP contructs to see if there is florescence with no scaffold. The duet plasmid is no longer useful because the split GFP will be tethered to PUF and the cell can support 2 plasmids. Can it be done through Genscript? IDT is offering 40% off to iGEM teams. After the split GFP, will help out and look into how to tether the PUF to the split GFP and other enzymes.
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Tuesday, 6/19/12
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- Anthony, PUF - calculated primer concentrations
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- Asha, PUF - inoculated E0030 which is the correct PCR template, skyped with Angela to clarify stuff
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- Divya, Isiah, Bob, Washington characterization - ran a gel to check the inoculation of the petrobrick and it appears to be the correct thing (5 kb plasmid backbone), tomorrow will go talk to Jin about part inconsistencies, Isiah and Divya will make the media tomorrow in the morning
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- Bob - helped Washington characterization, used the extra gel in the ice cream room, got the part with resveratrol and TAL, then plated it. Will check it in the morning and inoculate it tomorrow afternoon. for the wiki, finished putting up all the meeting minutes
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- Uros - need to insert both split GFP into a duet plasmid, because otherwise the plasmids will compete. Designed primers to insert restriction sites to the split GFP.
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- Need to update the daily work summaries.
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Wednesday, 6/20/12
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- Adi, corporate - revising the elevator pitch, working on the executive summary, going to carry out market research from a primary perspective, which will involve emailing a survey to companies. Weekend of July 6, will go to Chicago to meet Alex and finish the entrepreneurship website. Made excel sheet on a google doc of companies
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- Bob, Cara, PHAT - plated the 4CLSTS on 4 plates of different resistances.
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- Bob, webmaster - Angela sent suggestions for the wiki, changed the header a little, emailed Bhalerao to get a remote service to work with the server
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- Anthony - DCL access? work distribution is different.
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- Asha, PUF - PCR worked! Need HindIII! Need to email Will about enzymes in the big -20 (Uros will do this). Will talk to Courtney about the enzymes and traveling to the jamboree tomorrow. We got SORF funding. Will come up with a human practices website for SORF.
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Tshirt sizes: Adi (M), Bob (S), Uros (M), Asha (S), Cara (S), Divya (S), Isiah __, Angela (S)
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- Divya, Isiah, Washington characterization - talked with Jin, he wants a presentation at the advisor’s meeting, so Divya has been working on it. After the presentation he will discuss more of the project.
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- Cara - Dr. Metcalf is giving us a culture that has the last enzyme we need. After that will design primers and proceed to get it. Still trying to grow the yeast enzymes. Ordered the resveratrol and picetannol. Sent an email to Mark about the reimbursement (Melissa is handling it) Dr. Rafferty is talking to the Chem department about getting supplies for TLC. Brad suggested putting all of the enzymes in an operon under one promoter. Having some trouble with the agar stab that has the part.
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- Uros - ordered the part, but then got word from IDT that they can’t make it because of the large stem loops. Apparently the G block synthesis isn’t well suited for stem loops and secondary RNA structures. The IDT guy suggested another method of synthesis, but it’s only up to 200 bp. We might need to choose only 1 scaffold. Will consult with Todd again tomorrow.
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Thursday, 6/21/12
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- Adi, corporate - worked on executive summary, sent an email to Sarstedt (Courtney met their rep at a trade show), will send an email to NEB.
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- Divya - worked at presentation on Washington characterization for Dr. Jin, will work on finalizing it with Isiah tonight and then will send it to Uros. It will be presented at the advisor’s meeting tomorrow. Will be adding more blog entries.
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- Anthony - worked on GFP tethered to PUF stuff, will talk to a grad student tomorrow, is free after 1, but Todd is free after 10:30. Could also talk to Brad if he isn’t busy. Sequences are prepared, but need to adjust order and further edit it. Also have to figure out the actual manufacting synthesis (genscript money or PCR technique?)
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- Asha - ran a digest of PUF binding, contacted Courtney and Melissa about the high school iGEM trip, GMO video script is being made, Uros will look into getting cameras from the art department
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- Cara - got transfomed cells, will miniprep them, will sequence the part because it has been labeled as unreliable, need primers for it. Will order p cumaric acid (1 gram for $8). Will try to clone it and express it in e. coli.  (p cumaric gets turned into resveratrol). Will get rotobactercapsiaus that has the enzyme to turn tyrosine into p cumaric acid. Will make some constructs for the advisors meeting tomorrow.
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- Bob - got access to the server from Bhalerao. Needs to learn linux to work it (Ubuntu). Will work on human practices page with Asha.
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- Uros - advisor’s meeting at 3 tomorrow. Everyone should try to create some sort of presenation. (Anthony won’t be able to make it). Send presenations to Uros. miniprepped and made a glycerol stock of the pETDuet-1 from Todd. Also digested the first construct for it and will ligate it tomorrow. Also talked to Todd about synthesizing the RNA scaffold. A promising option is making a ‘mini-gene’ but it takes 2-4 days just to get a quote. Emailed Dr. Pamela Silver questions about using IDT as a synthesis (they did it without G block synthesis, so probably used the mini-gene option.)  If correspondence goes well, then hopefully we can get her to look at our sequence. It might be more expensive than anticipated, but we’ll see. Also working with Anthony on how to tether split GFP to PUF. will flip one of the PUF binding sites in order to put the split GFP closer together.
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Revision as of 21:33, 25 June 2012

Header

Protocols

Meeting Notes

Pre-April

  • 2/17/12
  • 2/19/12
  • 2/26/12
  • 3/4/12
  • 3/6/12
  • 3/7/12
  • 3/11/12
  • 3/25/12
  • 3/27/12
  • April

  • 4/1/12
  • 4/3/12
  • 4/4/12
  • 4/8/12
  • 4/14/12
  • 4/15/12
  • 4/17/12
  • 4/22/12
  • 4/24/12
  • May-July

  • 5/25/12
  • 5/29/12
  • 6/1/12
  • TBD
  • TBD
  • TBD
  • TBD
  • TBD
  • July-August

  • TBD
  • TBD
  • TBD
  • TBD
  • TBD
  • TBD
  • TBD
  • TBD
  • August-Jamboree

  • TBD
  • TBD
  • TBD
  • TBD
  • TBD
  • TBD
  • TBD
  • TBD
  • Select a date to read respective meeting notes.


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