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Team:Baltimore US/Notebook
From 2010.igem.org
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Notebook
June 10, 2010
Tonight we tested the hypothisis that the plasmid did not code for the antibiotic resistance/that we did not use enough dna. A Restriction Digest reaction was set up on the ligation reactions compleated on June 7. The reactions were cut with EcoR1 and Pst1. The reactions were allowed to incubate at 37 degrees C for one and a half hours. The digests were then ran on a electrophorasis gel. No DNA was present as there was not enough DNA, thus proving Duke's hypothisis.
June 9, 2010 In attendance: Duke, Tom, Ryan, Patrick, Lisa, Steven Missing: Kyle and Friend(Forgot his name)
1) Registration for iGEM site & Team affliation, required to update team wiki.
2) Access and update wiki.. Consider stylization, as well as information content. Who is our audience? Team info - blurb and caption of team members. Couple of sentences about you and your interests. Lab Notebook? - Openwetware connection.
3) Research biobrick parts by accessing in Registry of Standard Parts. XF to see if new combinations are already on file? If not begin documentation of the 3 new assemblies, with image using standard BioBrick icons. Document bp length of new parts to compare with Gel-Phoresis.
How do we test efficacy? (Part for PPM still in brick.) Is the media okay, is the antibiotic right. Positive tells you whether the cells themselves were capable of taking up our DNA. (Ideally, they should use the same antibiotic resistance, as our parts.
Negative groups tells us whether the antibiotic and media was effective and that the cells were not resistant to the media.
We know that cells were competent they were able to be transformed, and the antibiotic was effective. So the remaining question is whether they were able to be transformed.
The ligations are in question. Generally the restrictions and ligations go smoothly.
Tom's Hypothesis is questioning whether the media plates may have been mis-labelled with the wrong antibiotic resistance. Since we used a different resistance for controls, there was no telling.
Possible denaturing of enzymatic proteins from the heat shock on the initial restriction? 80c kill cycle. Vector ? - Linear plasmids - was the amount to small...? Parts - size already was confirmed, according to Tom
No Transformations.... so now what? Primers still on the way. Don't need to go to scratch.
The Core enzymes needed to perform the biobricks constructions... Spe1 pst1 ecor1 xba1 t4dna ligase polymerase
Project ideas... Polmerase in e.coli, tag, perhaps other enzymes could be self-manufactured/purified.
Basic tools/measurements -- Micropipetter's - Measuring volume. -- Measuring Mass.
---DV/HD camera - you tube videos and components.. --- Mini-preps. Growing the cells and isolating DNA. Cell competantcy Preparations...
Lac polymermerase - DIY-GEM
How do you purify?
What do you do with it... what is the process to create a project?
Hardware only takes you so far, these 5 basic tools. Restrictions Ligations Transformations/Plating PCR Gel Electrophoresis
The core will be good technique with these processes and then the ability to understand the existing database navigation with the proper questions to yield an experiment of interest.
Research educational tools from the MIT educator on IGEM site. Should we have an e-mail/Comments section added to wiki - openwetware, so observers can ask us questions?
June 8, 2010
In attendence: Colin, Patrick, Liz, Ryan, Duke and Tom. Missing: Andy, Scott.
So tonight we came in and took the 4 ligations/new part combinations from yesterday and transformed them into the competent cells, using a heat-shock transformation, while also preparing the Control groups (one with nothing/one with the ampicillan resistance). 3 of the parts were Tetracycline resistant, and 1 was Chlorephenecol. After the 90 minute transformation cycle we plated 6 versions of each of the 3 parts along with 1 plate of control and one negative group.
The 6 plates were done in a 0, -1, -2 dilutions in 2 concentrations one of 50 ul, and one of 200 ul.
They will be left for tomorrows team to run gel electrophoresis to determine whether they have the appropriate combination links.
June 7, 2010
In attendance: Colin, Patrick, Robert, Ryan, David, Gary, Miles, Duke and Tom. Missing: Melissa.
Tom greeted us with 4 separate sheets that contained 3 reactions each for us to begin restrictions and began heating to let the enzymes cut. A lesson in what not to do, was offered as we began the heating cycle of restriction in the PCR blocks and he timing had been set to 35 seconds instead of 35 minutes, after which it heated to a kill cycle of 80 degrees and we had to reapply the enzymes, in case the enzymes had been denatured.
We had 6 individuals building the 4 sheets, 2 in redundancy.
The legend for the various parts is as follows...
| 1PO | BBa_R0063 |
| 2PO | BBa_P0412 |
| 3PO | pSBIT3 |
| R (black marker) | BBa_R0062 |
| I (black marker) | BBa_I13507 |
| S (black marker) | pSBIT3 |
| F (green marker) | BBa_F2620 |
| I (green marker) | BBa_I13507 |
| S (green marker) | pSBIC3 |
| R10 (green marker) | BBa_R0010 |
| 462 (green marker) | BBa_I0462 |
| IT3 (green marker) | pSBIT3 |
| A/R10 (green marker) | BBa_R0010 |
| B/462 (green marker) | BBa_I0462 |
| C/IT3 (green marker) | pSBIT3 |
Patrick cut parts BBa_r0063 and BBa_p0412, and the plasmid backbone pSBIT3. The next step is to ligate them. Robert cut parts BBa_R0062 and BBa_I13507, and the plasmid backbone pSBIT3. Collin/Miles cut parts BBa_F2620, BBa_I13507 and the plasmid backbone pSBIC3 (labeled w/green marker).
After which we had a round table discussion about what kind of projects we may follow up with and the process of using the ncbi databases to discover pre-existing sequence information related to our various ideas. One idea we have discussed was the option of creating a smoother introductory curve for fellow DIY commmunity members and the creation of home-brewed enzymes that might be to pricey for the amateur scientists. We ended the night with the beginning of the various ligation reactions, as seen above.
- Ligation Reaction for R10+462+IT3 in 'LIGATE 05X
- Ligation Reaction for A/R10+B/462+C/IT3 in 'L/LIG
- Ligation Reaction for F2620+I13507+IC3 with "Green Asetrisk"
