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Team:Calgary/30 July 2009
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*Objective: Verify once more that B0015 has been cloned into the J13002-LuxOD47E construct before we send a colony down for sequencing. The previous gel looked a little strange and we saw some unexpected bands in the uncut lanes, so to be safe, we shall run the restriction digest again before sending anything down for sequencing. | *Objective: Verify once more that B0015 has been cloned into the J13002-LuxOD47E construct before we send a colony down for sequencing. The previous gel looked a little strange and we saw some unexpected bands in the uncut lanes, so to be safe, we shall run the restriction digest again before sending anything down for sequencing. | ||
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*Protocol: Cut with XbaI and PstI according to contruction technique protocol | *Protocol: Cut with XbaI and PstI according to contruction technique protocol | ||
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Visualized on a 1% agarose gel with uncut plasmid of the same colonies as a control. Also ran with the B0015-J13002-LuxOD47E construct as a size control. Bands of approximately 1.6 kb and 3 kb were expected represneting the construct and the psB1AC3 vector respectively. | Visualized on a 1% agarose gel with uncut plasmid of the same colonies as a control. Also ran with the B0015-J13002-LuxOD47E construct as a size control. Bands of approximately 1.6 kb and 3 kb were expected represneting the construct and the psB1AC3 vector respectively. | ||
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| - | *Results: Lane 1, 3 and 5 are J13002-LuxOD7E-B0015 colonies 1, 2 and 3 digested with XbaI and PstI | + | [[Image:ConstructRD]] |
| - | Lanes 2, 4 and 6 are colonies 1, 3 and 5 uncut. Lane 7 is B0015-J13002-LuxOD47E. | + | <Br> |
| + | *Results: Lane 1, 3 and 5 are J13002-LuxOD7E-B0015 colonies 1, 2 and 3 digested with XbaI and PstI. | ||
| + | Lanes 2, 4 and 6 are colonies 1, 3 and 5 uncut. Lane 7 is B0015-J13002-LuxOD47E. The bands are the expected sizes whixh is good. We will send colony 3 down for sequecing tomorrow as the band for the construct looks the higest, so it has the greatest chance of having the terminator in it. | ||
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Revision as of 05:14, 31 July 2009
UNIVERSITY OF CALGARY
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CAROL
Descriptive Title of What You’re Doing
WIKI CODING HERE
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CHINMOYEE
Descriptive Title of What You're Doing
WIKI CODING HERE
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EMILY
Verification Digest of J13002-LuxOD47E-B0015
Lanes 2, 4 and 6 are colonies 1, 3 and 5 uncut. Lane 7 is B0015-J13002-LuxOD47E. The bands are the expected sizes whixh is good. We will send colony 3 down for sequecing tomorrow as the band for the construct looks the higest, so it has the greatest chance of having the terminator in it.
Outreach
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FAHD
Outreach, Ethics and Marketing
I started of my day by exploring and getting familiar with the online virtual world called Second Life (TM). I attended a conference on the Science Centre Island. I browsed different ways for organizing the Ethics conference in Second Life.
For marketing, I did research on some more Oil & Gas companies starting off with Enbridge Pipelines and finishing off with Pajak Engineering. I e-mailed out newsletters to companies, updated our iGEM marketing list, filled out a grant application and printed posters for our Third University of Calgary iGEM Bake Sale. I also looked into potential organizations that would help us in our 2009 iGEM Education and Outreach Campaign. I have decided to contact the respective individuals as early as next week.
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IMAN
Descriptive Title of What You're Doing
WIKI CODING HERE
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JAMIE
Paper writing and T-shirt brainstorming
First draft of the paper is complete!
We also came up with some ideas for the Tshirt.
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JEREMY
Descriptive Title of What You're Doing
WIKI CODING HERE
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KATIE
Revision of Restriction Digest and Phosphatase Treatment Activities
Phosphatase treatment is now being combined with the restriction digest activity so I moved some of the script that was within the recipient tube for restriction digest, into the phosphatase treatment script and had to add new sections to the recipient tube so that the product you receive has to be taken to phosphatase treatment manually, before an avatar may receive the proper product to begin construction. This required the new method of searching for inventory, which is much more effective.
I completed instructions for the bacterial transformation activity and it was discovered that some of the items our avatars were using for PCR were named incorrectly, which was causing some major issues with testing out the equipment so those items have been renamed and the machine is in the process of being test once again.
Communication between Objects
I was also able to test the DNA extraction activity and it functions correctly as long as you follow the instructions provided throughout the activity. To improve upon it, we will have to get the objects to communicate with each other, which I have now started and the constant messaging would have to be reset for all steps within the product tube.
Since I find that the restriction digest is not unique compared to the other activity, tomorrow I believe that instead of moving the tube form water bath to heating block automatically, I will:
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KEVIN
Verification of the transformed reporter circuit
Now that hopefully the whole reporter circuit is transformed into TOP10 cells, I have performed a colony PCR of those colonies with Biobrick CP F/R primers and with the following conditions:
94°C for 3 min; 36x (94°C for 30s; 53°C for 45s; 72°C for 1 min and 20s;) 72°C for 10 min; held at 4°C.
Using Biobrick CP primers was a mistake, however, because I should have used Pqrr4 F primer and Biobrick CP reverse primer. This would have allowed me to verify whether or not Pqrr4 was not cut out during the construction. Another mistake was noticed, as I did not load any positive size control. Without any positive size controls to compare against, it is hard for me to tell whether or not it contains every piece of the circuit. Because of today's mistakes, I am planning to run another cPCR of the reporter circuit with 2 positive size controls, Pqrr4 by itself and Pqrr4 with B0034, and use Pqrr4 Forward and biobrick CP Reverse primers. The cPCR products were ran on 2% agarose gel, at 90 volts, and the following image is the picture of the gel. Figure 1. cPCR of Pqrr4+B0034(RBS)+K082003(GFP+LVA) 
Colonies 1 to 8 did not get amplified at all, and Colony 9 seemed to have been amplified, but not of the right size. The expected size is about 1043bp with some additional length added due to the primers annealing outside, and the band in Colony 9 lane is a bit higher than the expected size.
Modelling meeting
Anders, one of our facilitators, came and gave us an advise on modelling. We discussed about limitations, advantages of our characterization methods and what we should focus on.
Updated Wiki notebooks from May 26 to June 11
Because our wiki notebook page has been created recently by Mandy, we were not able to post our previous updates, so old updates are now being done along with the recent updates.
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MANDY
Descriptive Title of What You're Doing
WIKI CODING HERE
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PATRICK
Descriptive Title of What You're Doing
WIKI CODING HERE
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PRIMA
Descriptive Title of What You're Doing
WIKI CODING HERE
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STEFAN
Descriptive Title of What You're Doing
WIKI CODING HERE
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VICKI
Descriptive Title of What You're Doing
WIKI CODING HERE
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