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| + | I'm Back |
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| | <div class="desc"> | | <div class="desc"> |
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| - | WIKI CODING HERE
| + | Today we had a really great and important modelling meeting. We looked at the biochemistry of the circuit and gained new insight on different concept concerning the circuits. |
| | + | Iman showed us the visual representations he created . |
| | + | A few pictures for the APEGGA article was taken and the final article was revised. |
| | + | |
| | + | I revised the math modelling summary and sent it out to everyone. The simbiology simulations were also revised . New reactions were added to the old file. |
| | + | |
| | + | Researched information on GFP and thought about how that individual circuit/ mutant circuit could be characterized . |
| | + | |
| | + | Learned how to update on wiki. |
| | + | |
| | + | New Jobs to do : |
| | + | Prepare for the presentation on Friday : 12 min |
| | + | Gauntlet article due Friday |
| | + | Try to make an easier interface on simbiology ( eg . changing the initial concentration of ...) |
| | + | Think about flow/content of Jambouree presentation :5 min content |
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| + | J13002-LuxOD47E-B0015 curcuit finally completed construction and successfully sequenced! |
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| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | *Today we got the results back from my sequencing and they were good. The B0015 terminator is finally in my J13002-LuxOD47E construct and so my Mutant circuit is finished. Now as soon as Kevin makes his reporter circuit competant, we can start the testing of the two mutant circuits (LuxOD47A and LuxOD47E). |
| | + | |
| | + | *Today we had a Lab/Mathematical Modelling meeting. We summarized some of the work that has been done to date by both modelling groups. We briefly discussed how this work should be best presented at MIT. We also clarified some detalis of the Signalling pathway regarding protein size and the direction/ presence of certain equations. Our next meeting shall be on Thursday at 10:00 a.m. At Main Campus where we shall talk about the Membrane Computing project as a whole and how the different parts fit into the bigger picture. |
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| - | <a name="Iman"></a> | + | <a name="Jamie"></a> |
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| - | IMAN
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| + | luxPQ-B0015-R0040-luxOU-B0015 sequencing and construction into Surette vector |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| - | </html> | + | <ul><li>Sequencing results came back positive: signalling cascade is in psB1AC3. Resolution of <i>BamH</i>I and <i>Xho</i>I digested Surette vector on agarose gel: no bands? Redo digest tomorrow. </li> |
| - | WIKI CODING HERE
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| - | <html> | + | <li>Read up on AI-2 isolation from Salmonella.</li> |
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| - | <tr> | + | <li>Test the high-copy 'inducibility' of psB2K3 with IPTG induction. Prepare overnights of cl lambda for overnight induction with IPTG at concentrations of 0mM, 0.5mM, 1mM and 5.0mM. </li></ul> |
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| - | JAMIE
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| - | WIKI CODING HERE
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| + | Plasmid Isolation and Restriction Digest of cl lambda and PQ-OU |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | Plasmid was isolated from overnight cultures of cl lambda (two colonies – four tubes each) and PQ-B-R-OU-B in AK (4 colonies) using the QIAprep Spin MiniPrep Kit (QIAGEN). Plasmid purity and concentration were measured using the NanoDrop Spectrophotometer. The four tubes per colony of cl lambda were pooled and then vacufuged for two hours to increase the concentration of plasmid. RD was then set up with XbaI and PstI for 2 hours at 37 degrees for all the isolated and pooled plasmid. |
| | + | <br> |
| | + | <br> |
| | + | Sequencing results of LuxPQ-B0015-R0040-LuxOU-B0015 in psB1AC3 came back and the construct appears to be in the plasmid! Now we will be able to clone the PQ-OU construct into the Surrette vector and eventually start testing the promoter library. |
| | + | <br> |
| | + | <br> |
| | + | T-shirt companies are starting to be contacted concerning the awesome T-shirts that the U of C’s iGEM team will sport at the iGEM jamboree. |
| | + | |
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| + | Completion and Addition to Molecular Cloning and Transformation Activities |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | Construction zones one and two have been completed for the molecular cloning activity and are now going through testing. The third and final construction site will most likely be completed tomorrow since the most difficult part was determining the substrings required within a single note card that contains all the circuit parts to use for comparison purposes. This activity has a lot more ways to construct circuits then what they may do with the lab mission given so it is possible that other possible circuits may be included in case a user would like to test out the activity further. |
| | + | <br> |
| | + | <br> |
| | + | The order of the tasks within the DNA extraction activity have had their order set so it is not longer possible to go to the end or middle of the activity and still obtain the results you would like. The activity is reset every fifteen minutes or when an avatar completes the activity, which may be changed depending on how long it takes for an average avatar to finish the activity. |
| | + | <br> |
| | + | <br> |
| | + | Also, non-scripted items were moved to the second lab on the island when I had some free time, not including a lot of the smaller pieces, which may be linked together to be transported later. |
| | + | <br> |
| | + | <br> |
| | + | I have made additions to the transformation activity so that the plates that bacteria colonies develop on now will give objects to be used in other areas of the lab depending on what DNA an avatar’s competent cells were able to take up. The control plate will always give out the same informative note card, but the kanamycin and ampicilin plates may return one of two things: |
| | + | <br> |
| | + | <br> |
| | + | * A note card containing information about the resistance type depending on the DNA the competent cells take up |
| | + | * Invisibility or champion cells depending on what activity an avatar is doing, which may be stored in inventory until used elsewhere |
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| - | MANDY
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| - | WIKI CODING HERE
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| - | <a name="Patrick"></a>
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| - | PATRICK
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| - | WIKI CODING HERE
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| + | Marketing Success and Sponsors |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | I made several cold calls today. Sigma-Aldrich has generously donated to help fun iGEM Calgary's lab work. |
| | | | |
| | + | I also spoke to a representative of BioTeCanada about this year's proejct and possible sponsorship opportunities. He was very interested in our proejct and is willing to help our team. He also said he's trying to organize a get together for ALL Canadian teams at Boston (and he's probably going to come down too) and he wants to meet us there. I also spoke to him regarding the University of Calgary's membership with BioteCanada. |
| | + | |
| | + | The other comapanies which I had contacted were unavailable or required more time to think about our proposal. I will follow up with them later this week. |
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| + | Thinking about Squid |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | In order to make the Synthetic Kingdom more lively and to help people get familiar with it I have decided on some squid buddies for each station. There would be certain requirements and purposes which they serve: |
| | + | <br> |
| | + | <br> |
| | + | *Animated: Some squid should be animated in order to give a sense of being more alive |
| | + | *Interactive: At the very least they should be able to talk when you click them so a person will be more immersed |
| | + | *Notecards: Squid should give out notecards with more information about the station |
| | + | *Instructional: Help people not only understand more and learn about Second Life controls but tell them how to carry out the tasks at each station easily |
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| + | Modelling and lab meeting |
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| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | Our matlab, membrane computing and lab teams met today. On the matlab side, we have well-defined ideas for how we're going to approach simulation and characterisation, but they seem really disjoint. We will address this later this week. Thane also provided us with much greater detail on the biochemical foundation of the AI-2 signalling pathway, with special reference to kinases and non-specific phosphatases. This will help us find reaction constants for these particular bodies. Our teams will meet again on Thursday, where Afshin will give us a thorough briefing on membrane computing and we will begin to discuss how the two link together. |
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|
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CAROL
Modelling Meeting
- No lab experiments performed today (have to re-consider methods) - no colonies were found from the transformation that occured yesterday morning.
- For the modelling meeting, the following points were discussed:
1. A better organization of our work is required. We have both characterization and simulation from the mathematical team, but the work seems unlinked and not organized. Will have a more organized report for next week.
2. Greater detail was explained to us by Thane Kubik regarding the biochemical details that are behind the signalling pathway.
3. We need to start thinking about how we are going to present our two modelling system that we have created.
4. We will meet again on thursday and Afshin will give us a better overview of membrane computing.
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CHINMOYEE
I'm Back
Today we had a really great and important modelling meeting. We looked at the biochemistry of the circuit and gained new insight on different concept concerning the circuits.
Iman showed us the visual representations he created .
A few pictures for the APEGGA article was taken and the final article was revised.
I revised the math modelling summary and sent it out to everyone. The simbiology simulations were also revised . New reactions were added to the old file.
Researched information on GFP and thought about how that individual circuit/ mutant circuit could be characterized .
Learned how to update on wiki.
New Jobs to do :
Prepare for the presentation on Friday : 12 min
Gauntlet article due Friday
Try to make an easier interface on simbiology ( eg . changing the initial concentration of ...)
Think about flow/content of Jambouree presentation :5 min content
|
|
|
EMILY
J13002-LuxOD47E-B0015 curcuit finally completed construction and successfully sequenced!
- Today we got the results back from my sequencing and they were good. The B0015 terminator is finally in my J13002-LuxOD47E construct and so my Mutant circuit is finished. Now as soon as Kevin makes his reporter circuit competant, we can start the testing of the two mutant circuits (LuxOD47A and LuxOD47E).
- Today we had a Lab/Mathematical Modelling meeting. We summarized some of the work that has been done to date by both modelling groups. We briefly discussed how this work should be best presented at MIT. We also clarified some detalis of the Signalling pathway regarding protein size and the direction/ presence of certain equations. Our next meeting shall be on Thursday at 10:00 a.m. At Main Campus where we shall talk about the Membrane Computing project as a whole and how the different parts fit into the bigger picture.
|
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FAHD
Marketing for August 4th
Today, I put my energy towards marketing our project. I made preparations for our 2009 iGEM fundraising Bake Sale which will be held tomorrow (Wednesday August 5th 2009).
I also worked on some grant stream applications such as t=The Enbridge Pipeline Inc. Community Support Grants and also contacted some Oil & Gas companies. The following is the list of companies I contacted today:
1)Mackenzie Aborginal Corporation (MAC)
2) KMC Mining
3) Imperial Oil Resources.
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JAMIE
luxPQ-B0015-R0040-luxOU-B0015 sequencing and construction into Surette vector
- Sequencing results came back positive: signalling cascade is in psB1AC3. Resolution of BamHI and XhoI digested Surette vector on agarose gel: no bands? Redo digest tomorrow.
- Read up on AI-2 isolation from Salmonella.
- Test the high-copy 'inducibility' of psB2K3 with IPTG induction. Prepare overnights of cl lambda for overnight induction with IPTG at concentrations of 0mM, 0.5mM, 1mM and 5.0mM.
|
|
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JEREMY
Plasmid Isolation and Restriction Digest of cl lambda and PQ-OU
Plasmid was isolated from overnight cultures of cl lambda (two colonies – four tubes each) and PQ-B-R-OU-B in AK (4 colonies) using the QIAprep Spin MiniPrep Kit (QIAGEN). Plasmid purity and concentration were measured using the NanoDrop Spectrophotometer. The four tubes per colony of cl lambda were pooled and then vacufuged for two hours to increase the concentration of plasmid. RD was then set up with XbaI and PstI for 2 hours at 37 degrees for all the isolated and pooled plasmid.
Sequencing results of LuxPQ-B0015-R0040-LuxOU-B0015 in psB1AC3 came back and the construct appears to be in the plasmid! Now we will be able to clone the PQ-OU construct into the Surrette vector and eventually start testing the promoter library.
T-shirt companies are starting to be contacted concerning the awesome T-shirts that the U of C’s iGEM team will sport at the iGEM jamboree.
|
|
|
KATIE
Completion and Addition to Molecular Cloning and Transformation Activities
Construction zones one and two have been completed for the molecular cloning activity and are now going through testing. The third and final construction site will most likely be completed tomorrow since the most difficult part was determining the substrings required within a single note card that contains all the circuit parts to use for comparison purposes. This activity has a lot more ways to construct circuits then what they may do with the lab mission given so it is possible that other possible circuits may be included in case a user would like to test out the activity further.
The order of the tasks within the DNA extraction activity have had their order set so it is not longer possible to go to the end or middle of the activity and still obtain the results you would like. The activity is reset every fifteen minutes or when an avatar completes the activity, which may be changed depending on how long it takes for an average avatar to finish the activity.
Also, non-scripted items were moved to the second lab on the island when I had some free time, not including a lot of the smaller pieces, which may be linked together to be transported later.
I have made additions to the transformation activity so that the plates that bacteria colonies develop on now will give objects to be used in other areas of the lab depending on what DNA an avatar’s competent cells were able to take up. The control plate will always give out the same informative note card, but the kanamycin and ampicilin plates may return one of two things:
- A note card containing information about the resistance type depending on the DNA the competent cells take up
- Invisibility or champion cells depending on what activity an avatar is doing, which may be stored in inventory until used elsewhere
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KEVIN
Preparation for Plasmid switch of Pqrr4+I13500
Pqrr4+I13500(RBS+GFP) was constructed to verify the Mutants; however, we realized that both of our parts were in high copy plasmids, which a single cell can take one of. Thus the smaller Pqrr4+I13500 circuit is chosen to be plasmid switched into another vector (pSB2K3), which was obtained from the Q04510 (inverter). Today, both the Pqrr4+13500 and pSB2K3 were cut at xbaI+PstI via restriction digest, and it is going to be left in the waterbath(37˚C) overnight.
Preparation for Plasmid switch of Pqrr4+I13500
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PRIMA
Marketing Success and Sponsors
I made several cold calls today. Sigma-Aldrich has generously donated to help fun iGEM Calgary's lab work.
I also spoke to a representative of BioTeCanada about this year's proejct and possible sponsorship opportunities. He was very interested in our proejct and is willing to help our team. He also said he's trying to organize a get together for ALL Canadian teams at Boston (and he's probably going to come down too) and he wants to meet us there. I also spoke to him regarding the University of Calgary's membership with BioteCanada.
The other comapanies which I had contacted were unavailable or required more time to think about our proposal. I will follow up with them later this week.
|
|
|
STEFAN
Thinking about Squid
In order to make the Synthetic Kingdom more lively and to help people get familiar with it I have decided on some squid buddies for each station. There would be certain requirements and purposes which they serve:
- Animated: Some squid should be animated in order to give a sense of being more alive
- Interactive: At the very least they should be able to talk when you click them so a person will be more immersed
- Notecards: Squid should give out notecards with more information about the station
- Instructional: Help people not only understand more and learn about Second Life controls but tell them how to carry out the tasks at each station easily
|
|
|
VICKI
Modelling and lab meeting
Our matlab, membrane computing and lab teams met today. On the matlab side, we have well-defined ideas for how we're going to approach simulation and characterisation, but they seem really disjoint. We will address this later this week. Thane also provided us with much greater detail on the biochemical foundation of the AI-2 signalling pathway, with special reference to kinases and non-specific phosphatases. This will help us find reaction constants for these particular bodies. Our teams will meet again on Thursday, where Afshin will give us a thorough briefing on membrane computing and we will begin to discuss how the two link together.
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