Team:Calgary/9 July 2009

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Colony PCR
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WIKI CODING HERE
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* Overnight plates resulted in 3 colonies
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* Performed colony PCR on the three colonies using BBK CP reverse and forward primers.
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* The 0.6% agarose gel showed no viable results. Other smaller bands are found on the gel which suggests that we may be cloning primer dimers into the plasmid.
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* Might have to attempt gel extraction.
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Today I went to the modelling meeting in ICT building . Then I decided to make a summary about math modelling so that on Friday both the modelling teams could compare the two system . This will ensure uniformity in parameter values , reaction equations used etc. Also a good written record will be present.
Today I went to the modelling meeting in ICT building . Then I decided to make a summary about math modelling so that on Friday both the modelling teams could compare the two system . This will ensure uniformity in parameter values , reaction equations used etc. Also a good written record will be present.
   
   
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J13002-LuxOD47E-B0015 Construction Take Two
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*Today sequencing results came back and I was in fact successful in cloning in the J13002 promoter!  So now I can proceed to verification of my J13002-LuxOD47E-B0015 circuit.
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*So I ran a colony PCR of my J13002-LuxOD47E-B0015 colonies to verify the presence of the B0015 terminator in my construct.  BBK-CP forward and reverse primers were used with p Taq and cycling conditions were as follows: 94°C for 6 min, 36x(94°C for 30 s, 55°C for 45s, 72°C for 90s), 72°C for 10 min, held at 4°C. PCR products were visualized on a 1% agarose gel run at 120 V with J13002-LuxOD47E and LuxOD47E as size controls.  Gel is pictured below.  Lanes 1-4 are trial one where the B0015 terminator was treated as the insert.  Lanes 5-8 are trial 2 where the J13002-LuxOD47E construct was treated as the insert.  Lane 9 is J13002-LuxOD47E and Lane 10 is LuxOD47E.  Lane 11 is blank and Lane 12 is the negative control.
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[[Image:2009.07.09J13002-LuxOD47E-B0015.jpg|350px]]
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*Because all bands in the first 9 lanes appear to be the same size as the band in lane 9 with J13002-LuxOD47E, we can conclude that the B0015 terminator was not successfully cloned in and we will have to go back to contruction again.
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*Performed a restriction digest with EcoRI, XbaI and SpeI of B0015 and the J13002-LuxOD47E construct, digesting the insert with EcoRI and SpeI and digesting the recipient with EcoRI and XbaI.  Left the digestion in the 37C waterbath for 2 hours, transformed into TOP10 cells on both AC and C plates and left for overnight growth.
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*Today I also checked my KT1144 cells for glow.  There wasn't any, but we wil let them grow at room temperature for a couple more days.
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Marketing for July 9th 2009
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WIKI CODING HERE
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1) I contacted a number of travel agencies(including Travel Cuts) and the cheapest i got was through travel cuts and that was 595 CDN dollars(includes taxes and this price is with student discounts). However, Prima got a really good deal a few weeks ago( 412 CDN dollars) and i think(suggestion) that we should book these flights before somebody else grabs the booking. I am still waiting for our team members to respond me back with regards to the HOTELS e-mail i had sent out on WEDNESDAY about their preference. SO far only Patrick, Mandy, Stefan and Prima have told me about their preference.
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IMAN
 
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2) I did a research/invesyigation on the following research pharmaceutical companies:
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a-Ambion Inc.
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b-Charles River Labs
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c-Critical Outcome Technologies
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d- E-Z-EM Canada Inc.
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e- Genome Canada
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f- i3 Canada Inc.
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g- Ikaria Canada Inc.
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h- Inimex Pharmaceuticals
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i- Arc Pharma Canada Inc.
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j- Dalto Pharma Services
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k- Medicago Inc.
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l- Neuroimage Inc.
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m- Synbiosis
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I e-mailed only 4 of the companies above because i want to spend as much time as i can on a company. I also have to confirm them with my team before sending them out so it takes time but i hope they respond back to us in a positive manner.
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Signalling circuit construction and Response circuit preparation
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WIKI CODING HERE
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See Jeremy's updates regarding luxPQ-luxOU construction from hereonin.
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cIIambda and aiiA were transformed from registry plates into TOP10 cells for plasmid isolation and verification.
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Constructing LuxPQ-LuxOU signaling circuit
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WIKI CODING HERE
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Purpose: to construct LuxPQ-B0015-R0040-LuxOU-B0015 (hereafter PQ-B-R-OU-B) by inserting LuxPQ (AC) into B-R-OU-B (AK). Construction was performed by setting up a restriction digest by cutting the insert (LuxPQ) with EcoRI and SpeI and cutting the vector (B-R-OU-B in AK) with EcoRI and XbaI. After this restriction digest, phosphatase and ligation treatment was performed and the plasmid was subsequently transformed into TOP10 competent cells and plated overnight on LB+Kanamycin.
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I was also able to complete the script for the sequencing station as per Mandy’s request and it will now give any avatar who drops  ‘Amplified Colison E2’ into the sequencing object a notecard, which as of now does not contain any useful information. I will be adding various other amplified DNA products as objects to give back sequencing for on Friday, which may continue into next week.  
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I was also able to complete the script for the sequencing station as per Mandy’s request and it will now give any avatar who drops  ‘Amplified Colicin E2’ into the sequencing object a notecard, which as of now does not contain any useful information. I will be adding various other amplified DNA products as objects to give back sequencing for on Friday, which may continue into next week.  
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The results of the restreaks of J13002 and GFP/RFP
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The following is an image of the restreak:
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[[Image:Calgary_2009.07.10.I13502_E0040_J13002.png|500px]]
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From it, one can clearly see that RFP is glowing much brighter than the negative control, and that GFP is, although less obvious, also glowing.
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No other lab work was performed on this day.
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Second Life Biobert
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Today, we finished the prototype for ‘Biobert’, the lab helper robot. When clicked he can move and chat with people (using their names :D). He can also give instructions, note cards, and inventory like vectors. He also is the point where users can choose ‘lab missions’ to complete.
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I finished designing/planning the intermediate lab mission level, which is PCR/Gel electrophoresis verification and then bacterial transformation of a circuit. I started designing the more difficult lab mission that involves the compilation of a biobricked circuit.
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Biobert currently only responds to a couple phrases said to him by users. Tomorrow I plan to expand on both what he does and says (integrate him more in the lab, maybe have him give clues, etc.). Right now, he also likes to repeat himself a lot, which can get kind of annoying so I’m going to delete some of the scripting too.
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As soon as I learn exactly how Katie’s scripted restriction digest works, I will be finishing the designing/planning of the more difficult lab mission, and then figure out what can be an easy one.
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PATRICK
 
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Wiki Reformatting
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Today, I tried laying out the wiki more, and getting it ready for sponsors to see. NO SUCH LUCK, HOWEVER: here is what I was playing with, NOT on a wiki site: http://igemtest.blogspot.com
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(The purple is still uh…being debated). My css does not seem to combine with the wiki mark up, and Emily found that some teams used ‘templates’ with wiki markup to get around this problem, which I haven’t quite figured out how to do yet, but I’ve bookmarked some pages to read. THE WIKI pages have all been saved on Emily’s laptop and the pages online have been wiped in preparation for some trouble shooting (slowly adding elements and figuring out what isn’t working – why the formatting is off).
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THE BLOG is filling up rather nicely, helped Prima upload her video and retagged/formatted the current posts (so they will show up if people search iGEM on blogspot).
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Company contacts
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I updated the gmail contact list. Sent a Thank you letter to Corning Life Sciences.
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Called Worley Parsons – the contact they gave me was apparently the wrong person. It was the HR person and she said she’ll find out who deals with sponsorship and get back to me. But I might just inquire and find out myself just in case she forgets. I’ve been calling company 2 for some time now… I’ll call him again tomorrow.
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Sigma-Aldrich- called today but couldn’t get a hold of her so I left a message follow up tomorrow
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Cayman Chemicals ..called…needs a final confirmation from their President follow up July 31
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Followed up with numerous companies (including oil companies such as Shell and Husky) but they declined our proposal.
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I will continue to follow up and contact new companies.
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Freebies
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Most of today was spent traveling islands and the online Second Life marketplace XStreet in search of things to get for our sim. These included:
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*New textures
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*Rocks, coral and seaweed
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*Walkways
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*Particle effects
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Modelling meeting
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Team MatLab met with Team Mathematica in order to better coordinate our efforts and ensure that we have something in place that will have an impact at the jamboree. More comprehensive notes can be found in Chinee’s notebook. We watched a simulation of what Afshin and Iman have come up with for membrane computing and discussed how to go about streamlining our work so that our models will actually have the potential to support each other. This would involve a thorough literature search to find relevant phosphorylation and reaction constants (and an analysis of the inherent assumptions). As well, we agreed to write up a set of rules/reactions so that a team member from the other modelling school of thought (or otherwise) can better follow the work that each modelling crew has done on screen.
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Latest revision as of 21:53, 20 October 2009

University of Calgary

UNIVERSITY OF CALGARY



THIS MONTH

July
MTWTFSS
    [http://2009.igem.org/Team:Calgary/1_July_2009 1] [http://2009.igem.org/Team:Calgary/2_July_2009 2] [http://2009.igem.org/Team:Calgary/3_July_2009 3] [http://2009.igem.org/Team:Calgary/4_July_2009 4] [http://2009.igem.org/Team:Calgary/5_July_2009 5]
[http://2009.igem.org/Team:Calgary/6_July_2009 6] [http://2009.igem.org/Team:Calgary/7_July_2009 7] [http://2009.igem.org/Team:Calgary/8_July_2009 8] [http://2009.igem.org/Team:Calgary/9_July_2009 9] [http://2009.igem.org/Team:Calgary/10_July_2009 10] [http://2009.igem.org/Team:Calgary/11_July_2009 11] [http://2009.igem.org/Team:Calgary/12_July_2009 12]
[http://2009.igem.org/Team:Calgary/13_July_2009 13] [http://2009.igem.org/Team:Calgary/14_July_2009 14] [http://2009.igem.org/Team:Calgary/15_July_2009 15] [http://2009.igem.org/Team:Calgary/16_July_2009 16] [http://2009.igem.org/Team:Calgary/17_July_2009 17] [http://2009.igem.org/Team:Calgary/18_July_2009 18] [http://2009.igem.org/Team:Calgary/19_July_2009 19]
[http://2009.igem.org/Team:Calgary/20_July_2009 20] [http://2009.igem.org/Team:Calgary/21_July_2009 21] [http://2009.igem.org/Team:Calgary/22_July_2009 22] [http://2009.igem.org/Team:Calgary/23_July_2009 23] [http://2009.igem.org/Team:Calgary/24_July_2009 24] [http://2009.igem.org/Team:Calgary/25_July_2009 25] [http://2009.igem.org/Team:Calgary/26_July_2009 26]
[http://2009.igem.org/Team:Calgary/27_July_2009 27] [http://2009.igem.org/Team:Calgary/28_July_2009 28] [http://2009.igem.org/Team:Calgary/29_July_2009 29] [http://2009.igem.org/Team:Calgary/30_July_2009 30] [http://2009.igem.org/Team:Calgary/31_July_2009 31]


NOTEBOOK PAGE INDEX
Carol
Chinmoyee
Emily
Fahd
Iman
Jamie
Jeremy
Katie
Kevin
Mandy
Patrick
Prima
Stefan
Vicki



CALENDAR

May
MTWTFSS
        [http://2009.igem.org/Team:Calgary/1_May_2009 1] [http://2009.igem.org/Team:Calgary/2_May_2009 2] [http://2009.igem.org/Team:Calgary/3_May_2009 3]
[http://2009.igem.org/Team:Calgary/4_May_2009 4] [http://2009.igem.org/Team:Calgary/5_May_2009 5] [http://2009.igem.org/Team:Calgary/6_May_2009 6] [http://2009.igem.org/Team:Calgary/7_May_2009 7] [http://2009.igem.org/Team:Calgary/8_May_2009 8] [http://2009.igem.org/Team:Calgary/9_May_2009 9] [http://2009.igem.org/Team:Calgary/10_May_2009 10]
[http://2009.igem.org/Team:Calgary/11_May_2009 11] [http://2009.igem.org/Team:Calgary/12_May_2009 12] [http://2009.igem.org/Team:Calgary/13_May_2009 13] [http://2009.igem.org/Team:Calgary/14_May_2009 14] [http://2009.igem.org/Team:Calgary/15_May_2009 15] [http://2009.igem.org/Team:Calgary/16_May_2009 16] [http://2009.igem.org/Team:Calgary/17_May_2009 17]
[http://2009.igem.org/Team:Calgary/18_May_2009 18] [http://2009.igem.org/Team:Calgary/19_May_2009 19] [http://2009.igem.org/Team:Calgary/20_May_2009 20] [http://2009.igem.org/Team:Calgary/21_May_2009 21] [http://2009.igem.org/Team:Calgary/22_May_2009 22] [http://2009.igem.org/Team:Calgary/23_May_2009 23] [http://2009.igem.org/Team:Calgary/24_May_2009 24]
[http://2009.igem.org/Team:Calgary/25_May_2009 25] [http://2009.igem.org/Team:Calgary/26_May_2009 26] [http://2009.igem.org/Team:Calgary/27_May_2009 27] [http://2009.igem.org/Team:Calgary/28_May_2009 28] [http://2009.igem.org/Team:Calgary/29_May_2009 29] [http://2009.igem.org/Team:Calgary/30_May_2009 30] [http://2009.igem.org/Team:Calgary/31_May_2009 31]


June
MTWTFSS
[http://2009.igem.org/Team:Calgary/1_June_2009 1] [http://2009.igem.org/Team:Calgary/2_June_2009 2] [http://2009.igem.org/Team:Calgary/3_June_2009 3] [http://2009.igem.org/Team:Calgary/4_June_2009 4] [http://2009.igem.org/Team:Calgary/5_June_2009 5] [http://2009.igem.org/Team:Calgary/6_June_2009 6] [http://2009.igem.org/Team:Calgary/7_June_2009 7]
[http://2009.igem.org/Team:Calgary/8_June_2009 8] [http://2009.igem.org/Team:Calgary/9_June_2009 9] [http://2009.igem.org/Team:Calgary/10_June_2009 10] [http://2009.igem.org/Team:Calgary/11_June_2009 11] [http://2009.igem.org/Team:Calgary/12_June_2009 12] [http://2009.igem.org/Team:Calgary/13_June_2009 13] [http://2009.igem.org/Team:Calgary/14_June_2009 14]
[http://2009.igem.org/Team:Calgary/15_June_2009 15] [http://2009.igem.org/Team:Calgary/16_June_2009 16] [http://2009.igem.org/Team:Calgary/17_June_2009 17] [http://2009.igem.org/Team:Calgary/18_June_2009 18] [http://2009.igem.org/Team:Calgary/19_June_2009 19] [http://2009.igem.org/Team:Calgary/20_June_2009 20] [http://2009.igem.org/Team:Calgary/21_June_2009 21]
[http://2009.igem.org/Team:Calgary/22_June_2009 22] [http://2009.igem.org/Team:Calgary/23_June_2009 23] [http://2009.igem.org/Team:Calgary/24_June_2009 24] [http://2009.igem.org/Team:Calgary/25_June_2009 25] [http://2009.igem.org/Team:Calgary/26_June_2009 26] [http://2009.igem.org/Team:Calgary/27_June_2009 27] [http://2009.igem.org/Team:Calgary/28_June_2009 28]
[http://2009.igem.org/Team:Calgary/29_June_2009 29] [http://2009.igem.org/Team:Calgary/30_June_2009 30]


July
MTWTFSS
    [http://2009.igem.org/Team:Calgary/1_July_2009 1] [http://2009.igem.org/Team:Calgary/2_July_2009 2] [http://2009.igem.org/Team:Calgary/3_July_2009 3] [http://2009.igem.org/Team:Calgary/4_July_2009 4] [http://2009.igem.org/Team:Calgary/5_July_2009 5]
[http://2009.igem.org/Team:Calgary/6_July_2009 6] [http://2009.igem.org/Team:Calgary/7_July_2009 7] [http://2009.igem.org/Team:Calgary/8_July_2009 8] [http://2009.igem.org/Team:Calgary/9_July_2009 9] [http://2009.igem.org/Team:Calgary/10_July_2009 10] [http://2009.igem.org/Team:Calgary/11_July_2009 11] [http://2009.igem.org/Team:Calgary/12_July_2009 12]
[http://2009.igem.org/Team:Calgary/13_July_2009 13] [http://2009.igem.org/Team:Calgary/14_July_2009 14] [http://2009.igem.org/Team:Calgary/15_July_2009 15] [http://2009.igem.org/Team:Calgary/16_July_2009 16] [http://2009.igem.org/Team:Calgary/17_July_2009 17] [http://2009.igem.org/Team:Calgary/18_July_2009 18] [http://2009.igem.org/Team:Calgary/19_July_2009 19]
[http://2009.igem.org/Team:Calgary/20_July_2009 20] [http://2009.igem.org/Team:Calgary/21_July_2009 21] [http://2009.igem.org/Team:Calgary/22_July_2009 22] [http://2009.igem.org/Team:Calgary/23_July_2009 23] [http://2009.igem.org/Team:Calgary/24_July_2009 24] [http://2009.igem.org/Team:Calgary/25_July_2009 25] [http://2009.igem.org/Team:Calgary/26_July_2009 26]
[http://2009.igem.org/Team:Calgary/27_July_2009 27] [http://2009.igem.org/Team:Calgary/28_July_2009 28] [http://2009.igem.org/Team:Calgary/29_July_2009 29] [http://2009.igem.org/Team:Calgary/30_July_2009 30] [http://2009.igem.org/Team:Calgary/31_July_2009 31]


August
MTWTFSS
          [http://2009.igem.org/Team:Calgary/1_August_2009 1] [http://2009.igem.org/Team:Calgary/2_August_2009 2]
[http://2009.igem.org/Team:Calgary/3_August_2009 3] [http://2009.igem.org/Team:Calgary/4_August_2009 4] [http://2009.igem.org/Team:Calgary/5_August_2009 5] [http://2009.igem.org/Team:Calgary/6_August_2009 6] [http://2009.igem.org/Team:Calgary/7_August_2009 7] [http://2009.igem.org/Team:Calgary/8_August_2009 8] [http://2009.igem.org/Team:Calgary/9_August_2009 9]
[http://2009.igem.org/Team:Calgary/10_August_2009 10] [http://2009.igem.org/Team:Calgary/11_August_2009 11] [http://2009.igem.org/Team:Calgary/12_August_2009 12] [http://2009.igem.org/Team:Calgary/13_August_2009 13] [http://2009.igem.org/Team:Calgary/14_August_2009 14] [http://2009.igem.org/Team:Calgary/15_August_2009 15] [http://2009.igem.org/Team:Calgary/16_August_2009 16]
[http://2009.igem.org/Team:Calgary/17_August_2009 17] [http://2009.igem.org/Team:Calgary/18_August_2009 18] [http://2009.igem.org/Team:Calgary/19_August_2009 19] [http://2009.igem.org/Team:Calgary/20_August_2009 20] [http://2009.igem.org/Team:Calgary/21_August_2009 21] [http://2009.igem.org/Team:Calgary/22_August_2009 22] [http://2009.igem.org/Team:Calgary/23_August_2009 23]
[http://2009.igem.org/Team:Calgary/24_August_2009 24] [http://2009.igem.org/Team:Calgary/25_August_2009 25] [http://2009.igem.org/Team:Calgary/26_August_2009 26] [http://2009.igem.org/Team:Calgary/27_August_2009 27] [http://2009.igem.org/Team:Calgary/28_August_2009 28] [http://2009.igem.org/Team:Calgary/29_August_2009 29] [http://2009.igem.org/Team:Calgary/30_August_2009 30]
[http://2009.igem.org/Team:Calgary/31_August_2009 31]


September
MTWTFSS
  [http://2009.igem.org/Team:Calgary/1_September_2009 1] [http://2009.igem.org/Team:Calgary/2_September_2009 2] [http://2009.igem.org/Team:Calgary/3_September_2009 3] [http://2009.igem.org/Team:Calgary/4_September_2009 4] [http://2009.igem.org/Team:Calgary/5_September_2009 5] [http://2009.igem.org/Team:Calgary/6_September_2009 6]
[http://2009.igem.org/Team:Calgary/7_September_2009 7] [http://2009.igem.org/Team:Calgary/8_September_2009 8] [http://2009.igem.org/Team:Calgary/9_September_2009 9] [http://2009.igem.org/Team:Calgary/10_September_2009 10] [http://2009.igem.org/Team:Calgary/11_September_2009 11] [http://2009.igem.org/Team:Calgary/12_September_2009 12] [http://2009.igem.org/Team:Calgary/13_September_2009 13]
[http://2009.igem.org/Team:Calgary/14_September_2009 14] [http://2009.igem.org/Team:Calgary/15_September_2009 15] [http://2009.igem.org/Team:Calgary/16_September_2009 16] [http://2009.igem.org/Team:Calgary/17_September_2009 17] [http://2009.igem.org/Team:Calgary/18_September_2009 18] [http://2009.igem.org/Team:Calgary/19_September_2009 19] [http://2009.igem.org/Team:Calgary/20_September_2009 20]
[http://2009.igem.org/Team:Calgary/21_September_2009 21] [http://2009.igem.org/Team:Calgary/22_September_2009 22] [http://2009.igem.org/Team:Calgary/23_September_2009 23] [http://2009.igem.org/Team:Calgary/24_September_2009 24] [http://2009.igem.org/Team:Calgary/25_September_2009 25] [http://2009.igem.org/Team:Calgary/26_September_2009 26] [http://2009.igem.org/Team:Calgary/27_September_2009 27]
[http://2009.igem.org/Team:Calgary/28_September_2009 28] [http://2009.igem.org/Team:Calgary/29_September_2009 29] [http://2009.igem.org/Team:Calgary/30_September_2009 30]


October
MTWTFSS
      [http://2009.igem.org/Team:Calgary/1_October_2009 1] [http://2009.igem.org/Team:Calgary/2_October_2009 2] [http://2009.igem.org/Team:Calgary/3_October_2009 3] [http://2009.igem.org/Team:Calgary/4_October_2009 4]
[http://2009.igem.org/Team:Calgary/5_October_2009 5] [http://2009.igem.org/Team:Calgary/6_October_2009 6] [http://2009.igem.org/Team:Calgary/7_October_2009 7] [http://2009.igem.org/Team:Calgary/8_October_2009 8] [http://2009.igem.org/Team:Calgary/9_October_2009 9] [http://2009.igem.org/Team:Calgary/10_October_2009 10] [http://2009.igem.org/Team:Calgary/11_October_2009 11]
[http://2009.igem.org/Team:Calgary/12_October_2009 12] [http://2009.igem.org/Team:Calgary/13_October_2009 13] [http://2009.igem.org/Team:Calgary/14_October_2009 14] [http://2009.igem.org/Team:Calgary/15_October_2009 15] [http://2009.igem.org/Team:Calgary/16_October_2009 16] [http://2009.igem.org/Team:Calgary/17_October_2009 17] [http://2009.igem.org/Team:Calgary/18_October_2009 18]
[http://2009.igem.org/wiki/index.php?title=Team:Calgary/19_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 19] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/20_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 20] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/21_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 21] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/22_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 22] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/23_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 23] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/24_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 24] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/25_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 25]
[http://2009.igem.org/wiki/index.php?title=Team:Calgary/26_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 26] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/27_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 27] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/28_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 28] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/29_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 29] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/30_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 30] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/31_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 31]



JULY 9, 2009


CAROL

Colony PCR

  • Overnight plates resulted in 3 colonies
  • Performed colony PCR on the three colonies using BBK CP reverse and forward primers.
  • The 0.6% agarose gel showed no viable results. Other smaller bands are found on the gel which suggests that we may be cloning primer dimers into the plasmid.
  • Might have to attempt gel extraction.


CHINMOYEE

Math Model summary made

Today I went to the modelling meeting in ICT building . Then I decided to make a summary about math modelling so that on Friday both the modelling teams could compare the two system . This will ensure uniformity in parameter values , reaction equations used etc. Also a good written record will be present.


EMILY

J13002-LuxOD47E-B0015 Construction Take Two

  • Today sequencing results came back and I was in fact successful in cloning in the J13002 promoter! So now I can proceed to verification of my J13002-LuxOD47E-B0015 circuit.
  • So I ran a colony PCR of my J13002-LuxOD47E-B0015 colonies to verify the presence of the B0015 terminator in my construct. BBK-CP forward and reverse primers were used with p Taq and cycling conditions were as follows: 94°C for 6 min, 36x(94°C for 30 s, 55°C for 45s, 72°C for 90s), 72°C for 10 min, held at 4°C. PCR products were visualized on a 1% agarose gel run at 120 V with J13002-LuxOD47E and LuxOD47E as size controls. Gel is pictured below. Lanes 1-4 are trial one where the B0015 terminator was treated as the insert. Lanes 5-8 are trial 2 where the J13002-LuxOD47E construct was treated as the insert. Lane 9 is J13002-LuxOD47E and Lane 10 is LuxOD47E. Lane 11 is blank and Lane 12 is the negative control.

2009.07.09J13002-LuxOD47E-B0015.jpg

  • Because all bands in the first 9 lanes appear to be the same size as the band in lane 9 with J13002-LuxOD47E, we can conclude that the B0015 terminator was not successfully cloned in and we will have to go back to contruction again.
  • Performed a restriction digest with EcoRI, XbaI and SpeI of B0015 and the J13002-LuxOD47E construct, digesting the insert with EcoRI and SpeI and digesting the recipient with EcoRI and XbaI. Left the digestion in the 37C waterbath for 2 hours, transformed into TOP10 cells on both AC and C plates and left for overnight growth.
  • Today I also checked my KT1144 cells for glow. There wasn't any, but we wil let them grow at room temperature for a couple more days.


FAHD

Marketing for July 9th 2009

1) I contacted a number of travel agencies(including Travel Cuts) and the cheapest i got was through travel cuts and that was 595 CDN dollars(includes taxes and this price is with student discounts). However, Prima got a really good deal a few weeks ago( 412 CDN dollars) and i think(suggestion) that we should book these flights before somebody else grabs the booking. I am still waiting for our team members to respond me back with regards to the HOTELS e-mail i had sent out on WEDNESDAY about their preference. SO far only Patrick, Mandy, Stefan and Prima have told me about their preference.



2) I did a research/invesyigation on the following research pharmaceutical companies:

a-Ambion Inc.

b-Charles River Labs

c-Critical Outcome Technologies

d- E-Z-EM Canada Inc.

e- Genome Canada

f- i3 Canada Inc.

g- Ikaria Canada Inc.

h- Inimex Pharmaceuticals

i- Arc Pharma Canada Inc.

j- Dalto Pharma Services

k- Medicago Inc.

l- Neuroimage Inc.

m- Synbiosis

I e-mailed only 4 of the companies above because i want to spend as much time as i can on a company. I also have to confirm them with my team before sending them out so it takes time but i hope they respond back to us in a positive manner.


JAMIE

Signalling circuit construction and Response circuit preparation

See Jeremy's updates regarding luxPQ-luxOU construction from hereonin.

cIIambda and aiiA were transformed from registry plates into TOP10 cells for plasmid isolation and verification.


JEREMY

Constructing LuxPQ-LuxOU signaling circuit

Purpose: to construct LuxPQ-B0015-R0040-LuxOU-B0015 (hereafter PQ-B-R-OU-B) by inserting LuxPQ (AC) into B-R-OU-B (AK). Construction was performed by setting up a restriction digest by cutting the insert (LuxPQ) with EcoRI and SpeI and cutting the vector (B-R-OU-B in AK) with EcoRI and XbaI. After this restriction digest, phosphatase and ligation treatment was performed and the plasmid was subsequently transformed into TOP10 competent cells and plated overnight on LB+Kanamycin.


KATIE

Continuation of July 8th

I was able to complete scripts for three construction sites for the restriction digest activity that I planned out yesterday. The three construction sites will be used for creating a circuit from four parts: Promoter, RBS, terminator as well as a gene of the user’s choice. Currently it will only function for a general activity so I will have to modify it for specific missions. The construction sites consist of:

1. Single construction site for ligating two parts of the circuit together. These two parts must have been cut with the proper restriction enzymes to place one before the other ie. Promoter cannot be placed behind RBS.

2. Multiple construction site that works the same as the first but with two parts already together that must be connected to another part.

3. Multiple construction site with three pieces together already. There is also an option to ligate Promoter/RBS with Gene/Terminator, which can actually be considered a shortcut as long as users understand what they are doing.

One flaw in the activity is that you are only able to cut each piece once in the donor and recipient tubes, but I thought it would be unnecessarily tedious to cut at each step of construction once they have already succeeded in doing it once, but this can always be changed although I do not plan to in the upcoming week. It would involve possibly doubling the amount of comparisons within the donor and recipient tubes avatars may use to determine what they wish to cut. I also began to modify the recipient and donor tube scripts in order for them to cooperate with the three construction sites so they are no longer fully functional as I continue to change them. I have determined the names of the products an avatar may obtain from performing the activity so now I will have to create them and request they be given to inventory, which I hope to complete by next week and will be starting tomorrow.

I will most likely finish the restriction digest notecard in parallel with its corresponding activity and I will be sending these notecards to Mandy once again to look over and examine their validity, which I plan to have done by Monday (July 13). I was also able to construct the basic plates for streaking for the bacterial transformation activity.

I was also able to complete the script for the sequencing station as per Mandy’s request and it will now give any avatar who drops ‘Amplified Colicin E2’ into the sequencing object a notecard, which as of now does not contain any useful information. I will be adding various other amplified DNA products as objects to give back sequencing for on Friday, which may continue into next week.


KEVIN

The results of the restreaks of J13002 and GFP/RFP

The following is an image of the restreak:

Calgary 2009.07.10.I13502 E0040 J13002.png



From it, one can clearly see that RFP is glowing much brighter than the negative control, and that GFP is, although less obvious, also glowing.

No other lab work was performed on this day.


MANDY

Second Life Biobert

Today, we finished the prototype for ‘Biobert’, the lab helper robot. When clicked he can move and chat with people (using their names :D). He can also give instructions, note cards, and inventory like vectors. He also is the point where users can choose ‘lab missions’ to complete.

I finished designing/planning the intermediate lab mission level, which is PCR/Gel electrophoresis verification and then bacterial transformation of a circuit. I started designing the more difficult lab mission that involves the compilation of a biobricked circuit.

Biobert currently only responds to a couple phrases said to him by users. Tomorrow I plan to expand on both what he does and says (integrate him more in the lab, maybe have him give clues, etc.). Right now, he also likes to repeat himself a lot, which can get kind of annoying so I’m going to delete some of the scripting too.

As soon as I learn exactly how Katie’s scripted restriction digest works, I will be finishing the designing/planning of the more difficult lab mission, and then figure out what can be an easy one.

Wiki Reformatting

Today, I tried laying out the wiki more, and getting it ready for sponsors to see. NO SUCH LUCK, HOWEVER: here is what I was playing with, NOT on a wiki site: http://igemtest.blogspot.com (The purple is still uh…being debated). My css does not seem to combine with the wiki mark up, and Emily found that some teams used ‘templates’ with wiki markup to get around this problem, which I haven’t quite figured out how to do yet, but I’ve bookmarked some pages to read. THE WIKI pages have all been saved on Emily’s laptop and the pages online have been wiped in preparation for some trouble shooting (slowly adding elements and figuring out what isn’t working – why the formatting is off).

THE BLOG is filling up rather nicely, helped Prima upload her video and retagged/formatted the current posts (so they will show up if people search iGEM on blogspot).



PRIMA

Company contacts

I updated the gmail contact list. Sent a Thank you letter to Corning Life Sciences. Called Worley Parsons – the contact they gave me was apparently the wrong person. It was the HR person and she said she’ll find out who deals with sponsorship and get back to me. But I might just inquire and find out myself just in case she forgets. I’ve been calling company 2 for some time now… I’ll call him again tomorrow.

Sigma-Aldrich- called today but couldn’t get a hold of her so I left a message follow up tomorrow

Cayman Chemicals ..called…needs a final confirmation from their President follow up July 31

Followed up with numerous companies (including oil companies such as Shell and Husky) but they declined our proposal. I will continue to follow up and contact new companies.


STEFAN

Freebies

Most of today was spent traveling islands and the online Second Life marketplace XStreet in search of things to get for our sim. These included:

  • New textures
  • Rocks, coral and seaweed
  • Walkways
  • Particle effects


VICKI

Modelling meeting

Team MatLab met with Team Mathematica in order to better coordinate our efforts and ensure that we have something in place that will have an impact at the jamboree. More comprehensive notes can be found in Chinee’s notebook. We watched a simulation of what Afshin and Iman have come up with for membrane computing and discussed how to go about streamlining our work so that our models will actually have the potential to support each other. This would involve a thorough literature search to find relevant phosphorylation and reaction constants (and an analysis of the inherent assumptions). As well, we agreed to write up a set of rules/reactions so that a team member from the other modelling school of thought (or otherwise) can better follow the work that each modelling crew has done on screen.

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