Team:Calgary/21 July 2009

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* Prepared two 5 mL overnight cultures (LB broth) of Top 10 cells and XL Gold Ultracompetent cells.
* Prepared two 5 mL overnight cultures (LB broth) of Top 10 cells and XL Gold Ultracompetent cells.
* Helped the bioinformatics department (Bachelor of Health Sciences) take apart computers in the morning.
* Helped the bioinformatics department (Bachelor of Health Sciences) take apart computers in the morning.
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WIKI CODING HERE
 
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Sequencing
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Our sequencing came back and once again, it doesn't look like the B0015 terminator is present in the construct.  So we will go back to our most recent plates (from July 17th 2009) ad select different colonies and do verification on them.  So I set up a colony PCR with new colonies, following the protocol and the cycling conditions from from July 7th 2009.  We ran the PCR products on a 1% agarose gel with 1.0 kb+ DNA Ladder.  See gel photo below.
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[[Image:2009.07.21.J13002-LuxOD47E-B0015.jpg|350px]]
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*Analysis: Lanes 1-5 are J13002-LuxOD47E-B0015 trial 1 (with B0015 as the insert), lanes 6-10 are J13002-LuxOD47E-B0015 trial 2 (with J13002-LuxOD47E as the insert), lane 11 is a size control with J13002-LuxOD47E C3, lane 12 is another size control with BBk LuxOD47E and lane 13 is a negative control.
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*From this gel, we decided to prepare overnight cultures of colonies 5-8 in order to perform a verification digest and possibly send  a colony down for DNA sequencing.
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Marketing for July 21st 2009
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Today, I concentrated my energies at marketing our iGEM project and looking at the ethical aspect of our project. Here is what I did today:
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1)Helped in the Bio-info room till 11.15
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2) Called Bracco/E-Z-EM Canada and e-mailed him a sponsorship package
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3) Left a voicemail for Life Tech/Applied BioSystems.
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4) Talked to Dr Wolbring abt our Ethics Progress Via a webcam. Setup an appoinment for thursday at 10.00 am
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5) Read Ethics papers.
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6) Got an e-mail from Genome Canada; they said NO.
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Preparing for Competent Cells
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CaCl2 was prepared and sterilized.  Overnights of XL Gold and DH5a were made as well.
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Plasmid PCR to verify signaling circuit in AC plasmid
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Purpose: use PCR to verify the presence of PQ-B-R-OU-B in the psB1AC3 vector. A pTaq PCR was set up using BBK CP F/R primers using the following conditions: 94ºC for 3 minutes; 36X (94ºC for 30 seconds; 55ºC for 45 seconds; 72ºC for 6 min 30 sec); 72ºC for 10 minutes; held at 4ºC. The products were then run on a 0.8% agarose gel (see below). We can see that colonies 6 and 7 reveal the desired size of the construct (~6.0kb), however, the negative control lane shows two bands, when we want no bands. We must therefore repeat this PCR with colonies 6 and 7 to receive a clean negative control lane.
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[[Image:2009.07.21.PQ-B-R-OU-B-AC3-PCR-BBKCP.png|700px]]
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Blog Update
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WIKI CODING HERE
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I was able to make a video for the second life team for the blog. I finished editing it in the morning and it consisted of a very general overview of the scripting involved with what I have been doing in the virtual lab. I did not go into a lot of detail to prevent my video from going over ten minutes. I showed a little bit of the restriction digest and bacterial transformation activities for what I have so far.
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1. Plasmid Isolation
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I have isolated the <i>Pqrr4</i>+B0034 plasmids from yesterday's overnight cultures, and the purity and concentration of them were measured using nanodrop. They were pure enough to move on with.
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2. Restriction digest
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The isolated <i>Pqrr4</i>+B0034 plasmid was then cut with XbaI and PstI and ran on a 2% gel at 90V in order to verify the presence of the circuit. The following is an image of the gel:
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The lower bands of the colonies 1, 2, 4, 6, 8, 9, and 10 seem to be above the positive control bands, which is what was expected. Thus it is now ready for sequencing.
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Wiki Structure Completion
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WIKI CODING HERE
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All the pages we need are pretty much made/exist, so now it can be filled out.
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COMPLETED PAGES OF WIKI:
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*News (Campus Fair, all 3 AiF Meetings, all up/recoded, photos pending)
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*Synthetic Blogology (division of posts per team in each section still needs to be done, but the RSS feed of latest updates is there)
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*Gallery (also need to divide events and put on relevant news story pages)
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*Sponsors
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Icons will denote lab/second life/ human practices/ marketing / modelling sections of our project, providing a useful ‘guide’ around our wiki should people get lost in the many pages. Additionally, left side bars are mainly empty right now but will serve as quick indexes for each section. Icons will also link back to an overall site map which will make it easier to navigate.
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PAGES THAT NEED TO BE WORKED ON:
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*Main Pages for each section (esp reformatting patrick’s blog to fit our intro section for Second Life,  need to harass other team members for main intros for each project section)
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*Update pages for each section (taken from blog entries)
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Hotel search and Sponsors Continuation
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Today:
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All morning (pretty much) was spent helping with moving the computers in the Bio Inf. Lab.
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Here’s the real deal:
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I followed up with the Company 1 and they replied back saying that they’re unable to help. Also Company 3 and Company 3 have declined our offer.
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On a more positive note, I found GSK (GlaxoSmithKline) which is a  research-based pharmaceutical company devoted to developing innovative medicines and vaccines. I only found their phone number so I’ll give them a shout tomorrow and follow up with 4 other companies.
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I also finished writing and editing my email to Dr. Jay Ingram (Discovery Channel Co-host). Fahd, Jamie and Jeremy double checked it so I’ve attached it in this email. Dr. Jacob sent me Dr. Ingram’s wife’s email. They both know Dr. Jacob so I’ve mentioned him in the letter.
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I also searched up a few hotels which are not too far from MIT and have decent prices. I spoke to Thane about it and we were thinking of getting
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- And since the hotels are close, we could walk to MIT to avoid transportation costs. So far, we’ve managed to raise $3000 cash (excluding the lab reagents and equipment from sponsors)…so this will probably fly 6 students to Boston and back. This money came from first and second bake sales, and cash donations from sponsors. Accommodations will cost the 15 students  ± $1100 for the 4 nights. I haven't looked at rooms for facilitators so I can’t tell you much about it now.  In our next bake sale, our goal is to make around $500. :D The marketing team is trying their best to arrange meetings and getting sponsors.
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Tomorrow, I’ll call the other companies and send an email to Shawn Abbott (one of the Dragons) to set up a meeting with him to discuss iGEM sponsorship and if he can help us/give us advice. Once I set up a meeting, Jeremy and I plan to go visit him. Right now, the marketing team is reviewing the rough draft of the July newsletter which we hope to finalize by Friday and send out to companies early next week.
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Today was full of wonderful manual labour as you can probably tell
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Today was full of wonderful manual labour as you can probably tell from everyone's update. After that, I managed to read a Second Life ethics paper. I didn't think it was very good because it was poorly written and it seemed the person was not qualified to do it. However, I enjoyed the paper with the molecular orbitals. I think it is the same person that did the molecule rezzer as well. The paper showed how useful Second Life can be  to visually present something, which is excellent because synthetic biology is not very friendly to the naked eye. I also started to write the ethics blog post and put some thought into what to present on Friday.
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APEGGA article
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Carol and I started talking about how we’d approach it, but she was pretty busy in the lab so we didn’t make it too far. We’ll discuss it tomorrow and finish it by Aug 1, for sure. My preference would be to do a small profile of each engineer, where we discuss where we’re from, why we’re here and where we think we could go with synthetic biology. This would also include unifying paragraphs to start and finish the article, structured much like what I did for my showcase article for retiring teachers way way back in grade 12.
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Latest revision as of 23:19, 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 21, 2009


CAROL
Making Competent Cells

  • Prepared 500mL LB broth for making competent cells. Followed procedure that is outlined in the protocol page. Unfortunately, due to time constraints, we had to re-make the overnight cultures.
  • Prepared two 5 mL overnight cultures (LB broth) of Top 10 cells and XL Gold Ultracompetent cells.
  • Helped the bioinformatics department (Bachelor of Health Sciences) take apart computers in the morning.


EMILY

Sequencing

Our sequencing came back and once again, it doesn't look like the B0015 terminator is present in the construct. So we will go back to our most recent plates (from July 17th 2009) ad select different colonies and do verification on them. So I set up a colony PCR with new colonies, following the protocol and the cycling conditions from from July 7th 2009. We ran the PCR products on a 1% agarose gel with 1.0 kb+ DNA Ladder. See gel photo below.
2009.07.21.J13002-LuxOD47E-B0015.jpg

  • Analysis: Lanes 1-5 are J13002-LuxOD47E-B0015 trial 1 (with B0015 as the insert), lanes 6-10 are J13002-LuxOD47E-B0015 trial 2 (with J13002-LuxOD47E as the insert), lane 11 is a size control with J13002-LuxOD47E C3, lane 12 is another size control with BBk LuxOD47E and lane 13 is a negative control.
  • From this gel, we decided to prepare overnight cultures of colonies 5-8 in order to perform a verification digest and possibly send a colony down for DNA sequencing.


FAHD

Marketing for July 21st 2009

Today, I concentrated my energies at marketing our iGEM project and looking at the ethical aspect of our project. Here is what I did today:

1)Helped in the Bio-info room till 11.15

2) Called Bracco/E-Z-EM Canada and e-mailed him a sponsorship package

3) Left a voicemail for Life Tech/Applied BioSystems.

4) Talked to Dr Wolbring abt our Ethics Progress Via a webcam. Setup an appoinment for thursday at 10.00 am

5) Read Ethics papers.

6) Got an e-mail from Genome Canada; they said NO.


JAMIE

Preparing for Competent Cells

CaCl2 was prepared and sterilized. Overnights of XL Gold and DH5a were made as well.


JEREMY

Plasmid PCR to verify signaling circuit in AC plasmid

Purpose: use PCR to verify the presence of PQ-B-R-OU-B in the psB1AC3 vector. A pTaq PCR was set up using BBK CP F/R primers using the following conditions: 94ºC for 3 minutes; 36X (94ºC for 30 seconds; 55ºC for 45 seconds; 72ºC for 6 min 30 sec); 72ºC for 10 minutes; held at 4ºC. The products were then run on a 0.8% agarose gel (see below). We can see that colonies 6 and 7 reveal the desired size of the construct (~6.0kb), however, the negative control lane shows two bands, when we want no bands. We must therefore repeat this PCR with colonies 6 and 7 to receive a clean negative control lane.

2009.07.21.PQ-B-R-OU-B-AC3-PCR-BBKCP.png


KATIE

Blog Update

I was able to make a video for the second life team for the blog. I finished editing it in the morning and it consisted of a very general overview of the scripting involved with what I have been doing in the virtual lab. I did not go into a lot of detail to prevent my video from going over ten minutes. I showed a little bit of the restriction digest and bacterial transformation activities for what I have so far.


KEVIN

1. Plasmid Isolation

I have isolated the Pqrr4+B0034 plasmids from yesterday's overnight cultures, and the purity and concentration of them were measured using nanodrop. They were pure enough to move on with.

2. Restriction digest

The isolated Pqrr4+B0034 plasmid was then cut with XbaI and PstI and ran on a 2% gel at 90V in order to verify the presence of the circuit. The following is an image of the gel:
Calgary 2009.07.21.Pqrr4+B0034 edited.png

The lower bands of the colonies 1, 2, 4, 6, 8, 9, and 10 seem to be above the positive control bands, which is what was expected. Thus it is now ready for sequencing.


MANDY

Wiki Structure Completion

All the pages we need are pretty much made/exist, so now it can be filled out.

COMPLETED PAGES OF WIKI:

  • News (Campus Fair, all 3 AiF Meetings, all up/recoded, photos pending)
  • Synthetic Blogology (division of posts per team in each section still needs to be done, but the RSS feed of latest updates is there)
  • Gallery (also need to divide events and put on relevant news story pages)
  • Sponsors
  • MOST of team (waiting for descriptions)
  • 50% of main page :icons and other things all coded/made, still need to clean them up
  • Menu template links SHOULD be fixed.



Icons will denote lab/second life/ human practices/ marketing / modelling sections of our project, providing a useful ‘guide’ around our wiki should people get lost in the many pages. Additionally, left side bars are mainly empty right now but will serve as quick indexes for each section. Icons will also link back to an overall site map which will make it easier to navigate.

PAGES THAT NEED TO BE WORKED ON:

  • Site Map
  • Main Page
  • Main Pages for each section (esp reformatting patrick’s blog to fit our intro section for Second Life, need to harass other team members for main intros for each project section)
  • Update pages for each section (taken from blog entries)



PRIMA

Hotel search and Sponsors Continuation

Today:

All morning (pretty much) was spent helping with moving the computers in the Bio Inf. Lab. Here’s the real deal:

I followed up with the Company 1 and they replied back saying that they’re unable to help. Also Company 3 and Company 3 have declined our offer.

On a more positive note, I found GSK (GlaxoSmithKline) which is a research-based pharmaceutical company devoted to developing innovative medicines and vaccines. I only found their phone number so I’ll give them a shout tomorrow and follow up with 4 other companies.

I also finished writing and editing my email to Dr. Jay Ingram (Discovery Channel Co-host). Fahd, Jamie and Jeremy double checked it so I’ve attached it in this email. Dr. Jacob sent me Dr. Ingram’s wife’s email. They both know Dr. Jacob so I’ve mentioned him in the letter.

I also searched up a few hotels which are not too far from MIT and have decent prices. I spoke to Thane about it and we were thinking of getting <centre>

- And since the hotels are close, we could walk to MIT to avoid transportation costs. So far, we’ve managed to raise $3000 cash (excluding the lab reagents and equipment from sponsors)…so this will probably fly 6 students to Boston and back. This money came from first and second bake sales, and cash donations from sponsors. Accommodations will cost the 15 students ± $1100 for the 4 nights. I haven't looked at rooms for facilitators so I can’t tell you much about it now. In our next bake sale, our goal is to make around $500. :D The marketing team is trying their best to arrange meetings and getting sponsors. </centre>

Tomorrow, I’ll call the other companies and send an email to Shawn Abbott (one of the Dragons) to set up a meeting with him to discuss iGEM sponsorship and if he can help us/give us advice. Once I set up a meeting, Jeremy and I plan to go visit him. Right now, the marketing team is reviewing the rough draft of the July newsletter which we hope to finalize by Friday and send out to companies early next week.


STEFAN

Meeting at Christian's lab

Today was full of wonderful manual labour as you can probably tell from everyone's update. After that, I managed to read a Second Life ethics paper. I didn't think it was very good because it was poorly written and it seemed the person was not qualified to do it. However, I enjoyed the paper with the molecular orbitals. I think it is the same person that did the molecule rezzer as well. The paper showed how useful Second Life can be to visually present something, which is excellent because synthetic biology is not very friendly to the naked eye. I also started to write the ethics blog post and put some thought into what to present on Friday.


VICKI

APEGGA article

Carol and I started talking about how we’d approach it, but she was pretty busy in the lab so we didn’t make it too far. We’ll discuss it tomorrow and finish it by Aug 1, for sure. My preference would be to do a small profile of each engineer, where we discuss where we’re from, why we’re here and where we think we could go with synthetic biology. This would also include unifying paragraphs to start and finish the article, structured much like what I did for my showcase article for retiring teachers way way back in grade 12.

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