Team:Calgary/24 July 2009

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* Spent morning discussing ethics.
* Spent morning discussing ethics.
* Lab clean up
* Lab clean up
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* Lab Cleanup in the afternoon
* Lab Cleanup in the afternoon
* Worked on our ethics rough draft.  I read over some ethics reports form last year (Heidelberg and TUDelft) to get some ideas for format/ structure. I re-wrote the introduction that we used for our last ethics assignment for AIF to have a better explanation of synthetic biology and our project in general.  Fahd and I divided up sections to look at and add to this weekend (Economics and Legal for me and Social and environmental for Fahd) and then we will send it to Stefan to tie things together and make it more unified.  We made a list of few papers that will be helpful in doing this.  I also typed up some of my lab notebook to be used on the Wiki.   
* Worked on our ethics rough draft.  I read over some ethics reports form last year (Heidelberg and TUDelft) to get some ideas for format/ structure. I re-wrote the introduction that we used for our last ethics assignment for AIF to have a better explanation of synthetic biology and our project in general.  Fahd and I divided up sections to look at and add to this weekend (Economics and Legal for me and Social and environmental for Fahd) and then we will send it to Stefan to tie things together and make it more unified.  We made a list of few papers that will be helpful in doing this.  I also typed up some of my lab notebook to be used on the Wiki.   
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Marketing and Ethics 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) I called Edward Short at Charles River Labs. He is the HR director. Even though they said no, I am still on his case for contacts and sone money. I left a voicemail for him. Will call him on monday
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2) Called Julie Edwards at Boehringer Ingleheim Canada. She ws away from her office so i left her a voicemail. Will call her on Monday
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3) I called Mike Barr at Critical Outcome technologies. He is the Community Relations officer. He said that to call him on Wednesday July 29th.
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4) I called Heather Bourdeu at life technologies. She is the community relations officer. Left her a voicemail and i will call her on monday.
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5) I called Andrea Greene at EMD Bio-Chemicals. She is the Marketing/communications officer. Left her a voicemail and I will call her on monday.
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6) I called Nic Milligan at Teck Coal Ltd. He is the community relations officer. Left him a voicemail and I will call her on monday. 
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7) I called Cindy Bizon at ALPAC. She is the community relations officer. Left her a voicemail and I will call her on monday.
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8) I called Leon Zupan at Enbridge Pipelines Inc. He is the Director of Engineering and Development. Left him a voicemail and I will call him on monday.
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9) I called Ron Hall at Focus Corporation. He is the Branch Manager. He wants our sponsorship packgae so I e-mailed him one. He is also an Alumini.
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10) I called Dr Adolfo Cotter at Neuroimage Inc. for Contacts and Advice. Since his company is new, he will not be able to help us but he told nme to keep him in mind for next year and keep him updated. His advice was nothing new and was familiar to Derek Gratz's.
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11) Helped clean the Lab.
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12) Attended the meeting in the morning
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Review:
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So, after almost 3 months working on this model, we have the following components:
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- We have implemented the notations of rules, so that we can define various interaction rules for our system.
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- We have functions that take in an interaction rule and apply it to the system.
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- Gillespie's algorithm is implemented. As a quick review, this algorithm provides randomness for biological systems and also determines random time for each interaction.
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- We have defined cell life cycle for the simulated cells and now they divide after specific amount of time.
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- We can extract different kind of results such as concentration graphs, and matrices, and rule charts (I will attach a figure of available results).
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These components constitute the main framework of the system. Now we need a tutorial that helps biologists to understand this model. As a result, we have designed an animated tutorial which teaches the biological details of the system as well as the notations used to implement this system in Mathematica. One could look at these animations and realize how this model is related to the actual biological cascades of our circuits.
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This figure demonstrates a view of this animation.
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The biological system goes through two main cascades. Each cascade has its own interactions and agents involved. A nice interface has provided for users to watch the animation of the cascades separately in respect to the interaction occurring. The following figure shows this interface:
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Plasmid switch moving LuxPQ from the AK plasmid to the AC plasmid
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Purpose: to move LuxPQ (insert) into the AC plasmid (vector) so that we can subsequently move B-R-OU-B into this plasmid. A restriction digest was set up by cutting the insert and vector with XbaI and PstI. After this restriction digest, phosphotase and ligation treatment was performed and the plasmid was subsequently transformed into TOP10 competent cells and plated overnight on LB+Chlor.
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In order to construct the PQ-B-R-OU-B circuit, another approach was used in which the LuxPQ in AK is inserted into B-R-OU-B in AC. This was set up by cutting the insert with EcoRI and SpeI and by cutting the recipient with EcoRI and XbaI. Again, 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+Chlor.
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The note cards for the ligation activity for molecular cloning have been created, consisting of parts from the registry:
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* J13002 – promoter + rbs
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* B0015 - terminator
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I also made up a note card for a gene that was selected for one of the missions in the lab (AFP Gene) as well as note cards to give for each step of construction. Now I am in the process of renaming everything for restriction digest, phosphatase treatment and construction to work using these note cards and creating the substrings within the master note cards that I will need to compare with the note cards dropped into each object used for construction.
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I also created a DNA polymerase for the DNA replication display that will move in a straight line and nucleotides will appear behind it as it moves. I also made a backbone for the strand that I was trying to create, but the backbone attached to each individual nucleotide does not line up perfectly together yet even though they are the exact same size so I will have to go back to the polymerase script to change the position that the nucleotides are rezzed at. I am aware that nucleotides are not produced by the DNA polymerase, but it is the only way to get the nucleotides to the position I want easily and it is hard to tell that they appear out of the DNA polymerase anyway. I am working on setting the position of the polymerase to a section on the leading strand of DNA that I also finished constructing today. I have also made helicase and DNA ligase, which presently do not do anything, but I will start working on the other enzyme’s functionality once I get the DNA polymerase running smoothly.
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1. Sequencing
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After today’s meeting, I have sent Pqrr4+I13500 for sequencing with BBK CP F/R sequencing primers to verify if it is actually in the plasmid. After the verification, I will make it competent again so that Emily can test her mutants. It has been sent before 1pm, so I am hoping to get it by Monday.
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2. Lab clean up
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After lunch, we had a huge clean up time, as our lab was getting dirtier every day.
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Fixing DNA Extraction and Further Planning in Second Life
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Today, tested out the DNA extraction activity I did last week. It worked up until the last few steps, where I think I have my parts miscommunicating with each other and the centrifuge near the end, so I am in the process of working backwards to check all my scripts and change this. After this, I can make start on biobrick PCR, using the PCR that Katie has already scripted. This will allow us to work on the ‘restriction digest and ligation’ of the circuit that is required for the third lab mission. Once this is finished, we will evaluate if we have time to do cell culture for the first lab mission. Either way, the first mission has bacterial transformation which has been scripted in the form of a 10 question quiz by Katie, which is easier to understand than the equipment used in the more difficult levels, allowing the user to get used to dialogue box controls.
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Once the lab missions are finished, we will clone the entire thing into the green island and make everything green. After the labs are complete, we will begin working on the base of Patrick’s biobrick simulator. Katie and I have a few notecards already written up on the basics, we just need to organize it in an easy to understand format with something creative that is more interesting than just reading notecards. Katie is working on having a moving ‘diagrams’ eg of DNA polymerase, etc. I am going to figure out how to embed streaming video in Second Life (maybe show a moving visualization of transcription).
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We had a mini-meeting to list out all the commands and controls we thought users needed to know in the labs and the biobrick simulator so that Stefan could design some activities around teaching those. We also began to layout how we wanted the path in Synthetic Kingdom to work. Today I spent 5 minutes staring at Katie’s DNA Polymerase, which is SO CUTE. <3
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Working While Dodging Meetings
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Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.
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Unlike the title, most of today was spent in meetings, so little work on my corner of the project got accomplished as a result. But now I understand everyone else's work a little better!
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Moving objects around in three dimensions is neat, but it can be a bit of a pain in second life. I worked on changing the way the objects bind and unbind so that they mostly stay in the same plane, which makes them much easier to deal with.
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I also started planning what elements I would show when my turn to do a [http://igemcalgary.blogspot.com/2009/07/patrick-and-biobrick-simulator.html video blog] came around.
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Marketing & RD of PQ-B-R-OU-B
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Today:
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In Marketing:
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I called Courtyard Marriot Hotel in Boston. They offered 279/night with 2 queen beds per room. I wanted to know if they offer any quotes for students but apparently Marriot hotels, in general, don’t offer any sort of quotes/discounts.
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I mailed the sponsorship pkg to GSK (GlaxoSmithKline) just as the Charitable Donations lady asked me to. Although she didn’t think iGEM’s goal this year matches the company’s objectives but she’s still willing to have a look at it.
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I didn’t call any companies today because I’ve been continuously calling them for the past few weeks. I’ll do it Monday though.
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Company 1’s donation committee reviewed our pkg and said that since that company does not have a presence in Calgary and they only support communities where they have operations so they declined our proposal. I sent her a thank you letter and asked for contacts.
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In lab:
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(shadowing Jeremy) I made a 0.7% agarose gel for restriction digest of Colony 6 and colony 7. (we took C6 +7 from a plasmid PCR that was done earlier by Jeremy to verify the presence of LuxPQ-B-R-OU-B in AC plasmid. C6 +7 looked the most accurate after Jeremy ran it on a gel so we used it for the restriction digest today. )
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The purpose of this restriction digest was to verify the size of the PQ-B-R-OU-B. He let me do almost everything on my own while he was there.  After we ran it on a gel, wells 2 and 4 (cut) was blank but the wells 3 and 5 (uncut) was clearly visible. We assumed there must’ve been a problem with the RD perhaps so we redid everything again. I made the gel again, etc. Yesterday, Jeremy did a RD of luxPQ and ccdb and left it overnight. Today we did a plasmid switch to transfer PQ  from AK to AC. We antartic phosphatased it and ligated it, then we did a transformation to transfer PQ plasmid into top 10 cells. Finally we plated it on Chlroramphenical plates and left it overnight.
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The rest of the time was spent in the ethics meeting this morning and major lab clean up in the afternoon.
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Bringing credibility to my introduction
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I found 4 papers that would be really useful: 2 that describe the AI-2 signalling pathway (Chen et al, 2008; Bassler et al, 1994); 1 that describes the AHL signalling pathway in depth (Cao et al, 1989); and some justification for why we’d bring in AI-2 in addition to AHL in that AI-2 is much more prevalent in nature, which should make it more versatile in its potential applications (Rasmussen, 2006).
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Latest revision as of 23:30, 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 24, 2009


CAROL

Team Meeting and Lab Clean Up

  • Spent morning discussing ethics.
  • Lab clean up


EMILY

Team Meeting, Lab Cleanup and Ethics

  • Lab Meeting: Discussed Ethics Conference and paper
  • Lab Cleanup in the afternoon
  • Worked on our ethics rough draft. I read over some ethics reports form last year (Heidelberg and TUDelft) to get some ideas for format/ structure. I re-wrote the introduction that we used for our last ethics assignment for AIF to have a better explanation of synthetic biology and our project in general. Fahd and I divided up sections to look at and add to this weekend (Economics and Legal for me and Social and environmental for Fahd) and then we will send it to Stefan to tie things together and make it more unified. We made a list of few papers that will be helpful in doing this. I also typed up some of my lab notebook to be used on the Wiki.


FAHD

Marketing and Ethics 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) I called Edward Short at Charles River Labs. He is the HR director. Even though they said no, I am still on his case for contacts and sone money. I left a voicemail for him. Will call him on monday

2) Called Julie Edwards at Boehringer Ingleheim Canada. She ws away from her office so i left her a voicemail. Will call her on Monday

3) I called Mike Barr at Critical Outcome technologies. He is the Community Relations officer. He said that to call him on Wednesday July 29th.

4) I called Heather Bourdeu at life technologies. She is the community relations officer. Left her a voicemail and i will call her on monday.

5) I called Andrea Greene at EMD Bio-Chemicals. She is the Marketing/communications officer. Left her a voicemail and I will call her on monday.

6) I called Nic Milligan at Teck Coal Ltd. He is the community relations officer. Left him a voicemail and I will call her on monday.

7) I called Cindy Bizon at ALPAC. She is the community relations officer. Left her a voicemail and I will call her on monday.

8) I called Leon Zupan at Enbridge Pipelines Inc. He is the Director of Engineering and Development. Left him a voicemail and I will call him on monday.

9) I called Ron Hall at Focus Corporation. He is the Branch Manager. He wants our sponsorship packgae so I e-mailed him one. He is also an Alumini.

10) I called Dr Adolfo Cotter at Neuroimage Inc. for Contacts and Advice. Since his company is new, he will not be able to help us but he told nme to keep him in mind for next year and keep him updated. His advice was nothing new and was familiar to Derek Gratz's.

11) Helped clean the Lab.

12) Attended the meeting in the morning


IMAN

Review:

So, after almost 3 months working on this model, we have the following components: - We have implemented the notations of rules, so that we can define various interaction rules for our system.

- We have functions that take in an interaction rule and apply it to the system.

- Gillespie's algorithm is implemented. As a quick review, this algorithm provides randomness for biological systems and also determines random time for each interaction.

- We have defined cell life cycle for the simulated cells and now they divide after specific amount of time.

- We can extract different kind of results such as concentration graphs, and matrices, and rule charts (I will attach a figure of available results).

These components constitute the main framework of the system. Now we need a tutorial that helps biologists to understand this model. As a result, we have designed an animated tutorial which teaches the biological details of the system as well as the notations used to implement this system in Mathematica. One could look at these animations and realize how this model is related to the actual biological cascades of our circuits.

ObjectsNames.png

This figure demonstrates a view of this animation.

The biological system goes through two main cascades. Each cascade has its own interactions and agents involved. A nice interface has provided for users to watch the animation of the cascades separately in respect to the interaction occurring. The following figure shows this interface:

Tutorial.png


JEREMY

Plasmid switch moving LuxPQ from the AK plasmid to the AC plasmid

Purpose: to move LuxPQ (insert) into the AC plasmid (vector) so that we can subsequently move B-R-OU-B into this plasmid. A restriction digest was set up by cutting the insert and vector with XbaI and PstI. After this restriction digest, phosphotase and ligation treatment was performed and the plasmid was subsequently transformed into TOP10 competent cells and plated overnight on LB+Chlor.
In order to construct the PQ-B-R-OU-B circuit, another approach was used in which the LuxPQ in AK is inserted into B-R-OU-B in AC. This was set up by cutting the insert with EcoRI and SpeI and by cutting the recipient with EcoRI and XbaI. Again, 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+Chlor.


KATIE

Notecards

The note cards for the ligation activity for molecular cloning have been created, consisting of parts from the registry:

  • J13002 – promoter + rbs
  • B0015 - terminator

I also made up a note card for a gene that was selected for one of the missions in the lab (AFP Gene) as well as note cards to give for each step of construction. Now I am in the process of renaming everything for restriction digest, phosphatase treatment and construction to work using these note cards and creating the substrings within the master note cards that I will need to compare with the note cards dropped into each object used for construction.

I also created a DNA polymerase for the DNA replication display that will move in a straight line and nucleotides will appear behind it as it moves. I also made a backbone for the strand that I was trying to create, but the backbone attached to each individual nucleotide does not line up perfectly together yet even though they are the exact same size so I will have to go back to the polymerase script to change the position that the nucleotides are rezzed at. I am aware that nucleotides are not produced by the DNA polymerase, but it is the only way to get the nucleotides to the position I want easily and it is hard to tell that they appear out of the DNA polymerase anyway. I am working on setting the position of the polymerase to a section on the leading strand of DNA that I also finished constructing today. I have also made helicase and DNA ligase, which presently do not do anything, but I will start working on the other enzyme’s functionality once I get the DNA polymerase running smoothly.


KEVIN

1. Sequencing

After today’s meeting, I have sent Pqrr4+I13500 for sequencing with BBK CP F/R sequencing primers to verify if it is actually in the plasmid. After the verification, I will make it competent again so that Emily can test her mutants. It has been sent before 1pm, so I am hoping to get it by Monday.


2. Lab clean up

After lunch, we had a huge clean up time, as our lab was getting dirtier every day.


MANDY

Fixing DNA Extraction and Further Planning in Second Life

Today, tested out the DNA extraction activity I did last week. It worked up until the last few steps, where I think I have my parts miscommunicating with each other and the centrifuge near the end, so I am in the process of working backwards to check all my scripts and change this. After this, I can make start on biobrick PCR, using the PCR that Katie has already scripted. This will allow us to work on the ‘restriction digest and ligation’ of the circuit that is required for the third lab mission. Once this is finished, we will evaluate if we have time to do cell culture for the first lab mission. Either way, the first mission has bacterial transformation which has been scripted in the form of a 10 question quiz by Katie, which is easier to understand than the equipment used in the more difficult levels, allowing the user to get used to dialogue box controls.

Once the lab missions are finished, we will clone the entire thing into the green island and make everything green. After the labs are complete, we will begin working on the base of Patrick’s biobrick simulator. Katie and I have a few notecards already written up on the basics, we just need to organize it in an easy to understand format with something creative that is more interesting than just reading notecards. Katie is working on having a moving ‘diagrams’ eg of DNA polymerase, etc. I am going to figure out how to embed streaming video in Second Life (maybe show a moving visualization of transcription).

We had a mini-meeting to list out all the commands and controls we thought users needed to know in the labs and the biobrick simulator so that Stefan could design some activities around teaching those. We also began to layout how we wanted the path in Synthetic Kingdom to work. Today I spent 5 minutes staring at Katie’s DNA Polymerase, which is SO CUTE. <3



PATRICK

Working While Dodging Meetings

Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.

Unlike the title, most of today was spent in meetings, so little work on my corner of the project got accomplished as a result. But now I understand everyone else's work a little better!

Moving objects around in three dimensions is neat, but it can be a bit of a pain in second life. I worked on changing the way the objects bind and unbind so that they mostly stay in the same plane, which makes them much easier to deal with.

I also started planning what elements I would show when my turn to do a [http://igemcalgary.blogspot.com/2009/07/patrick-and-biobrick-simulator.html video blog] came around.


PRIMA

Marketing & RD of PQ-B-R-OU-B

Today: In Marketing: I called Courtyard Marriot Hotel in Boston. They offered 279/night with 2 queen beds per room. I wanted to know if they offer any quotes for students but apparently Marriot hotels, in general, don’t offer any sort of quotes/discounts.

I mailed the sponsorship pkg to GSK (GlaxoSmithKline) just as the Charitable Donations lady asked me to. Although she didn’t think iGEM’s goal this year matches the company’s objectives but she’s still willing to have a look at it. I didn’t call any companies today because I’ve been continuously calling them for the past few weeks. I’ll do it Monday though.

Company 1’s donation committee reviewed our pkg and said that since that company does not have a presence in Calgary and they only support communities where they have operations so they declined our proposal. I sent her a thank you letter and asked for contacts.

In lab: (shadowing Jeremy) I made a 0.7% agarose gel for restriction digest of Colony 6 and colony 7. (we took C6 +7 from a plasmid PCR that was done earlier by Jeremy to verify the presence of LuxPQ-B-R-OU-B in AC plasmid. C6 +7 looked the most accurate after Jeremy ran it on a gel so we used it for the restriction digest today. )

The purpose of this restriction digest was to verify the size of the PQ-B-R-OU-B. He let me do almost everything on my own while he was there. After we ran it on a gel, wells 2 and 4 (cut) was blank but the wells 3 and 5 (uncut) was clearly visible. We assumed there must’ve been a problem with the RD perhaps so we redid everything again. I made the gel again, etc. Yesterday, Jeremy did a RD of luxPQ and ccdb and left it overnight. Today we did a plasmid switch to transfer PQ from AK to AC. We antartic phosphatased it and ligated it, then we did a transformation to transfer PQ plasmid into top 10 cells. Finally we plated it on Chlroramphenical plates and left it overnight. The rest of the time was spent in the ethics meeting this morning and major lab clean up in the afternoon.


STEFAN

Decisions, Decisions

Today was mostly meeting...

BUT our team decided on a bunch of Second Life stuff afterward. The most important part was deciding what to teach people when they first come to our island. In particular: flying, teleporting, opening your own and other object inventories, and manipulating objects. Some of these would be taught on the starting island, and others will be taught in the Synthetic Kingdom (for practice). For example, you click on a jellyfish to receive GFP and then open the inventory of a bacteria, put it in, and then the bacteria glows. Speaking of that wacky place, we brainstormed some rough ways to structure it. I think it is still a good idea to have all the bacteria floating around to give it a sense of awe, however, it could benefit from a path. This would make it very similar to a zoo exhibition. The path would preferably be lighted for maximum awesomeness and each "station" would hold a different engineered bacteria. There would also be signs pointing the way and a little notecard giver that would give you more information.

This weekend will spent on the paper. Emily and Fahd were working on it today and I'll complete it on Sunday.


VICKI

Bringing credibility to my introduction

I found 4 papers that would be really useful: 2 that describe the AI-2 signalling pathway (Chen et al, 2008; Bassler et al, 1994); 1 that describes the AHL signalling pathway in depth (Cao et al, 1989); and some justification for why we’d bring in AI-2 in addition to AHL in that AI-2 is much more prevalent in nature, which should make it more versatile in its potential applications (Rasmussen, 2006).

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