Team:Calgary/21 May 2009

From 2009.igem.org

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MAY 21, 2009
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* Prepared 0.7% Agarose gel
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*From the results, there is contamination in the negative control, but it did amplify the 6KB <i>LUXCDABE</i>. The large bands is a result of loading too much DNA.
*From the results, there is contamination in the negative control, but it did amplify the 6KB <i>LUXCDABE</i>. The large bands is a result of loading too much DNA.
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Visualization of PCR Product
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WIKI CODING HERE
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*This morning we had WHMIS training on Main Campus.
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*This afternoon our lab team members visualized our PCR from yesterday.  We learned how to prepare agarose gels, load gels and visualize them in the G-Box.  See photo of gel below.  Lanes 1-4 is Kevin's Pqrr4, lane 5 is Kevin's negative control, lanes 6-7 are left blank, lane 8 is a negative control and lanes 9-12 are LuxOD47E colony 2.
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[[Image:2009_05_21Pqrr4_LuxOD47E.jpeg]]
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*Analysis: It is good that the negative control is clean as this indicates that there is no contamination.  The presence of bands also indicates that we were able to amplify something, also good!  It looks like LuxOD47E is likely there, as we see band around the expected size of 1.4 kb, however the lanes appear to be overloaded with DNA, so it is not conclusive.  The bands are not very clean, so we will try this PCR gain next week.
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WHMIS TRAINING and First Sponsorship May 21st 2009
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WIKI CODING HERE
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We had our WHMIS training today at the University of Calgary Main Campus. It is a required course to take if we are working in a lab. In the afternoon, I was greeted with some great news: NEB (New England BioLabs) Canada had agreed to sponsor us with lab equipment and reagents. It was our first ever sponsorship. It was also an exciting moment for our entire team as it would save us loads and loads of money because our WetLab team uses a lot of reagents from NEB Canada.
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This afternoon our lab team members ran a gel from yesterday's PCR.  We learned how to prepare agarose gels, load gels and visualize them in the G-Box. The gel that we collectively ran did have a clean negative control; however, we definitely overloaded DNA into the wells of the gel. We learned what to expect when loading gels, and that sometimes you may not even get any bands on the gel. I'm quite excited to break off into our respective mini-projects and start practicing and performing all these lab techniques.
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Planning PCR Activity
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Started to make an outline of what I will be required to do for PCR machine:
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* Need some way to add items to the machine to make it more interactive then just telling the machine what is required
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* Looked through the lsl wiki and found llAllowInventoryDrop, which is a function that seems to allow for addition of objects to another as long as it is set to true
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* If anything can be added then I need to have a way to get rid of everything that is added
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* I will need some way to incorporate other information besides materials, such as temperatures and times for each cycle
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The whole morning was spent learning about safety.
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In the afternoon, we brainstormed about our team logo.
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Verification of amplification of <i>luxCDABE</i> from polymerase chain reaction (PCR)
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* Prepared 0.7% Agarose gel
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*From the results, there is contamination in the negative control, but it did amplify the 6KB <i>LUXCDABE</i>. The large bands is a result of loading too much DNA.
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Today, most of the team had WHMIS training on main campus. The afternoon was spent brainstorming potential ideas for an iGEM Calgary team logo (and possibly mascot). Ideas were bounced around in order to prepare some prototypes for a future logo meeting.
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Early Development
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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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First came up with the polymer linking system that I would eventually use without too much modification: each piece of DNA knows the name of the next piece in the polymer. Figuring out what to use as that 'name', and how to store it, would be a much longer process. I noticed very quickly that the internal identifier assigned by SL to each object changed every time the object was copied from the user's inventory, so would not be suitable for tracking polymer structure over time.
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Began to notice how important a consistent scheme for inter-object communication would be. Ultimately, the objects that make up the Biobrick simulator would send something like 70 distinct message types, a number which is only set to increase. In the case of the HUD, there would be more than a hundred possible destination objects!
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Decided that as a first working goal, I would try to implement the TetR operon, something that as of this writing (August 20 2009) I have not yet fully completed!
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Latest revision as of 07:44, 18 October 2009

University of Calgary

UNIVERSITY OF CALGARY



THIS MONTH

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]


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]



MAY 21, 2009


CAROL

Verification of amplification of luxCDABE from polymerase chain reaction (PCR)

  • Prepared 0.7% Agarose gel
  • Used orange G dye
  • Ran gel at 90V for 90 minutes

RESULTS: LuxCDABEPCR.png

  • From the results, there is contamination in the negative control, but it did amplify the 6KB LUXCDABE. The large bands is a result of loading too much DNA.


EMILY

Visualization of PCR Product

  • This morning we had WHMIS training on Main Campus.
  • This afternoon our lab team members visualized our PCR from yesterday. We learned how to prepare agarose gels, load gels and visualize them in the G-Box. See photo of gel below. Lanes 1-4 is Kevin's Pqrr4, lane 5 is Kevin's negative control, lanes 6-7 are left blank, lane 8 is a negative control and lanes 9-12 are LuxOD47E colony 2.

File:2009 05 21Pqrr4 LuxOD47E.jpeg

  • Analysis: It is good that the negative control is clean as this indicates that there is no contamination. The presence of bands also indicates that we were able to amplify something, also good! It looks like LuxOD47E is likely there, as we see band around the expected size of 1.4 kb, however the lanes appear to be overloaded with DNA, so it is not conclusive. The bands are not very clean, so we will try this PCR gain next week.


FAHD

WHMIS TRAINING and First Sponsorship May 21st 2009

We had our WHMIS training today at the University of Calgary Main Campus. It is a required course to take if we are working in a lab. In the afternoon, I was greeted with some great news: NEB (New England BioLabs) Canada had agreed to sponsor us with lab equipment and reagents. It was our first ever sponsorship. It was also an exciting moment for our entire team as it would save us loads and loads of money because our WetLab team uses a lot of reagents from NEB Canada.


JEREMY

Continuation of Training in the Labs

This afternoon our lab team members ran a gel from yesterday's PCR. We learned how to prepare agarose gels, load gels and visualize them in the G-Box. The gel that we collectively ran did have a clean negative control; however, we definitely overloaded DNA into the wells of the gel. We learned what to expect when loading gels, and that sometimes you may not even get any bands on the gel. I'm quite excited to break off into our respective mini-projects and start practicing and performing all these lab techniques.


KATIE

Planning PCR Activity

Started to make an outline of what I will be required to do for PCR machine:

  • Need some way to add items to the machine to make it more interactive then just telling the machine what is required
  • Looked through the lsl wiki and found llAllowInventoryDrop, which is a function that seems to allow for addition of objects to another as long as it is set to true
  • If anything can be added then I need to have a way to get rid of everything that is added
  • I will need some way to incorporate other information besides materials, such as temperatures and times for each cycle


KEVIN

WHMIS traning

The whole morning was spent learning about safety.

Logo

In the afternoon, we brainstormed about our team logo.

MANDY

General Team Affairs

Today, most of the team had WHMIS training on main campus. The afternoon was spent brainstorming potential ideas for an iGEM Calgary team logo (and possibly mascot). Ideas were bounced around in order to prepare some prototypes for a future logo meeting.


PATRICK

Early Development

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

First came up with the polymer linking system that I would eventually use without too much modification: each piece of DNA knows the name of the next piece in the polymer. Figuring out what to use as that 'name', and how to store it, would be a much longer process. I noticed very quickly that the internal identifier assigned by SL to each object changed every time the object was copied from the user's inventory, so would not be suitable for tracking polymer structure over time.

Began to notice how important a consistent scheme for inter-object communication would be. Ultimately, the objects that make up the Biobrick simulator would send something like 70 distinct message types, a number which is only set to increase. In the case of the HUD, there would be more than a hundred possible destination objects!

Decided that as a first working goal, I would try to implement the TetR operon, something that as of this writing (August 20 2009) I have not yet fully completed!


PRIMA

Marketing

We had the WHMIS training on main campus all morning (9:00am - 12:00 noon).

In the afternoon, I continued my follow-ups with companies via email. Jeremy, Vicki and I wrote up Thank You letters to the Dragons from Dragon's Den for taking the time out of their busy schedules to watch our marketing pitches, provide feedback, advising us on marketing and business initiatives and way to sell our project.

I researched a few more companies that I had found, wrote up emails and updated the Gmail marketing document.

Retrieved from "http://2009.igem.org/Team:Calgary/21_May_2009"