Team:Calgary/3 July 2009

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Colony PCR
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* plates resulted in two colonies and a colony PCR was initiated. After the PCR was completed, we ran the product on a 0.6% agarose gel but no bands appeared suggesting that colonies did not uptake plasmid that had the gene of interest ligated to it.
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EMILY
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Team Presentations
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Today we had our team presentations. I presented on behalf of the Human Practices aspect of our project.
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DIVISION
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As it was mentioned, division function gets an environment as its input. Then it looks at the elements existing in the cells. Those elements that should be doubled before the divisions (like Qrr4 promoter, RNA polymerase, LuxPQ and etc) are doubled and those elements that should be equally divided between new cells (like AI2, LuxU.p, LuxO.p, etc) are divided between cells. For those elements that are divided between new cells, it is not 100% that each new cell gets an equal amount of each one. There is a random generator function which produces a number between 1.90 and 2.10, and this number is used to divide the elements between the cells. Each rule has a label that determines this rule belongs to which cell. When division occurs, rules of the new cells should be labelled. Another challenge is to label all the rules of all the new existing cells. Moreover, we need to determine a time period as life cycle for each generation of the cells. We used the time that Gillespie’s algorithm assigns to the system for this purpose. At this stage, we have added an important aspect of “emergent properties” to our bacteria population by adding division to it.
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Once again, two meetings this week. One on Thursday with Lindsay project, and the other one on Friday with iGEM.
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JAMIE
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Verification of LuxPQ into psB1AC3 construction
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Purpose: to verify the presence of LuxPQ into psB1AC3 by colony PCR; to isolate plasmid; to send isolated plasmid for sequencing. A pTaq colony PCR was set up using the following sets of forward and reverse primers: LuxPQ and BBK CP. The following conditions were used for both sets of primers: 94ºC for 6 minutes; 36X (94ºC for 30 seconds; 55ºC for 45 seconds; 72ºC for 4 minutes); 72ºC for 10 minutes; held at 4ºC. The products were then run on a 0.8% agarose gel (see figures below). We can see that colonies 1, 6 and 7 all have bands of the expected size (~3.9kb) for both primers, indicating a successful transformation of LuxPQ into psB1AC3. Plasmid was isolated from these colonies using the GenElute Plasma MinPrep Kit. Colonies 6 and 7 were then sent to the University of Calgary’s DNA sequencing laboratory with BBK-CP-F/R primers.
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KATIE
 
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[[Image:2009.07.02.BBKluxPQ_ColPCR_PQPrimers.png|700px]]
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PATRICK
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iGEM Island Terrain
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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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We finally gained access to our new home LINDSAY Island not long ago, but did not have any permissions to create objects there, or edit the terrain. That all changed today, after meeting with out supervisor (and keeper of admin passwords) Dr. Christian Jacob. It was a sight to behold, the *instant* the terraforming permission was switched on, the whole team began creating mountains and gouging our canyons everywhere, right from beneath their own feet.
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After a while, we got more organized about the island's terrain, and found a program called Backhoe for designing SL terrain externally. Today saw an upgrade to the island's terrain, expanding the underwater zone assigned to the Synthetic Kingdom (which would grow ever larger over the summer, slowly submerging more and more land).
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The rest of the day was spent on more HUD development, determining which navigation buttons will belong on which screens, and setting up a script to 'listen' for binding events (such as TetR subunits binding each other, or binding DNA after dimerizing). This unbind list could then be called on to send messages dismissing the binding, giving the user back their separate parts and control over their biobricks.
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First occurred to me that, if I meant for multiple copies of this system to be in use by multiple people in the same area, I might have to insulate one person's biobricks from the the others! Began a campaign to upgrade all of the publicly visible messages in the simulator's components to include their owner's ID, and to check for that ID on all incoming messages. Now your friend's HUD won't have the power to unbind your complexes, for example.
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Isolate Plasmids
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-Shadowed Jeremy today.
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Purpose: isolate plasmids from overnight cultures containing Top 10 competent cells with Lux PQ in psB1AC3
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Protocol: Geneflute Plasmid mini prep kit
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After mini-prep we nano-dropped to determine the plasmid concentration at 260 wavelength
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| '''Plasmid''' || '''260/280'''    || '''260/230''' || '''Concentration [ng/μL]'''
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| ''LuxPQ Top 10 C24C11  || 1.82 || 2.23 || 160.2
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| ''LuxPQ Top 10 C24C12|| 1.89 ||  2.34 ||112.8
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| ''LuxPQ psB1AC3 C11|| 1.89|| 2.17|| 89.4
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| ''LuxPQ psB1AC3 C6|| 1.88|| 2.11|| 82.5
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| ''LuxPQ psB1AC3 C7|| 1.88|| 2.09|| 79.0
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For sequencing:
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C7 = send 8.34 microL
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Sequencing Table
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Canada day make-up
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| '''Reaction #'' || '''Name'''    || '''size''' || '''Primer''' ||'''Tm'''
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| ''1  || LuxPQ-BBK-C6-F || 6680 || BBK-CP-F || 55
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| ''2|| LuxPQ-BBK-C6-R ||  6680 ||BBK-CP-R || 55
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| ''3|| LuxPQ-BBK-C7-F|| 6680|| BBK-CP-F || 55
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| ''4|| LuxPQ-BBK-C7-R|| 6680|| BBK-CP-R || 55
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Latest revision as of 18:50, 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 3, 2009


CAROL

Colony PCR

  • plates resulted in two colonies and a colony PCR was initiated. After the PCR was completed, we ran the product on a 0.6% agarose gel but no bands appeared suggesting that colonies did not uptake plasmid that had the gene of interest ligated to it.


FAHD

Team Presentations

Today we had our team presentations. I presented on behalf of the Human Practices aspect of our project.


IMAN

DIVISION

As it was mentioned, division function gets an environment as its input. Then it looks at the elements existing in the cells. Those elements that should be doubled before the divisions (like Qrr4 promoter, RNA polymerase, LuxPQ and etc) are doubled and those elements that should be equally divided between new cells (like AI2, LuxU.p, LuxO.p, etc) are divided between cells. For those elements that are divided between new cells, it is not 100% that each new cell gets an equal amount of each one. There is a random generator function which produces a number between 1.90 and 2.10, and this number is used to divide the elements between the cells. Each rule has a label that determines this rule belongs to which cell. When division occurs, rules of the new cells should be labelled. Another challenge is to label all the rules of all the new existing cells. Moreover, we need to determine a time period as life cycle for each generation of the cells. We used the time that Gillespie’s algorithm assigns to the system for this purpose. At this stage, we have added an important aspect of “emergent properties” to our bacteria population by adding division to it.

Once again, two meetings this week. One on Thursday with Lindsay project, and the other one on Friday with iGEM.


JEREMY

Verification of LuxPQ into psB1AC3 construction

Purpose: to verify the presence of LuxPQ into psB1AC3 by colony PCR; to isolate plasmid; to send isolated plasmid for sequencing. A pTaq colony PCR was set up using the following sets of forward and reverse primers: LuxPQ and BBK CP. The following conditions were used for both sets of primers: 94ºC for 6 minutes; 36X (94ºC for 30 seconds; 55ºC for 45 seconds; 72ºC for 4 minutes); 72ºC for 10 minutes; held at 4ºC. The products were then run on a 0.8% agarose gel (see figures below). We can see that colonies 1, 6 and 7 all have bands of the expected size (~3.9kb) for both primers, indicating a successful transformation of LuxPQ into psB1AC3. Plasmid was isolated from these colonies using the GenElute Plasma MinPrep Kit. Colonies 6 and 7 were then sent to the University of Calgary’s DNA sequencing laboratory with BBK-CP-F/R primers.

2009.07.02.BBKluxPQ ColPCR PQPrimers.png

2009.07.02.BBKluxPQ ColPCR BBKCPPrimers.png


KEVIN

Transformation of fluorescent proteins

I transformed E0040 (GFP), E0032 (YFP), E0022 (CFP), I13500 (GFP+RBS), and I13502 (RFP+RBS) into TOP10 cells for testing of R0040 and... for drawing bacterial pictures! Orange FP and Blue FP were not available for distribution, and purple FP was not added to the iGEM registry.

Calgary 2009.07.03.GFP YFP.png

Calgary 2009.07.03.GFP+RBS.png

Calgary 2009.07.03.RFP+RBS CFP.png


PATRICK

iGEM Island Terrain

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

We finally gained access to our new home LINDSAY Island not long ago, but did not have any permissions to create objects there, or edit the terrain. That all changed today, after meeting with out supervisor (and keeper of admin passwords) Dr. Christian Jacob. It was a sight to behold, the *instant* the terraforming permission was switched on, the whole team began creating mountains and gouging our canyons everywhere, right from beneath their own feet.

After a while, we got more organized about the island's terrain, and found a program called Backhoe for designing SL terrain externally. Today saw an upgrade to the island's terrain, expanding the underwater zone assigned to the Synthetic Kingdom (which would grow ever larger over the summer, slowly submerging more and more land).

The rest of the day was spent on more HUD development, determining which navigation buttons will belong on which screens, and setting up a script to 'listen' for binding events (such as TetR subunits binding each other, or binding DNA after dimerizing). This unbind list could then be called on to send messages dismissing the binding, giving the user back their separate parts and control over their biobricks.

First occurred to me that, if I meant for multiple copies of this system to be in use by multiple people in the same area, I might have to insulate one person's biobricks from the the others! Began a campaign to upgrade all of the publicly visible messages in the simulator's components to include their owner's ID, and to check for that ID on all incoming messages. Now your friend's HUD won't have the power to unbind your complexes, for example.


PRIMA

Isolate Plasmids

-Shadowed Jeremy today. Purpose: isolate plasmids from overnight cultures containing Top 10 competent cells with Lux PQ in psB1AC3

Protocol: Geneflute Plasmid mini prep kit

After mini-prep we nano-dropped to determine the plasmid concentration at 260 wavelength

Plasmid 260/280 260/230 Concentration [ng/μL]
LuxPQ Top 10 C24C11 1.82 2.23 160.2
LuxPQ Top 10 C24C12 1.89 2.34 112.8
LuxPQ psB1AC3 C11 1.89 2.17 89.4
LuxPQ psB1AC3 C6 1.88 2.11 82.5
LuxPQ psB1AC3 C7 1.88 2.09 79.0

For sequencing: C7 = send 8.34 microL Sequencing Table



Reaction # Name' size Primer Tm
1 LuxPQ-BBK-C6-F 6680 BBK-CP-F 55
2 LuxPQ-BBK-C6-R 6680 BBK-CP-R 55
3 LuxPQ-BBK-C7-F 6680 BBK-CP-F 55
4 LuxPQ-BBK-C7-R 6680 BBK-CP-R 55

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