Team:Calgary/20 August 2009
From 2009.igem.org
CAROL
Descriptive Title of What You’re Doing
WIKI CODING HERE
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CHINMOYEE
Wiki Modelling page planning and Modelling meeting
MatLab paper formatting
Abstract Introduction – talk about our system , have a system diagram Methodology —algorithms , lab procedures etc Results and discussions —graphs , pics of glow bac Conclusions (Do in LaTeX) Wiki Formatting
Left frame
Matlab modeling --- The tab contains definitions and overview of methodology like
Membrane computing--- this tab contain pics and relavant information for overview of concepts Paper 1 Matlab Modelling--- Paper 2 Membrane computing--- pdf file , made with LaTeX The Meeting
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EMILY
Descriptive Title of What You're Doing
WIKI CODING HERE
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FAHD
Human Practices for August 20th 2009
Today, I continued to work on the ethics paper. I started reading literature on the environmental, legal and societal issues surrounding Quorum Sensing and I found a lot of interesting information that I can add on to the ethics paper. I will continue to work on the ethics paper over the next couple of days and try to improve it further.
I also contacted some companies that were on my marketing list. Most of these companies were Oil and gas development companies. I will do a follow-up with these companies next week.
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IMAN
Descriptive Title of What You're Doing
WIKI CODING HERE
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JAMIE
Setting up the V. harveyi MM32 AI-2 Assay and Testing Experiments in Second Life's Virtual Lab
Using a 96 well microplate, AI-2 isolated from Salmonella typhimurium 14028 supernatant will be tested. V. harveyi reporter strain MM32 (luxS- and luxN-) will luminesce in the presence of AI-2. Controls used in the experiment include S. typhimurium SS007, V. harveyi BB120 and E. coli DH5a. Overnight OD600 and luminescence (CPS) readings will be taken by a VICTOR (thank you Surette lab, especially Margot!).
Preliminary testing was done on the bacterial transformation and genomic DNA isolation activities in the virtual lab. Additionally, I now have transparent wings which glow. |
JEREMY
Descriptive Title of What You're Doing
WIKI CODING HERE
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KATIE
Fundamental Displays
I recently remembered that I will have to start making cleaning scripts for a lot of the equipment in the lab to prevent clutter for easy maintenance. I started to make these and added them to bacterial transformation, the sequencing station and DNA extraction. It is not imperative that these be completed immediately since this type of abuse is not expected for testing.
Added rho termination, but I am not satisfied with it yet and will continue to change where objects travel too although the pushing part looks satisfactory I need a better place for the mRNA strand. I have no idea how I am going to do the hairpin termination at this time but it will probably mean I have to fiddle with rotation again. There is now a complementary strand of DNA that will change its bases when an avatar makes changes to the template strand (the bottom one strand in this animation) so that the two strands will remain complementary to one another. Also did some more wiki updates.
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KEVIN
1. Measuring fluorescence of GFP
Yesterday, varieties of bacterial cultures were grown in order to test the expression of GFP's. The fluorescence of GFP are measured by the plate reader, and following are the results that Emily and I were able to get today:
2. Sequencing results
The sequencing results of Pqrr4+B0034+K082003 came back today. Unfortunately, B0034 was still not there despite the change of Pqrr4+B0034 colonies from C9 to C1. Surprisingly, the sequence for the previous construction that used Pqrr4+B0034 C9 actually match the sequence that came back today, which used Pqrr4+B0034 C1. (99% match) The following is the alignment of the two sequences:
>lcl|28877 Length=801 Score = 1472 bits (797), Expect = 0.0 Identities = 800/801 (99%), Gaps = 1/801 (0%) Strand=Plus/Plus Query 9 GGTGACACCTTGCCCTTTTTTGCCGGACTGCAGCGGCCGCTACTAGTATTAAGCTACTAA 68 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1 GGTGACACCTTGCCCTTTTTTGCCGGACTGCAGCGGCCGCTACTAGTATTAAGCTACTAA 60 Query 69 AGCGTAGTTTTCGTCGTTTGCAGCAGGCCTTTTGTATAGTTCATCCATGCCATGTGTAAT 128 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 61 AGCGTAGTTTTCGTCGTTTGCAGCAGGCCTTTTGTATAGTTCATCCATGCCATGTGTAAT 120 Query 129 CCCAGCAGCTGTTACAAACTCAAGAAGGACCATGTGGTCTCTCTTTTCGTTGGGATCTTT 188 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 121 CCCAGCAGCTGTTACAAACTCAAGAAGGACCATGTGGTCTCTCTTTTCGTTGGGATCTTT 180 Query 189 CGAAAGGGCAGATTGTGTGGACAGGTAATGGTTGTCTGGTAAAAGGACAGGGCCATCGCC 248 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 181 CGAAAGGGCAGATTGTGTGGACAGGTAATGGTTGTCTGGTAAAAGGACAGGGCCATCGCC 240 Query 249 AATTGGAGTATTTTGTTGATAATGGTCTGCTAGTTGAACGCTTCCATCTTCAATGTTGTG 308 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 241 AATTGGAGTATTTTGTTGATAATGGTCTGCTAGTTGAACGCTTCCATCTTCAATGTTGTG 300 Query 309 TCTAATTTTGAAGTTAACTTTGATTCCATTCTTTTGTTTGTCTGCCATGATGTATACATT 368 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 301 TCTAATTTTGAAGTTAACTTTGATTCCATTCTTTTGTTTGTCTGCCATGATGTATACATT 360 Query 369 GTGTGAGTTATAGTTGTATTCCAATTTGTGTCCAAGAATGTTTCCATCTTCTTTAAAATC 428 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 361 GTGTGAGTTATAGTTGTATTCCAATTTGTGTCCAAGAATGTTTCCATCTTCTTTAAAATC 420 Query 429 AATACCTTTTAACTCGATTCTATTAACAAGGGTATCACCTTCAAACTTGACTTCAGCACG 488 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 421 AATACCTTTTAACTCGATTCTATTAACAAGGGTATCACCTTCAAACTTGACTTCAGCACG 480 Query 489 TGTCTTGTAGTTCCCGTCATCTTTGAAAAATATAGTTCTTTCCTGTACATAACCTTCGGG 548 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 481 TGTCTTGTAGTTCCCGTCATCTTTGAAAAATATAGTTCTTTCCTGTACATAACCTTCGGG 540 Query 549 CATGGCACTCTTGAAAAAGTCATGCTGTTTCATATGATCTGGGTATCTCGCAAAGCATTG 608 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 541 CATGGCACTCTTGAAAAAGTCATGCTGTTTCATATGATCTGGGTATCTCGCAAAGCATTG 600 Query 609 AACACCATAACCGAAAGTAGTGACAAGTGTTGGCCATGGAACAGGTAGTTTTCCAGTAGT 668 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 601 AACACCATAACCGAAAGTAGTGACAAGTGTTGGCCATGGAACAGGTAGTTTTCCAGTAGT 660 Query 669 GCAAATAAATTTAAGGGTAAGTTTTCCGTATGTTGCATCACCTTCACCCTCTCCACTGAC 728 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 661 GCAAATAAATTTAAGGGTAAGTTTTCCGTATGTTGCATCACCTTCACCCTCTCCACTGAC 720 Query 729 AGAAAA-TTTGTGCCCATTAACATCACCATCTAATTCAACAAGAATTGGGACAACTCCAG 787 |||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 721 AGAAAAATTTGTGCCCATTAACATCACCATCTAATTCAACAAGAATTGGGACAACTCCAG 780 Query 788 TGAAAAGTTCTTCTCCTTTAC 808 ||||||||||||||||||||| Sbjct 781 TGAAAAGTTCTTCTCCTTTAC 801 And the following is the previous sequencing result that I have gotten for Pqrr4+B0034 that was used for construction: Sequence of Pqrr4+B0034 (RBS) C1
GGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATCCTTAGCTTTCGCTAAGGATGATTTCTG GAATTCGCGGCCGCTTCTAGAGTATCAGCAAAAACACTACGGTGGATAATCAGTAAAACCATGAAACTAGAGCCCCGCA CACTTGCGGGGCTTTTTAATTTTGAATTTCTTTCTTATTAAAACGCCATTTTTCTGATAAATGTATTAGTAGCAA TGCGCATGGTGGCATATTTGCATCATTTTGCATTTTGCAAATGCGATTTGCAAAATGCGTGCTCAATAAAGCACC AATATGCATCAGGATCGAAGAAAAAAGGCGTTTTTAAAAGTTGGCACGCATCGTGCTTTATACAGATACTAGAGAAAGAGGAGAAA TACTAGTAGCGGCCGCTGCAG TCCGGCAAAAAAGGGCAAGGTGTCACCACCCTGCCCTTTTTCTTTAAAACCGAAAAGATTACTT CGCGTTATGCAGGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGG CGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCG TAAAAAGGCCGCGTTGCTGGCGTTTTTCCACAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGG TGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGC CGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTC GGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTAT CGTCTTGAGTCCAACCCGGTAGACACGACTTATCGCCACTG
...AGATACTAGAGAAAGAGGCTAGATGCGTA...
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MANDY
Descriptive Title of What You're Doing
WIKI CODING HERE
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PATRICK
The Next Big Thing: Levels
As the iGEM season starts winding up, it is becoming very urgent to make the second life project publicly presentable! I spent today getting organized and nailing down the design for the last big feature that will live in the Biobrick Simulator heads up display object: levels.
The simulator is not a game (though it will be fun), but the 'playing through levels' concept is widely known amongst young people these days, and it's much more appealing than something like 'concepts', or 'chapters', even though those terms are better descriptions of what a 'level' will be. Each level is a self contained set of parts, with the goal of introducing one or two new features of the simulator and concepts in molecular biology to the user. The preliminary list of levels is a good illustration of the progression I'm looking for:
Unfortunately, there are also a good number of systems I had wanted to make into levels, but whose features aren't yet supported by the simulator's engine! Including, but not limited to:
In addition, a number of the levels I will be building would benefit from features these other systems require, especially inducers for LacI and TetR. Inducers make a huge amount of sense for systems like the toggle switches, for getting from one state to another; and also for positive autoregulation, for turning on/off cellular memory. That's to say nothing of incorporating environmental signals like temperature, osmolarity, and light, each of which have sensor parts within the registry, leading to more systems and more levels... but I digress! In a perfect world I'd have a chance to implement all of these things before putting together a selection of levels. But since I would like a version of the simulator with most of its *features* in place before the end of summer, choices have to be made about content. And who knows, there might still be time. Fortunately, none of the code that remains to be written for the levels is very complicated. The Level Selection screen makes the levels and their parts available, the Home screen gives some basic guidance for each level, and the Parts screen makes supplementary objects, and replacement objects in case you happen to delete the ones you're working with (or wish to combine multiple levels' parts together. That will work just fine!) All three screens are necessary for the levels to work, and none have new or complicated features, it's mostly a question of adapting code I've already written for other purposes. And all of that isn't even the last major portion of the island that needs to be developed! To support all of this biobrickery, users will first visit a zone describing the basics of molecular biology and biochemistry (in Second Life's interactive style). Katie is already working on a display of DNA replication for this zone. Also fortunately, each of the exhibits I have in mind are more or less stand-alone displays, as compared to the biobrick simulator where every part interacts with half a dozen others, so I don't anticipate it taking as long. But, with development as with biology, a good safe bet is to multiply all your time estimates by three...
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PRIMA
Marketing and tieing up loose ends
I ran the gene-specifc PCR with aiiA-F/R primers and ran it with a 1% gel at 100V.
I followed up with couple pharmaceutical companies. Some of our potential sponsors are currently deciding on sponsoring iGEM Calgary. Again, I couldn't get hold of other companies by phone but I left a message with a call back number. I also emailed those companies with a follow- up email. The good news is that Beckman Coulter has generously donated $200.00 to our iGEM Team this year. Unfortuantely, Alda Phamaceuticals Corporation is unable to sponsor our team this year. I updated some of the days on the wiki notebook. I also worked on my lab notebook to make sure all the gels were labeled and all pages are numbered. Finally, I began working on the iGEM articles for media purposes and for our meeting with Leanne next week. I should have that completed by this weekend. Tomorrow, I'll discuss my gel with Thane and Sonja and decide where to go from here in the lab. For marketing, I'll continue to contact companies (mostly via email) for sponsorship for this year and next year.
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STEFAN
Testing...Testing
Today, a generic avatar was created (aptly named Generic Lennie) that was in a separate group that had access to our island. He was used to test each area on our sim. We don't want visitors to be able to move, objects, change script and make new permanent objects. For the synthetic Kingdom everything was in order:
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VICKI
...And some more work on the modelling front
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