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CAROL
Descriptive Title of What You’re Doing
WIKI CODING HERE
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CHINMOYEE
More Simbiology
Exploration Results :
Simbiology assumes that all reactions are elementary reactions. For stochastic simulation only the Chemical kinetic and Hill kinetic equations work. Simbiology also produces a diagram of all the reactions input . The diagram view is helpfull in establishing the connections between species when they react or form.
The simbiology simulation graphs produced have a generic y-axis value of state which signifies concentration .
Started to look at other Toolboxes given with the Matlab package.
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EMILY
Visualization of Previous Restriction Digest
- Visualization of psB1AC3, psB1AK3 and LuxOD47E in pCR.2.1-TOPO vector restriction digest
- Added 10X Orange dye and ran on a 1% agarose gel, expected band sizes: psB1AC3/psB1AK3 ~ 3.0 KB,
Lanes 2-6 psB1AC3
Lanes 7-11 psB1AK3
Lane 8- LuxOU
Lane 9-Lux PQ
Lane 10- Lux CDABE
Lane 11- LuxOD47E
Lane 12- LuxOD47A
- Analysis: From this gel we can conclude that LuxPQ and LuxCDABE were not cut with EcoRI as we do not see the expected band sizes in these lanes. The others look good. We will proceed by sending LuxPQ in TOPO vector and LuxCDABE in TOPO vector for DNA sequencing.
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FAHD
Descriptive Title of What You're Doing
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IMAN
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JAMIE
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JEREMY
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KATIE
Working with the Listen Event
Everything has to be added into chat so answers to questions are entered into the chat window, which I do not really like since mistakes are easy to make and I also keep communicating with a black board that uses one of the channels I am using as well.
Learned about the listen event:
- Uses channels and messages and keeps track of a avatar’s id so this will be very useful for: Giving out inventory, dividing messages up
Cycle of the PCR are complete now and an amplified piece of DNA, which is rezzed beside it and can be taken into the avatar’s inventory to be used for something else later on like running a gel.
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KEVIN
Cloning Technique
Began looking into biobrick cloning techniques. Reviewed how the parts are put together. If A part is the recepient and B part is the donor, and when B part needs to be put behind of A, the recepient A is cut with SpeI and PstI sites and the donor is cut with XbaI and PstI. When B needs to be put in front of A, the recepient A is cut with EcoRI and Xba, and the donor B is cut with EcoRI and SpeI. When cut Xba and Spe sites meet, it creates a scar, making the construction permenant. (It won't cut apart with the enzymes we use)
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MANDY
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PATRICK
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PRIMA
CTV interviews
Today, I continued to follow up with companies to whom I had sent the sponsorship package. I made a couple cold calls to companies who didn't provide an email address on their websites. First I tried to get a hold of the person in-charge of marketing/sponsorship, tell them a little about the project, what iGEM is and why we're looking for sponsors. I spoke to a few company representatives and most of them were very excited about the project. I asked for their email address and sent the sponsorship package to them. I'll follow up with them next week.
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STEFAN
Descriptive Title of What You're Doing
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VICKI
Gel of the vector verification performed yesterday
Purpose: to visualise the results of yesterday’s vector verification
Expected restriction digest output:
Biobrick digest (2 fragments)
- psB1AC3/psB1AK3: ~3.0 kb
- ccdB (p1010): ~675 bp
TOPO digest (2 fragments)
- TOPO (T/A and Blunt): ~3.5 kb
- LuxOU: ~2.0 kb
- LuxPQ: ~4.0 kb
- LuxCDABE: ~6.0 kb
- LuxOD47E: ~1.4 kb
- LuxOD47A: ~1.4 kb
Results:
Gel and lane description is included below. LuxPQ did not work, so it will need to be sequenced.
Sequencing of LuxPQ in TOPO Blunt II
Purpose: As mentioned above, the results for LuxPQ are very questionable. Since they cannot be explained with restriction digests, hopefully sequencing will alleviate some of the confusion.
Materials and methods:
We inserted 7.3 uL of LuxPQ in TOPO into a mini PCR tube so that around 730 ng of DNA were present for sequencing. We used the sp6 forward primer and the T7 reverse primer.
Results:
Much like our previous sequencing attempts, these were questionable. The electronic copy will be inserted shortly.
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