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| + | As everyone know, we are modeling a signaling system within bacteria. As a result, we have to be able to simulate hundreds of cells in each simulation. To do so, this model should perform very fast and it is not going to happen unless our codes are super efficient. That is why we have spent a week just to clean up the codes, rewrite some functions, and to polish it. |
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CAROL
Presentation Preparations
- Prepared presentations for Modelling and Lab
- Presented only in modelling presentation
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CHINMOYEE
Presentations Day
Prepaired for Presentation for Modelling .
Recieved good feedback on how to present well and what exactly to focus on . Give formulas and explain concepts that are being discussed. Focuse on why modelling is important to biologists. Good transitions required between presenting of each sub team . Coordinate closely between membrane computing and matlab modelling. Have nice pictures. We were supposed to have presented as if we were at the jambouree but we didn't format ourselves in that way .
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EMILY
Team Presentations
Today we spent a large portion of the morning preparing for our team meeting this afternoon where each team had 12 minutes to present all of their work up to date. The purpose of this was to get practice presenting as well as to start thinking about what the most important parts of each subproject are as we have limited time to present at MIT. I presented as part of the human practices team (Marketing, Outreach and Ethics) as well as part of the Lab team.
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FAHD
Marketing and Presentations for August 7th 2009
Today, I contacted a couple of Syn-bio companies that I had found on the Synbio 4.0 conference brochure. I send them a sponsorship proposal and I will do a follow-up on these companies next week. I also e-mailed out our July Newsletter to our current and future potential sponsors.
We also had our team presentations today: I was part of the human practices presentation. I presented the ethical aspect of the human practices section.
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IMAN
Polishing:
As everyone know, we are modeling a signaling system within bacteria. As a result, we have to be able to simulate hundreds of cells in each simulation. To do so, this model should perform very fast and it is not going to happen unless our codes are super efficient. That is why we have spent a week just to clean up the codes, rewrite some functions, and to polish it.
It is interesting to know that with doing that, our simulation is 5 times faster than before.
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JAMIE
Preparing for Fort McMurray and AI-2 Fun
Researching on individuals who would be present at our trip up North so we can have a better understanding of their goals and aims etc.
Emily, Jeremy and I also spent some time talking with Margot from the Surette lab about her experience working with Salmonella and AI-2.
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JEREMY
Presentation Skills and looking ahead in the lab
Purpose: Practice presentation skills and answering questions in preparation for aGEM and iGEM competitions. A large portion of the morning preparing for our team meeting in which each facet of our team had 12 minutes to present all of their work up to date. I helped to present the Lab section of iGEM Calgary's overall project. We also prepared for AI-2 isolation in the coming weeks and the trip to Ft. McMurray on Monday.
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KATIE
Presentation Critiques
We had our meeting today and were given some suggestions regarding our second life presentation:
1. The storyline is very important to a presentation and our presentation was static, using titles, point form notes and pictures. To fully demonstrate second life. To fully demonstrate second life, especially for the iGEM competition, it would be best to take one avatar through the domains of the island as a visual aid
2. Pick one person as our team’s presenter
3. Hold off on releasing our island to the public until we have something that is extremely novel to the Second Life environment
4. Testing for next year to gauge the effectiveness of the island activities
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KEVIN
1. Plasmid Isolation
The Pqrr4+I13500 plasmid was isolated from TOP10 cells in order for them to be verified via Restriction digest. This would then be made competent in order to transform mutants in.
2. Restriction Digest
The Pqrr4+I13500 isolated plasmid was digested with XbaI and PstI enzymes, then ran on 1% gel at 100V. The following gel was obtained.
As one can see, the upper bands of the colonies 4, 5, and 6 match the upper band in the pSB2K3 size control, meaning the plasmid switch to pSB2K3 seems to have been successful. Also, the bottom bands of the colonies 4, 5, and 6 match the one in the Pqrr4+I13500 in pSB1AC3 lane, meaning that the construction seems to have worked. These two lower bands might look as if they do not match; however, if you consider the slanting of the ladders at right compared to the left, it seems that the two match.
3. Sequencing
Yesterday's sequencing of Pqrr4+B0034+K082003 had been received and analyzed. The forward sequencing did not work; however, the reverse did, and an unusual problem was noticed. K082003 had matched 100% with the sequence provided by the parts registry, and Pqrr4 matched 99%, which made sense because the Pqrr4 is almost at the 1000bp region starting from behind and polymerase often reads inaccurately after reading about 1kb, but the part in the middle, B0034, was not present. This is unusual because I have sequenced the Pqrr4+B0034 construct before constructing K082003 behind. An explanation might be that the scar did not form between Pqrr4+B0034 which caused the B0034 part to be cut out. Another reason that may explain this result may be that I simply used a non-verified isolated plasmid of Pqrr4+B0034. Either way, I would have to carry out the construction procedure from the start.
Actual matching of the sequences is soon to come, as now the sequencing website is down.
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PRIMA
Understanding circuits and Construction procedures
I spent some time going over the basic biology and lab procedures with Jeremy. I drew out the response circuit, vectors, restriction sites, promoters to make sense of what I will be constructing in the lab later next week.
I worked on the construction plan which I will submit to Sonja and Thane tomorrow. I decided taht since C1 lambda is currently in 2K3 plasmid and Pqrr4 is in an 1AC3 plasmid, it would make sense to move C1 lambda (1kb) behind Pqrr4 and grow the colonies on Chlroramphenical plates. Then I could move my construct (RBS-aiiA-B0015) behind the C1 lambda. Since my construct is only about 900 kb, it shouldn't be too hard to move. This would be the ideal method of construction because my construct is in psB1AK3. Cloning the aiiA construct after C1 lambda would allow me to grow the colonies on Chloramphenical plates. This method of construction does not require a plasmid switch.
I did a bit of research of aiiA to get a better understanding of my construct and how it "fits" into the response circuit.
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STEFAN
Stations almost complete!
Finished most of the notecards except for the eukaryotic cell station since I am still trying to figure that out and the smelly bacteria station because that might be change. The problem there is that it's not really very interactive. The bacteria are there but don't really do anything and the squid just tells you about them. I was thinking of a quiz but that might be too superficial in the questions that can be asked.
Various seaweed and rock were added, some terraforming was done so people will not wander off the path and a starting area was made. This consists of Professor Squidmund Freud giving directions, a sign saying "Welcome to the Synthetic Kingdom" and a map.
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VICKI
Presentation preparation
I prepared slides for the lab presentation and I edited the slides for the modelling powerpoint that I prepared last night. I also presented on the modelling side.
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