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| | * Prepared two 5 mL overnight cultures (LB broth) of Top 10 cells and XL Gold Ultracompetent cells. | | * Prepared two 5 mL overnight cultures (LB broth) of Top 10 cells and XL Gold Ultracompetent cells. |
| | * Helped the bioinformatics department (Bachelor of Health Sciences) take apart computers in the morning. | | * Helped the bioinformatics department (Bachelor of Health Sciences) take apart computers in the morning. |
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| - | WIKI CODING HERE
| + | Our sequencing came back and once again, it doesn't look like the B0015 terminator is present in the construct. So we will go back to our most recent plates (from July 17th 2009) ad select different colonies and do verification on them. So I set up a colony PCR with new colonies, following the protocol and the cycling conditions from from July 7th 2009. We ran the PCR products on a 1% agarose gel with 1.0 kb+ DNA Ladder. See gel photo below. |
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| | + | [[Image:2009.07.21.J13002-LuxOD47E-B0015.jpg|350px]] |
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| | + | *Analysis: Lanes 1-5 are J13002-LuxOD47E-B0015 trial 1 (with B0015 as the insert), lanes 6-10 are J13002-LuxOD47E-B0015 trial 2 (with J13002-LuxOD47E as the insert), lane 11 is a size control with J13002-LuxOD47E C3, lane 12 is another size control with BBk LuxOD47E and lane 13 is a negative control. |
| | + | *From this gel, we decided to prepare overnight cultures of colonies 5-8 in order to perform a verification digest and possibly send a colony down for DNA sequencing. |
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| | 6) Got an e-mail from Genome Canada; they said NO. | | 6) Got an e-mail from Genome Canada; they said NO. |
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| + | CaCl2 was prepared and sterilized. Overnights of XL Gold and DH5a were made as well. |
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| - | WIKI CODING HERE
| + | Purpose: use PCR to verify the presence of PQ-B-R-OU-B in the psB1AC3 vector. A pTaq PCR was set up using BBK CP F/R primers using the following conditions: 94ºC for 3 minutes; 36X (94ºC for 30 seconds; 55ºC for 45 seconds; 72ºC for 6 min 30 sec); 72ºC for 10 minutes; held at 4ºC. The products were then run on a 0.8% agarose gel (see below). We can see that colonies 6 and 7 reveal the desired size of the construct (~6.0kb), however, the negative control lane shows two bands, when we want no bands. We must therefore repeat this PCR with colonies 6 and 7 to receive a clean negative control lane. |
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| - | WIKI CODING HERE
| + | I was able to make a video for the second life team for the blog. I finished editing it in the morning and it consisted of a very general overview of the scripting involved with what I have been doing in the virtual lab. I did not go into a lot of detail to prevent my video from going over ten minutes. I showed a little bit of the restriction digest and bacterial transformation activities for what I have so far. |
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| | The lower bands of the colonies 1, 2, 4, 6, 8, 9, and 10 seem to be above the positive control bands, which is what was expected. Thus it is now ready for sequencing. | | The lower bands of the colonies 1, 2, 4, 6, 8, 9, and 10 seem to be above the positive control bands, which is what was expected. Thus it is now ready for sequencing. |
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| - | WIKI CODING HERE | + | All the pages we need are pretty much made/exist, so now it can be filled out. |
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| | + | COMPLETED PAGES OF WIKI: |
| | + | *News (Campus Fair, all 3 AiF Meetings, all up/recoded, photos pending) |
| | + | *Synthetic Blogology (division of posts per team in each section still needs to be done, but the RSS feed of latest updates is there) |
| | + | *Gallery (also need to divide events and put on relevant news story pages) |
| | + | *Sponsors |
| | + | *MOST of team (waiting for descriptions) |
| | + | *50% of main page :icons and other things all coded/made, still need to clean them up |
| | + | *Menu template links SHOULD be fixed. |
| | + | <br><Br> |
| | + | Icons will denote lab/second life/ human practices/ marketing / modelling sections of our project, providing a useful ‘guide’ around our wiki should people get lost in the many pages. Additionally, left side bars are mainly empty right now but will serve as quick indexes for each section. Icons will also link back to an overall site map which will make it easier to navigate. |
| | + | <br><br> |
| | + | PAGES THAT NEED TO BE WORKED ON: |
| | + | *Site Map |
| | + | *Main Page |
| | + | *Main Pages for each section (esp reformatting patrick’s blog to fit our intro section for Second Life, need to harass other team members for main intros for each project section) |
| | + | *Update pages for each section (taken from blog entries) |
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| - | - And since the hotels are close, we could walk to MIT to avoid transportation costs. So far, we’ve managed to raise $3000 cash (excluding the lab reagents and equipment from sponsors)…so this will probably fly 6 students to Boston and back. This money came from first and second bake sales, and cash donations from sponsors. Accommodations will cost the 15 students ± $1100 for the 4 nights. I havn’t looked at rooms for facilitators so I can’t tell you much about it now. In our next bake sale, our goal is to make around $500. :D The marketing team is trying their best to arrange meetings and getting sponsors.
| + | - And since the hotels are close, we could walk to MIT to avoid transportation costs. So far, we’ve managed to raise $3000 cash (excluding the lab reagents and equipment from sponsors)…so this will probably fly 6 students to Boston and back. This money came from first and second bake sales, and cash donations from sponsors. Accommodations will cost the 15 students ± $1100 for the 4 nights. I haven't looked at rooms for facilitators so I can’t tell you much about it now. In our next bake sale, our goal is to make around $500. :D The marketing team is trying their best to arrange meetings and getting sponsors. |
| | </centre> | | </centre> |
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| | Tomorrow, I’ll call the other companies and send an email to Shawn Abbott (one of the Dragons) to set up a meeting with him to discuss iGEM sponsorship and if he can help us/give us advice. Once I set up a meeting, Jeremy and I plan to go visit him. Right now, the marketing team is reviewing the rough draft of the July newsletter which we hope to finalize by Friday and send out to companies early next week. | | Tomorrow, I’ll call the other companies and send an email to Shawn Abbott (one of the Dragons) to set up a meeting with him to discuss iGEM sponsorship and if he can help us/give us advice. Once I set up a meeting, Jeremy and I plan to go visit him. Right now, the marketing team is reviewing the rough draft of the July newsletter which we hope to finalize by Friday and send out to companies early next week. |
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| - | Today was full of wonderful manual labour as you can probably tell | + | Today was full of wonderful manual labour as you can probably tell from everyone's update. After that, I managed to read a Second Life ethics paper. I didn't think it was very good because it was poorly written and it seemed the person was not qualified to do it. However, I enjoyed the paper with the molecular orbitals. I think it is the same person that did the molecule rezzer as well. The paper showed how useful Second Life can be to visually present something, which is excellent because synthetic biology is not very friendly to the naked eye. I also started to write the ethics blog post and put some thought into what to present on Friday. |
| - | from everyone's update. After that, I managed to read a Second Life | + | |
| - | ethics paper. I didn't think it was very good because it was poorly | + | |
| - | written and it seemed the person was not qualified to do it. However, | + | |
| - | I enjoyed the paper with the molecular orbitals. I think it is the | + | |
| - | same person that did the molecule rezzer as well. The paper showed how | + | |
| - | useful Second Life can be tovisually present something, which is | + | |
| - | excellent because synthetic biology is not very friendly to the naked | + | |
| - | eye. I also started to write the ethics blog post and put some thought into | + | |
| - | what to present on Friday. | + | |
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CAROL
Making Competent Cells
- Prepared 500mL LB broth for making competent cells. Followed procedure that is outlined in the protocol page. Unfortunately, due to time constraints, we had to re-make the overnight cultures.
- Prepared two 5 mL overnight cultures (LB broth) of Top 10 cells and XL Gold Ultracompetent cells.
- Helped the bioinformatics department (Bachelor of Health Sciences) take apart computers in the morning.
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EMILY
Sequencing
Our sequencing came back and once again, it doesn't look like the B0015 terminator is present in the construct. So we will go back to our most recent plates (from July 17th 2009) ad select different colonies and do verification on them. So I set up a colony PCR with new colonies, following the protocol and the cycling conditions from from July 7th 2009. We ran the PCR products on a 1% agarose gel with 1.0 kb+ DNA Ladder. See gel photo below.
- Analysis: Lanes 1-5 are J13002-LuxOD47E-B0015 trial 1 (with B0015 as the insert), lanes 6-10 are J13002-LuxOD47E-B0015 trial 2 (with J13002-LuxOD47E as the insert), lane 11 is a size control with J13002-LuxOD47E C3, lane 12 is another size control with BBk LuxOD47E and lane 13 is a negative control.
- From this gel, we decided to prepare overnight cultures of colonies 5-8 in order to perform a verification digest and possibly send a colony down for DNA sequencing.
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FAHD
Marketing for July 21st 2009
Today, I concentrated my energies at marketing our iGEM project and looking at the ethical aspect of our project. Here is what I did today:
1)Helped in the Bio-info room till 11.15
2) Called Bracco/E-Z-EM Canada and e-mailed him a sponsorship package
3) Left a voicemail for Life Tech/Applied BioSystems.
4) Talked to Dr Wolbring abt our Ethics Progress Via a webcam. Setup an appoinment for thursday at 10.00 am
5) Read Ethics papers.
6) Got an e-mail from Genome Canada; they said NO.
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JAMIE
Preparing for Competent Cells
CaCl2 was prepared and sterilized. Overnights of XL Gold and DH5a were made as well.
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JEREMY
Plasmid PCR to verify signaling circuit in AC plasmid
Purpose: use PCR to verify the presence of PQ-B-R-OU-B in the psB1AC3 vector. A pTaq PCR was set up using BBK CP F/R primers using the following conditions: 94ºC for 3 minutes; 36X (94ºC for 30 seconds; 55ºC for 45 seconds; 72ºC for 6 min 30 sec); 72ºC for 10 minutes; held at 4ºC. The products were then run on a 0.8% agarose gel (see below). We can see that colonies 6 and 7 reveal the desired size of the construct (~6.0kb), however, the negative control lane shows two bands, when we want no bands. We must therefore repeat this PCR with colonies 6 and 7 to receive a clean negative control lane.
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KATIE
Blog Update
I was able to make a video for the second life team for the blog. I finished editing it in the morning and it consisted of a very general overview of the scripting involved with what I have been doing in the virtual lab. I did not go into a lot of detail to prevent my video from going over ten minutes. I showed a little bit of the restriction digest and bacterial transformation activities for what I have so far.
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KEVIN
1. Plasmid Isolation
I have isolated the Pqrr4+B0034 plasmids from yesterday's overnight cultures, and the purity and concentration of them were measured using nanodrop. They were pure enough to move on with.
2. Restriction digest
The isolated Pqrr4+B0034 plasmid was then cut with XbaI and PstI and ran on a 2% gel at 90V in order to verify the presence of the circuit. The following is an image of the gel:
The lower bands of the colonies 1, 2, 4, 6, 8, 9, and 10 seem to be above the positive control bands, which is what was expected. Thus it is now ready for sequencing.
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MANDY
Wiki Structure Completion
All the pages we need are pretty much made/exist, so now it can be filled out.
COMPLETED PAGES OF WIKI:
- News (Campus Fair, all 3 AiF Meetings, all up/recoded, photos pending)
- Synthetic Blogology (division of posts per team in each section still needs to be done, but the RSS feed of latest updates is there)
- Gallery (also need to divide events and put on relevant news story pages)
- Sponsors
- MOST of team (waiting for descriptions)
- 50% of main page :icons and other things all coded/made, still need to clean them up
- Menu template links SHOULD be fixed.
Icons will denote lab/second life/ human practices/ marketing / modelling sections of our project, providing a useful ‘guide’ around our wiki should people get lost in the many pages. Additionally, left side bars are mainly empty right now but will serve as quick indexes for each section. Icons will also link back to an overall site map which will make it easier to navigate.
PAGES THAT NEED TO BE WORKED ON:
- Site Map
- Main Page
- Main Pages for each section (esp reformatting patrick’s blog to fit our intro section for Second Life, need to harass other team members for main intros for each project section)
- Update pages for each section (taken from blog entries)
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PRIMA
Hotel search and Sponsors Continuation
Today:
All morning (pretty much) was spent helping with moving the computers in the Bio Inf. Lab.
Here’s the real deal:
I followed up with the Company 1 and they replied back saying that they’re unable to help. Also Company 3 and Company 3 have declined our offer.
On a more positive note, I found GSK (GlaxoSmithKline) which is a research-based pharmaceutical company devoted to developing innovative medicines and vaccines. I only found their phone number so I’ll give them a shout tomorrow and follow up with 4 other companies.
I also finished writing and editing my email to Dr. Jay Ingram (Discovery Channel Co-host). Fahd, Jamie and Jeremy double checked it so I’ve attached it in this email. Dr. Jacob sent me Dr. Ingram’s wife’s email. They both know Dr. Jacob so I’ve mentioned him in the letter.
I also searched up a few hotels which are not too far from MIT and have decent prices. I spoke to Thane about it and we were thinking of getting
<centre>
- And since the hotels are close, we could walk to MIT to avoid transportation costs. So far, we’ve managed to raise $3000 cash (excluding the lab reagents and equipment from sponsors)…so this will probably fly 6 students to Boston and back. This money came from first and second bake sales, and cash donations from sponsors. Accommodations will cost the 15 students ± $1100 for the 4 nights. I haven't looked at rooms for facilitators so I can’t tell you much about it now. In our next bake sale, our goal is to make around $500. :D The marketing team is trying their best to arrange meetings and getting sponsors.
</centre>
Tomorrow, I’ll call the other companies and send an email to Shawn Abbott (one of the Dragons) to set up a meeting with him to discuss iGEM sponsorship and if he can help us/give us advice. Once I set up a meeting, Jeremy and I plan to go visit him. Right now, the marketing team is reviewing the rough draft of the July newsletter which we hope to finalize by Friday and send out to companies early next week.
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STEFAN
Meeting at Christian's lab
Today was full of wonderful manual labour as you can probably tell from everyone's update. After that, I managed to read a Second Life ethics paper. I didn't think it was very good because it was poorly written and it seemed the person was not qualified to do it. However, I enjoyed the paper with the molecular orbitals. I think it is the same person that did the molecule rezzer as well. The paper showed how useful Second Life can be to visually present something, which is excellent because synthetic biology is not very friendly to the naked eye. I also started to write the ethics blog post and put some thought into what to present on Friday.
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VICKI
APEGGA article
Carol and I started talking about how we’d approach it, but she was pretty busy in the lab so we didn’t make it too far. We’ll discuss it tomorrow and finish it by Aug 1, for sure. My preference would be to do a small profile of each engineer, where we discuss where we’re from, why we’re here and where we think we could go with synthetic biology. This would also include unifying paragraphs to start and finish the article, structured much like what I did for my showcase article for retiring teachers way way back in grade 12.
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