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| | |{{#calendar: query=preload=Team:Calgary/NotebookPreload | year=2009 | month=06 | title=Team:Calgary}} | | |{{#calendar: query=preload=Team:Calgary/NotebookPreload | year=2009 | month=06 | title=Team:Calgary}} |
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| | <html> | | <html> |
| | </center> | | </center> |
| | </div> | | </div> |
| | <br> | | <br> |
| - | <div class="heading">NOTEBOOK PAGE INDEX</div>
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| - | <div class="desc">
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| - | <a href="#Carol">Carol</a><br>
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| - | <a href="#Chinmoyee">Chinmoyee</a><br>
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| - | <a href="#Emily">Emily</a><br>
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| - | <a href="#Fahd">Fahd</a><br>
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| - | <a href="#Iman">Iman</a><br>
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| - | <a href="#Jamie">Jamie</a><br>
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| - | <a href="#Jeremy">Jeremy</a><br>
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| - | <a href="#Katie">Katie</a><br>
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| - | <a href="#Kevin">Kevin</a><br>
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| - | <a href="#Mandy">Mandy</a><br>
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| - | <a href="#Patrick">Patrick</a><br>
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| - | <a href="#Prima">Prima</a><br>
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| - | <a href="#Stefan">Stefan</a><br>
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| - | <a href="#Vicki">Vicki</a><br>
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| - | </div>
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| - | </p></div>
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| - | <br>
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| - | <div class="heading">CALENDAR</div>
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| - | <div class="desc">
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| - | <center>
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| | </html> | | </html> |
| - | {| style="background:transparent;" | + | {{Template:CalgaryNotebook}} |
| - | |{{#calendar: query=preload=Team:Calgary/NotebookPreload | year=2009 | month=05 | title=Team:Calgary}}
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| - | |{{#calendar: query=preload=Team:Calgary/NotebookPreload | year=2009 | month=06 | title=Team:Calgary}}
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| - | |{{#calendar: query=preload=Team:Calgary/NotebookPreload | year=2009 | month=07 | title=Team:Calgary}}
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| - | |{{#calendar: query=preload=Team:Calgary/NotebookPreload | year=2009 | month=08 | title=Team:Calgary}}
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| - | {| style="background:transparent;"
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| - | |{{#calendar: query=preload=Team:Calgary/NotebookPreload | year=2009 | month=09 | title=Team:Calgary}}
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| - | <br>
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| - | {| style="background:transparent;"
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| - | |{{#calendar: query=preload=Team:Calgary/NotebookPreload | year=2009 | month=10 | title=Team:Calgary}}
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| | <center> | | <center> |
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| | * Used GenElute Plasmid Miniprep Kit (Sigma-Aldrich), used as according to the manufacturers instructions. | | * Used GenElute Plasmid Miniprep Kit (Sigma-Aldrich), used as according to the manufacturers instructions. |
| | *Results: | | *Results: |
| - | <Br>
| |
| | <center> | | <center> |
| | {| border="1" | | {| border="1" |
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| | |} | | |} |
| | </center> | | </center> |
| | + | <br> |
| | * Set up restriction enzyme digest to ensure that biobrick sites are in the vector. The following are the reactions that were done: | | * Set up restriction enzyme digest to ensure that biobrick sites are in the vector. The following are the reactions that were done: |
| | Reaction 1: pSB1AC3 - cut with NotI | | Reaction 1: pSB1AC3 - cut with NotI |
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| | </tr> | | </tr> |
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| - | <tr>
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| - | <td height="10px" bgcolor="#222222">
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| - | </td>
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| - | </tr>
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| - | <tr>
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| - | <td>
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| - | <a name="Chinmoyee"></a>
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| - | <br>
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| - | <div class="heading">
| |
| - | CHINMOYEE
| |
| - | </div>
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| - | <br>
| |
| - | <div class="heading">
| |
| - | Descriptive Title of What You're Doing
| |
| - | </div>
| |
| - | <br>
| |
| - | <div class="desc">
| |
| - | </html>
| |
| - | WIKI CODING HERE
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| - |
| |
| - | <html>
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| - | </div>
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| - | </td>
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| - | </tr>
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| | <div class="heading"> | | <div class="heading"> |
| | Purification of psB1AC3 & psB1AK3 vectors | | Purification of psB1AC3 & psB1AK3 vectors |
| - |
| |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | *Protocol: Used GenElute Plasmid Miniprep Kit (Sigma-Aldrich), lot # 048k6062, used as according to the manufacturers instructions. | + | *Protocol: Used GenElute Plasmid Miniprep Kit (Sigma-Aldrich), lot # 048k6062, used as according to the manufacturer's instructions. |
| | <Br> | | <Br> |
| | *Results: | | *Results: |
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| | Left to digest overnight in waterbath at 37°C. | | Left to digest overnight in waterbath at 37°C. |
| | | | |
| - | <Br>
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| | <html> | | <html> |
| - | <Br>
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| | </div> | | </div> |
| | </td> | | </td> |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Marketing and Media for June 2nd 2009 |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | Today, I started filling out funding applications for some pharmaceutical companies. Some of these companies include Pfizer Canada, Merck Frosst Canada and Glaxosmithkline Canada. I did not get a chance to complete them but I am still working on it. |
| - | | + | |
| - | <html>
| + | |
| - | </div>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | | + | |
| - | <tr>
| + | |
| - | <td height="10px" bgcolor="#222222">
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | | + | |
| - | <tr>
| + | |
| - | <td>
| + | |
| - | <a name="Iman"></a>
| + | |
| | <br> | | <br> |
| - | <div class="heading">
| |
| - | IMAN
| |
| - | </div>
| |
| | <br> | | <br> |
| - | <div class="heading">
| + | I also set up a TV media appointment with the NUTV news for June the 16th 2009. |
| - | Descriptive Title of What You're Doing
| + | |
| - | </div>
| + | |
| - | <br>
| + | |
| - | <div class="desc">
| + | |
| - | </html>
| + | |
| - | WIKI CODING HERE
| + | |
| | | | |
| | <html> | | <html> |
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| | </td> | | </td> |
| | </tr> | | </tr> |
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| | <tr> | | <tr> |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Biobrick Vector Isolation and Verification + Sponsorship Package work |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| - | </html> | + | Today the iGEM Lab team worked on isolating psB1AC3 and psB1AK3. Digestion with all enzymes in the prefix and suffix was used to confirm the presence of the restriction sites.<br /><br /> |
| - | WIKI CODING HERE
| + | |
| | + | I also spent some time drafting up the sponsorship package for companies. |
| | | | |
| - | <html>
| |
| | </div> | | </div> |
| | + | <br> |
| | </td> | | </td> |
| | </tr> | | </tr> |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Isolation and verification of pSB1AC3 and pSB1AK3 |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | The iGEM lab team members worked together today to help each other perfect the method of plasmid isolation. Plasmids psB1AC3 and psB1AK3 were isolated using Sigma GenElute Plasmid Mini-prep kit, and the concentration and purity of plasmid was measured using the NanoDrop Spectrophotometer. See Emily’s notebook for today (above) for results. |
| | + | <br> |
| | + | <br> |
| | + | In order to verify that these vectors only had the death gene ccdB (675bp) in them, RD was set up with combinations of the following restriction enzymes: EcoRI, XbaI, PstI, NotI and SpeI. A gel was run with these products, as well as products from a RD set up with various genes of interest in their respective TOPO vectors (all cut with EcoRI). |
| | | | |
| | <html> | | <html> |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Genome Island |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | I got a chance to finally explore Genome Island properly and went through some of the activities on the island, which contains informative areas on Mendelian genetics and includes quizzes, slide shows etc. There was a tour of the island, a scavenger hunt, a garden containing plasmids as well as a tower with a variety of lab equipment where Mandy was able to talk to the owner of the island. |
| | + | <br> |
| | + | <br> |
| | + | I am hoping we will be able to make our island more interactive than this, but it will depend on how difficult I find the scripting language. |
| | | | |
| | <html> | | <html> |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive of What You're Doing
| + | Plasmid Purification/isolation and verification of pSB1AC3 |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | <b>Plasmid Isolation</b> |
| | + | To isoloate pSB1AC3 plasmid from TOP10 cells, a miniprep on them was done using Sigma's GenElute plasmid Miniprep Kit (sigma). pSB1AC3 plasmids are needed for potential plasmid switches. |
| | + | <br> |
| | + | <br> |
| | + | <center> |
| | + | Table 1. Purity and concentration of pSB1AC3 measured with Nanodrop utility and Spectrophotometer |
| | + | {| border="1" |
| | + | | '''Plasmid''' || '''260/280''' || '''260/230''' || '''Concentration [ng/μL]''' |
| | + | |- |
| | + | | pSB1AC3 C3 || 2.05 || 2.42 || 134.4 |
| | + | |- |
| | + | | pSB1AC3 C4 || 1.95 || 2.23 || 55.6 |
| | + | |} |
| | + | </center> |
| | + | <br> |
| | + | <Br> |
| | + | <b>Restriction Digest</b> |
| | + | To verify if the biobrick restriction sites are present in pSB1AC3, restrition digest was done using all the different combinations of enzymes:<br> |
| | + | NotI, EcorI+SpeI, XbaI+PstI, EcorI+PstI and XbaI+SpeI |
| | + | <br> |
| | + | [[Image:Calgary_2009.06.03.BBK_Verification_RD_copy.png|700px]] |
| | | | |
| | <html> | | <html> |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Second Life Teleporter |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | The teleportation grid now has buttons that turn black, indicating that the corresponding biobrick sphere is in use, and they remain that way for half an hour. Unfortunately, now that we look back on the spheres, it is dificult to have enough room to get all the parts for biobricking into them, as they can only be 10x10x10 in size as a maximum. |
| - | | + | Today was also our shopping day in preparation for activity materials for the University Campus Fair. |
| | <html> | | <html> |
| | </div> | | </div> |
| - | </td>
| |
| - | </tr>
| |
| - |
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| - | <tr>
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| - | <td height="10px" bgcolor="#222222">
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| - | </td>
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| - | </tr>
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| - |
| |
| - | <tr>
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| - | <td>
| |
| - | <a name="Patrick"></a>
| |
| | <br> | | <br> |
| - | <div class="heading">
| |
| - | PATRICK
| |
| - | </div>
| |
| - | <br>
| |
| - | <div class="heading">
| |
| - | Descriptive Title of What You're Doing
| |
| - | </div>
| |
| - | <br>
| |
| - | <div class="desc">
| |
| - | </html>
| |
| - | WIKI CODING HERE
| |
| - |
| |
| - | <html>
| |
| - | </div>
| |
| | </td> | | </td> |
| | </tr> | | </tr> |
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| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Biotech companies |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | Today I made an general email which I could sent to all Biotech companies. I had it checked by the rest of the marketing team. I had tailored some of the emails to target companies who had sponsored the building of the O'Brian labs and donated/offered quotes in the past. Since we had established a friendly long-term relationship with some of these companies, I wrote an email specifically to them regarding sponsoring this year's iGEM project. |
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| | <html> | | <html> |
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| | <tr> | | <tr> |
| | <td> | | <td> |
| - | <a name="Stefan"></a> | + | <a name="Vicki"></a> |
| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | STEFAN
| + | VICKI |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="heading"> | | <div class="heading"> |
| - | Descriptive Title of What You're Doing
| + | Verification of vectors |
| | </div> | | </div> |
| | <br> | | <br> |
| | <div class="desc"> | | <div class="desc"> |
| | </html> | | </html> |
| - | WIKI CODING HERE
| + | Purpose: Check the BBk and TOPO vector tubes and confirm that they actually contain what the labels claim they do. |
| | | | |
| - | <html>
| + | Materials and methods: |
| - | </div>
| + | 1. The plasmids (BBk and ccdB) came in E. coli. We performed a mini-prep to isolate them from the bacteria, in accordance with our plasmid isolation procedure. We were dealing with both psB1AC3 and psB1AK3 plasmids. |
| - | </td>
| + | |
| - | </tr>
| + | |
| | | | |
| - | <tr>
| + | 2. We evaluated the DNA concentrations with the Nanodrop spectrophotometer |
| - | <td height="10px" bgcolor="#222222">
| + | |
| - | </td>
| + | 3. We confirmed the contents with a restriction digest. |
| - | </tr>
| + | |
| | | | |
| - | <tr>
| + | Restriction digest volumes |
| - | <td>
| + | |
| - | <a name="Vicki"></a>
| + | For TOPO plasmids: take 10 uL LuxPQ, 7 uL ddHOH |
| - | <br>
| + | |
| - | <div class="heading">
| + | For restriction digest: 1 uL of each restriction enzyme, 2 uL of the relevant buffer, 8 uL of the plasmid and 9 uL of ddHOH – for a total volume of 20 uL |
| - | VICKI
| + | |
| - | </div>
| + | Reactions (enzymes that were used in cutting and relevant buffers): |
| - | <br>
| + | * Tube 1 – NotI (REact 3) |
| - | <div class="heading">
| + | * Tube 2 – EcoRI and SpeI (REact 4) |
| - | Descriptive Title of What You're Doing
| + | * Tube 3 – XbaI and PstI (REact 2) |
| - | </div>
| + | * Tube 4 – EcoRI and PstI (REact 2) |
| - | <br>
| + | * Tube 5 – XbaI and SpeI (REact 4) |
| - | <div class="desc">
| + | * Tube 6 – TOPO with EcoRI (REact 3) |
| - | </html>
| + | |
| - | WIKI CODING HERE
| + | Results: |
| | + | |
| | + | The restriction digest products were visualised on an agarose gel the following day. |
| | | | |
| | <html> | | <html> |
|
|
CAROL
Isolation of Plasmids (pSB1AC3 and pSB1AK3)for Cloning
- Isolated plasmids (pSB1AK3 and pSB1AC3) from overnight cultures prepared by Thane.
- Used GenElute Plasmid Miniprep Kit (Sigma-Aldrich), used as according to the manufacturers instructions.
- Results:
| Plasmid | 260/280 | 260/230 | Concentration [ng/μL]
|
| psB1AC3 1 | 1.96 | 3.48 | 76.9
|
| psB1AC3 2 | 1.93 | 2.29 | 98.1
|
| psB1AC3 3 | 1.87 | 1.88 | 48.5
|
| psB1AC3 4 | 1.90 | 2.11 | 118.9
|
| psB1AK3 1 | 2.05 | 2.42 | 134.4
|
| psB1AK3 2 | 1.95 | 2.23 | 55.6
|
| psB1AK3 3 | 1.91 | 2.22 | 97.9
|
| psB1AK3 4 | 2.03 | 1.92 | 44.5
|
- Set up restriction enzyme digest to ensure that biobrick sites are in the vector. The following are the reactions that were done:
Reaction 1: pSB1AC3 - cut with NotI
Reaction 2: pSB1AC3 - cut with EcoRI and SpeI
Reaction 3: pSB1AC3 - cut with XbaI and PstI
Reaction 4: pSB1AC3 - cut with XbaI and SpeI
Reaction 5: pSB1AK3 - cut with NotI
Reaction 6: pSB1AK3 - cut with EcorI and SpeI
Reaction 7: pSB1AK3 - cut with XbaI and PstI
Reaction 8: pSB1AK3 - cut with XbaI and SpeI
- Incubate reactions at 37oC
|
|
|
EMILY
Purification of psB1AC3 & psB1AK3 vectors
- Protocol: Used GenElute Plasmid Miniprep Kit (Sigma-Aldrich), lot # 048k6062, used as according to the manufacturer's instructions.
| Plasmid | 260/280 | 260/230 | Concentration [ng/μL]
|
| psB1AC3 1 | 1.96 | 3.48 | 76.9
|
| psB1AC3 2 | 1.93 | 2.29 | 98.1
|
| psB1AC3 3 | 1.87 | 1.88 | 48.5
|
| psB1AC3 4 | 1.90 | 2.11 | 118.9
|
| psB1AK3 1 | 2.05 | 2.42 | 134.4
|
| psB1AK3 2 | 1.95 | 2.23 | 55.6
|
| psB1AK3 3 | 1.91 | 2.22 | 97.9
|
| psB1AK3 4 | 2.03 | 1.92 | 44.5
|
Restriction digest of psB1AC3 and psB1AK3 vectors as well as LuxOD47E in pCR.2.1-TOPO vector
- Objective: To verify the presence of restriction sites in the two BBK vectors as well as in our BBK gene in the pCR.2.1-TOPO vector
5 reactions for psB1AC3 vector, 5 reactions for psB1AK3 vector, 1 reaction for gene of interest (LuxOD47E in pCR2.1-TOPO vector).
BBK Vector Reaction List
Reaction 1- Not1 + React 3 Buffer
Reaction 2- EcoRI + SpeI + React Buffer 4
Reaction 3- XbaI + PstI + React 2 Buffer
Reaction 4- EcoRI + PstI + React 2 Buffer
Reaction 5- XbaI + SpeI + React 4 Buffer
BBK vector tube preparation
8 uL Plasmid (psB1AC3 or psB1AK3)
2 uL appropriate React Buffer
1 uL of each appropriate restrcition enzyme
ddH20 up to 20 uL
TOPO vector tube preparation
10 uL DNA (LuxOD47E in pCR2.1- TOPO vector)
7 uL ddH20
2 uL React 3 Buffer
1 uL NotI restriction enzymes
Left to digest overnight in waterbath at 37°C.
|
|
|
FAHD
Marketing and Media for June 2nd 2009
Today, I started filling out funding applications for some pharmaceutical companies. Some of these companies include Pfizer Canada, Merck Frosst Canada and Glaxosmithkline Canada. I did not get a chance to complete them but I am still working on it.
I also set up a TV media appointment with the NUTV news for June the 16th 2009.
|
|
|
JAMIE
Biobrick Vector Isolation and Verification + Sponsorship Package work
Today the iGEM Lab team worked on isolating psB1AC3 and psB1AK3. Digestion with all enzymes in the prefix and suffix was used to confirm the presence of the restriction sites.
I also spent some time drafting up the sponsorship package for companies.
|
|
|
JEREMY
Isolation and verification of pSB1AC3 and pSB1AK3
The iGEM lab team members worked together today to help each other perfect the method of plasmid isolation. Plasmids psB1AC3 and psB1AK3 were isolated using Sigma GenElute Plasmid Mini-prep kit, and the concentration and purity of plasmid was measured using the NanoDrop Spectrophotometer. See Emily’s notebook for today (above) for results.
In order to verify that these vectors only had the death gene ccdB (675bp) in them, RD was set up with combinations of the following restriction enzymes: EcoRI, XbaI, PstI, NotI and SpeI. A gel was run with these products, as well as products from a RD set up with various genes of interest in their respective TOPO vectors (all cut with EcoRI).
|
|
|
KATIE
Genome Island
I got a chance to finally explore Genome Island properly and went through some of the activities on the island, which contains informative areas on Mendelian genetics and includes quizzes, slide shows etc. There was a tour of the island, a scavenger hunt, a garden containing plasmids as well as a tower with a variety of lab equipment where Mandy was able to talk to the owner of the island.
I am hoping we will be able to make our island more interactive than this, but it will depend on how difficult I find the scripting language.
|
|
|
KEVIN
Plasmid Purification/isolation and verification of pSB1AC3
Plasmid Isolation
To isoloate pSB1AC3 plasmid from TOP10 cells, a miniprep on them was done using Sigma's GenElute plasmid Miniprep Kit (sigma). pSB1AC3 plasmids are needed for potential plasmid switches.
Table 1. Purity and concentration of pSB1AC3 measured with Nanodrop utility and Spectrophotometer
| Plasmid | 260/280 | 260/230 | Concentration [ng/μL]
|
| pSB1AC3 C3 | 2.05 | 2.42 | 134.4
|
| pSB1AC3 C4 | 1.95 | 2.23 | 55.6
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Restriction Digest
To verify if the biobrick restriction sites are present in pSB1AC3, restrition digest was done using all the different combinations of enzymes:
NotI, EcorI+SpeI, XbaI+PstI, EcorI+PstI and XbaI+SpeI
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MANDY
Second Life Teleporter
The teleportation grid now has buttons that turn black, indicating that the corresponding biobrick sphere is in use, and they remain that way for half an hour. Unfortunately, now that we look back on the spheres, it is dificult to have enough room to get all the parts for biobricking into them, as they can only be 10x10x10 in size as a maximum.
Today was also our shopping day in preparation for activity materials for the University Campus Fair.
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PRIMA
Biotech companies
Today I made an general email which I could sent to all Biotech companies. I had it checked by the rest of the marketing team. I had tailored some of the emails to target companies who had sponsored the building of the O'Brian labs and donated/offered quotes in the past. Since we had established a friendly long-term relationship with some of these companies, I wrote an email specifically to them regarding sponsoring this year's iGEM project.
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VICKI
Verification of vectors
Purpose: Check the BBk and TOPO vector tubes and confirm that they actually contain what the labels claim they do.
Materials and methods:
1. The plasmids (BBk and ccdB) came in E. coli. We performed a mini-prep to isolate them from the bacteria, in accordance with our plasmid isolation procedure. We were dealing with both psB1AC3 and psB1AK3 plasmids.
2. We evaluated the DNA concentrations with the Nanodrop spectrophotometer
3. We confirmed the contents with a restriction digest.
Restriction digest volumes
For TOPO plasmids: take 10 uL LuxPQ, 7 uL ddHOH
For restriction digest: 1 uL of each restriction enzyme, 2 uL of the relevant buffer, 8 uL of the plasmid and 9 uL of ddHOH – for a total volume of 20 uL
Reactions (enzymes that were used in cutting and relevant buffers):
- Tube 1 – NotI (REact 3)
- Tube 2 – EcoRI and SpeI (REact 4)
- Tube 3 – XbaI and PstI (REact 2)
- Tube 4 – EcoRI and PstI (REact 2)
- Tube 5 – XbaI and SpeI (REact 4)
- Tube 6 – TOPO with EcoRI (REact 3)
Results:
The restriction digest products were visualised on an agarose gel the following day.
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