Team:Calgary/26 May 2009

From 2009.igem.org

(Difference between revisions)
 
(79 intermediate revisions not shown)
Line 52: Line 52:
text-align: justify;
text-align: justify;
}
}
 +
 +
.center {
 +
text-align: center;
 +
display: block;
 +
margin-left: auto;
 +
margin-right: auto;
 +
}
 +
</style>
</style>
Line 59: Line 67:
<tr>
<tr>
<div id="leftmenu">
<div id="leftmenu">
-
<td width="210" rowspan=13 bgcolor="#414141" valign="top">
+
<td width="210" rowspan=30 bgcolor="#414141" valign="top">
<br>
<br>
-
<div class="heading">NOTEBOOK PAGE INDEX</div>
+
<div class="heading">THIS MONTH</div>
<div class="desc">
<div class="desc">
-
<a href="#Carol">Carol</a><br>
+
<center>
-
<a href="#Emily">Emily</a><br>
+
</html>
-
<a href="#Jamie">Jamie</a><br>
+
{| style="background:transparent;"
-
<a href="#Jeremy">Jeremy</a><br>
+
|{{#calendar: query=preload=Team:Calgary/NotebookPreload | year=2009 | month=05 | title=Team:Calgary}}
-
<a href="#Kevin">Kevin</a><br>
+
|}
-
<a href="#Vicki">Vicki</a><br>
+
<html>
 +
</center>
</div>
</div>
-
</p></div>
+
<br>
 +
</html>
 +
{{Template:CalgaryNotebook}}
 +
 
 +
<html>
 +
<center>
 +
</desc>
</td>
</td>
-
<td width="10" rowspan=13 bgcolor="#222222">
+
<td width="10" rowspan=30 bgcolor="#222222">
</div>
</div>
<td width="750" bgcolor="#414141" valign="top">
<td width="750" bgcolor="#414141" valign="top">
Line 97: Line 112:
<br>
<br>
<div class="heading">
<div class="heading">
-
DESCRIPTIVE TITLE OF WHAT YOU'RE DOING - ALL CAPS UNLESS YOU ARE USING TERMINOLOGY THAT REQUIRES NO CAPS
+
Plasmid Isolation of ''luxCDABE'' in TOPO vector
</div>
</div>
<br>
<br>
<div class="desc">
<div class="desc">
</html>
</html>
-
WIKI CODING HERE
+
The purpose of plasmid isolation is to extract plasmids from ''E. coli'' that has topo vector with ''luxCDABE''. Overnight cultures were prepared and Sigma Mini Prep kit was used to to isolate plasmids (see protocols for detailed procedures). The plasmids was finally eluted in the elution buffer provided by the kit to a total of 50uL.
 +
 
 +
The concentration of plasmids was determined using the nano-drop apparatus at 260nm wavelength (see protocols for detailed procedures) and the following table summarizes the concentrations of plasmids.
 +
 
 +
<br>
 +
<br>
 +
<center>
 +
{| border="1"
 +
| '''Plasmid''' || '''260/280'''    || '''260/230''' || '''Concentration [ng/μL]'''
 +
|-
 +
| ''luxCDABE'' TOPO C1  || 2.21 || 4.58 || 47.6
 +
|-
 +
| ''luxCDABE'' TOPO C2|| 2.09 ||  3.39 || 56.0
 +
|}
 +
</center>
<html>
<html>
Line 108: Line 137:
</td>
</td>
</tr>
</tr>
 +
<tr>
<tr>
Line 123: Line 153:
<br>
<br>
<div class="heading">
<div class="heading">
-
DESCRIPTIVE TITLE OF WHAT YOU'RE DOING - ALL CAPS UNLESS YOU ARE USING TERMINOLOGY THAT REQUIRES NO CAPS
+
Plasmid Isolation of <i>LuxOD47E</i> in pCR2.1 TOPO and psB1AC3 vectors
 +
 
</div>
</div>
<br>
<br>
<div class="desc">
<div class="desc">
</html>
</html>
-
WIKI CODING HERE
+
*Objective: To extract plasmids of LuxOD47E in pCR2.1-TOPO vector from overnight cultures.
 +
 
 +
*Protocol: Used Sigma GenElute Plasmid Miniprep Kit (Sigma), lot # 048k6062, used as according to the manufacturers instructions, eluting in 50 μL ddH20.
 +
 
 +
*Results: Used Nanodrop 1000 Spectrophotometer read at 260 wavelength to determine DNA concentrations
 +
 
 +
<center>
 +
{| border="1"
 +
| '''Plasmid''' || '''260/280'''    || '''260/230''' || '''Concentration [ng/μL]'''
 +
|-
 +
| ''LuxO''D47E TOPO C1  || 1.88 || 2.21 || 409.5
 +
|-
 +
| ''LuxO''D47E TOPO C2|| 1.86 ||  2.18 ||551.4
 +
|-
 +
| ''LuxO''D47E BBK C1|| 2.04|| 5.01|| 551.4
 +
|-
 +
| ''LuxO''D47E BBK C2|| 1.77|| 1.39|| 92.9
 +
|}
 +
</center>
<html>
<html>
Line 139: Line 188:
</td>
</td>
</tr>
</tr>
 +
<tr>
<tr>
Line 149: Line 199:
<br>
<br>
<div class="heading">
<div class="heading">
-
PLASMID ISOLATION OF <i>luxOU</i> in pCR-Blunt II-TOPO
+
Plasmid Isolation of <i>luxOU</i> in pCR-Blunt II-TOPO and psB1AC3
</div>
</div>
<br>
<br>
<div class="desc">
<div class="desc">
-
</html>
 
-
Sigma Genelute Plasmid Mini-prep kit was used. Standard manufacturer protocol used; elution in 50 &#181; L
 
-
<html>
+
Sigma Genelute Plasmid Mini-prep kit (lot # 048k6062)as used. Standard manufacturer protocol used; elution in 50&#181;L of ddH<sub>2</sub>O.
 +
<br><br>
 +
<style>
 +
.center {
 +
display: block;
 +
margin-left: auto;
 +
margin-right: auto;
 +
}
 +
</style>
 +
<div class="center">
 +
<table style="border-collapse:collapse; font-variant: small-caps;">
 +
<tr style="border-bottom:1px solid #fff; border-top:1px solid #fff;">
 +
<td width="100px">Plasmid sample</td>
 +
<td width="50px">260/280</td>
 +
<td width="50px">260/230</td>
 +
<td width="150px">Concentration(ng/&#181;L)</td>
 +
</tr>
 +
<tr>
 +
<td>TOP10 <i>luxOU</i> C1</td>
 +
<td>1.91</td>
 +
<td>2.58</td>
 +
<td>365.6</td>
 +
</tr>
 +
<tr>
 +
<td>TOP10 <i>luxOU</i> C2</td>
 +
<td>1.90</td>
 +
<td>2.52</td>
 +
<td>287.2</td>
 +
</tr>
 +
<tr>
 +
<td>BBK <i>luxOU</i> C1</td>
 +
<td>1.87</td>
 +
<td>2.22</td>
 +
<td>534.2</td>
 +
</tr>
 +
<tr>
 +
<td>BBK <i>luxOU</i> C2</td>
 +
<td>1.92</td>
 +
<td>2.24</td>
 +
<td>715.2</td>
 +
</tr>
 +
</table>
</div>
</div>
 +
</div>
 +
<br>
</td>
</td>
</tr>
</tr>
Line 175: Line 266:
<br>
<br>
<div class="heading">
<div class="heading">
-
DESCRIPTIVE TITLE OF WHAT YOU'RE DOING - ALL CAPS UNLESS YOU ARE USING TERMINOLOGY THAT REQUIRES NO CAPS
+
Plasmid Isolation of luxOD47A in pCR2.1 TOPO and psB1AC3 vectors
</div>
</div>
<br>
<br>
<div class="desc">
<div class="desc">
</html>
</html>
-
WIKI CODING HERE
+
The purpose was to isolate plasmid containing luxOD47A, as a means of starting the construction of the mutant circuits. TOPO T/A and psB1AC3 vectors containing luxOD47A were isolated using the Sigma GenElute Plasmid Mini-prep kit. 100μL of ddH2O were used to elute, and the purity and concentration of each plasmid were measured using the NanoDrop Spectrophotometer.
 +
 
 +
<html>
 +
</div>
 +
</td>
 +
</tr>
 +
 
 +
<tr>
 +
<td height="10px" bgcolor="#222222">
 +
</td>
 +
</tr>
 +
 
 +
<tr>
 +
<td>
 +
<a name="Katie"></a>
 +
<br>
 +
<div class="heading">
 +
KATIE
 +
</div>
 +
<br>
 +
<div class="heading">
 +
Challenges Faced with PCR
 +
</div>
 +
<br>
 +
<div class="desc">
 +
</html>
 +
* Working on the virtual PCR machine and completed a general PCR first
 +
* Making it work for PCR with three different types of DNA and placed it initially in three separate scripts and only one would run if it had all of its items. I really want to find a better way to do this so I will continue to work on this.
 +
 
 +
Problem: Items are not being found and it is causing an error on the debug channel and it was not happening before so I will have to find what I have changed in the past day to see what went wrong. It seems to be something that goes wrong within the for loop I have since it seems to be locating everything when there are items missing. I will most likely see to this problem tomorrow.
<html>
<html>
Line 201: Line 321:
<br>
<br>
<div class="heading">
<div class="heading">
-
DESCRIPTIVE TITLE OF WHAT YOU'RE DOING - ALL CAPS UNLESS YOU ARE USING TERMINOLOGY THAT REQUIRES NO CAPS
+
Plasmid Isolation of <i>Pqrr4</i> for Reporter circuit
</div>
</div>
<br>
<br>
<div class="desc">
<div class="desc">
 +
The <i>Pqrr4</i> was isolated from TOPO T/A and biobrick AC (pSB1AC3) using Sigma’s Genelute Plasmid Mini-prep kit (sigma) according to the specifications of the manufacturer. Nanodrop utility along with the Spectrophotometer was used to measure the concentration and purity of the isolated plasmid. The wavelength was set at 260nm.
 +
<br>
 +
<br>
 +
<center>
 +
<b>HTML Code, just as an example for now</b>
 +
<table border="1">
 +
<tr>
 +
<td> <b>Plasmid</b> </td><td> <b>260/280</b>    </td><td> <b>260/230</b> </td><td> <b>Concentration [ng/μL]</b>
 +
</td></tr>
 +
<tr>
 +
<td> <i>Pqrr4</i> TOPO Blue tube </td><td><center> 1.81 </center></td><td><center> 2.24 </center></td><td> 181
 +
</td></tr>
 +
<tr>
 +
<td> <i>Pqrr4</i> TOPO Pink tube </td><td><center> 1.81 </center></td><td><center> 2.02 </center></td><td> 231.3
 +
</td></tr>
 +
<tr>
 +
<td> <i>Pqrr4</i> BBK Green tube </td><td><center> 1.76 </center></td><td><center> 1.66 </center></td><td> 51.2
 +
</td></tr>
 +
<tr>
 +
<td> <i>Pqrr4</i> BBK Pink tube </td><td> 1.85 </td><td> 1.45 </td><td> 60.6
 +
</td></tr></table></center>
 +
<br>
 +
*The two TOPO vectors were from the same colony, thus labelled "Green tube" instead of C1. The two BBK plasmids were also from same colony, so same label applies.
</html>
</html>
-
WIKI CODING HERE
+
<center>
 +
<br>
 +
<b>Wiki Code</b> <br>
 +
Table 1. Purity and concentration of <i>Pqrr4</i> measured with Nanodrop utility and Spectrophotometer
 +
{| border="1"
 +
| '''Plasmid''' || '''260/280'''    || '''260/230''' || '''Concentration [ng/μL]'''
 +
|-
 +
| ''Pqrr4'' TOPO Blue Tube|| 1.81 || 2.24 || 181
 +
|-
 +
| ''Pqrr4'' TOPO Pink Tube|| 1.81 || 2.02 ||231.3
 +
|-
 +
| ''Pqrr4'' BBK Green Tube|| 1.76 || 1.66 || 51.2
 +
|-
 +
| ''Pqrr4'' BBK Pink Tube|| 1.85 || 1.45 || 60.6
 +
|}
 +
</center>
<html>
<html>
Line 217: Line 375:
</td>
</td>
</tr>
</tr>
 +
 +
<tr>
 +
<td>
 +
<a name="Patrick"></a>
 +
<br>
 +
<div class="heading">
 +
PATRICK
 +
</div>
 +
<br>
 +
<div class="heading">
 +
What's in a (DNA Part) Name?
 +
</div>
 +
<br>
 +
<div class="desc">
 +
</html>
 +
Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.
 +
 +
Continued developing the script for sending names from one part to the next, so that each could learn where the other was. The problem was that each DNA part in a polymer needs to know the key of the next part, in order to direct the RNA Polymerase to the next part when it visits the current one. Yet object keys weren't stable between sessions, so we needed some additional internal name for each part to go by. Each part would know its internal name, and the name of the next part in the sequence. Then it can use that name to obtain the key of the next part via a message and reply.
 +
 +
I first began to use comma separated values (CSV) to encode my messages, which worked so well I never needed to change it. This is thanks to some good built in tools for CSV handling in the linden scripting language.
 +
 +
<html>
 +
</div>
 +
</td>
 +
</tr>
 +
 +
<tr>
 +
<td height="10px" bgcolor="#222222">
 +
</td>
 +
</tr>
 +
 +
<tr>
 +
<td>
 +
<a name="Prima"></a>
 +
<br>
 +
<div class="heading">
 +
PRIMA
 +
</div>
 +
<br>
 +
<div class="heading">
 +
Back from Dragon's Den
 +
</div>
 +
<br>
 +
<div class="desc">
 +
</html>
 +
We returned home on the evening of May 26th, weary from the experience and yet somehow craving more of it. Having satisfied both of our original ambitions, we were pleased with the result and thankful that we were more than just another meal for a few Dragons in the vicinity. Armed with a new sense of promotional direction, more contacts who can help support our initiatives, and the same stunning good looks that we had before we left, we are excited to implement some of these ideas to help capitalize on our marketing potential.
 +
 +
<html>
 +
</div>
 +
</td>
 +
</tr>
 +
 +
<tr>
 +
<td height="10px" bgcolor="#222222">
 +
</td>
 +
</tr>
 +
<tr>
<tr>
Line 227: Line 442:
<br>
<br>
<div class="heading">
<div class="heading">
-
DESCRIPTIVE TITLE OF WHAT YOU'RE DOING - ALL CAPS UNLESS YOU ARE USING TERMINOLOGY THAT REQUIRES NO CAPS
+
Plasmid isolation with mini-prep
</div>
</div>
<br>
<br>
<div class="desc">
<div class="desc">
</html>
</html>
-
WIKI CODING HERE
+
 
 +
<b>Purpose:</b><br>
 +
To isolate the plasmid DNA from the rest of the bacteria for colonies containing LuxPQ on TOPO II Blunt and LuxPQ BBk on psB1AC3.
 +
 
 +
<br>
 +
Reference: The user manual and the Sigma Aldrich site
 +
 
 +
<br>
 +
Kit: MP70 GeneElute Plasmid mini-prep kit. Note that it had been previously used, which may be a problem for contamination.
 +
 
 +
<br>
 +
<b>Materials and methods:</b><br>
 +
Procedure was carried out in accordance with our Plasmid Isolation protocol. When complete, we stored our isolated plasmids in the freezer for concentration measurement and content analysis over the next 2 days.
 +
 
 +
<br>
 +
<b>Results:</b><br>
 +
We were left with tubes containing the described plasmids. Quantifiable details on their concentrations and actual contents are outlined on the May 27 and May 28 entries.
 +
 
 +
<html>
 +
<br>
 +
<div class="heading">
 +
DNA concentration measurements with the Nanodrop spectrophotometer
 +
</div>
 +
<br>
 +
<div class="desc">
 +
</html>
 +
 
 +
<b>Purpose:</b><br> To measure the DNA concentration of LuxPQ plasmids that were isolated in the May 26 miniprep
 +
 
 +
<br>
 +
<b>Materials and Methods:</b><br> The DNA measurement area was cleaned with isopropanol and KimWipes to clear off any trace residue from previous uses. The sample wavelength was set to 260 nm. A blank measurement was made with 1 uL of ddHOH. 1 uL of the sample in question was added to the Nanodrop measurement area. The measurement was made; the sample area was wiped down; and a new sample was measured.
 +
 
 +
<br>
 +
<b>Results:</b>
 +
<br>
 +
<br>
 +
<center>
 +
{| border="1"
 +
| '''Plasmid''' || '''260/280'''    || '''260/230''' || '''Concentration [ng/μL]'''
 +
|-
 +
| ''LuxPQ'' TOPO C1  || 1.83 || 1.86 || 338.2
 +
|-
 +
| ''LuxPQ'' TOPO C2|| 1.81 || 1.87 || 284.2
 +
|-
 +
| ''LuxPQ'' BBK C1|| 1.90 || 2.34 || 295.5
 +
|-
 +
| ''LuxPQ'' BBK C2|| 1.90 || 2.29 || 313.2
 +
|}
 +
</center>
<html>
<html>

Latest revision as of 02:54, 19 October 2009

University of Calgary

UNIVERSITY OF CALGARY



THIS MONTH

May
MTWTFSS
        [http://2009.igem.org/Team:Calgary/1_May_2009 1] [http://2009.igem.org/Team:Calgary/2_May_2009 2] [http://2009.igem.org/Team:Calgary/3_May_2009 3]
[http://2009.igem.org/Team:Calgary/4_May_2009 4] [http://2009.igem.org/Team:Calgary/5_May_2009 5] [http://2009.igem.org/Team:Calgary/6_May_2009 6] [http://2009.igem.org/Team:Calgary/7_May_2009 7] [http://2009.igem.org/Team:Calgary/8_May_2009 8] [http://2009.igem.org/Team:Calgary/9_May_2009 9] [http://2009.igem.org/Team:Calgary/10_May_2009 10]
[http://2009.igem.org/Team:Calgary/11_May_2009 11] [http://2009.igem.org/Team:Calgary/12_May_2009 12] [http://2009.igem.org/Team:Calgary/13_May_2009 13] [http://2009.igem.org/Team:Calgary/14_May_2009 14] [http://2009.igem.org/Team:Calgary/15_May_2009 15] [http://2009.igem.org/Team:Calgary/16_May_2009 16] [http://2009.igem.org/Team:Calgary/17_May_2009 17]
[http://2009.igem.org/Team:Calgary/18_May_2009 18] [http://2009.igem.org/Team:Calgary/19_May_2009 19] [http://2009.igem.org/Team:Calgary/20_May_2009 20] [http://2009.igem.org/Team:Calgary/21_May_2009 21] [http://2009.igem.org/Team:Calgary/22_May_2009 22] [http://2009.igem.org/Team:Calgary/23_May_2009 23] [http://2009.igem.org/Team:Calgary/24_May_2009 24]
[http://2009.igem.org/Team:Calgary/25_May_2009 25] [http://2009.igem.org/Team:Calgary/26_May_2009 26] [http://2009.igem.org/Team:Calgary/27_May_2009 27] [http://2009.igem.org/Team:Calgary/28_May_2009 28] [http://2009.igem.org/Team:Calgary/29_May_2009 29] [http://2009.igem.org/Team:Calgary/30_May_2009 30] [http://2009.igem.org/Team:Calgary/31_May_2009 31]


NOTEBOOK PAGE INDEX
Carol
Chinmoyee
Emily
Fahd
Iman
Jamie
Jeremy
Katie
Kevin
Mandy
Patrick
Prima
Stefan
Vicki



CALENDAR

May
MTWTFSS
        [http://2009.igem.org/Team:Calgary/1_May_2009 1] [http://2009.igem.org/Team:Calgary/2_May_2009 2] [http://2009.igem.org/Team:Calgary/3_May_2009 3]
[http://2009.igem.org/Team:Calgary/4_May_2009 4] [http://2009.igem.org/Team:Calgary/5_May_2009 5] [http://2009.igem.org/Team:Calgary/6_May_2009 6] [http://2009.igem.org/Team:Calgary/7_May_2009 7] [http://2009.igem.org/Team:Calgary/8_May_2009 8] [http://2009.igem.org/Team:Calgary/9_May_2009 9] [http://2009.igem.org/Team:Calgary/10_May_2009 10]
[http://2009.igem.org/Team:Calgary/11_May_2009 11] [http://2009.igem.org/Team:Calgary/12_May_2009 12] [http://2009.igem.org/Team:Calgary/13_May_2009 13] [http://2009.igem.org/Team:Calgary/14_May_2009 14] [http://2009.igem.org/Team:Calgary/15_May_2009 15] [http://2009.igem.org/Team:Calgary/16_May_2009 16] [http://2009.igem.org/Team:Calgary/17_May_2009 17]
[http://2009.igem.org/Team:Calgary/18_May_2009 18] [http://2009.igem.org/Team:Calgary/19_May_2009 19] [http://2009.igem.org/Team:Calgary/20_May_2009 20] [http://2009.igem.org/Team:Calgary/21_May_2009 21] [http://2009.igem.org/Team:Calgary/22_May_2009 22] [http://2009.igem.org/Team:Calgary/23_May_2009 23] [http://2009.igem.org/Team:Calgary/24_May_2009 24]
[http://2009.igem.org/Team:Calgary/25_May_2009 25] [http://2009.igem.org/Team:Calgary/26_May_2009 26] [http://2009.igem.org/Team:Calgary/27_May_2009 27] [http://2009.igem.org/Team:Calgary/28_May_2009 28] [http://2009.igem.org/Team:Calgary/29_May_2009 29] [http://2009.igem.org/Team:Calgary/30_May_2009 30] [http://2009.igem.org/Team:Calgary/31_May_2009 31]


June
MTWTFSS
[http://2009.igem.org/Team:Calgary/1_June_2009 1] [http://2009.igem.org/Team:Calgary/2_June_2009 2] [http://2009.igem.org/Team:Calgary/3_June_2009 3] [http://2009.igem.org/Team:Calgary/4_June_2009 4] [http://2009.igem.org/Team:Calgary/5_June_2009 5] [http://2009.igem.org/Team:Calgary/6_June_2009 6] [http://2009.igem.org/Team:Calgary/7_June_2009 7]
[http://2009.igem.org/Team:Calgary/8_June_2009 8] [http://2009.igem.org/Team:Calgary/9_June_2009 9] [http://2009.igem.org/Team:Calgary/10_June_2009 10] [http://2009.igem.org/Team:Calgary/11_June_2009 11] [http://2009.igem.org/Team:Calgary/12_June_2009 12] [http://2009.igem.org/Team:Calgary/13_June_2009 13] [http://2009.igem.org/Team:Calgary/14_June_2009 14]
[http://2009.igem.org/Team:Calgary/15_June_2009 15] [http://2009.igem.org/Team:Calgary/16_June_2009 16] [http://2009.igem.org/Team:Calgary/17_June_2009 17] [http://2009.igem.org/Team:Calgary/18_June_2009 18] [http://2009.igem.org/Team:Calgary/19_June_2009 19] [http://2009.igem.org/Team:Calgary/20_June_2009 20] [http://2009.igem.org/Team:Calgary/21_June_2009 21]
[http://2009.igem.org/Team:Calgary/22_June_2009 22] [http://2009.igem.org/Team:Calgary/23_June_2009 23] [http://2009.igem.org/Team:Calgary/24_June_2009 24] [http://2009.igem.org/Team:Calgary/25_June_2009 25] [http://2009.igem.org/Team:Calgary/26_June_2009 26] [http://2009.igem.org/Team:Calgary/27_June_2009 27] [http://2009.igem.org/Team:Calgary/28_June_2009 28]
[http://2009.igem.org/Team:Calgary/29_June_2009 29] [http://2009.igem.org/Team:Calgary/30_June_2009 30]


July
MTWTFSS
    [http://2009.igem.org/Team:Calgary/1_July_2009 1] [http://2009.igem.org/Team:Calgary/2_July_2009 2] [http://2009.igem.org/Team:Calgary/3_July_2009 3] [http://2009.igem.org/Team:Calgary/4_July_2009 4] [http://2009.igem.org/Team:Calgary/5_July_2009 5]
[http://2009.igem.org/Team:Calgary/6_July_2009 6] [http://2009.igem.org/Team:Calgary/7_July_2009 7] [http://2009.igem.org/Team:Calgary/8_July_2009 8] [http://2009.igem.org/Team:Calgary/9_July_2009 9] [http://2009.igem.org/Team:Calgary/10_July_2009 10] [http://2009.igem.org/Team:Calgary/11_July_2009 11] [http://2009.igem.org/Team:Calgary/12_July_2009 12]
[http://2009.igem.org/Team:Calgary/13_July_2009 13] [http://2009.igem.org/Team:Calgary/14_July_2009 14] [http://2009.igem.org/Team:Calgary/15_July_2009 15] [http://2009.igem.org/Team:Calgary/16_July_2009 16] [http://2009.igem.org/Team:Calgary/17_July_2009 17] [http://2009.igem.org/Team:Calgary/18_July_2009 18] [http://2009.igem.org/Team:Calgary/19_July_2009 19]
[http://2009.igem.org/Team:Calgary/20_July_2009 20] [http://2009.igem.org/Team:Calgary/21_July_2009 21] [http://2009.igem.org/Team:Calgary/22_July_2009 22] [http://2009.igem.org/Team:Calgary/23_July_2009 23] [http://2009.igem.org/Team:Calgary/24_July_2009 24] [http://2009.igem.org/Team:Calgary/25_July_2009 25] [http://2009.igem.org/Team:Calgary/26_July_2009 26]
[http://2009.igem.org/Team:Calgary/27_July_2009 27] [http://2009.igem.org/Team:Calgary/28_July_2009 28] [http://2009.igem.org/Team:Calgary/29_July_2009 29] [http://2009.igem.org/Team:Calgary/30_July_2009 30] [http://2009.igem.org/Team:Calgary/31_July_2009 31]


August
MTWTFSS
          [http://2009.igem.org/Team:Calgary/1_August_2009 1] [http://2009.igem.org/Team:Calgary/2_August_2009 2]
[http://2009.igem.org/Team:Calgary/3_August_2009 3] [http://2009.igem.org/Team:Calgary/4_August_2009 4] [http://2009.igem.org/Team:Calgary/5_August_2009 5] [http://2009.igem.org/Team:Calgary/6_August_2009 6] [http://2009.igem.org/Team:Calgary/7_August_2009 7] [http://2009.igem.org/Team:Calgary/8_August_2009 8] [http://2009.igem.org/Team:Calgary/9_August_2009 9]
[http://2009.igem.org/Team:Calgary/10_August_2009 10] [http://2009.igem.org/Team:Calgary/11_August_2009 11] [http://2009.igem.org/Team:Calgary/12_August_2009 12] [http://2009.igem.org/Team:Calgary/13_August_2009 13] [http://2009.igem.org/Team:Calgary/14_August_2009 14] [http://2009.igem.org/Team:Calgary/15_August_2009 15] [http://2009.igem.org/Team:Calgary/16_August_2009 16]
[http://2009.igem.org/Team:Calgary/17_August_2009 17] [http://2009.igem.org/Team:Calgary/18_August_2009 18] [http://2009.igem.org/Team:Calgary/19_August_2009 19] [http://2009.igem.org/Team:Calgary/20_August_2009 20] [http://2009.igem.org/Team:Calgary/21_August_2009 21] [http://2009.igem.org/Team:Calgary/22_August_2009 22] [http://2009.igem.org/Team:Calgary/23_August_2009 23]
[http://2009.igem.org/Team:Calgary/24_August_2009 24] [http://2009.igem.org/Team:Calgary/25_August_2009 25] [http://2009.igem.org/Team:Calgary/26_August_2009 26] [http://2009.igem.org/Team:Calgary/27_August_2009 27] [http://2009.igem.org/Team:Calgary/28_August_2009 28] [http://2009.igem.org/Team:Calgary/29_August_2009 29] [http://2009.igem.org/Team:Calgary/30_August_2009 30]
[http://2009.igem.org/Team:Calgary/31_August_2009 31]


September
MTWTFSS
  [http://2009.igem.org/Team:Calgary/1_September_2009 1] [http://2009.igem.org/Team:Calgary/2_September_2009 2] [http://2009.igem.org/Team:Calgary/3_September_2009 3] [http://2009.igem.org/Team:Calgary/4_September_2009 4] [http://2009.igem.org/Team:Calgary/5_September_2009 5] [http://2009.igem.org/Team:Calgary/6_September_2009 6]
[http://2009.igem.org/Team:Calgary/7_September_2009 7] [http://2009.igem.org/Team:Calgary/8_September_2009 8] [http://2009.igem.org/Team:Calgary/9_September_2009 9] [http://2009.igem.org/Team:Calgary/10_September_2009 10] [http://2009.igem.org/Team:Calgary/11_September_2009 11] [http://2009.igem.org/Team:Calgary/12_September_2009 12] [http://2009.igem.org/Team:Calgary/13_September_2009 13]
[http://2009.igem.org/Team:Calgary/14_September_2009 14] [http://2009.igem.org/Team:Calgary/15_September_2009 15] [http://2009.igem.org/Team:Calgary/16_September_2009 16] [http://2009.igem.org/Team:Calgary/17_September_2009 17] [http://2009.igem.org/Team:Calgary/18_September_2009 18] [http://2009.igem.org/Team:Calgary/19_September_2009 19] [http://2009.igem.org/Team:Calgary/20_September_2009 20]
[http://2009.igem.org/Team:Calgary/21_September_2009 21] [http://2009.igem.org/Team:Calgary/22_September_2009 22] [http://2009.igem.org/Team:Calgary/23_September_2009 23] [http://2009.igem.org/Team:Calgary/24_September_2009 24] [http://2009.igem.org/Team:Calgary/25_September_2009 25] [http://2009.igem.org/Team:Calgary/26_September_2009 26] [http://2009.igem.org/Team:Calgary/27_September_2009 27]
[http://2009.igem.org/Team:Calgary/28_September_2009 28] [http://2009.igem.org/Team:Calgary/29_September_2009 29] [http://2009.igem.org/Team:Calgary/30_September_2009 30]


October
MTWTFSS
      [http://2009.igem.org/Team:Calgary/1_October_2009 1] [http://2009.igem.org/Team:Calgary/2_October_2009 2] [http://2009.igem.org/Team:Calgary/3_October_2009 3] [http://2009.igem.org/Team:Calgary/4_October_2009 4]
[http://2009.igem.org/Team:Calgary/5_October_2009 5] [http://2009.igem.org/Team:Calgary/6_October_2009 6] [http://2009.igem.org/Team:Calgary/7_October_2009 7] [http://2009.igem.org/Team:Calgary/8_October_2009 8] [http://2009.igem.org/Team:Calgary/9_October_2009 9] [http://2009.igem.org/Team:Calgary/10_October_2009 10] [http://2009.igem.org/Team:Calgary/11_October_2009 11]
[http://2009.igem.org/Team:Calgary/12_October_2009 12] [http://2009.igem.org/Team:Calgary/13_October_2009 13] [http://2009.igem.org/Team:Calgary/14_October_2009 14] [http://2009.igem.org/Team:Calgary/15_October_2009 15] [http://2009.igem.org/Team:Calgary/16_October_2009 16] [http://2009.igem.org/Team:Calgary/17_October_2009 17] [http://2009.igem.org/Team:Calgary/18_October_2009 18]
[http://2009.igem.org/wiki/index.php?title=Team:Calgary/19_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 19] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/20_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 20] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/21_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 21] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/22_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 22] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/23_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 23] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/24_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 24] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/25_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 25]
[http://2009.igem.org/wiki/index.php?title=Team:Calgary/26_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 26] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/27_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 27] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/28_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 28] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/29_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 29] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/30_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 30] [http://2009.igem.org/wiki/index.php?title=Team:Calgary/31_October_2009&preload=Team:Calgary/NotebookPreload&action=edit 31]



MAY 26, 2009


CAROL

Plasmid Isolation of ''luxCDABE'' in TOPO vector

The purpose of plasmid isolation is to extract plasmids from E. coli that has topo vector with luxCDABE. Overnight cultures were prepared and Sigma Mini Prep kit was used to to isolate plasmids (see protocols for detailed procedures). The plasmids was finally eluted in the elution buffer provided by the kit to a total of 50uL.

The concentration of plasmids was determined using the nano-drop apparatus at 260nm wavelength (see protocols for detailed procedures) and the following table summarizes the concentrations of plasmids.



Plasmid 260/280 260/230 Concentration [ng/μL]
luxCDABE TOPO C1 2.21 4.58 47.6
luxCDABE TOPO C2 2.09 3.39 56.0


EMILY

Plasmid Isolation of LuxOD47E in pCR2.1 TOPO and psB1AC3 vectors

  • Objective: To extract plasmids of LuxOD47E in pCR2.1-TOPO vector from overnight cultures.
  • Protocol: Used Sigma GenElute Plasmid Miniprep Kit (Sigma), lot # 048k6062, used as according to the manufacturers instructions, eluting in 50 μL ddH20.
  • Results: Used Nanodrop 1000 Spectrophotometer read at 260 wavelength to determine DNA concentrations
Plasmid 260/280 260/230 Concentration [ng/μL]
LuxOD47E TOPO C1 1.88 2.21 409.5
LuxOD47E TOPO C2 1.86 2.18 551.4
LuxOD47E BBK C1 2.04 5.01 551.4
LuxOD47E BBK C2 1.77 1.39 92.9


JAMIE

Plasmid Isolation of luxOU in pCR-Blunt II-TOPO and psB1AC3

Sigma Genelute Plasmid Mini-prep kit (lot # 048k6062)as used. Standard manufacturer protocol used; elution in 50µL of ddH2O.

Plasmid sample 260/280 260/230 Concentration(ng/µL)
TOP10 luxOU C1 1.91 2.58 365.6
TOP10 luxOU C2 1.90 2.52 287.2
BBK luxOU C1 1.87 2.22 534.2
BBK luxOU C2 1.92 2.24 715.2


JEREMY

Plasmid Isolation of luxOD47A in pCR2.1 TOPO and psB1AC3 vectors

The purpose was to isolate plasmid containing luxOD47A, as a means of starting the construction of the mutant circuits. TOPO T/A and psB1AC3 vectors containing luxOD47A were isolated using the Sigma GenElute Plasmid Mini-prep kit. 100μL of ddH2O were used to elute, and the purity and concentration of each plasmid were measured using the NanoDrop Spectrophotometer.


KATIE

Challenges Faced with PCR

  • Working on the virtual PCR machine and completed a general PCR first
  • Making it work for PCR with three different types of DNA and placed it initially in three separate scripts and only one would run if it had all of its items. I really want to find a better way to do this so I will continue to work on this.

Problem: Items are not being found and it is causing an error on the debug channel and it was not happening before so I will have to find what I have changed in the past day to see what went wrong. It seems to be something that goes wrong within the for loop I have since it seems to be locating everything when there are items missing. I will most likely see to this problem tomorrow.


KEVIN

Plasmid Isolation of Pqrr4 for Reporter circuit

The Pqrr4 was isolated from TOPO T/A and biobrick AC (pSB1AC3) using Sigma’s Genelute Plasmid Mini-prep kit (sigma) according to the specifications of the manufacturer. Nanodrop utility along with the Spectrophotometer was used to measure the concentration and purity of the isolated plasmid. The wavelength was set at 260nm.

HTML Code, just as an example for now
Plasmid 260/280 260/230 Concentration [ng/μL]
Pqrr4 TOPO Blue tube
1.81
2.24
181
Pqrr4 TOPO Pink tube
1.81
2.02
231.3
Pqrr4 BBK Green tube
1.76
1.66
51.2
Pqrr4 BBK Pink tube 1.85 1.45 60.6

*The two TOPO vectors were from the same colony, thus labelled "Green tube" instead of C1. The two BBK plasmids were also from same colony, so same label applies.


Wiki Code
Table 1. Purity and concentration of Pqrr4 measured with Nanodrop utility and Spectrophotometer

Plasmid 260/280 260/230 Concentration [ng/μL]
Pqrr4 TOPO Blue Tube 1.81 2.24 181
Pqrr4 TOPO Pink Tube 1.81 2.02 231.3
Pqrr4 BBK Green Tube 1.76 1.66 51.2
Pqrr4 BBK Pink Tube 1.85 1.45 60.6


PATRICK

What's in a (DNA Part) Name?

Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.

Continued developing the script for sending names from one part to the next, so that each could learn where the other was. The problem was that each DNA part in a polymer needs to know the key of the next part, in order to direct the RNA Polymerase to the next part when it visits the current one. Yet object keys weren't stable between sessions, so we needed some additional internal name for each part to go by. Each part would know its internal name, and the name of the next part in the sequence. Then it can use that name to obtain the key of the next part via a message and reply.

I first began to use comma separated values (CSV) to encode my messages, which worked so well I never needed to change it. This is thanks to some good built in tools for CSV handling in the linden scripting language.


PRIMA

Back from Dragon's Den

We returned home on the evening of May 26th, weary from the experience and yet somehow craving more of it. Having satisfied both of our original ambitions, we were pleased with the result and thankful that we were more than just another meal for a few Dragons in the vicinity. Armed with a new sense of promotional direction, more contacts who can help support our initiatives, and the same stunning good looks that we had before we left, we are excited to implement some of these ideas to help capitalize on our marketing potential.


VICKI

Plasmid isolation with mini-prep

Purpose:
To isolate the plasmid DNA from the rest of the bacteria for colonies containing LuxPQ on TOPO II Blunt and LuxPQ BBk on psB1AC3.


Reference: The user manual and the Sigma Aldrich site


Kit: MP70 GeneElute Plasmid mini-prep kit. Note that it had been previously used, which may be a problem for contamination.


Materials and methods:
Procedure was carried out in accordance with our Plasmid Isolation protocol. When complete, we stored our isolated plasmids in the freezer for concentration measurement and content analysis over the next 2 days.


Results:
We were left with tubes containing the described plasmids. Quantifiable details on their concentrations and actual contents are outlined on the May 27 and May 28 entries.


DNA concentration measurements with the Nanodrop spectrophotometer

Purpose:
To measure the DNA concentration of LuxPQ plasmids that were isolated in the May 26 miniprep


Materials and Methods:
The DNA measurement area was cleaned with isopropanol and KimWipes to clear off any trace residue from previous uses. The sample wavelength was set to 260 nm. A blank measurement was made with 1 uL of ddHOH. 1 uL of the sample in question was added to the Nanodrop measurement area. The measurement was made; the sample area was wiped down; and a new sample was measured.


Results:

Plasmid 260/280 260/230 Concentration [ng/μL]
LuxPQ TOPO C1 1.83 1.86 338.2
LuxPQ TOPO C2 1.81 1.87 284.2
LuxPQ BBK C1 1.90 2.34 295.5
LuxPQ BBK C2 1.90 2.29 313.2

Retrieved from "http://2009.igem.org/Team:Calgary/26_May_2009"