Team:Caltech/Week 3

From 2011.igem.org

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Line 12: Line 12:
Checked DDT and nonylphenol cultures, will wait until tomorrow to transfer<br/>
Checked DDT and nonylphenol cultures, will wait until tomorrow to transfer<br/>
Ethanol precipitation of DNA extractions from LA river samples following protocol<br/>
Ethanol precipitation of DNA extractions from LA river samples following protocol<br/>
-
Streak out cells from fosmid kit<br/>
 
Prepare antibiotic stocks (Ampicillin, Chloramphenicol)<br/><br/>
Prepare antibiotic stocks (Ampicillin, Chloramphenicol)<br/><br/>
===Results===
===Results===
Line 55: Line 54:
Analysis of sequencing results from yesterday<br/>
Analysis of sequencing results from yesterday<br/>
Transfer DDT and nonylphenol cultures to new media <br/>
Transfer DDT and nonylphenol cultures to new media <br/>
-
Transform mCherry ([http://partsregistry.org/Part:BBa_J06702 J06702]), Lac Promoter ([http://partsregistry.org/Part:BBa_R0010 R0010]), double terminator ([http://partsregistry.org/Part:BBa_B0014 B0014] and [http://partsregistry.org/Part:BBa_B0015 B0015]) and Tet Promoter ([http://partsregistry.org/Part:BBa_R0040 R0040])for creation of glycerol stocks
+
Transform mCherry ([http://partsregistry.org/Part:BBa_J06702 J06702]), Lac Promoter ([http://partsregistry.org/Part:BBa_R0010 R0010]), double terminator ([http://partsregistry.org/Part:BBa_B0014 B0014] and [http://partsregistry.org/Part:BBa_B0015 B0015]) and Tet Promoter ([http://partsregistry.org/Part:BBa_R0040 R0040]) for creation of glycerol stocks
===Results===
===Results===
Line 117: Line 116:
</tr>
</tr>
<tr>
<tr>
-
<td>6/28 3</td>
+
<td>6/28 [http://partsregistry.org/Part:BBa_B0014 B0014]</td>
<td>15.2</td>
<td>15.2</td>
</tr>
</tr>
<tr>
<tr>
-
<td>6/28 4</td>
+
<td>6/28 [http://partsregistry.org/Part:BBa_R0040 R0040]</td>
<td>49.1</td>
<td>49.1</td>
</tr>
</tr>
<tr>
<tr>
-
<td>6/28 5</td>
+
<td>6/28 [http://partsregistry.org/Part:BBa_K123001 K123001]</td>
<td>42.0</td>
<td>42.0</td>
</tr>
</tr>
<tr>
<tr>
-
<td>6/28 6</td>
+
<td>6/28 [http://partsregistry.org/Part:BBa_B0015 B0015]</td>
<td>112.0</td>
<td>112.0</td>
</tr>
</tr>
<tr>
<tr>
-
<td>6/29 1</td>
+
<td>6/29 [http://partsregistry.org/Part:BBa_R0010 R0010]</td>
<td>112.7</td>
<td>112.7</td>
</tr>
</tr>
<tr>
<tr>
-
<td>6/29 2</td>
+
<td>6/29 [http://partsregistry.org/Part:BBa_K123000 K123000]</td>
<td>168.0</td>
<td>168.0</td>
</tr>
</tr>
Line 149: Line 148:
===Results===
===Results===
[[File: 630pcrgel.png|thumb|PCR of parts for pNT001 and pNT002: 1 & 2 [http://partsregistry.org/Part:BBa_B0014 B0014]; 3 & 4 [http://partsregistry.org/Part:pSB4A5 pSB4A5]; 5 blank; 6 ladder]]
[[File: 630pcrgel.png|thumb|PCR of parts for pNT001 and pNT002: 1 & 2 [http://partsregistry.org/Part:BBa_B0014 B0014]; 3 & 4 [http://partsregistry.org/Part:pSB4A5 pSB4A5]; 5 blank; 6 ladder]]
-
B0014 appeared in the gel. But [http://partsregistry.org/Part:pSB4A5 pSB4A5] did not. We are redoing PCR of [http://partsregistry.org/Part:pSB4A5 pSB4A5] with primers to add the prefix and suffix with longer annealing and elongating times.
+
B0014 appeared in the gel, but [http://partsregistry.org/Part:pSB4A5 pSB4A5] did not. We are redoing PCR of [http://partsregistry.org/Part:pSB4A5 pSB4A5] with primers to add the prefix and suffix with longer annealing and elongating times.<br/>
 +
 
 +
Concentration of the 5 K145001 minipreps:
 +
<table border="1">
 +
<tr>
 +
<th>Miniprep</th>
 +
<th>Concentration (ng/ul)</th>
 +
</tr>
 +
<tr>
 +
<td>1</td>
 +
<td>154.7</td>
 +
</tr>
 +
<tr>
 +
<td>2</td>
 +
<td>356.7</td>
 +
</tr>
 +
<tr>
 +
<td>3</td>
 +
<td>153.2</td>
 +
</tr>
 +
<tr>
 +
<td>4</td>
 +
<td>146.4</td>
 +
</tr>
 +
<tr>
 +
<td>5</td>
 +
<td>138.2</td>
 +
</tr>
 +
</table>
 +
 
<div><div>
<div><div>
==July 1==
==July 1==
<p>Dpn1 digest and purification of [http://partsregistry.org/Part:pSB4A5 pSB4A5] PCR<br/>
<p>Dpn1 digest and purification of [http://partsregistry.org/Part:pSB4A5 pSB4A5] PCR<br/>
Run a gel of [http://partsregistry.org/Part:pSB4A5 pSB4A5] PCR<br/>
Run a gel of [http://partsregistry.org/Part:pSB4A5 pSB4A5] PCR<br/>
-
Gibson assemble pNT001 and pNT002 and negative controls following Joe's protocol.<br/>
 
-
Transform pNT001 and pNT002 into competent cells<br/>
 
Check sequencing of K145001<br/>
Check sequencing of K145001<br/>
-
Check if enrichment cultures are ready for transfer</p>
+
Check if enrichment cultures are ready for transfer<br/>
 +
Try running PCR at different annealing temperatures (55˚, 60˚, 65˚ C)<br/>
 +
Try the PCR, using the 4x5backbone primers on [http://partsregistry.org/Part:pSB4K5 pSB4K5]<br/>
 +
Order more 4x5 backbone primer<br/>
 +
Transform [http://partsregistry.org/PartpSB4A5 pSB4A5] from the distribution plate into XL-10 gold competent cells in case our source of plasmid is bad</p>
 +
 
 +
===Results===
 +
[[File: 7-1 PCRgelpSB4A5.jpg|thumb|PCR of pSB4A5: 1 ladder; 2 blank; 3, 4, 5 pSB4A5]]
 +
[[File:7-1temppcr4x5.jpg|thumb|left|PCR of 4x5 primers with pSB4A5 and pSB4K5 at different annealing temperatures: 1 ladder; 2 blank; 3 pSB4A5 55˚C; 4 pSB4K5 55˚C; 5  pSB4A5 60˚C; 6 pSB4K5 60˚C; 7 pSB4A5 65˚C; 8 pSB4K5 65˚C]]
 +
No bands appeared in the first gel (right), indicating that the PCR did not work.<br/><br/>
 +
PCR using different annealing temperatures had bands in every experimental lane, indicating that the PCR worked.<br/><br/>
 +
Aligned K145001 to sequence reads of the five samples. Sample 2 is most likely one containing the T7 polymerase, as the alignment seems best and BLASTn searches through Geneious of forward and reverse sequence reads both give a hit of NC_001604, part of the T7 genome.<br/><br/>
 +
<table border="1">
 +
<tr>
 +
<th>6/30 B0014 PCR purification</th>
 +
<th>Concentration (ng/ul)</th>
 +
</tr>
 +
<tr>
 +
<td>1</td>
 +
<td>30.3</td>
 +
</tr>
 +
<tr>
 +
<td>2</td>
 +
<td>31.5</td>
 +
</tr>
 +
</table>
==July 2==
==July 2==
-
<p>Check plates from Gibson transformations. Do colony PCR if necessary<br/>
+
<p>Gibson assemble pNT001 and pNT002 with negative controls and transform into competent cells<br/>
Check if enrichment cultures are ready for transfer</p>
Check if enrichment cultures are ready for transfer</p>
 +
 +
===Results===
 +
Concentration of pSB4A5 PCRs:
 +
<table border="1">
 +
<tr>
 +
<th>pSB4A5 PCR temp. (C)</th>
 +
<th>Concentration (ng/ul)</th>
 +
</tr>
 +
<tr>
 +
<td>55</td>
 +
<td>73.4</td>
 +
</tr>
 +
<tr>
 +
<td>60</td>
 +
<td>127.5</td>
 +
</tr>
 +
<tr>
 +
<td>65</td>
 +
<td>83.9</td>
 +
</tr>
 +
</table>
 +
All of the enrichment cultures remain clear.
}}
}}

Latest revision as of 23:15, 11 July 2011


Caltech iGEM 2011



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June 26

Start overnight cultures of T7 polymerase ([http://partsregistry.org/Part:BBa_K145001 K145001]), mCherry ([http://partsregistry.org/Part:BBa_J06702 J06702]), Lac Promoter ([http://partsregistry.org/Part:BBa_R0010 R0010]), double terminator ([http://partsregistry.org/Part:BBa_B0014 B0014] and [http://partsregistry.org/Part:BBa_B0015 B0015]) and Tet Promoter ([http://partsregistry.org/Part:BBa_R0040 R0040])

June 27

Miniprep of T7 polymerase ([http://partsregistry.org/Part:BBa_K145001 K145001]), mCherry ([http://partsregistry.org/Part:BBa_J06702 J06702]), Lac Promoter ([http://partsregistry.org/Part:BBa_R0010 R0010]), double terminator ([http://partsregistry.org/Part:BBa_B0014 B0014] and [http://partsregistry.org/Part:BBa_B0015 B0015]) and Tet Promoter ([http://partsregistry.org/Part:BBa_R0040 R0040]) and submit for sequencing
Transfer 0.5 mL aliquots of BPA and 5 mL aliquots 17a-ethynylestradiol cultures from June 23 to fresh minimal media
Checked DDT and nonylphenol cultures, will wait until tomorrow to transfer
Ethanol precipitation of DNA extractions from LA river samples following protocol
Prepare antibiotic stocks (Ampicillin, Chloramphenicol)

Results

Miniprep

Part Concentration(ng/ul)
B0014 230.5
B0015 254.1
J06702 301.3
K145001 205.6
R0010 117.3
R0040 156.8

We found growth in one of our BPA enrichment cultures, and slight growth in our ethinyl estradiol cultures. We transferred these vials today.

June 28

Send off continued forward sequencing for HER
PCR for Gibson assembly of PNT001 and PNT002
Gel and PCR purification of PCR products
Analysis of sequencing results from yesterday
Transfer DDT and nonylphenol cultures to new media
Transform mCherry ([http://partsregistry.org/Part:BBa_J06702 J06702]), Lac Promoter ([http://partsregistry.org/Part:BBa_R0010 R0010]), double terminator ([http://partsregistry.org/Part:BBa_B0014 B0014] and [http://partsregistry.org/Part:BBa_B0015 B0015]) and Tet Promoter ([http://partsregistry.org/Part:BBa_R0040 R0040]) for creation of glycerol stocks

Results

Sequencing: All biobricks showed correct sequence except T7 Polymerase

PCR of parts for pNT001 and pNT002(BioBricks + primers for Gibson): From left to right: 1 ladder; 2 blank; 3 [http://partsregistry.org/Part:BBa_R0010 R0010]; 4 [http://partsregistry.org/Part:BBa_K123000 K123000]; 5 [http://partsregistry.org/Part:BBa_B0014 B0014]; 6 [http://partsregistry.org/Part:BBa_R0040 R0040]; 7 [http://partsregistry.org/Part:BBa_K123001 K123001]; 8 [http://partsregistry.org/Part:BBa_B0015 B0015]

Ran a gel of the PCR products. Strangely, lanes 3 and 4 show no DNA. We will repeat the PCR of lanes 3-5 and Gibson assemble pNT001 ([http://partsregistry.org/Part:BBa_R0010 R0010], [http://partsregistry.org/Part:BBa_K123000 K123000], [http://partsregistry.org/Part:BBa_B0014 B0014]) later in the week.

EtOH precipitation of Soil Extractions from June 21

Tube/Location Number Concentration(ng/ul)
1 13.6
2 15.2
4 8.3
5 11.4
6 25.5
7 23.5
9 261.3
10 74.0

June 29

Redo PCR of [http://partsregistry.org/Part:BBa_R0010 R0010] and [http://partsregistry.org/Part:BBa_K123000 K123000]
Analyze sequence of ER, design new primer for continued sequencing
Prepare overnight cultures of K145001 colonies for sequencing and overnight cultures of other biobrick plates for creating glycerol stocks
Plan experiments using pNT001 and pNT002

Results

PCR of parts for pNT001(BioBricks+primers for Gibson): 1 ladder; 2 blank; 3 [http://partsregistry.org/Part:BBa_R0010 R0010]; 4 [http://partsregistry.org/Part:BBa_K123000 K123000]; 5 [http://partsregistry.org/Part:BBa_B0014 B0014]; 6 primers from lane 3 for negative control

Estrogen receptor ([http://partsregistry.org/Part:BBa_K123003 K123003]) sequencing is back. Again, the translation is right, but the bases don't match. The stop codon is not in this read. We will keep sequencing.

[http://partsregistry.org/Part:BBa_B0014 B0014] was not amplified in PCR. We will PCR this part and primers again, as the PCR from June 28 has a rather low concentration to be used for Gibson Assembly.

Concentration of Purified PCR products from June 28 and June 29

Tube Number Concentration(ng/ul)
6/28 [http://partsregistry.org/Part:BBa_B0014 B0014] 15.2
6/28 [http://partsregistry.org/Part:BBa_R0040 R0040] 49.1
6/28 [http://partsregistry.org/Part:BBa_K123001 K123001] 42.0
6/28 [http://partsregistry.org/Part:BBa_B0015 B0015] 112.0
6/29 [http://partsregistry.org/Part:BBa_R0010 R0010] 112.7
6/29 [http://partsregistry.org/Part:BBa_K123000 K123000] 168.0

June 30

Miniprep 5 K145001 cultures and send them off for sequencing
Make glycerol stocks of mCherry ([http://partsregistry.org/Part:BBa_J06702 J06702]), Lac Promoter ([http://partsregistry.org/Part:BBa_R0010 R0010]), double terminator ([http://partsregistry.org/Part:BBa_B0014 B0014] and [http://partsregistry.org/Part:BBa_B0015 B0015]) and Tet Promoter ([http://partsregistry.org/Part:BBa_R0040 R0040])
Repeat PCR of B0014 and perform PCR to linearize backbone vector (pSB4A5)
Digest PCR products with DpnI and purify

Results

PCR of parts for pNT001 and pNT002: 1 & 2 [http://partsregistry.org/Part:BBa_B0014 B0014]; 3 & 4 [http://partsregistry.org/Part:pSB4A5 pSB4A5]; 5 blank; 6 ladder

B0014 appeared in the gel, but [http://partsregistry.org/Part:pSB4A5 pSB4A5] did not. We are redoing PCR of [http://partsregistry.org/Part:pSB4A5 pSB4A5] with primers to add the prefix and suffix with longer annealing and elongating times.

Concentration of the 5 K145001 minipreps:

Miniprep Concentration (ng/ul)
1 154.7
2 356.7
3 153.2
4 146.4
5 138.2

July 1

Dpn1 digest and purification of [http://partsregistry.org/Part:pSB4A5 pSB4A5] PCR
Run a gel of [http://partsregistry.org/Part:pSB4A5 pSB4A5] PCR
Check sequencing of K145001
Check if enrichment cultures are ready for transfer
Try running PCR at different annealing temperatures (55˚, 60˚, 65˚ C)
Try the PCR, using the 4x5backbone primers on [http://partsregistry.org/Part:pSB4K5 pSB4K5]
Order more 4x5 backbone primer
Transform [http://partsregistry.org/PartpSB4A5 pSB4A5] from the distribution plate into XL-10 gold competent cells in case our source of plasmid is bad

Results

PCR of pSB4A5: 1 ladder; 2 blank; 3, 4, 5 pSB4A5
PCR of 4x5 primers with pSB4A5 and pSB4K5 at different annealing temperatures: 1 ladder; 2 blank; 3 pSB4A5 55˚C; 4 pSB4K5 55˚C; 5 pSB4A5 60˚C; 6 pSB4K5 60˚C; 7 pSB4A5 65˚C; 8 pSB4K5 65˚C

No bands appeared in the first gel (right), indicating that the PCR did not work.

PCR using different annealing temperatures had bands in every experimental lane, indicating that the PCR worked.

Aligned K145001 to sequence reads of the five samples. Sample 2 is most likely one containing the T7 polymerase, as the alignment seems best and BLASTn searches through Geneious of forward and reverse sequence reads both give a hit of NC_001604, part of the T7 genome.

6/30 B0014 PCR purification Concentration (ng/ul)
1 30.3
2 31.5

July 2

Gibson assemble pNT001 and pNT002 with negative controls and transform into competent cells
Check if enrichment cultures are ready for transfer

Results

Concentration of pSB4A5 PCRs:

pSB4A5 PCR temp. (C) Concentration (ng/ul)
55 73.4
60 127.5
65 83.9

All of the enrichment cultures remain clear.


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