Team:Caltech/Week 3

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Revision as of 17:59, 30 June 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
Streak out cells from fosmid kit
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 3	15.2
6/28 4	49.1
6/28 5	42.0
6/28 6	112.0
6/29 1	112.7
6/29 2	168.0

June 30

Miniprep 5 K145001 cultures and send them off for sequencing before noon 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
Digest PCR products with DpnI and purify
Make gibson mix, run gibson reaction and transform
For gels tomorrow: Use Joe's sybr safe.

@@ Line 104: / Line 104: @@
 Redo PCR of [http://partsregistry.org/Part:BBa_R0010 R0010] and [http://partsregistry.org/Part:BBa_K123000 K123000]<br/>
 Analyze sequence of ER, design new primer for continued sequencing<br/>
+Prepare overnight cultures of K145001 colonies for sequencing and overnight cultures of other biobrick plates for creating glycerol stocks<br/>
 Plan experiments using pNT001 and pNT002</p>
 ===Results===
@@ Line 144: / Line 145: @@
 <p>Miniprep 5 K145001 cultures and send them off for sequencing before noon
 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])<br/>
-Ask Joe if we need to PCR plasmid or if he has linear plasmid<br/>
+Repeat PCR of B0014 and perform PCR to linearize backbone vector <br/>
-If we need to linearize: Borrow plasmid primers and plasmid, do PCR. Repeat failed PCR (Primers 9 and 10 and DNA B0014) along with it <br/>
+Digest PCR products with DpnI and purify<br/>
-If we don't, then repeat failed PCR <br/>
+Make gibson mix, run gibson reaction and transform<br/>
-Get recipe from Joe for gibson mix and gibson protocol, make gibson mix, and run gibson reaction and transform<br/>
 For gels tomorrow: Use Joe's sybr safe.</p>
-== This Week ==
-<p>
-Email other teams <br/>
-Use pNT001 and pNT002 to test degradation parts</p>
-}}