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
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
Gibson assemble pNT001 and pNT002 and negative controls following Joe's protocol.
Transform pNT001 and pNT002 into competent cells
Check sequencing of K145001
Check if enrichment cultures are ready for transfer
July 2
Check plates from Gibson transformations. Do colony PCR if necessary
Check if enrichment cultures are ready for transfer
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