Team:TU Delft/Notebook
Notebook
Workspace
Our lab
We have our own iGEM TU Delft lab in the new Applied Science building on the edge of the TU Delft campus. It is classified as an ML-1 lab, the lowest safety level to work with modified organisms, which is enough for our experiments. Apart from this lab, we are also working in an optical lab, which is also ML-1 classified. In here built our own laser set-up.
Our office
Our office is our homebase for when we're not working in the lab. Here we work on things like the safety tool, the wiki, the modeling, and processing our results. This summer the Bionanoscience department moved to a new building, so it took some time before we had our own office. When we finally got our office, we quickly made it our home. Next to our office, there is a meeting room, where we have a weekly meeting with our TA’s and PI’s to keep everyone up to date and discuss problems we might encounter.
Lab safety
Our lab is classified the lowest safety level (level 1), meaning that our experiments involve low to no risk. All the members of the team have successfully completed the following safety tests: Lab safety test General safety test of the building we currently work in Biological safety test for ML-1 lab General safety test of the building we worked in before June All the members of the team have received safety training, including: Introduction to sterile working General lab training (using a PCR machine, making gels, etc.) General safety information, regarding contact persons and locations The safety of our experiments was supervised by Erwin van Rijn (Safety Manager of the lab) and Jeremie Capoulade (Safety Manager of the lasers). The supplies we needed in the lab were provided with the help of our instructor Esengül Yildirim. The research has been conducted with respect to the regulations of biosafety for The Netherlands, that can be found here.
Day Notes
29th June 2016
María
Prepare 10mL of antibiotic stocks of both antibiotics that are going to be used during the project: Chloramphenicol (Cm) and Ampicillin (Amp). Make 500µL and 1mL aliquots.
Prepare 1L of LB medium and 3 400mL bottles of LB Agar. Send to autoclave.
30th June 2016
María
Add antibiotics to the LB Agar bottles prepared the previous day and pour plates to have them ready for when we start transforming.
4th July 2016
Lycka
Digestion gBlocks mVenus and mKate with EcoRI and PstI.
Made liquid culture of strain containing pSB4A5 bakcbone with RFP.
María
Digestion of pSB1C3 linearized backbone from the distribution kit with EcoRI and PstI.
5th July 2016
María
Dissolution of necessary parts from distribution kit: GFP BioBrick BBa_E0840 and promoters BBa_J23100, BBa_J23105, BBa_J23108, BBa_J23113 and BBa_J23117.
Dissolution of K1149051 (a kind gift of Imperial College), which was sent dry on filter paper.
Lycka
Ligation of mKate into backbone pSB1C3.
Transformation of ligation product mKate and the BioBricks dissolved by María into Escherichia coli Top10 cells. These were plated on LB medium supplemented with Cm.
6th July 2016
Lycka
Stocked primers VF2 and VR: storage stock (100µM) and working stock (10µM).
Colony PCR of transformants from yesterday with primers VF2 and VR followed by gel electrophoresis. Gel picture yielded no bands. This might be attributed to a fault in the transformation.
7th July 2016
María
Transformation of same BioBricks as on 5th July using a different transformation protocol since we believed that the negative result was due to a mistake during transformation.
8th July 2016
María
Finally, the plasmids containing K1149051 and BBa_E0840 yielded a few colonies. However, the ones containing the promoters did not. Thus, we believe that the distribution kit plate containing the promoters is defective and the mKate ligation also featured some problems.
11th July 2016
Lycka
To test whether the distribution kit might be the problem, transformation of BBa_J23113 in OneShot® TOP10 chemically competent cells (Invitrogen) to make sure the transformation process is not the cause of the negative results. Also, a plasmid containing TU Delft 2015 csgA Biobrick was used as a positive control.
For the mKate construct we will obtain the backbone from another construct instead of the linearized backbones from the iGem distribution kit.
12th July 2016
Lycka
Measure DNA concentration of biobricks from registry by nanodrop.
Nanodrop
| Product | Concentration (ng/µl) |
|---|---|
| J23113 | 89.3 |
| J23117 | 91.7 |
| J23105 | 89.3 |
| J23108 | 92.7 |
| J23100 | 93.4 |
| E0840 | 81.9 |
As can be seen from the table, there is DNA presence in the samples. Therefore, something else should be causing the transformations not to work. Since last year's distribution kit plates are still available in the lab and those plasmids were not taken we will try to get these parts from 2015 distribution kit.
María
Transfer colonies for K1149051 and BBa_E0840 to overnight LB+Cm culture. A colony containing CsgA was transfered as well to be able to isolate and use that plasmid as standard backbone for all synthesized parts.
13th July 2016
María
Plasmid isolation of overnight cultures prepared yesterday and preparation of K1149051 and BBa_E0840 samples for sequencing.
Lycka
Cryostocks of K1149051 and BBa_E0840 overnight culures. Stored at -80 degrees.
Digestion of backbones pSB1C3, pSB4A5 and all gBlocks with EcorI and PstI.
14th July 2016
Lycka
Gel purification of digested backbones. Dissolved in nuclease free water, stored at -20 degrees.
Ligation of synthesized fragments into backbones.
María
After all the problems transforming in the past weeks, we tested if we could use our homemade chemically competent cells for future transformations by transforming a couple of positive controls, which were taken from last year's plasmids. The transformations worked so these cells can still be used.
15th July 2016
María
Transformation of Lycka's ligation products from yesterday and the BioBricks from the distribution kit were given one last chance. Transformed cells were plated after doubling their concentration.
Lycka
Dissolution of promoter BioBricks from 2015 iGEM distribution kit.
18th July 2016
Lycka
Restriction of backbones pSB1C3 and pSB4A5 with EcorI and PstI. Gel electrophoresis of digested fragments. Gel picture yielded no bands.
19th July 2016
Lycka
Transformation of BioBricks from the distribution kit of 2015, since the ones from 2016 yielded no colonies. Positive control: csgA. Negative control: water. Biobricks: J23100, J23108, J23105, J23117, J23113. Overnight cultivation yielded no result, we decide to drop this and add the promoters to the parts that need it by PCR.
María
Restriction of pSB1C3 and pSB4A5 backbones with EcoRI and PstI
Ligation of synthesized parts that could not be ligated on 14th of July: INP_Sil_Sdom in pSB1C3 and BolA_ind and BolA_con in both pSB1C3 and pSB4A5.
20th July 2016
Lycka and Tessa
Transformation of plasmids ligated by Maria (19th of July) together with the ones ligated on 14th of July. After overnight culture the following plates contained colonies. pSB1C3: INP_Sil_Sdom, OmpA_Sil_Taur, Sil_Sdom, SulA, BolA_ind, BolA_con, phaP. pSB4A5: BolA_con. The ones with a negative result were ligated again the next day.
21th July 2016
María
Colony PCR of yesterday's transformation results from Lycka and Tessa. However, not all transformations yielded colonies.
Lycka
Ligation of mKate, mVenus, mCerulean, OmpA_Sil_Sdom and LacI into pSB1C3. Ligation of OmpA_Sil_Taur, OmpA_Sil_Sdom, Sil_Sdom, SulA and BolA_ind into pSB4A5. Left at room temperature overnight.
22th July 2016
Lycka
Transformation of ligation products from yesterday. Cells containing backbones pSB1C3 or pSB4A5 were plated on plates supplemented with chloramphenicol or ampicilin, respectively. After overnight cultivation the following plates contained colonies: mKate, mVenus, mCerulean, OmpA_Sil_Sdom, Sil_Sdom, SulA, BolA_ind.
24th July 2016
Lycka
Cryostocking and minipreping of colonies picked by Maria (23th of July). Cryostocks stored at -80 degrees, minipreped plasmid stored at -20 degrees.
25th July 2016
Lycka
Nanodrop and prepare for sequencing minipreped plasmids yesterday. Sequencing resulted in the following. Correct sequence: Sil_Sdom (pSB1C3), OmpA_Sil_Taur (pSB1C3), Sil_Sdom (pSB4A5), SulA (pSB4A5). Sequence with mutations: SulA (pSB1C3), BolA_ind (pSB1C3), J23108 (pSB1C3), BolA_con (pSB4A5), BolA_ind (pSB4A5). Different sequence: BolA_con (pSB1C3), INP_sil_Sdom (pSB1C3), OmpA_Sil_Sdom (pSB4A5). Mutated sequences can be repaired by PCR and blunt end ligation.
27th July 2016
Lycka
Colony PCR of plates transformed yesterday.
Picture on the left shows simulated agarose gel. Pictures in the middle and on the right show the actual agarose gel. Picked colonies marked with an arrow were cultivated in selective LB overnight.
29th July 2016
Lycka and Célina
Repeat of the colony PCR of plates from the 26th of July that yielded a negative result.
Picture on the left shows simulated agarose gel. Pictures in the middle and on the right show the actual agarose gel. Picked colonies marked with an arrow were cultivated in LB and the applicable antibiotic overnight.
Transformation of OmpA_Sil_Sdom in both different backbones.
30th July 2016
Lycka
Colony PCR of OmpA_Sil_Sdom in both backbones from the 29th of July. The PCR machine was filled with colonies from older plates which had not yielded any good colonies yet: mKate (26th of July), mKate (mKate 30th of June), INP_Sdom (20th of July).
Picture on the left shows simulated agarose gel. Pictures in the middle and on the right show the actual agarose gel. Picked colonies marked with an arrow were cultivated in LB and the applicable antibiotic overnight.
Cryostocking and minipreping of colonies picked by on 29th of July. Cryostocks stored at -80 degrees, minipreped plasmid stored at -20 degrees.
2nd August 2016
Tessa
Amplified E0840 (GFP) out of a pSB1C3-GFP plasmid using Phusion PCR. Four reactions of 50µl.
Nanodropped PCR products.
Nanodrop
| Product | Concentration (ng/µl) |
|---|---|
| E0840 | 339.6 |
| E0840 | 554.1 |
| E0840 | 596.9 |
| E0840 | 567.6 |
Ran a 1% agarose gel of the PCR product.
Stored product 2 and 4 in the fridge for later use.
10th August 2016
Tessa
Restricted PCR product of 3rd August, J23100 E0840, J23113 E0840 and J23117 E0840, with EcoRI-HF and PstI.
Purified restriction product.
Nanodropped purified product.
Nanodrop
| Product | Concentration (ng/µl) |
|---|---|
| J23100 E0840 | 14.7 |
| J23113 E0840 | 21.3 |
| J23117 E0840 | 23.3 |
Ligated purified product into pSB1C3.
Transformed ligation product into TOP10 strain. Using RFP as positive control and sterile MiliQ as negative control. Plated on plates with LB agar and CM.
11th August 2016
Tessa
Colony PCR'd colonies from yesterdays transformation.
Ran a 1% agarose gel of the PCR product.
Transferred colony 14 (J23113 E0840 pSB1C3) and 21 (J23117 E0840 pSB1C3) into liquid LB.
12th August 2016
Tessa
Miniprepped colony 14 and 21.
Nanodropped miniprep product.
Nanodrop
| Product | Concentration (ng/µl) |
|---|---|
| J23113 E0840 in pSB1C3 | 140.6 |
| J23117 E0840 in pSB1C3 | 325.6 |
Cryostocked colony 14 and 21.
Send miniprepped product for sequencing. [Sequence Confirmed]
