iGEM 2015 — Team CSU_Fort_Collins

# Team:CSU Fort Collins/Notebook

**COLORADO STATE**
**UNIVERSITY iGEM**

![](https://static.igem.org/mediawiki/2015/1/1d/CSU_iGEMLogo.jpg)

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* PROJECT
  [+ Description](https://2015.igem.org/Team%3ACSU_Fort_Collins/Description)
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[* NOTEBOOK](https://2015.igem.org/Team%3ACSU_Fort_Collins/Notebook)
[* ATTRIBUTIONS](https://2015.igem.org/Team%3ACSU_Fort_Collins/Attributions)
[* COLLABORATIONS](https://2015.igem.org/Team%3ACSU_Fort_Collins/Collaborations)
[* HUMAN PRACTICES](https://2015.igem.org/Team%3ACSU_Fort_Collins/Practices)
[* SAFETY](https://2015.igem.org/Team%3ACSU_Fort_Collins/Safety)
[* INTERLAB STUDY](https://2015.igem.org/Team%3ACSU_Fort_Collins/Measurement)

[* ENTREPRENEURSHIP](https://2015.igem.org/Team%3ACSU_Fort_Collins/Entrepreneurship)

##### Contents

[1 March](#Mar)
[2 April](#Apr)
[3 May](#May)
[4 June](#Jun)
[5 July](#Jul)
[6 August](#Aug)
[7 September](#Sep)

# Notebook

#### March:

##### 3/12/15:

Made overnight cultures of lac promoter in pSB1C3 and of KillerRed and trans-zeatin in backbones from synthesis.

##### 3/13/15:

Prepared minipreps from overnight cultures of lac promoter, KillerRed, and trans-zeatin plasmids.

##### 3/14/15:

Completed digestion, ligation, and transformation of *E. coli* with lac:KillerRed and lac:trans-zeatin.

##### 3/17/15:

Checked colonies with colony PCR protocol. Used annealing temperature of 65℃ and extension time of 2 minutes. Ran gel of results. lac:KillerRed colonies 4, 9 were successful.

![](https://static.igem.org/mediawiki/2015/8/8a/CSU_Jell_March17.png)
![](https://static.igem.org/mediawiki/2015/7/75/CSU_Gel2March17.png)

From left to right: Ladder 1, KillerRed colonies 1-9, ladder 2, trans-zeatin colonies 10-16, positive control

##### 3/18/15:

Miniprepped lac:KillerRed colonies from overnight cultures using kit instructions. Nanodropped results. Re-tried construction of lac:trans-zeatin.

##### 3/19/15:

Checked colonies of lac:trans-zeatin. Results successful.

#### May:

##### 5/15/15:

Miniprepped overnight cultures of KillerRed in pSB1C3. Attempted to create RBS:KillerRed using SLIM procedure. Made new LB, LB + Amp100 plates, and LB + Kn50 plates.

##### 5/18/15:

Checked May 15th results for RBS:KillerRed on gel; results unsuccessful. Retried procedure using a different thermocycler.

#### June:

##### 6/4/15:

Miniprepped RBS and P\_lac.

##### 6/5/15:

Used PCR to amplify FadD. Annealed at 48.5 ℃ , 55 ℃ , and 62.5 ℃ . Extension for 2 minutes.

##### 6/6/15:

Used PCR to amplify FadD. Annealed at 48.5 ℃ , 55 ℃ , and 62.5 ℃ . Extension for 2 minutes.

##### 6/9/15:

Ran gel on PCR product from FadD

![](https://static.igem.org/mediawiki/2015/c/c7/CSU_GelJun9.png)

Lane 1: 1 kb ladder Lane 2 & 3: FadD

##### 6/11/15:

Digested Biobrick backbone pSB1C3 (cut sites Spe, Pst), FadD (cut sites Xba, Pst), and P\_lac (cut sites Spe, Pst). Ligated FadD+P\_lac and FadD+pSB1C3 at 16 ℃ overnight.

##### 6/12/15:

Miniprepped P\_trp and Ribosome binding site (RBS) + KR and set up for sequencing. Transformed P\_lac + FadD and FadD into pSB1C3

##### 6/14/15:

Made overnight cultures of (RBS+KR)

##### 6/15/15:

Prepare media and overnight cultures for trans-zeatin growth experiment. Ran PCR check on P\_lac + FadD and FadD.

![](https://static.igem.org/mediawiki/2015/9/95/CSU_Gel1June15.png)![](https://static.igem.org/mediawiki/2015/0/03/CSU_Gel2June15.png)

Gel 1: Lanes 1 & 2 are FadD in pSB1c3 Gel 2: Lanes 6 & 7 are P\_lac +FadD

##### 6/16/15:

Followed procedure for trans-zeatin growth experiment up to a final growth time of 1 day.

##### 6/17/15:

Miniprepped the two successful FadD + pSB1C3 colonies and the two successful P\_lac + FadD colonies.

##### 6/18/15:

Ran HPLC procedure for analysis of [fermentative products](%E2%80%9Dhttps%3A//2015.igem.org/Team%3ACSU_Fort_Collins/Results#prod”). Miniprepped P\_trp again and re-digested and ligated. RBS+KR came back from sequencing correct so this was ligated with P\_trp

**InterLab:** Reconstitute BioBrick parts BBa\_J23106: 2015 Kit Plate 1, Well 22A. Size: 35 bp CmR and BBa\_I13504: 2015 Kit Plate 4, Well 21J. Size: 875 bp AmpRTransform J23106 and BBa\_I13504.

##### 6/19/15:

Transformed P\_trp+RBS+KR

##### 6/22/15:

Taq checked P\_trp+RBS+KR

**InterLab:** Reconstitute BioBrick parts BBa\_J23101: 2015 Kit Plate 1, Well 20K. Size: 35 bp. CmRTransform J23101 (Two plates: unconcentrated and concentrated) . Performed colony PCR on BBa\_J23106 and BBa\_I13504 transformed colinies.

##### 6/23/15:

Ran gel on Taq check from June 22nd and got no visible results.
Received sequencing results for FadD in pSB1C3 and P\_lac+FadD and overnight cultures were made to glycerol stock these products.

**InterLab:** Annotate and restreak. Pick and annotate 16 colonies onto new LB+Cm25 plates. Leave at 37°C overnight. Made overnight cultures of BBa\_J23106 and BBa\_I13504 transformed colinie

##### 6/24/15:

Made glycerol stocks of FadD in pSB1C3 and P\_lac+FadD
Attempted to dephosphorylate P\_trp backbone but was unsuccessful

**InterLab:** Colony PCR (16 rxns total). Run PCR products in 2% agarose gel.

![](https://static.igem.org/mediawiki/2015/5/58/CSU_Gel1Jun24.png)![](https://static.igem.org/mediawiki/2015/e/e4/CSU_Gel2June24.png)

The expected size of J23101 sequenced is 318bp, so all colonies look correct. We will move forward using colonies A and F because their bands are clear. Minipreped BBa\_J23106 and BBa\_I13504 overnights and sent them off for sequencing. Digested J23106 and I13504.

##### 6/25/15:

**InterLab:** Make overnight cultures of J23101 colonies A and F for Miniprep. Use 2mL of LB + 2uL of Cm (25mg/mL). Leave at 37°C overnight.

##### 6/26/15:

>

**InterLab:** Miniprep J23101 A and F using Promega kit and sent them off for sequencing.Decided to move ahead because the sizes from the gel looked correct. Digested 1ug of J23101 F. Decided to start more overnights from A and F J23101 colonies in case digestion doesn’t work. Sequencing confirmed for J23106 and I13504, digested J23106 and I13504 was done incorrectly because no PCR clean up was used.

##### 6/29/15:

**InterLab:** Miniprep J23101 A and F. J23106 and I13504 overnight cultures made for glycerol stocking and Miniprep.

##### 6/30/15:

**InterLab:** Overnight culture of J23101 F for glycerol stock. Minipreped, digested, and overnight ligation performed on J23106 and I13504.

#### July:

##### 7/1/15:

**InterLab:**Digest I13504 with XbaI and PstI.Glycerol stock J23101 F. Transformed J23106 and 13504 and grew on Amp25 plates.

##### 7/2/15:

**InterLab:** Ligation: J23101 and I13504. J23106 and 13504 had no growth. Religated J23106 into 13504

##### 7/3/15:

**InterLab:** Transformation of ligation reaction didn’t work. Transformed J23106 into 13504 and grew on Amp25 plates.

##### 7/6/15:

Made overnight cultures of P\_lac and P\_lac+KR in LB+Chloramphenicol (CM)

**InterLab:** Redo J23101 and I13504 digestions, ligation and transformation. Performed colony PCR on J23106 and I13504 colonies.

##### 7/7/15:

**InterLab:** Ran J23106 and I13504 colonies PCR results on 1% gel.

![](https://static.igem.org/mediawiki/2015/f/fa/CSU_GelJul7.png)

colonies from well 3 and 4 showed improper ligation.

##### 7/8/15:

Performed Quick and Dirty experiment and got a lawn of growth so protocol was rethought.

**InterLab:** Ligation transformation didn’t work. Redid digestions.Performed colony PCR on 14 new colonies from J23106 and I13504 transformation.

##### 7/9/15:

**InterLab:** Redo J23101 and I13504 ligation and transformation.Ran J23106 and I13504 colonies PCR results on 1% gel.

![](https://static.igem.org/mediawiki/2015/a/aa/CSU_Gel1Jul9.png)

gels show that transformation was unsuccessful.

##### 7/10/15:

**InterLab:** Transformation plates had lots of colonies.
Annotate and restreak colonies Pick and annotate onto new LB+Cm25 plates. Leave in incubator at 37°C overnight.Re-digest J23106 and I13504 and use heat inactivation instead of PCR clean up kit.

##### 7/13/15:

Performed Quick and Dirty experiment (see google drive) and got a lawn of growth so protocol was rethought.

**InterLab:** Run PCR products in agarose gel.

![](https://static.igem.org/mediawiki/2015/e/e1/CSU_Gel1Jul13.png)![](https://static.igem.org/mediawiki/2015/2/20/CSU_Gel2Jul13.png)

Colony #2 looks like the (only) ligated product. J23117+I13504 is about 1.2kb.Ligated J23106 into I13504 and transformed. Grew transformed cells on Amp25 plates.

##### 7/14/15:

Performed Killer Red Experiment (see drive) and KR was expressed.

>

**InterLab:** Make 2 overnight cultures of J23101+I13504 Colony 2.
2mL LB + 2uL Cm (25mg/mL). Ran colony PCR on 14 J23106 and I13504 transformed colonies.

##### 7/15/15:

Killer Red Experiment did not work as planned.

**InterLab:** Miniprep both cultures. Send one for sequencing with VF2 and VR. Ran J23106 andI13504 PCR products on 1% gel.

![](https://static.igem.org/mediawiki/2015/5/58/CSU_Gel1Jul15.png)

Successful

##### 7/15/15:

**InterLab:** Made J23106 and I13504 overnight cultures for sequencing.

##### 7/17/15:

Created media and prepared flasks for trans-zeatin growth experiment. The experiment needed to be repeated because we suspected that 1 day was not long enough for the trans-zeatin to be created in detectable amounts.

**InterLab:** Minipreped J23106 and I13504 and sent the off for sequencing.

##### 7/19/15:

Created overnight cultures of strains for trans-zeatin growth experiment.

##### 7/20/15:

Day 1 of trans-zeatin growth experiment.

.

**InterLab:** Although the prefix and J23101sequences are correct, I13504 and the suffix are unclear. The chromatogram signals for these last two regions were also very weak. I think the sequence is correct because Construct 2 group (Dylan, Dakota, Sam and Aidan) sequenced I13504. I will send for sequencing again.

##### 7/21/15:

Day 2 of trans-zeatin growth experiment.

##### 7/22/15:

Day 3 of trans-zeatin growth experiment. Collected final samples of liquid culture. Cells were accidentally thrown away, so the experiment needed to be repeated.

##### 7/28/15:

Started overnight culture of P\_lac+KR for Miniprep.

##### 7/29/15:

Anthony Miniprepped P\_lac+KR

##### 7/30/15:

Attempted transform, but used wrong competent cells

##### 7/31/15:

Did P\_lac+KR transformation with cells with strong LacI promoter

#### August:

##### 8/1/15:

Plate was too overgrown to do Taq polymerase check so transformation will be redone.

##### 8/3/15:

Transformation on P\_lac+KR

**Interlab:** Reconstitute J23177: 2015 kit, plate 1, Well 22K, Size: 35 bp, and transformed

##### 8/4/15:

Performed Taq check using Promega “GO Taq”

**Interlab:** Plates for J23117 transformed successfully and annotated on a LB+Cm plate.

##### 8/5/15:

Ran gel on PCR and results came back inconclusive as even ladder did not appear under UV light.

##### 8/6/15:

**Interlab:** Colony PCR for all 9 colonies.

##### 8/10/15:

**Interlab:** Take out samples from thermocycler. Start overnight culture of colony #6 for miniprep. Run 1.5% agarose gel.

![](https://static.igem.org/mediawiki/2015/e/e5/CSU_GelAug10.png)

##### 8/11/15:

**InterLab:** Send J23101+I13504 Colony 2 for sequencing again using VR primer.

**Interlab:** No growth in overnight. Accidentally used Amp instead of Cm.

##### 8/12/15:

**InterLab:** Miniprep J23117.

##### 8/17/15:

Overnight cultures of P\_lac and P\_lac+FadD were started.

**InterLab:** If the suffix sequence is correct, I think the I13504 sequence is most likely correct as well. At the mismatched sequences, there was a high background signal. I think this part is good for use in the Interlab measurements. Digestion J23117, ligation: J23117 and I13504, and transformed. Need to make glycerol stock of J23117. Prepare overnight culture.

##### 8/18/15:

ODs were taken on overnight samples of P\_lac and P\_lac+FadD. Results were inconclusive as P\_lac cells grew to a higher OD and much faster than the P\_lac+FadD cells.
KR+P\_lac was transformed and an overnight culture was started. Foil was used the whole time to prevent cells from being exposed to light.
Trans-Zeatin+FadD was transformed and an overnight culture was started.

**InterLab:** J23117+I13504 Colony PCR Check

![](https://static.igem.org/mediawiki/2015/e/e2/CSU_gelsAug18.png)

##### 8/19/15:

Made media, autoclaved flasks, and prepared overnight cultures to run trans-zeatin growth experiment. Both plates from August 18th had an acceptable number of colonies and the KR+P\_lac colonies were not red.

##### 8/20/15:

Day 1 of trans-zeatin growth experiment.

##### 8/21/15:

Day 2 of trans-zeatin growth experiment.

**InterLab:**J23117 Digestion and J23117+I13504 Ligation and Transformation.

Redo J23117+I13504 ligation. Make overnight of J23117 just in case ligation didn’t work because we don’t have any more plasmid stock.

##### 8/22/15:

Day 3 of trans-zeatin growth experiment.

**InterLab:** Check sequencing results for J23117+I13504-12 Colony PCR, and run 1.5% agarose gel.

![](https://static.igem.org/mediawiki/2015/f/fe/CSU_GelsAug22.png)

##### 8/23/15:

**InterLab:**Make overnights for J23117+I13504 #6, I20270 #20, I20270 #21 l.

##### 8/24/15:

**InterLab:** Miniprep and send for sequencing..

##### 8/25/15:

Ran PCR with F’i^2 cells and primers for the FadL gene using Phusion DNA polymerase. Reaction was ran in duplicate (2 total)

##### 8/26/15:

Gel was run and results were inconclusive (smear for product 1 and mark around 500bp for product 2)
SIx overnight KR cultures were started which contained 5ml LB, 5ul CM, and 2.5ul IPTG. 3 of these were inoculated with colonies of KR+P\_lac from 8-8-15. The other 3 were inoculated with P\_lac cells from glycerol stocks.

##### 8/27/15:

Ran PCR on FadL. Gel results came back with band of the right size indicating presence of FadL.
Started overnight of Lipase L1 from Bacillus Stearothermophilusfor sequencing and an overnight of both P\_lac and P\_lac+FadD.

**InterLab:** Check sequencing results.

#### September:

##### 9/7/15:

Made media and prepared bioreactors for trans-zeatin prototype (bioreactor experiment).

##### 9/8/15:

Transformed P\_lac+Lipase L1, P\_lac+FadL, P\_lac+FadD+FadL, and P\_lac+KR cultures.

##### 9/9/15:

PCR check done for all four transformations in replicates of 8. Taq DNA pol was used and the “Go Taq” DNA polymerase protocol from Promega was used.

##### 9/10/15:

Made 50 mL overnight cultures for bioreactor experiment.

##### 9/11/15:

Day 1 of bioreactor experiment. Gels were run on products 1-7 of P\_lac+Lipase L1, P\_lac\_FadD+FadL, and P\_lac + FadL.

##### 9/12/15:

Day 2 of bioreactor experiment.

##### 9/13/15:

Day 3 of bioreactor experiment.

##### 9/14/15:

Extracted zeatin from bioreactor and previous experimental results using single-phase extraction procedure. Set up for KillerRed experiment. Created overnights for part submissions.

##### 9/15/15:

Ran HPLC to detect zeatin production. Ran KillerRed experiment. Set up for 0.04% frying oil experiment. Miniprepped plasmids for submission to registry.

##### 9/16/15:

Ran 0.04% frying oil experiment. Prepared sample plate for submission.

##### 9/17/15:

Ran 100% and 50% frying oil experiment.