iGEM 2014 — Team SDU-Denmark

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# Team:SDU-Denmark/Notebook

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| Lab Journal | | |
| Week 25 (16/6 - 22/6) | | |
| Monday 16/6 | | |
| The lab crash course began. We talked a lot about the project goal and the way of getting there. The team is now on the same page and ready for a great summer of exciting and interesting work to begin. In the lab we learned where everything was located and learned how to run a PCR. - Sarah || Tuesday 17/6 | | |

| In the lab: The PCR from yeasterday didn't work, so they were repeated. This time 50 µL PCR reaction were prepared. Gel purification was performed on the PCR products and the final concentration was measured by nanodrop.- We digested the products by using restriction enzymes XbaI og SpeI. We detected that the plasmid was only linearized, meaning that only one restriction enzyme/ restriction site was functional.- We worked on the basics in the iGEM concept. We discussed the definitions of biobrick, basis part, composite part and deviced. We learned the "Standard Assembly Method", it's condition, uses and limitations.- We defined the conditions for our own device and started searching for the necessary parts in the iGEM registry -Victoria || Wednesday 18/6 | | |

| The XbaI enzyme didn't work to cut plasmid 161 tuesday and we wanted to find out what was wrong. We had different theories as to what went wrong tuesday:  * Maybe the XbaI didn't have enough time to cut the plasmid. We only gave it 5 minutes. * Maybe the restriction site on plasmid 161 didn't work.  To find out which of these theories was right we made three experiments:  1. We wanted to do the same as on tuesday, but allow the enzyme to work for 15 minutes instead of 5 minutes, in case this was our mistake. 2. We wanted to use the same plasmid as tuesday but cut it with EcoRI to see if this restriction site worked. 3. We wanted to try to cut a new plasmid (RFP) with the same enzyme for the same amount of time (5 minutes), to find out if the enzyme worked or not.  We ran these three experiments and also a control for each of the two plasmids on a PCR, and observed which plasmids where cut. We found out that something was wrong with the X restriction site of plasmid 161, since XbaI didn't cut plasmid 161 (not with 15 minutes either) but did in fact cut pRFP. Furthermore we found out that the E restriction site on plasmid 161 worked, since EcoRI was able to cut it. Besides the worked in the lab, we learned to design primers for Standard Assembly Method - Sarah We also recieved lab safety training || Friday 20/6 | | |

| Team page and Notebook page added to the wiki. - Sarah We tried to construct the TetR without the LVA-tag, 3 PCRs were made.- PCR 1 consisted of template 2:2P, primer yellow#5 and yellow#6. - PCR 2 consisted of template from previous made PCR2 and primers yellow#5 and yellow#7. - PCR 3 consisted of template 2:24D, primer yellow#8 and yellow#9. Standard operating procedure was used for creating the 3 reactions with 50µL. Our gel was odd, which turned out to be caused by mixing two different gel mixs. However, we were still able to cut out the bands anyhow , and they seemed to be okay. The gels were purified as the SOPs described. We had to stop our work here, since we lacked enzymes and were therefore not able to digest the PCR products. - Martin || Saturday 21/6 | | |

| All the pipettes were calibrated - [Odor-free strain - Yale](http://cgsc.biology.yale.edu/Strain.php?ID=64826) - [Odor-free strain - iGEM](http://parts.igem.org/Part%3ABBa_J45999)  A K12 MG1655 strain was plated out on agar, to colonize overnight, in order for us to produce more plasmid later on. - Martin || Sunday 22/6 | | |

| A coloni from the overnight plate was transferred to a bulb with 10 µL LB and TSB buffer was prepared using the SOB. 1,5 µL plasmid (65,3 ng/µL) was added and 1 hour at 37\*C were given for fenotypical expression. Everything else was done according to the SOP. The transformation was put on a chloramphenicol agar plate and left overnight in the heating cabinet. - Martin || Week 26 (23/6 - 29/6) | | |

| Monday 23/6 | | |
| The transformation from yesterday did not work.  Agar plates with antibiotics were created. Ampicillin (50µg/mL), Kanamycin (25µg/mL) and Chloramphenicol (33µg/mL). || Wednesday 25/6 | | |

| Transformation is attempted again today.  The e. Coli coloni was taken from the agarplate made on Saturday 21/6  Transformation was attempted with the four different plasmids: aza (from Ann Zahle), pSB1C3, pSB1A3, pSB1K3 (taken from igem kit 2013).  The transformed E. coli with the different plasmids, are spread onto agar plates with antibiotics (chloramphenicol, chloramphenicol, ampicillin, kanamycin respectively), and grown overnight.  Tomorrow the agar plates should be examined for any colonies.  - Jens J and Anne K || Thursday 26/6 | | |

| The results from yesterday's transformation showed that the E. coli culture with the plasmid aza (from Ann Zahle) had grown on the agar plate with ampicillin. The transformation of the E. coli culture with pSB1A3 was also successful. The transformation of the E. coli with pSB1C3 and pSB1K3 respectively were not successful, and should therefor be repeated.  A colony from each of the successful cultures were prepared for overnight growth in LB medium with ampicillin. Additionally an overnight culture of the wild type E. coli strain without the plasmid was prepared.  The cultures should be prepared for storage at -80°C tomorrow.  - Jens J | Friday 27/6 | | | |
| The overnight cultures from yesterday were prepared for storage at -80°C by mixing a sample from each culture with glycerol. The samples were then stored at -80°C.  - Jens J and Camilla|  |  |  | | --- | --- | --- | | Saturday 28/6 | | | |
| A new transformation was attempted with the plasmids pSB1C3 and pSB1K3. Two transformations were done of each plasmid. The cultures were put on agar plates with chloramphenicol and kanamycin respectively. Tomorrow the plates should be examined for cultures.  - Jens J and Camilla|  |  |  | | --- | --- | --- | | Sunday 29/6 | | | |
| The transformation was partially successful. There were some, but very few, visible colonies on the agar plates. Two overnight cultures were prepared from one colony respectively of the strain with kanamycin and chloramphenicol resistance.  - Jens J and Camilla|  |  |  | | --- | --- | --- | | Week 27 (30/6 - 6/7) | | | |
| Monday 30/6 | | |
| The overnight culture was not red, which means that something was wrong with the plasmid. Therefor a new overnight culture was prepared, so that colony pcr can be performed on the cultures. Furthermore an overnight culture was prepared of the wild type E. coli strain, so that it can be used for transformation tomorrow.  - Jens J|  |  |  | | --- | --- | --- | | Tuesday 1/7 | | | |
| Today colony PCR (iGEM2014\_SOP0021) was performed on the E. coli MG1655 strains with the plasmids: pSB1A3, pSB1C3, pSB1K3 and J04450 (also known as aza). The results showed that the constructs all had approximately the same weight, just below 1500 bp. This corresponds to the theoretical weight of the constructs, which is 1382 bp.  The development of the construct used to produce lacI was commenced. This was done by first running Phusion PCR (igem2014\_SOP010) on lacI (BBa\_I732100, Template 8A, Plate 3). The PCR product was then analysed on gel-electrophoresis and purified.  Transformation was performed on the plasmids pSB1C3 and pSB1K3 as the former transformation was unsuccessful. Furthermore transformation was also performed on the parts BBa\_R0010 (lacP promoter) and BBa\_E0840 (GFP coding seq.). The transformed E. coli were put on agar plates with antibiotic according to their respective resistance. The plates were placed in the heating cabinet and should be examined for colonies tomorrow.  -JJ|  |  |  | | --- | --- | --- | | Wednesday 2/7 | | | |
| Because the PCR on lacI from yesterday yielded a low concentration, Phusion PCR was repeated today, where both the PCR product from yesterday and BBa\_I732100 from iGEM were used as template. The results showed that the PCR product from yesterday was too short and still yielded a low concentration. While the PCR reaction with BBa\_I732100 as template produced a higher concentration of lacI.  The transformation on the parts BBa\_R0010 (lacP promoter) and BBa\_E0840 (GFP coding seq.) from yesterday was unsuccesful so the experiment was repeated today.  Freezing stocks of E. coli with pSB1C3 and pSB1K3 were stored at -80°C. Each culture were mixed with 50% glycerol  Furthermore fast digest on our 3 PCR products were made with XbaI and SpeI- PCR 1 consisted of template 2:2P, primer yellow#5 and yellow#6. - PCR 2 consisted of template from previous made PCR2 and primers yellow#5 and yellow#7. - PCR 3 consisted of template 2:24D, primer yellow#8 and yellow#9.  PCR 1 and 3 were ligated and PCR 2 and 3 were ligated. they are stored at 16°C overnight. - Anne | Thursday 3/7 | | | |
| Today the ligated PCR1/3 and PCR2/3 was purified by running them through a gel. The concentration of the purified constructs were measured by nano drop: - PCR1/3 = 2.8 ng/µL - PCR2/3 = 2.9 ng/µL  In order to create "sticky ends" on PCR1/3 and PCR2/3, the parts were fast digested. Also pSB1C3 was fast digested, so that it could be used as a backbone. The different fast digested parts were gel purified. PCR1/3 was then ligated to the backbone (pSB1C3) and PCR2/3 was ligated to the backbone (pSB1C3).  Colony PCR was performed on a colony from the yesterday transformation of the lacP promoter (BBa\_R0010) and GFP coding seq. (BBa\_E0840). Because the results showed that the sequences consisted of more base pairs than they theoretically should, a new colony PCR was performed on a different colony. The results from the new colony PCR were the same as before, with the weight of GFP just above 1000 bp and the weight of lacP promoter just around 500 bp.  - Jens Jakob | Friday 4/7 | | | |
| Today we startet with miniprep on our e. Coli containing lacP promoter (BBa\_R0010) and GFP coding seq. (BBa\_E0840)  A freezing stock was then made from the e. Coli with lacP promotor and with the GFP coding seq.  Further more there was made PCR on the products from the miniprep. Unfortunatly the PCR didn't work because the gel didn't show any products.  Because the PCR didn't work we found the products from the iGEM kit from 2014 and made PCR again.  This time the PCR worked and the products were gel purified and we then measured the concentration with nanodrop:- lacP promoter (BBa\_R0010) = 20,1 ng/µL - GFP coding seq. (BBa\_E0840) = 27,9 ng/µL || Saturday 5/7 | | |

| PCR was preformed on LVA less GFP with tet promoter using primers yellow#8 and yellow#9. The PCR was purified using the gel purification SOP.  A digest was done on PCR products #11 and #12 in an attempt to ligate these. Ligation was done in 30 mins at RT whereupon the ligase was inactivated at 65 °C for 10 mins. Purification of the ligation product was done, diverging from the SOP and resulting in an unusable amount of product.  - Daniel || Sunday 6/7 | | |

| The lacP promoter (BBa\_R0010)and GFP coding seq. (BBa\_E0840) have been ligated but the concentration was low and therefore we made PCR on the product.  The PCR product was run on gel. The band was hard to separate from other bands around the same length (1400bp). We cut the right length out and purified it. Nanodrop was measured to 53,3 ng/µL  PCR1 (consisting of template 2:2P, primers yellow#5 and yellow#6) and PCR2 (consisting of template 2:2P and primers yellow#5 and yellow#7) has both been cut with SpeI. PCR3 (consisting of template 2:24D and primers yellow#8 and yellow#9) has been cut with Xbai. PCR1 and PCR3 was attempted ligated (for 30 min) and so was PCR2 and PCR3. These ligations did not show any bands around the expected length (1700 bp) during gel purification. Two new ligations (of the same), with higher concentrations of digested PCR products, are reacting overnight.  - Anne and Ulrika || Week 28 (7/7 - 13/7) | | |

| Monday 7/7 | | |
| We realized that we have to step back in the process by inserting the different parts we want to ligate into a plasmid before ligating them to each other.  We then started our day in the lab by doing a PCR reaction on PCR1 (consisting of template 2:2P, primers yellow#5 and yellow#6) and PCR2 (consisting of template 2:2P and primers yellow#5 and yellow#7). Unfortunately PCR2 didn't show the right sequence when run on gel. This means we will have to repeat our PCR 2 from before to se if it works in second round.  PCR was also done on the lacP promoter (BBa\_R0010)and GFP coding seq. (BBa\_E0840). The sequences machted the the lenght seen in the gel. The band from the gel was cut out and purified.  - Anne || Tuesday 8/7 | | |

| Yesterday the following products were digested:- PCR 1, Pcon\_rbs\_BBa\_C0040(LVAtag\_removed)\_term - PCR 3, Ptet\_BBa\_E0840 - LacP, BBa\_R0010  These products were purified today.  Furthermore PCR on PCR 2 (Pcon\_rbs\_BBa\_C0040\_term) was repeated, this time with a gradient spanding from 53°C - 58°C. Our results were good this time. The products were purified and their concentrations varied from 10 ng/µL - 11,7 ng/µL.  - Anne || Wednesday 9/7 | | |

| Tet construct: The plasmid pSB1C3 was concentrated before it was digested with the enzymes Xbai and SpeI. The plasmid was ligated with the following:- The digested PCR1, Pcon\_rbs\_BBa\_C0040(LVAtag\_removed)\_term, from yesterday was ligated into plasmid - PCR2, Pcon\_rbs\_BBa\_C0040\_term, was digested with XbaI and SpeI to begin with and then ligated into plasmid - The digested PCR3, Ptet\_BBa\_E0840, from yesterday was ligated into plasmid Lac Construct:- Pcon\_rbs\_LacI(withoutLVA)\_term, BBa\_C0012, was digested with EcoRI and SpeI - GFP, BBa\_E0840 in plasmid has beed ligated - LacP, BBa\_R0010, was ligated with our C part in plasmid Transformation is made and we will have the results tomorrow. || Thursday 10/7 | | |

| The transformation from yesterday was successful. To examine if the digestion and ligation were a success, colony PCR was performed on all of the cultures. Four colonies were tested from each agar plate. The result showed that part B (Bba\_R0010) and C (Bba\_E0840) had been ligated successfully. Unfortunately nothing could be seen on the gel with regard to PCR1, PCR2 and PCR3. Therefor a new colony PCR was performed on the colonies with PCR1, PC2 and PCR3, but with VF2 and VR primers. |
| Friday 11/7 | | |
| Today we realized that XbaI didn't work well when we used green buffer for fast digest of our products. This leaded to an experiment where we compared digestion with green buffer and a colorless buffer, which we ran on gel afterwards. We saw that the green buffer didn't work optimally because the gel showed smear and there was very little of the disired product in general. We puridied our PCR products 1 (Pcon\_rbs\_BBa\_C0040(LVAtag\_removed)\_term) and 3 (Ptet\_BBa\_E0840) and digested these with the colorless buffer this time. || Saturday 12/7 | | |

| Ligation of our digested product, PCR 1 (Pcon\_rbs\_BBa\_C0040(LVAtag\_removed)\_term), PCR2 (Pcon\_rbs\_BBa\_C0040\_term) and PCR3 (Ptet\_BBa\_E0840), into a backbone, pSB1C3. Ligation of B(LacP, BBa\_R0010) and C (GFP, BBa\_E0840) konstruct into pSB1C3. Transformation on PCR 1(Pcon\_rbs\_BBa\_C0040(LVAtag\_removed)\_term),PCR2 (Pcon\_rbs\_BBa\_C0040\_term), PCR3 (Ptet\_BBa\_E0840) and BC (LacP, BBa\_R0010 + GFP, BBa\_E0840) into E. coli. || Sunday 13/7 | | |

| We made miniprep to get more plasmid pSB1C3, which can be used in experiments. || Week 29 (14/7 - 20/7) | | |

| Monday 14/7 | | |
| Over night culture was made on our wild type E. coli from freezing stock. The agar plates with our transformated plasmids from Saturday showed colonies with different colors. Colony PCR on the colonies that seemed to have worked was made and run on gel. The lenghts from colony PCR products had the right lengths. There was also made plate streaking from the colonies used for the colony PCR. || PCR was made on PCR 1 (Pcon\_rbs\_BBa\_C0040(LVAtag\_removed)\_term) (green 20), PCR2 (Pcon\_rbs\_BBa\_C0040\_term) (green 22), PCR3 (Ptet\_BBa\_E0840) (green 21) & lacI (part B, blue 7) using the protocol iGEM2014\_SOP0010\_v01\_Phusion PCR. Added 1μL template to each reaction -> 13,4 μL water. |

PCR program:

1. 98˚C 2 min.
2. 98 ˚C 10 sec.
3. 53 ˚C 30 sec.
4. 72 ˚C 15 sec.
5. GOTO 2REP 30
6. 72 ˚C 10 min.
7. HOLD 4 ˚C

PCR didn’t work on PCR2, PCR3 and lacI (part B, blue 7)

- Camilla J

| Tuesday 15/7 | | |
| Today we made colony PCR from the colonies we plate streaked yesterday. The PCR was repeated from yesterday to double check if our results were right. We had good results again which means we can make freezing stocks on our transformed E. coli. || Wednesday 16/7 | | |

| Today we started by doing miniprep of the ON cultures from yesterday (PCR 1, PCR 2, PCR3 and B+C in plasmid). Though the concentration was not high enough to be sent in to sequencing. The samples were therefor placed in the centrifugal evaporator to increase the concentration.  A new ON culture of these strains is prepared, in case that something goes wrong  Also the ordered parts from iGEM arrived today, and these were plated on agar plates with the appropriate antibiotics and placed in the incubator. \_MVM || Thursday 17/7 | | |

| The plasmids that were prepared yesterday (PCR 1, PCR 2, PCR 3 and B+C) were digested today with: - PCR 1: EcoRI + SpeI - PCR 2: EcoRI + SpeI - PCR 3: EcoRI + XbaI - B+C: EcoRI + XbaI  The products were then run on gel and gel purified. The products were dissolved in 20 µL ultra pure water. The following concentrations were obtained: - PCR 1: 37.3 ng/µL - PCR 2: 8.0 ng/µL - PCR 3: 15.1 ng/µL - B+C: 16.4 ng/µL  The following digested parts were then ligated: - PCR 1 + PCR 3 - PCR 2 + PCR 3 - A + (B+C) - A + B  Furthermore the plasmids with PCR 1, PCR 2, PCR 3 and B+C were prepared to be sent to Eurofins for DNA sequencing.  As mentioned yesterday a ON-culture was prepared yesterday. The culture was attempted mini-prepped, but the mini-prep was unsuccessful. Consequently a new ON-culture was prepared today.  The parts from iGEM that were plated yesterday, were today prepared for ON-culture, so that a freezing stock can be made tomorrow.  - Jens Jakob || Friday 18/7 | | |

| We prepared a freezing stock of the parts we had ordered and received from iGEM, and the remaining sample from the ON culture used for the freezing stocks, was miniprepped and catalogued. Some of the minipreps, were prepared with a wash buffer not containing any ethanol, and therefore we has miserable results. New ON cultures of those was prepared.| Saturday 19/7 | | | |
| The ON cultures of the iGEM parts from yesterday, were miniprepped with fine results.  Colony PCR was performed on the cultures transformed with PCR1+3, PCR2+3, ABC and AB. There were no colonies on plate 5.10 (AB-part).  Plate streaking was performed on each colony taken for colony PCR.  At first sight the results from the colony PCR seems to suggest that something went wrong during the digestion or ligation, since only re-ligations seems to be present. | Sunday 20/7 | | | |
| As we were not successful in transforming the samples from th 19th of June a new batch was initiated. That is PCR1, 2, and 3 together with B and BC was digested, ligated, and transformed.  In accordance with our decision to make the nutrient producing strain taste good transformations of parts; I742111 (RBS+limonene synthase), K118024 (dsx+LIMS1+appY), J23119 (constitutive promoter), and B0015 (double terminator) was commenced. These are going to constitute the construct for producing lemon taste and scent.  /Daniel | Monday 21/7 | | | |
| Text  /Name | Tuesday 22/7 | | | |
| Minipreps were made on (yields were measured in nanodrop):- Blue#51: J23119 (104,7 ng/μL) - Blue#52: I742111 (58,8 ng/μL) - Blue#53: K118024 (71,7 ng/μL) - Blue#54: Lac promoter (BBa\_R0010) (40 ng/μL) - Blue#55: pSB1AT3 (84,9 ng/μL)  /Daniel | Wednesday 23/7 | | | |
| Today we ran colony PCR on transformations:- PCR 1+3 - PCR 2+3 - A+B - A+BC - B0015 terminator  Also J23119 and K118024 were ligated and J23119 and I742111 were also ligated.  /Daniel | Thursday 24/7 | | | |
| We recieved a delta 12 desaturase from Julius Fredens today, it is a Fat2 desaturase originating from C. elegans, we are planing on testing it and we might add it to the iGEM parts registry since it does not seem to be registered.  /Daniel | Friday 25/7 | | | |
| Over night cultures have been made for (started at 3:30 PM):- PCR 1 - PCR 2 - PCR 3 - B - C - BC  /Daniel | friday 25/7 | | | |
| We ran a PCR on PCR1,2,3 and part A, B, C & BC to check if they had the correct lenghts. After running a gel, the bands were blurry so the PCR was repeated, only this time using a Tm=51 degrees, and for parts with a length of 1000 bp or fewer got at step 4 15 sec. and parts over 1000 bp got 30 sec. After running a gel, it was indicated that PCR2, 3, part BC & A (using Lac\_F & Lac\_R on this part) didn't have the correct lenghts. Anne, Sarah & Camilla || Saturday 26/7 | | |

| Miniprep has been made of the ON cultures from 25/7 (these can be used for cloning later on):- PCR 1 - PCR 2 - PCR 3 - B - C - BC  PCR reactions of PCR 1, 2 and 3 was made from different templates, these are to be purified tomorrow.  /Daniel | Saturday 26/7 | | | |
| To see if we could get a more cleat band of part A, a gradient PCR was made with Lac\_R and Lac\_F primers, using Tm gradient 51-70 degrees with 5 samples. Gradient mix: 2,5 uL template, 31 uL water. PCR program:1: 98 deg., 2 min. 2: 98 deg., 10 sec. 3: 51-70 deg., 30 sec. 4: 72 deg., 45 sec. 5: GO TO 2 rep 30. 6: 72 deg., 5 min. Tm for the different samples, were set to be: 50,8; 52,4; 58,9; 66,3; 70,0. The PCR showed blurry bands and no correct product/lenght. The reason for this, was found to be due to a too high concentration of primers, which were then diluted. Then we did a touch down PCR on part A, starting at 66 degrees going 1 degree lower per cycle, for 10 cycles thus ending at 56 degrees. Running a gel showed clear band at the correct leght. In order for us to be able to ligate PCR1 and PCR2 into PCR3, repectively, we needed a higher concentration of PCR1 & PCR2. Therefor we ran a PCR with the program: 1: 98 deg., 2 min. 2: 98 deg., 10 sec. 3: 50 deg., 30 sec. 4: 72 deg., 20 sec. 5: GO TO 20 sec. 6: 72 deg., 5 min. After running a gel bands showed at the wrong lenghts, but wasn't religations. Thus we concluded that we had the sample was wrong. Due to this, we ran a PCR on all PCR1, 2 and 3 samples using VF2 & and VR as primers, in order for us to check id they had the correct leghts. Luckily it turned out that all other samples were of the correct lenghts.  Anne, Sarah & Camilla || Sunday 27/7 | | |

| PCR products made yesterday has been purified, this was PCR 1, 2 and 3 from different templates.  /Daniel  Digest of I74211, K118024, B0015 and what was thoght to be J23119. Because I didn't think of the fact that the inserts had to be after the promoter, i started out digesting with the wrong enzymes, which was repeated afterwards with the correct enzymes. What was thought to be J23119 wasn't J23119 but BBa\_I15008. The parts were digested as follow: I742111; E+S & X+P K118024; E+S & X+P B0015; E+S & X+P J23119('''BBa\_I15008''') /Camilla | thursday 31/7 | | | |
| Mini-prep was made on overnight culture with J23119. Overnight culture on PCR3 was made. Camilla |  |  |

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