Team:DTU-Denmark/Blog

Welcome to our blog

This aim of this blog is keep you up-to date with the happenings of our iGEM team! This will mostly include the softer side of our iGEM project. For more techical details please check out our Notebook.

September

September 24th 2010

Meeting with supervisors and the 2009 team

No one was able to be in the lab this morning, so Maya, Patrick and I started the lab work at 12:30, after lunch. Patrick and I were happy to see that the transformations I did yesterday looked good, meaning the ligations Patrick did Wednesday most likely went well! We have a few colonies on our negative controls, but not at all as many as we have on the actual ligations, which is a great sign. We restreaked 4 colonies from each ligation so we can start overnight cultures of them on Monday. We also ran verification PCRs of the ligations we did last week and gave Maya a hand with the 20 minipreps and 40 verification PCRs she had to do! Hopefully they all work out, because working in the lab until 18:00 really sucks :P.

September 23rd 2010

Meeting with supervisors and the 2009 team

Today we had a meeting with Mogens and Chris, our supervisors, Sebastien, our instructor, as well as Hans and Christian from last years iGEM team. We prepared a rough draft of our jamboree presentation and presented it to them to get their feedback. We got alot of great input about things we could add/change in the presentation to make it more understandable, so that was great. Hans and Christian also told us about their last 5 weeks before the wiki freeze last year and gave us alot of great tips. It was really great that they were able to answer all our questions about the jamboree, the poster we have to make as well as the wiki. We also talked about the requirements for the Gold Medal, and how we plan to fulfill one of them, and got some great input from everyone. All in all it was a great meeting.

Since we had to prepare for the meeting, not a whole lot got done in the lab. I transformed some ligations that had been done the day before, with the help of Anja from the Repressor group. The Repressor group started 20 overnight cultures of their ligations so they can miniprep them tomorrow and run some verification PCRs on the plasmids.

September 22nd 2010

In the quest of the missing transformants!

The transformations we made last Thursday containing the backbone plasmid pSB1C3 and one of the four inserts Gifsy1/2 promoters or the promoter region plus repressor had grown on the plates. We unfortunately had a lot of background growth on our negative controls. But as we are a very positive group, we decided to check our colonies to see if we would be lucky enough to have the right plasmids somewhere in the transformants. And so the quest began.

Lisa did a very beautiful colony PCR of some of the transformants which indicated that the right plasmids are among the colonies. Sadly the colonies did not want to be marked, so they were not be found on the plates.

The quest for the missing transformants will continue.

September 20th & 21st 2010

PCR’s are finally alive and working!

Today was the deadline for having to send in our track selection, project abstracts and team rosters. Having to make the track selection was a bit tricky as our project theoretically can fall under many of the areas available; we picked the most relevant and interesting one though.

So after many attempts of running PCR’s, we switched back to the old PCR buffer which seems to be the contributing factor in making them successful once again. The repressor group still seems to be having some issues with their PCR’s, but this could be due to several reasons, i.e issues with the primers they’re using, PCR mix, etc.

Many restrictions need to be performed this week as we still require a good amount of ligated products towards the final construct in the anti-terminator; so far so good though, many hours have been spent these past two days in the lab with a lot of good results, hope my lucky streak continues.

September 17th 2010

Successful ligations!!

As soon as I arrived at the lab today after my morning course, I rushed to the incubator to take a look at the plates and I was very pleased to see that we had a decent amount of colonies on all the plates we expected to see growth on, and only a small number of colonies on the negative controls. Malthe from my group, the Antiterminator group, started a load of PCRs to amplify the backbone plasmids that we're going to need later on when constructing our systems, as well as a PCR of the GFP we're going to be using as a reporter. The Repressor group did PCRs of the pBAD promotor, an inducible promoter that both groups plan to use as part of our charaterizations, as well as ligations of the parts they plan to submit to the Registry.

Outside the lab we are putting the finishing touches on our Project Description, which we must send to the people at iGEM by Monday. We also spent a bit of time discussing what we would like to put on the poster we have to make for the jamboree. All in all a great week, here's hoping that next week will be as successful as this one!

September 16th 2010

Spaghetti and restrictions

A lot of stuff got done in the lab today as well. It feels like we are really on the right track now. My group, the Repressor group, did some restrictions that we will hopefully be able to transform tomorrow. The Antiterminator group did ligations, ligating parts to the pSB1C3 backbone plasmid, which is the plasmid you use to submit parts to the Parts registry. The ligations were also transformed and we'll see tomorrow if they were successful.

Today we also started our ”spaghetti” meetings. That included some nice spaghetti bolognese that Thomas and Annemi prepared for us. It was so good, and it was much easier to stay awake and focused during the late meeting with some food in your stomach.

September 15th 2010

Back in the lab!

When we started designing our approach to constructing our switch back at the beginning of June, I don't think anyone imagined how hectic the next 3 months would be. Highlights include redoing our approach twice, multiple tries at inserting FPs into plasmids, insane amounts of colony PCRs and lots of frustrations with the poor performance of our restriction enzymes. However, that is all in the past now. After realising that constructing our whole switch would be unrealistic, we designed our third and final plan, focusing on good characterization of our biobricks, as well as a couple of new standards for measuring other biobricks that will hopefully net us a gold medal at the jamboree! The plan included splitting ourselves into two groups, Repressor group and the Antiterminator group, enabling us to work on two very different parts of our switch. The repressor group will funnily enough be working with the repressors GogR and GtgR and their interactions with the Gifsy1 and 2 promoters and antirepressors. The Antiterminator group will be working with the antiterminator N from lambda and how it, together with the nutR site, affects a variety of terminators.

We finally received our primers yesterday and things are finally starting to happen in the lab. We've done a bunch of sucessful PCRs so far, as well as some digestions that will hopefully also turn out well. I'll try to post a blog entry each weekday (not necessarily written by me though! :P), detailing the work that has happened that day, so tune in again to see how we're doing during the last 6 weeks before the jamboree :).

August

August 13th, 2010

Hello world and welcome to our blog!

We are a team of 10 DTU students who have come together in the name of Systems Biology to compete in the prestigious iGEM (international Genetic Engineered Machine) competition. This blog will keep you updated with our progress, so stay tuned and enjoy the journey with us.

This is the second year that DTU will be represented at the Jamboree in Boston, USA. Last years team did a brilliant job and won a Gold medal. We hope to follow in their footsteps and come back home from with a Gold medal.