Team:DTU-Denmark/Blog

October

October 12th, 2010

Time flies...

Jeez, where's the time going?? It's weird to think that we have about 2 weeks left and also very scary. It's full speed ahead here with us in the lab, but also in the dry lab. The SDU-iGEM team came to our part of the world for a wee visit and we had our own little conference and it was very beneficial as we gave each other good feedback and ideas. It was also brilliant to finally get a fresh pair of eyes to look at our project.
Juliet
iGEM DTU 2010

October 8th/9th, 2010

So today some of us have been here at DTU from 8 in the morning until 02 am working in the lab, on the wiki, the economy, planning our SDU/DTU event, poster and powerpoint presentation. It's been a tres busy day, but there's no rest for the weary ;) and we had a dinner together in preparation for our long evening...

October 5th, 2010

So far so good…

Despite all the stress about making the deadline on the 27th of October, it seems like we’re progressing forwards with pleasing results. Up until now, all our ligated constructs seem to have worked successfully after having verified them via verification PCR’s from minipreps.

The last stretch of work will hopefully go smoothly as well cause its here where we really need everything to work especially as they’ll be for our measurements!

The first construct out of 5 needed for running measurements will be made today; this differs from the other 4 as it doesn’t contain any terminators within the construct, this will be used to illustrate how the system will function containing an anti-terminator and nut site though no terminator. So firstly a ligation will be made, followed by a transformation and finally the transformants will be plated and tomorrow we’ll know if this ligation was successful or not, hopefully yes!!

And the picture of the day is…

Ever since we started working in the lab in June, the lab coats we got had some rather interesting drawings, name tags, and other biological warfare scars like holes and chemical stains. This one here is of “Mr. Anderson”, some of you might know him from the Matrix, you should know then that his alter ego is Thomas Trolle. ;)

October 4th, 2010

Where's the time going?

October 4th.. time is passing way to fast!!! We had a nice working weekend, we got things done in the lab and for the poster and presentation. The poster and presentation needs to be finished since we will be presenting it this saturday for the SDU team at our pre-Boston conference here at DTU.

What I found out this morning is that my group, the repressor group have some serious problems with verification PCRs of our transformations. Maybe we should get the other group to do the PCR for us, since they don’t have any problems in verifying their constructs..?? We are trying other alternatives now, such as biological assays. And it actually seems that some of our ligations/transformations are working. Still need to redo a bunch, but I’m optimistic!

October 3rd, 2010

Sunday with iGEM

A bunch of the iGEM team met up today on a Sunday to do some lab work and work on our poster. It's been a while since I've been in the lab as I have been working on some of the more practical and non-wet lab side of iGEM. But you know what? It was fun to put on a lab coat again. We ran a gel of the PCR restrictions. Thomas and I then did some ligations. We then amplified our inserts using PCR. It was good with a refresher course in the lab! All in all it was a productive day!

In the picture of the day you can see Maya, Greg and I (Juliet) working away on our laptops ;)

October 1st, 2010

October!

1st October... The days are slipping by really quickly now, 26 days and counting until the wiki freeze! I was alone in the lab today, and since I had a course until 12, it sort of limited the amount of work I was able to do. I just ran some gels and did a PCR purification of the PCR products Anastasiya and I ran yesterday after the meeting. I also did restriction digests of the PCR products, but I managed to forget to take them out of the Thermoblock.. Good job, Thomas, that was a total waste of two hours... Luckily, Anastasiya and Patrick are coming in tomorrow, so they'll be able to redo the digests before we actually have to use them :P. Lisa and Maya from the Repressor group redid some ligations in the morning and transformed them in the afternoon. Both groups made overnight cultures of the restreaks done yesterday, so the people coming in tomorrow can miniprep the plasmids and run verifications PCRs to check if Wednesdays ligations went well.

I'd also like to start a new feature on this blog: Picture of the day! Maya has kindly offered to leave one of her cameras at the lab, so we can better document the stuff we're doing here. I'm certain we'll get some fun and cool pictures taken. Today we'll start with a picture of Maya doing transformations

September

September 30th 2010

Positive results from the lab!

Today was a great day for the Antiterminator group. Anastasiya and I ran some verification PCRs on the 5 ligations we did last Thursday. We finally confirmed that all the constructs we had hoped to make were successfully ligated! Other than that, both groups did restreaks of the ligations that were transformed yesterday. The Repressor groups seemed somewhat successful, but they decided to play it safe and redo some restrictions so they can redo the ligations tomorrow. For the Antiterminator group 3/4 of the ligations seem very promising. The last one, however, seems like it may have failed. We'll have to redo it next week if it has.

We also had our weekly meeting today. Nothing too exciting, we just talked about how to send in the biobricks we are submitting to the iGEM registry, buying plane tickets for Boston as well as who is going to be presenting at the jamboree in November, among other things.

September 29th 2010

Chugging along

Things seem to be going quite nicely in the lab at the moment. There are a few screw ups here and there, but it really feels like most of us have enough lab experience to get things done right more often than not. That, or we're just feeling the pressure now, the iGEM wiki freeze is in just 4 weeks now! Today, both groups did ligations, the Repressor group did 10, and the Antiterminator group did 7. Annemi and Patrick did the 19 transformations we had to do. I was glad that I was away during the afternoon because of my TA job, 19 transformations is a LOT and must've been boring to do ;). Unfortunately, it's going to take 3 more days before we're able to continue working on the constructs we made today, our little bugs have to grow! Luckily, people are dedicated enough to come in on weekends from now on, so the pace should pick up quite a bit. Hopefully the Repressor group will be done with their constructs next friday, ready for characterization!

September 27th 2010

Another one of those days...

Today was one of those very frustrating days when nothing works. We had many plans in the lab for today: doing PCRs, preparing overnight cultures, doing digestion, etc. However, as it has turned out we could not do the cultures, because the resteaks of ligation products from Friday had some problems, so we had to figure them out first and to redo them again. We have also run into some problems with our PCRs, which sometimes would not work for some strange reason. Then we could not start digestions because we have spend too much time focusing on smaller tasks in the lab and organising different things. Nevertheless, we still managed to finish many things during the day and hopefully we would be able to solve our problems tomorrow.

September 24th 2010

Lab work until 18:00 on a friday!

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.