Diary of the TU Delft team

11th June 2009

Dear Diary, it was quite a disappointing day. First of all, we had a small presentation in the morning, but about half an hour before it we had a terrible realization: our idea is fundementally wrong!!! :-(
How did that happen? Well, when we electropalate selection markers into the plasmids, expressing them will allow the host for the plasmid to pass the selection. Unfortunately, expressing them would express the entire plasmid, including the self-destructing gene, meaning that after selection the plasmid will be destroyed before we even use it. On the other hand, if we don't apply any selection but give the host a plasmid with a selection marker, the plasmid is not used and is ejected from the host, so it doesn't have the self-destructing gene anymore.
Luckily, we came up with an alternative idea: Fucking Conjugates (literally). The essential idea is based on bacterial [http://en.wikipedia.org/wiki/Bacterial_conjugation conjugation], where an F plasmid in F+ E.coli is transfered into an F- E.coli. In an experiment done by [http://parts.mit.edu/wiki/images/d/df/IGEM2006-Berkeley-Powerpoint.pdf Berkeley in iGEM 2006], they took the origin in the F plasmid (which is a signal to transfer the F plasmid from one E.coli to another) and put it in a micro F plasmid instead.

Yours in unity, TUD iGEM '09

5th June 2009

Dear Diary, did we have a long discussion today! First of all, we determined how to divide the work among us (each one said what his skills were, and we decided who will do what in the project). Obviously, some of us took more managerial positions (taking care of planning, logistics and what not), and some were more on the employer/slave side (Emreh even suggested that a whip might come in handy...)
Later, we discussed the initial steps of working with the self-destructive plasmid, which pretty quickly turned into several simultaneous conversations: whether we should use a selection marker or not (somewhat pointless, since the marker would be already given in the plasmid supplied from MIT), methylation of the plasmid nucleotides (which no one really knew how it is affected after replication of E.coli) and the rate of plasmid degradation compared to gluing them back together. In the end, we gave some tasks out: Daniel was responsible for finding the top 10 restriction sites in the E.coli plasmid, Sriram was in charge of going over the registry of the bio-bricks of iGEM to seek a useful promoter, and Orr would look into methylation in E.coli to expand more on how it works and how it is affected by replication.
In short, much to do, for all of us. LET'S GET WORKING!!! :-D

Yours in unity, TUD iGEM '09

26th May 2009

Dear Diary, today had a brainstorm about our main 6 topics again, and we realised that the most feasible idea we can choose is the self-destructive plasmids (some of us already had PR ideas, like a poster of James Bond with a gun-shaped plasmid in his hand). Finally, we agreed to write a short plan on what we will do and how each one of us shall contribute to the project.

Yours in unity, TUD iGEM '09

14th May 2009

Dear Diary, today we looked at the different ideas we had for the project. Needless to say, most of the ideas seemed more appealing as we started looking deeper into them, although it was somewhat disappointing when we found out the salt water desalination using bacteria was not quite feasible. The micro-organism muscle idea also turned out to be a flop. However, there were some nice developments in the other 4 ideas, and the buoyant bacteria application in mines seemed quite promising.

Yours in unity, TUD iGEM '09

8th May 2009

Dear Diary, as we decided in last meeting, we chose the top 5 ideas from the list of subjects we had so far. We came to the following conclusion based on democratic voting:

1. Salt water purification
2. Buoyant Bacteria
3. Impulse Signal
4. Melatonin Compensation
5. Micro-organism Muscle
6. Enzyme Modulation (shared 5th place)

We agreed to devide the subjects and look at the possibilities, opportunities, feasibility and applications for the top 5 ideas, so that next meeting we could inform each other on the subjects, and possibly narrow down the list to a top 3.

Yours in unity, TUD iGEM '09

28th April 2009

Dear diary, today we had a meeting regarding the practical aspects of the iGEM project (we divided the task of looking at the project ideas among all the group members, and decided that each person would look at 3 ideas, make a small research about them and publish it on the website, so that we can choose the top 5 ideas, and out of them choose the most attractive one). We also agreed on starting to look for financial support, but then we agreed we should wait a bit longer until we have a concrete idea for our project. We also agreed on meeting with the designer of the Delft Wiki page from last year, so we can learn from his wisdom and bask in his glory.

Yours in unity, TUD iGEM '09

23rd April 2009

Dear diary, today we had a brainstorm session, where we invited various people, including professors and experts in different fields of biology, chemistry and engineering. Sadly, only 3 people outside our team have come to our aid, yet we got some good ideas and feedback from them. We ended with 21 ideas, some of them being highly general and highly important (e.g. salt-water purification), some started as a joke (e.g. flashing dog poo brought an idea of fast degradation of dog excrements) and some were simply cool (e.g. flashing bacteria colony). In the end, we did not decide which project we shall do, but we decided to look at all the projects ideas and look at the feasibility, advantages and disadvantages of each idea.

Yours in unity, TUD iGEM '09

17th April 2009

Dear diary, today we continued with looking over past projects. We also discussed the possible sponsors we might be able to recruit, including the town of Delft (by advertising them on the Jamboree as a town worth visiting) and various beer companies (specifically in case we would make a project involving beer). We also discussed the Teacher workshop in London (30th-31st of May), and since only one student can accompany the instructors, we decided to hold a fight among all students who would like to go, and last one standing would go (if this would not work, we'll just make a lottery). We also agreed to have a brainstorm regarding the project we will choose on the 23rd of April, where we will invite people to come and give remarks on our ideas after Daniel would give a short introduction of iGEM and our project ideas. Hopefully, enough people will come to make it worthwhile.

Yours in unity, TUD iGEM '09

7th April 2009

Dear diary, today we gave some presentations about iGEM projects of previous years. Some of them were pretty good (the Slovenian team of 2006 came up with the idea of making a sepsis-free cells, and the 2007 Slovenian team came up with ubiqiotinating methods against HIV infected cells) and some were just highly extensive with little concrete results (the 2008 Cambridge team attempt at making an artificial neuronal network for E.coli was not quite a success...) We also saw some 'cool' experiments (gladiator bacteria and generation marking in bacteria), but we still haven't found the project we want to work on. Nevertheless, we had some excitement about a project by a TU Delft Masters student working on a bacteria that can sense whether it is in an environment with low insulin concentration and produce insulin in response (could be a good diabetes treatment).

Yours in unity, TUD iGEM '09

25th March 2009

Dear diary, today we went over some general points, regarding the booking of the hotel in Boston and how we can take an extended vacation in the US after going to the Jamboree.

Yours in unity, TUD iGEM '09