iGEM 2012 — Team Baskent-Meds

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# Team:Baskent-Meds/Notebook

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Brainstorming Part

December 15th 2011, Thursday

In our very first meeting, we were excited as hell. Almost none of us know how to work in the lab we didn’t know the lab rules. We began to learn about practicing in lab and lab rules. We are not so great on the theoric basis so , we’re gonna have to work hard and learn all about molecular genetics, bacteria and iGEM.

22.12 .11 December 22nd 2011, Thursday

We realized that it’s a long road to walk. We are learning new stuff almost every day about bioengineering and it’s exciting. We began our brainstorming meetings. Every member of our team thinks about what we can do to save the world every week! J After a week, we have lots of new ideas and we spend the rest of our time to search about if it’s possible to carry them to the benchtop and then to real life!

December 29th 2011, Sunday

We were discussing about “detecting methane gas in the air” and we were so hopeful about it but while we were searching online we saw that another Turkish team already performed it for last year’s iGEM competition. We were so frustrated that we felt that we would never gonna find an original, bright idea.Anyway, it looks like our brainstorming meetings will be beginning again!

05.01.12 January 5th 2011,

Happy new year! Here is some exciting and impossible ideas from our last meeting:

> - Human epithelial cells making photosynthesis resulting in green men!!! (So weard)
>
> - Bacteria sensing an approaching subject to be used in cars as a park sensor
>
> - Dancing bacteria- we thought it as it is without a utility
>
> - Bacteria sensing earthquake with a gene sensing pressure changes

Some of them just for fun of course but we liked the other ones and we’re gonna spend the rest of the week about making a search for them.

12.01.12

It turns out it’s really not that possible to create those last weeks’ ideas and some of them had already had been done by other iGEM teams. So we didn’t stop our brainstorming and come up with even crazier ideas to our meeting!

> - Bacteria detecting the purity of gold and silver
>
> - Bacteria changing color with daytime accorsding to the light spectrum from the sun, used as a sun clock
>
> - Bacteria produced to change the irresistable smell of waste water with a rose flavour !

19.01.12

We spent the week by thinking about last week’s ideas and trying to find new ones. Two people came with the same idea to this week’s meeting; lightning moment! We decided to work with detection and destruction of legionella pnomophilia, by using its quorum sensing gene parts! That legionella disease is still killing so many people every year and it’s especially common in our country. We couldn’t find a an IGEM team that worked with it before but we’re gonna look around more and more. Of course we wouldn’t wanna do the same project .

24.01.12

So let’s begin to work in our lovely lab, finally! We are officially gonna study about creating an E. coli that’s gonna find and kill legionella pnomophilia in every place it could hide. We can’t wait to get to work and do some real experiments!

30.01.12

Today, in our first real lab experience we created competent cells that can take our plasmids by using JM109, DH5α, XL-1Blue E. coli strains. We used calcium chloride (CaCl2) treatment while forming it.

It’s just like building a home for our plasmids to live in happily ever after. By the way, we need to start thinking about our application to the big competition, we have big exams every month as med students, we can even forget the last date of sign in to iGEM! We need to accomplish every mission we have, and we need to do it well.

09.02.12

This week we began with transformation experiments. We don’t know how to do them, we are not experienced and we need to learn a lot. These first transformation experiments are very informative for every member of our group. We started with E. Coli JM109 strain. We used pUCBM20 (pNT-1) (includes *lqs*locus), pMMB207C-RBS (pTS-2) (expression vector which includes *lqsA* gene), pUSEamp(+) (includes *luc*gene), and pGEM-3Z (control) for transformation. It was very fun to do it as a group, team spirit is rising! Heat shock transformation sounds very kicka\*\*. Our instructor told us that we may have to do it until transformation became successful.

16.02.12

YAY! pGEM-3Z and pUSEamp(+) was successfully transformated to our E. coli strains. It took a month to have successfully transformated cells. But it turns out our plasmids that include lqs gene locus are not very likely to be transformed.

We learned so many things. We can prepare LB medium, and our component cells stays alive thanks to us, and we transform plasmids into them! What a success, even for now!

23.02.12

We came back from our semester break and we are now officially an iGEM team. We paid our registration fee. There are so much to do, like preparing a wiki page for our team, It’s so important and we checked out some old wikis, we should create a better one, actually why can’t we create the best wiki page ever?

01.03 .12

We now continue to do experiments. Preparing compotent cells, plasmid transformation, pcr, plasmid isolation… We’re going pretty well. Rise and shine, Baskent\_Meds! (It’s our official team name. We loved it.)

15.06.12

Hard and stressful times. This year’s last comitee exam was today and now we’re gonna have our final exam, if we couldn’t get enough notes to pass, we’re gonna have to repeat this year. We have to study all the time for two weeks because if we couldn’t finish this year our project will crash down L that was our deal with our mentors for starting this in the beginning. See you in two weeks little lovely bacteria families.

04.07.12

We had our final exam and started to work in our lab while waiting our exam results. Excitiment still goes on but we really missed that place. There are so much to do so we made a “to do list” and we’re gonna finish everything we need to do by the end of july. Yeah we will! Everything goes on according to plan.

05.07.12

It looks like there is so much to do and to be honest we are a little afraid about it. We started to come study in lab as much as possible. It’s finally our summer break now, the lab is very very hot. Everything is still in progress.

06.07.12

Next week we’re gonna start to prepare component cells, transformation experiments and plasmid isolation. We’re gonna need hundreds of thousands cc and plasmids and so many other things when our vector design is finally over. So we should be prepared.

13.07.12

It’s. So. Hot. We spend this hot week with experiments. We designed a (actually another) lovely logo and it’s just so cool. In two weeks we’re gonna have our team t-shirts! Our t-shirt design is already finished, all we need to do is add our new team logo on t-shirt’s back! J

16.07.12

Now I am gonna write a list of the things we need to finish as soon as possible: vector design, finding the plasmids, enzyms we need (if we already don’t have them), printing our team t-shirts, finishing our wiki page.

And no, we’re feeling very good about it and our team spirit never was as shiny as it is now.

17.07.12

While we were working in our lovely lab everyday, we try to arrange a meeting with METU iGEM team. But it’s really hard to find a day that works both of our teams. It looks like we’re gonna have a barbeque this Thursday! Only two days left and we’re exciting about meeting them and working together. Xx collaboration rocks xX

19.07.12

Today we took a break to our works and met with METU iGEM team! Two of our team members were on vacation and we were only five J We met ten members of METU team today, we had so much fun, ate delicious meals, enjoyed the warm weather! We decided to see each other’s lab and work together. I think we are gonna be at their iGEM party next Saturday have fun and talk about how we can help each other again.

25.07.12

The hardest part of whole iGEM competition: designing a vector. Be sure that you trust in yourself about vector design before you sign up for competition!

Here comes the big news! We have been working so hard, since it and it is almost finished! We feel like we’re gonna fly, at least i know i feel that way. It, really, is a long road to walk.

30.07.12

We are trying transformation experiments with our iGEM kits and we fail every single time and wonder why. We arranged another meeting with METU iGEM team in their school, visited their lab and talked about our problems. They told the same issue too. Why our transformation experiments doesn’t work?? We both don’t know why yet but we wrote and e-mail to iGEM Headquarters and try to use their suggestions about transformation. We hope it’s gonna be successful this time. Today we tried two of them, we will get the results tomorrow. Exciting. Isn’t it?

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