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December,2011

 

11.12.2011 :First Meeting: Today the all that responded our announcements to be a part of the iGEM competition representing the METU-IGEM team got together for the first time. In total we have got 50 interested students, 2 instructors and 1 adviser. We started by introducing ourselves then we talked about our past IGEM experiences. Here, with the audiences we decided to make a brainstorming session which should be after reading enough about more on synthetic biology. Furthermore, we decided to make a brainstorming session to decide on our project after 1 week.

18.12.2011: Brainstorming Session Part 1: To make a successful plan we know that the first think should be done is coming together and adding the ideas each other. In the first part of the brainstorming we simply think everything and write them on the board!

25.12.2011: Brainstorming Session Part 2: In the second part of the brainstorming we continue to storm the ideas and writing down to the board. Then we made a schedule to think the ideas for their feasibility and if it is possible making circuits of the plans.

   

January,2012

 

03.01.2012: Eliminating the Ideas: The imagination of our team was extremely high because ,our team consists mainly first and second year students. At the end of the brainstorming sessions, there were lots of crazy ideas; however, we had to eliminate them. Finally we ended up with two main project. By trying to choose our main project, the several managerial tasks were divided among the team members. By doing so everyone got the chance to use their experience while learning from each other. Then we divided our team as a 4 different sub-groups; Wetlab workers, Software workers, People who interested in funding and Human Practice group.There were ofcourse some interactions between groups.

   

February,2012

 

13.02.2012: Article Reading: In the middle of the semester holiday, we did a meeting to give some homeworks to team members. We decided to prepare an article pool about our two main projects. By collecting information, we could have decided which one was more possible or which parts we had to add or remove from our projects.

27.02.2012: Deciding to main project :CO FILTER must done! After semester holiday, we had read and summarized so many articles. With this huge amount of information we prepared lots of presentations to transfer the information and to discuss about them. After reading and discussing the so many articles related to our two main topics, we chose CO filter as our main project.

   

March,2012

 

06.03.2012: Building up the Project: Because our team members were unexperienced ,we had mini classes in which the basis of genetic engineering is taught. After this time, we all were excellent article readers. We tried to access all possible information about our project and try to build up the system, by finding available promoters ,genes,etc. We finally built the system and we presented it to our advisors.

13.03.2012: Searching for sponsorship: Just after deciding our project, we started to search for sponsorship for our team. We started to make telephone calls to every single company or government unit about our project. In this time , we started to search for a new lab.

20.03.2012: Building our own iGEM laboratory : Our instructor ,Mrs. Akkaya had already offered her lab for our experiments. However, this wasn`t enough for us. So after this search, we found a new lab in the basement of Chemistry Building. This lab was being used as storage for this building and was full of unnecessary stuff. By the time, we collected the last parts of our system and we all started to clean our new lab.

   

April,2012

 

04.04.2012: Software Meetings: Our software team started to do their own meetings. At first , they gather information about the model of our project. At the same time, they started to discussions about the design of our wiki page. By this time, they design a draft logo which is: (eski logo resmi)

11.04.2012: Human Practice Meetings: At this time, human practice sub team started to collect their ideas and present them to all group members. They made lots of presentation about their projects. Moreover, they implemented almost all of their ideas; making a short movie, organizing a iGEM party and a picnic with the other iGEM team of Turkey:Baskent University team,going to funfair to tell people about iGEM,etc.

18.04.2012: Hardworking software team: Software team was arranging lots of meetings to talk about the design of our wiki page and the logo. After so many crazy ideas we ended with our current logo. After deciding our logo, software team started to ask the ideas of all team about wiki design.

25.04.2012: : Meetings with presidency of METU : Our funding team arranged meetings with the rector of our university. After those meetings, we found some money necessary for our wet lab practices.

   

May,2012

 

02.05.2012:Readdyyy for wet lab!! After cleaning, we designed our laboratory .Because our lab was a radioactive working place, we had to remove lots of stuff and check whole lab for radioactive substances. Because of our limited budget ,we can only place an old PCR machine named as UMUT. Then we had opened the box sent by iGEM with big excitement for the first time.

09.05.2012: Lets go into autoclave together!! We all introduced with autoclave at this times. All equipment that we had collected was autoclaved patiently and this procedure has been done often up to now.

23.05.2012: Preparing plates.. As a beginning of our wet lab work, we prepared lots of plates with agar medium. It was necessary to prepare them continuously during our working period. The first preparation was so excited for every one of us; however after time passing, this part has become the most boring part of study.

   

June,2012

 

06.06.2012: Lab cleaning List done: We all had started to live and work in this lab, so we have to keep it clean. We made a cleaning list and paste it on to our door. And we arrange a post stage for our lab notes, and as a compulsory work, we had to have a lab notebook to write down all procedures.

13.06.2012:Now Transformation List: From iGEM kit we started to extract our parts and after diluting store them in fridges. Addition to this, we prepared competent cell series. Because we are very crowded wet lab team , we had to divide people into sub groups for transformation.

14.06.2012: Protocols, have you seen my protocols? The senior members of our team started to search for their reliable protocols. We collected all protocols that we could find. Then we copied all to our lab notebooks, and collected in a shared network.

15.06.2012: Competent cells were prepared according to our protocol. A new list was done to do competent cell.

16.06.2012:Let the transformations begin! All the members of our team started to learn how to do transformation. All parts, removed and diluted, were ready to do transformation. There were almost ten groups for doing transformation. All started to their work one by one.

18.06.2012:We did the transformation of PLasR and JD.

19.06.2012: Transformation of CI and Elowitz were done by second group.

20.06.2012: KS and RBS were done ,too.

21.06.2012: Plates were cleaned and the contaminated LB was poured.

22.06.2012: Meeting Time

• Were these protocols true , why didn`t they work, who are we :S
• All transformations, except Berke`s , were failed. So we started to change our protocols and repeated all the procedures with these new protocols. After that time, transformations started to work.
• Funding team; They all started to telephone calls to companies. They found some companies who are ready to help us . And they arranged meetings with Güven Vakfi , Vendeka and Atasim. Also they collect the information for application of TUBITAK.

23.06.2012: With the new protocols transformations were started to repeat.

24.06.2012: With our new protocol , the transformation of PLasR and JD were succeed.

25.06.2012: The parts,CI and Elowitz, were also done .

26.06.2012: Our third group also succeeded the transformation of KS and RBS parts.

27.06.2012:Our last group did the transformation of LacI ,LasR and J23116. They also did LB agar with ampicillin according to LB agar protocol.

28.06.2012: The primers arrived and we dilute them according to their special value 1:10 ratio. We tested our primers with PCR.

29.06.2012: Meeting Time:

• Wetlab: Protocols were being collected for next procedures.
• Software: Software team started to build the model of kill switch and quorum sensing. They needed some parameters for these models .So lots of homework was given to all team to do some research about them.
• Funding: Our rectorship started to give some funding for our wet lab procedures. Then they started to search funding for our plane tickets and accommodation.

30.06.2012: We did the colony PCR from plates which we cultivate. The iGEM team of Baskent University came to our university for meeting .We decided for collaboration.

   

July,2012

 

02.07.2012: Colony PCR didn`t work for the first times.

03.07.2012: Colony PCR still didn`t work. By the way we are trying to be success in transformations. Starting to cahenge the plan accordiging to tarnsformations works.

04.07.2012: By changing some conditions we tried colony pcr several times ,to find the error.

07.07.2012:After some tries ,colony PCR was succeed and run samples on agorose gel according to its protocol. According to results, we put ONC into the shaker.

08.07.2012: However, we realized that our gel electrophoresis has some problems. we couldn`t get any results. So we conclude that our ladder didn`t work.

09.07.2012: We tried to find new ladder from our colleagues.

10.07.2012: We control our ONCs and we did plasmid isolation of some genes that work with transformation according to this protocol, and started to make stocks with them. After plasmid isolation we took nanodrop values of our plasmids.

11.07.2012: We ran the plasmids which we isolated in agorose gel electrophoresis. We prepared LB Broth, LB Agar and plates.

12.07.2012: We prepared antibiotics ampicillin and kanamycin according to protocol1 and protocol2.

13.07.2012: We cleaned up our lab.

14.07.2012: Meeting

• Wetlab: Protocols were being collected for next procedures.
• Software: Software team started to build the model of kill switch and quorum sensing. They needed some parameters for these models .So lots of homework was given to all team to do some research about them.
• Funding: Our rectorship started to give some funding for our wet lab procedures. Then they started to search funding for our plane tickets and accommodation.

15.07.2012: LB Broth ,LB agar and plates were prepared .

16.07.2012: Funding team went to Interlab for sponsorship discussion.

17.07.2012: We did double digestion of our plasmids according to its protocol. Then put the samples in Agorose Gel Electrophoresis and we did gel extraction according to its protocol.

18.07.2012: Competent cells were done again.

19.07.2012: We had a picnic with Baskent iGEM team .We all had great time and get fun together.

20.07.2012: We had a mini meeting for logo ideas. And we decided some details , so it was ready to professionally drawn.

21.07.2012: Meeting:

• Preparation for iGEM party... With the wet lab works, we also carried out our human practice works. And we found a place for our party. And we designed our party tickets and party posters.(resimler) .We started to deliver our party flyers.
• Software: After collecting homework, software team did some parts of models and parameters. They also started to talk about logo design.
• Human Practice: They started to talk about the activities which were going to do in METU.

22.07.2012:We did ligation to our samples according the cloniing protocol.

23.07.2012: We controlled our samples with Agorose Gel electrophoresis. We did transformation from our ligated parts and spread them onto agar plate and we did ONC.

24.07.2012:Preparation for party is done and last controls were done.

25.07.2012: Lab cleaning was done.

28.07.2012: Party Timee for Synthetic biology lovers! At that night, we had our party with 300 visitors. We had lots of surprises, which introduces iGEM, for our guests. We wore our lab coats and had great fun through all night. Up to early in the morning, the music wasn`t closed. We left a great impression in our visitors?mind about iGEM competition.

   

August,2012

 

02.08.2012: We did plasmid isolation optimization in 4 test isolation condition according to its protocol.

03.08.2012: Meeting:

• Software:Modelling works of KillSwitch and Cell limiter parts are divided into two in the Software team. We started to search up for parameters
• Funding:We started to go sponsorship meetings

04.08.2012: We did agorose gel electrophoresis and measure the nanodrop of the parts.

05.08.2012: We did ONC from samples.

06.08.2012: We did plasmid isolation and measure their nanodrop , and put samples into agorose gel electrophoresis.

07.08.2012: We did double digestion .

08.08.2012: We controlled our parts , however ; we saw digestion hadn`t worked.

09.08.2012: We repeated our digestion procedure according to its protocol.

10.08.2012: Our final logo was drawn and we loved it.

11.08.2012: We did ligation and gel electrophoresis.

12.08.2012: We did transformation of ligated parts, and realized some of the ligations were not successfully done.

13.08.2012: The unsuccessful ligations were repeated.

14.08.2012:The last ligations were also be controlled by transformation.

15.08.2012: We prepared competent cell with CaCl2 treatment.

16.08.2012: Meeting

• Wetlab: We tried to collect all the equipment that we used to write them down to sponsorship list.
• Software: Models were nearly completed and wiki codes were also nearly completed.
• Funding: Our funding team said us that our plane tickets were bought?

17.08.2012: We did plasmid isolation for the parts; pLacI, KS, SD, J23116,pLasR and measure their nanodrop. We did competent cells and digestion.

18.08.2012: We did transformations of RBS,CI,LVA and minC parts.

19.08.2012: We did gel electrophoresis and we saw the DT-1 and pLacI.

21.08.2012: We did gel extraction.

22.08.2012: Meeting Time:

• Software:We started to build up the wiki page. First of all we constructed general structure of it.
• Wetlab: All wetlab workers gave feedbacks about the parts.

23.08.2012: We did competent cells.

24.08.2012: We talked about our wiki page and its design. We added some new parts to our wiki draft.

25.08.2012: These times since the sine rises a lot, some students go for a bit holiday, so we foced on more reading about articles.

26.08.2012: We started to collect the articles in our dropbox for references.

   

September,2012

 

06.09.2012: To be sure about the parts that we tought they have done, we all run them in a gel.

06.09.2012: We scaned the procedures again and from this time we decided to use 3Assebly kits.

10.09.2012: Plasmid isolation of the parts that have left one one before to ONC are done and run in the gel.

11.09.2012: New competent cells are prepared by Selin and Özge. Elowitz and Double terminater parts are grown at ONC. Moreover, we made some transformations (Min C and the ligated part RBS+cI)

12.09.2012: We made some restriction digestions. And the parts J23116 and Sender device are ligated.

13.09.2012: Ligated parts are transformated. PCR checks are done also. Today is Emre`s birthday!! Happy b-day!!

14.09.2012: Successful transformations were left for ONC. Ligation of the plasmids were done.

15.09.2012: PCR of the parts were done. Then their gel control was done. Plasmid isolation of the parts are done.

16.09.2012: Transformations of the ligated parts are done. Successful ones are left for ONC.

17.09.2012: Morning, plasmid isolation of the parts were done, nonodrop measurements are handled and run in the gel.

19.09.2012: Lab is cleaned, with team workers meetings are done. Wiki works getting more and more hard, nearly all files are uploaded into the IGEMs official side.

20.09.2012: New competent cells are prepared. Furthermore, we decided to get together of the videos that we shoot just for fun. Oguz put the video together and while he was woking and hungering there, we forgot about him and ate some delicious pizza! Yeah!

21.09.2012: We started to get very good feedbacks about our video. Moreover, some transformations are done. Ligations are done also. Hey, today is Oguz`s and Özge`s birtday! Let`s go out, ... Wait! We can`t. Too much stuff to do... ********!!!!!

22.09.2012: Ligated parts were transformed. Yesterdays transformants made ONC. By the way, wiki works getting more and more hard. Wiki page however, nearly ready!

23.09.2012: Plasmid isolation of the parts are done. Some ready parts had gone to PCR checking up. For this we again made Emre to preapare gel:)

24.09.2012: Again, ligation of the parts were done. Transformations are prepared. ONC of the ready plates were prepared. From the parts are going it seems that the parts won`t be ready to submit :( One of the parts seems ready and we think characterization of CODH can be done at least.