Collaboration with Turkish teams in iGEM 2011
Since iGEM 2007, there is a team to research and prepare a project for iGEM competition from Middle East Technical University(METU). On behalf, there are advisors and instructors who are familiar with competition and content of it. In this year there are 4 registered teams from Turkey and 3 of them are new participants. Therefore in order to come together and criticize our projects and any deficiencies or ambugity related with project. So we organized and arranged a meeting on Synthetic Biology and iGEM competition which is the first in our country.The participants of this meeting were teams;Fatih Turkey, Bilkent_UNAM, METU-BIN
and researchers who related with Synthetic Biology and company owners in Biotechnology field also there was special guests via online talk, Drew Endy, he is an assistant Professor of Bioengineering, Stanford University and Scott Mohr Professor of Biological Chemistry, Boston University This meeting was held in September 10, that was close to Regional Jamboree in order to also check the presentation preparations of teams. The news agencies were also invited and the interviews were done with all teams publicity of teams were enhanced.
Except from this, we established a collaboration with METU-BIN Software iGEM 2011
team on their software program. This year their project, M4B: Mining for BioBricks
is on enhancement and simplification of parts registry and gene library usage to ease the wet lab researchers job. They requested us to use and try their software program. One of our parts in this year, kill switch is composite of this year distributions. By the way we tried their program to search and try on this composite. we gave them the following as feedback and also according to our comments on visual of program, we had collaborated this year.
“We are constructing a device that is induced by IPTG and that gives lysis enzymes and GFP as the outputs because, in order to elute methanol we need to kill our modified cells that convert ambient methane to methanol and the reason why we want GFP as one output is to be sure that it works. Our modelled device has promoter induced by IPTG, RBS, gene coding GFP and lysis cassette ending with cell death and we are glad to have it and it's working how we expected. So then, we use M4B to see that if it finds the exact device or the device that can do the same job. Since the software has only one place for output, we queried IPTG as an input and GFP as an output on the software and got corresponding 117 results. These results contain devices exactly what we have one for the same operation. However, we couldn't find the lysozyme output for the IPTG input in the software.”
We had requested them to support us on wiki page design and same tricks on loading the links on wiki page. We had prepared the self evaluating lab safety questionnaire and they made them manipulable on wiki page and the methane release meter on home page is their work.
Helping to other new Turkish teams in the future
Our university, METU has an online lecture application; METU OpenCourseware to support the open information source not only members of METU and to reach people to inform in all ages. In this online application, For Synthetic Biology field, last year the sessions were loaded and this year it is upgraded. The protocols for Synthetic biology methods were downloaded and supported with tutorials of procedures that taken during experiments. We established this page and enhanced for Synthetic Biology to reach more students to meet with Synthetic Biology in any region of Turkey. We had requested from President of METU made people to reach this webpage from universities with related departments in an official way. By the way, we believe to reach more students or researchers to iGEM competition and Synthetic Biology.
Collaboration with 2011 Uppsala Sweeden iGEM Team
We asked them to use and give feedback to our software tool on our wiki. This tool is named as BioGuide which was first studied on last year’s competition iGEM 2010 and gained silver medal. This year this team joined with wet lab team. While they were progressing the BioGuide project, this software tool also supported the web page and experiments of METU_Ankara team. We publish this software program on our wiki page to made other iGEM teams to reach and benefit from program on part and path choices. Uppsala-Sweeden team was one of the teams that use and try the BioGuide program. They tried to reach their used parts in kit distributions and then gave us feedback on them.
They tried this software tool according to parts of their project As an input parameters they tried to type red light 'cph8', blue light 'LovTAP', green light 'Ccas', IPTG(PT5-Lac), YF1
and as output parameters they typed amil GFP, amil CP and mCHERRY
. However they found the library of program restricted and they could not reach all parts because BioGuide software tool library is designed and programmed on parts that are in 2010 and 2011kit plate distributions. By the way, they found this software program managable. Given part names or input and output data results with Biobrick codes of parts in parts registry library. Therefore, it made easier their job on longstanding assembly plans. For mutual collaboration, we read and evaluated their Biosafety web page and gave feedback below
“You replied the first question having main title “materials used in your project” as bacteria strain used in your project. We suggest that you should focus on chemical or any other material to answer this question.However we also used the E.coli Top 10 as host strain and found that these strains are classified as hazard group 2 pathogen by the UK Advisory Committee on the Dangerous Pathogens (ACDP).
In the question 3 that you explained “Institutional Biosafety Committee”, you described the threats of Synthetic biology in 3 main items based on your interview, we think you should expand content of items.
And lastly, it would be better if you give more detail on your last question to be more clear for future iGEM teams.”