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METUGEM '07
Middle East Technical University
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Somebody (an undergrad) learned
about synthetic biology
and told others…
They found out iGEM’06
and asked themselves…
Why aren’t we there?
and they set up a team…
METUGEM ‘07
Why nobody else around me know
about it?
and asked himself…
HOW ?
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But then… Not everything went as planned..!
First time on our own…
We were inexperienced!
The bureaucracy was taking so
long;
Our schedule was not aligning with
that of iGEM;
Nobody else around us knew
about SB;
• Educating ourselves
• Convincing others
Information…
Timing…
Money…
• Summer practice requirement
• Money coming late • Lab stuff not in
stocks
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Still… We were determined!
• To draw attention to Synthetic Biology in
Turkey
• To pioneer the first
undergraduate project in our department
• To attend to the Jamboree
We;* made presentations* talked to students and instructors
* worked on 3 project ideas theoretically
and now we are here…
* got ready for the iGEM’08; allocated lab space and bought materials
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Mexican Wave
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AimTo create a mechanism that can signal an
event in a funny manner
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Signal protein that is result of an event
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What do we expect to observe?
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Chase Simulator
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AimTo create 2 kinds of invader cells that compete
on lawn of neutral cells
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Mechanism
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Metal Transporter
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Metal-binding domainseg. CVNGCVPSKfor Mercury
Cu, Cd, Ag, Hg, Sb, Tl,Zn, Co, As, Cr, Mb, Mg,Fe, K, Te...
F
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BacteriorhodopsinTransmembrane protein
Cis-trans isomerization
Proton pumping
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Phototaxis
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Fusion constructs for Phototaxis
Jung et al. (2001)
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Stage 1
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Stage 2: Metal Binding
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Stage 3: Moving towards light
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Stage 4. Reaching to destination
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Stage 5: Releasing metal ions
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Stage 6: Returning…
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References In silico identification of putative metal binding motifs, Richard Thilakaraj,
Krishnan Raghunathan, Sharmila Anishetty and Gautam Pennathur, 2007 Bioinformatics, Vol. 23 no. 3, pages 267–271
An Archaeal Photosignal-Transducing Module Mediates Phototaxis in Escherichia coli, Kwang-Hwan Jung, Elena N. Spudich, Vishwa D. Trivedi, and John L. Spudich, 2001, Journal of Bacteriology,Vol 183 No:21, p. 6365–6371
Engineering the Escherichia coli outer membrane protein OmpC for metal bioadsorption, Norberto Cruz, Sylvie Le Borgne, Georgina Hern´andez-Ch´avez, Guillermo Gosset, Fernando Valle & Francisco Bolivar, 2000, Biotechnology Letters 22: 623–629
Molecular basis of transmembrane signalling by sensory rhodopsin II–transducer complex, Valentin I. Gordeliy, Jorg Labahn, Rouslan Moukhametzianov, Rouslan Efremov, Joachim Granzin, Ramona Schlesinger,Georg Buldt, Tudor Savopol, Axel J. Scheidig, Johann P. Klare & Martin Engelhard, 2002, Nature, Vol 419, 484-486
Genetic cloning and functional expression in Escherichia coli of an archaerhodopsin gene from Halorubrum xinjiangens, Jie Feng, Hong-Can Liu, Jin-Fang Chu, Pei-Jin Zhou, Ji-An Tang Æ Shuang-Jiang Liu, 2005, Extremophiles, 10: 29-33
http://www.cocuksepeti.com/images/7011-b.gif
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What have we learnt?Organizational manners:
* starting a team, * funding, * preparing a whole money and time
planning,* ordering lab equipments and materials,
Biobrick Strategy:* designing parts,* using the wiki and the registry
Protocols:practicing synthetic biology
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Special Thanks to:SYNBIOCOMM and Sven PANKE
TÜBİTAK
METU
Gülay ÖZCENGİZ, Mahinur AKKAYA and Sertaç ÖNDE
Pamela SILVER from HMS