Team:Bilkent UNAM Turkey

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<!--- The Mission, Experiments --->
 
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
 
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!align="center"|[[Team:Bilkent_UNAM_Turkey|Home]]
 
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!align="center"|[[Team:Bilkent_UNAM_Turkey/Team|Team]]
 
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!align="center"|[https://igem.org/Team.cgi?year=2011&team_name=Bilkent_UNAM_Turkey Official Team Profile]
 
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!align="center"|[[Team:Bilkent_UNAM_Turkey/Project|Project]]
 
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!align="center"|[[Team:Bilkent_UNAM_Turkey/Parts|Parts Submitted to the Registry]]
 
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!align="center"|[[Team:Bilkent_UNAM_Turkey/Modeling|Modeling]]
 
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!align="center"|[[Team:Bilkent_UNAM_Turkey/Notebook|Notebook]]
 
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!align="center"|[[Team:Bilkent_UNAM_Turkey/Safety|Safety]]
 
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!align="center"|[[Team:Bilkent_UNAM_Turkey/Attributions|Attributions]]
 
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{|align="justify"
 
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|You can write a background of your team here.  Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
 
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''Our major project's abstract and motivation of us;
 
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According to encyclopaedia algae have wide strand from unicellular to multicellular and they are photosynthetic. They are really good species to study on to produce biodiesel as a lot of people do. We choose working on algae for four major reasons:
 
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Firstly; getting protein from algae is cheap and they can grow in wide area from soil to pink water. When we added our plasmid backbone to biobrick database other group can use it to get protein easily and amount also is a major problem for getting it from prokaryotes to clinical usage.|
 
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Secondly; Chlamydomonas reinhardtii is a common used model organism and it is easy to handle. With last decades people are really condense studying on it. This organism can also grow in dark with adding acetate as a source of carbon.
 
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Thirdly; trinitrotoluene is a toxic material for the environment. After Edinburgh Team project we recognise it could be improved by this way. We have chosen NfsI gene as a nitroreductase which isolated from Enterobacter cloacae.  Efficiency of NfsI gene for TNT reduction is good to accept to work with it.
 
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And lastly; losing a family member because of mine is enough reason to put effort on it. We could have been a child of a dead man. Reality is that hundreds of thousands of people have been injured or killed by anti-personnel landmines. In Afghanistan, 350,000–500,000 have been killed or injured due to landmine explosions, and more occur daily. In Angola, there are approximately 26,000 amputees, and in Cambodia 30,000. In Mozambique, 6,000 people, mostly civilians, have been killed or maimed by landmines since 1980. Landmine Monitor reports have estimated that annually, 5,000 to 7,000 new casualties are caused by landmines and unexploded ordnance, the majority occurs in countries no longer involved in conflict. A child could die just for running after ball.
 
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To conclude with; taking action to produce protein has some benefits and working with oxygen insensitive nitroreductase also has an advantage. We try to what scientists do.  
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(Save the people, save the world!)
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|[[Image:Bilkent_UNAM_Turkey_team.png|right|frame|Your team picture]]
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|align="center"|[[Team:Bilkent_UNAM_Turkey | Team Example]]
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<span class='tab_item'>
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PROJECT
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<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Project_Overview">Background</a>
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<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Project_Description">Project_Description</a>
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TEAM
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<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Gallery">Gallery</a>
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LABWORKS
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<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Protocols">Protocols</a>
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<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Experiment">Experiment</a>
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                                        <a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Safety">Lab Safety</a>
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HUMAN PRACTICE
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<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/BBQ_Party">BBQ Party</a>
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<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Team_Meetup">Team Meetup</a>
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                                        <a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/iGEM_Everywhere">iGEM Everywhere</a>
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<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Collaboration">Collaboration</a>
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BIOBRICK PARTS
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ATTRIBUTIONS
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<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>Biodegradation of TNT and TNT derivatives by <i>nfsI</i>-transfected <i>Chlamydomonas_reinhardtii</i><o:p></o:p></span></b></p>
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<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>Abstract<o:p></
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Our aim is to modify the unicellular microalga <i>Chlamydomonas reinhardtii</i> for effective trinitrotoluene (TNT) biodegradation by expression of Enterobacter cloacae nitroreductase gene nfsI.  <i>C. reinhardtii</i> is a ubiquitous species capable of thriving in soil, freshwater and marine environments, making this alga a suitable choice for removal of TNT from a wide variety of biomes. We have opted for the use of nfsI as the gene in question is a well-characterized nitroreductase with a known sequence. Our experimental procedure involves (a) development of a synthetic nfsI gene with flanking prefix and suffixes of standard Biobricks, (b) ligation of this sequence to the C. heinhardtii expression vector pRbcBRL, (c) transfection of <i>C. reinhardtii</i> with the recombinant plasmid and (d) TNT tolerance and biodegradation capacity assessment of the modified alga.
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        <li>Bilkent UNAM Turkey team established in January 2011 and member list has grown and changed in time. We shared a lot by that time and are extremely thankful to our former members. We did many brainstorming meetings, some of them was inconclusive. Team went through several problems that cause slightly negative impact on team. For a team to join from Turkey, money always becomes a problem. That’s why we are just able to send just two of our members to the regional jamboree. Moreover, laboratory equipment shipping takes very much time, even a restriction enzyme received one month after the ordering. Our team survive those restrictions and did its best. The force that always give impetus to ourselves is the friendship that we have.
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<td><img src="https://static.igem.org/mediawiki/2011/e/ee/01089.jpg" width="440" height="300"></td>
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<p>
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In this summer; we learned about iGEM, how it works, what the biggest part of competition is and how we can win a medallion.<p>
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When we were newbie, we organized a lot of meeting to find out our main project than we got idea for improving human welfare so we choose an idea from brainstorm results. We searched to get a gene to work on. As a result; lab works began.
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We added our protocols which are helpful to transform <i>Chlamydomonas reinhardtii</i> and <i>Escherichia coli</i>. Basic cloning protocols are available on our protocol page. Experiments and safety questions also available from link at the top section.
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IGEM Project is our number one priority. As we worked really hard for our project it is important for us to make our dreams come true which is taking a gold medal. Questioning different items like experiment time, materials and methods and the efficiency of the experiments improved our skills and we started to look as a scientist to problems we faced. There were lots of challenging parts and sometimes we thought to quit but we listened to “Eye of The Tiger” and we did not give up from our experiments we delayed them yes, but we never gave up. <p>
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IGEM team- meet-up was a great opportunity for us to communicate with the other groups, understood their projects and share our ideas. As we had a chance for an interview with Anatolia Agency, we also used media power to get attention to our project, iGEM and the importance of synthetic biology. <p>
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Apart from that we did not forget having fun apart from our lab. As we planned a BBQ party, it was also a great chance for us to relax and gain some energy for our experiments, I did not even mention about the delicious foods and how joyful was our activities. Also like in iGEM team meeting up, we had a chance to introduce our project and main aim to other scientists and researchers in different areas.<p>
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Links at above lead you to specific event and its photos suppose to be at that link. If not, look at gallery link.
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Thanks and get great time.<p>
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<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2011&group=Bilkent_UNAM_Turkey"><img src="https://static.igem.org/mediawiki/2011/e/ea/Our_parts.png" width="700"> </img></a>
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<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K596001"><img src="https://static.igem.org/mediawiki/2011/f/f3/BBa_K596001.JPG" width="700" height="300"> </img></a>
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<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K596004"><img src="https://static.igem.org/mediawiki/2011/0/05/Algae_protein_expression_vector_pAPEV.png" width="450" height="450"> </img></a>
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<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>DNA Submission to Registry<p></b>
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We find it our duty to thank Gulce Itir Percin, Aydan Torun and Ömer Faruk
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Sarıoglu for their valuable assistance in conducting the experiments
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within our project’s scope, without which we could scarcely have expected
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to complete our project in time. We must also extend our thanks to
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Sustainable Technologies Laboratory Manager Zeynep E. Ülger for providing
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the necessary instructions and training for the use of a wide variety of
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laboratory equipment. We would like to acknowledge Prof. Dr. Tayfun Özçelik and Prof. Dr. Engin Umut Akkaya for their sincere support on our team and efforts for getting finanical support from Bilkent University. We thank the Turkish National Nanotechnology
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Institute (UNAM) for the administration of routine training sessions regarding
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laboratory safety, which allowed all our team members to operate without
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any personal danger throughout the experiments so far. We are also
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grateful to Assistant Professor Ayse Begum Tekinay and her laboratory for
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supplying much-needed reagents and assistance, both of which allowed our
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small team to work much faster than it otherwise could. And lastly we must
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thank our supervisor Turgay Tekinay for making this project possible and
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granting us a summer that was as entertaining as it was informative.
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<h1>Sponsors</h1>
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<a href="http://www.bilkent.edu.tr"><img src="http://www.bilkent.edu.tr/~yayinbir/amblem/ing-amblem.jpg" height="100"></img></a>
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<a href="http://www.nano.org.tr/index1.html"><img src="http://www.nano.org.tr/files/Unam_logo.jpg" height="100"></img></a>
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<a href="http://www.sentegen.com/"><img src="https://static.igem.org/mediawiki/2011/8/8d/Sentegen_logo.jpg" width="150" height="100"></img></a>
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<h2>Share</h2>
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<span  class='st_email_large' ></span><span  class='st_facebook_large' ></span><span  class='st_twitter_large' ></span></span><span  class='st_yahoo_large' ></span><span  class='st_friendfeed_large' ></span><span  class='st_blogger_large' ></span><span  class='st_delicious_large' ></span><span  class='st_linkedin_large' ></span>
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Latest revision as of 03:44, 22 September 2011

 
PROJECT
Background Project_Description
TEAM
Gallery Team_Page
LABWORKS
Protocols Experiment Lab Safety
HUMAN PRACTICE
BBQ Party Team Meetup iGEM Everywhere Collaboration
BIOBRICK PARTS ATTRIBUTIONS

    Biodegradation of TNT and TNT derivatives by nfsI-transfected Chlamydomonas_reinhardtii

    Abstract

    Our aim is to modify the unicellular microalga Chlamydomonas reinhardtii for effective trinitrotoluene (TNT) biodegradation by expression of Enterobacter cloacae nitroreductase gene nfsI. C. reinhardtii is a ubiquitous species capable of thriving in soil, freshwater and marine environments, making this alga a suitable choice for removal of TNT from a wide variety of biomes. We have opted for the use of nfsI as the gene in question is a well-characterized nitroreductase with a known sequence. Our experimental procedure involves (a) development of a synthetic nfsI gene with flanking prefix and suffixes of standard Biobricks, (b) ligation of this sequence to the C. heinhardtii expression vector pRbcBRL, (c) transfection of C. reinhardtii with the recombinant plasmid and (d) TNT tolerance and biodegradation capacity assessment of the modified alga.
  • Bilkent UNAM Turkey team established in January 2011 and member list has grown and changed in time. We shared a lot by that time and are extremely thankful to our former members. We did many brainstorming meetings, some of them was inconclusive. Team went through several problems that cause slightly negative impact on team. For a team to join from Turkey, money always becomes a problem. That’s why we are just able to send just two of our members to the regional jamboree. Moreover, laboratory equipment shipping takes very much time, even a restriction enzyme received one month after the ordering. Our team survive those restrictions and did its best. The force that always give impetus to ourselves is the friendship that we have.

  • In this summer; we learned about iGEM, how it works, what the biggest part of competition is and how we can win a medallion.

    When we were newbie, we organized a lot of meeting to find out our main project than we got idea for improving human welfare so we choose an idea from brainstorm results. We searched to get a gene to work on. As a result; lab works began. We added our protocols which are helpful to transform Chlamydomonas reinhardtii and Escherichia coli. Basic cloning protocols are available on our protocol page. Experiments and safety questions also available from link at the top section.

  • IGEM Project is our number one priority. As we worked really hard for our project it is important for us to make our dreams come true which is taking a gold medal. Questioning different items like experiment time, materials and methods and the efficiency of the experiments improved our skills and we started to look as a scientist to problems we faced. There were lots of challenging parts and sometimes we thought to quit but we listened to “Eye of The Tiger” and we did not give up from our experiments we delayed them yes, but we never gave up.

    IGEM team- meet-up was a great opportunity for us to communicate with the other groups, understood their projects and share our ideas. As we had a chance for an interview with Anatolia Agency, we also used media power to get attention to our project, iGEM and the importance of synthetic biology.

    Apart from that we did not forget having fun apart from our lab. As we planned a BBQ party, it was also a great chance for us to relax and gain some energy for our experiments, I did not even mention about the delicious foods and how joyful was our activities. Also like in iGEM team meeting up, we had a chance to introduce our project and main aim to other scientists and researchers in different areas.

    Links at above lead you to specific event and its photos suppose to be at that link. If not, look at gallery link. Thanks and get great time.

    Favorite Parts

    BBa_K596001

    BBa_K596004

    DNA Submission to Registry

  • We find it our duty to thank Gulce Itir Percin, Aydan Torun and Ömer Faruk Sarıoglu for their valuable assistance in conducting the experiments within our project’s scope, without which we could scarcely have expected to complete our project in time. We must also extend our thanks to Sustainable Technologies Laboratory Manager Zeynep E. Ülger for providing the necessary instructions and training for the use of a wide variety of laboratory equipment. We would like to acknowledge Prof. Dr. Tayfun Özçelik and Prof. Dr. Engin Umut Akkaya for their sincere support on our team and efforts for getting finanical support from Bilkent University. We thank the Turkish National Nanotechnology Institute (UNAM) for the administration of routine training sessions regarding laboratory safety, which allowed all our team members to operate without any personal danger throughout the experiments so far. We are also grateful to Assistant Professor Ayse Begum Tekinay and her laboratory for supplying much-needed reagents and assistance, both of which allowed our small team to work much faster than it otherwise could. And lastly we must thank our supervisor Turgay Tekinay for making this project possible and granting us a summer that was as entertaining as it was informative.

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