Team:Bilkent UNAM Turkey

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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.
Sponsors

Share

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-					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Project_Overview">Overview</a>
+					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Project_Overview">Background</a>
+		</span>
+                                        <span class='sliding_item'>
+					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Project_Description">Project_Description</a>
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-                                         <a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/safety">Lab Safety</a>
+                                         <a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Safety">Lab Safety</a>
                                  </span>
 			</div>
 		</span>
 		<span class='tab_item'>
-			HUMAN PRACTİCE
+			HUMAN PRACTICE
 			<div class='sliding_menu'>
 				<span class='sliding_item'>
@@ Line 220: / Line 223: @@
 				<span class='sliding_item'>
                                          <a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/iGEM_Everywhere">iGEM Everywhere</a>
+				</span>
+				<span class='sliding_item'>
+					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Collaboration">Collaboration</a>
 				</span>
 			</div>
@@ Line 246: / Line 252: @@
-<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>
+<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>
 <p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>Abstract<o:p></
 o:p></span></b></p>
 <table width="880" height="225" cellpadding="5" cellspacing="0" style="background:transparent !important;">
-        <td><img src="https://static.igem.org/mediawiki/2011/5/54/But.png" width="370" height="340"></td>
+<tr>
-<td>
+       <td rowspan="2"> <img src="https://static.igem.org/mediawiki/2011/5/54/But.png" width="370" height="340"></td>
+	<td><img src="https://static.igem.org/mediawiki/2011/e/eb/Nbt1201-1168-F1.gif" width="400"></td>
+</tr>
+     <tr><td>
-<p><span lang=3DTR>We aim for the genetic modification of the unicellular microalga <i
+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.
-style=3D'mso-bidi-font-style:normal'>Chlamydomonas reinhardtii</i>  by introducing the
-<i style=3D'mso-bidi-font-style:normal'>nfsI</i> gene belonging to the bacterium <i
-style=3D'mso-bidi-font-style:normal'>Enterobacter cloacae</i> in order to
-investigate how nitroreductase expressing-microalgae respond to trinitrotoluene
-(TNT) exposure. Our experimental design is as follows:
-firstly, obtain a synthetic gene of <i style=3D'mso-bidi-font-style:normal'>nfsI</i> with flanking prefix and suffix of standard Biobricks, and ligate this insert to pRbcBRL, a vector with
-appropriate expression and selection system for <i style=3D'mso-bidi-font-style:
-normal'>Chlamydomonas reinhardtii</i> and obtain pRbcnfsI. Then, <i style=3D'mso-bidi-font-style:normal'>Chlamydomonas reinhardtii</i> will be transfected with the with the designed plasmid. The transfected algae will then be grown in presence of TNT and/or TNT derivatives and the effectiveness of nitroreductase activity on
-biological degradation of TNT will be investigated.<b style=3D'mso-bidi-font-weight:normal'><o:p
-></o:p></b></span></p>
          </td>
-        </tr>
+       </tr>
          </table>
@@ Line 282: / Line 281: @@
 	</li>
-         <li>Something about spirit of being team
+         <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.
          </li>
          </td>
@@ Line 310: / Line 309: @@
 <ul>
 	<li>
-		<p> 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>
+		<p>
+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>
 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>
 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>
 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.<p>
 	</li>
 </ul>
@@ Line 323: / Line 323: @@
 <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>
-<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>Favorite Parts<p>
+<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>Favorite Parts<p></b>
-<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>BBa_K596001<p>
+<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>BBa_K596001<p></b>
 <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>
-<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>BBa_K596004<p>
+<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>BBa_K596004<p></b>
 <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>
-<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>DNA Submission to Registry<p>
+<p><b style=3D'mso-bidi-font-weight:normal'><span lang=3DTR>DNA Submission to Registry<p></b>
+<img src="https://static.igem.org/mediawiki/2011/9/9f/DNA_submission_to_registry.JPG" width="700"><p>
-<a href="https://2011.igem.org/File:DNA_submission_to_registry.JPG"><img src="https://static.igem.org/mediawiki/2011/f/f3/DNA_submission_to_registry.JPG" width="700" height="300"> </img></a>
@@ Line 354: / Line 356: @@
 <ul>
 	<li>
-We are really grateful to Gulce Itir Percin, Aydan Torun and Zeynep E.
+We find it our duty to thank Gulce Itir Percin, Aydan Torun and Ömer Faruk
-Ulger for their help and especially guidance of Mrs. Ulger about unknown
+Sarıoglu for their valuable assistance in conducting the experiments
-lab equipments. Prof. Dr. Tayfun Özçelik and Assistant Prof. Ali Güre are helped us to start iGEM team. Assistant Prof. Ayşe Tekinay and her lab were assisted our project a lot. Also we thanks to other members of SBL and NBT for patience.
+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.
 <h1>Sponsors</h1>
-<img src="https://static.igem.org/mediawiki/2011/3/32/Bilkent.gif" height="100"></img>
+<a href="http://www.bilkent.edu.tr"><img src="http://www.bilkent.edu.tr/~yayinbir/amblem/ing-amblem.jpg" height="100"></img></a>
-<img src="https://static.igem.org/mediawiki/2011/a/a1/Unam.gif" height="100"></img>
+<a href="http://www.nano.org.tr/index1.html"><img src="http://www.nano.org.tr/files/Unam_logo.jpg" height="100"></img></a>
-<img src="https://static.igem.org/mediawiki/2011/8/8d/Sentegen_logo.jpg" width="150" height="100"></img>
+<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>
+<h2>Share</h2>
+<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>
+<g:plusone></g:plusone>
 	</li>
 </ul>
-<ul>
-	<li>
-		This matches the 7tab
-	</li>
-</ul>
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