Team:Bilkent UNAM Turkey

From 2011.igem.org

(Difference between revisions)

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

There is a problem with poping up if you see this note.

@@ Line 4: / Line 4: @@
 <script type="text/javascript" src="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/js/dropdowncontent.js?action=raw&amp;ctype=text/css\"></script>
 <script type="text/javascript" src="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/wordlist.js?action=raw&amp;ctype=text/css\"></script>
+<script type="text/javascript" src="https://apis.google.com/js/plusone.js"></script>
 <script type="text/javascript">
@@ Line 63: / Line 64: @@
 #menubar.right-menu {
 	margin-top: -15px;
+}
+#menubar.left-menu {
+	top:0;
 }
 .right-menu ul {
@@ Line 71: / Line 75: @@
 	z-index: 25;
 }
+.left-menu noprint{
+	top:0;
+}
 * html body {
 	overflow: hidden;
@@ Line 104: / Line 110: @@
 img[src*="/wiki/skins/common/images/wiki.png"] {
 	width: 0;
-	height: 20px;
+	height:0px;
 }
@@ Line 122: / Line 128: @@
 	padding:0px -15px -2px -15px;
 	z-index:999;
-}
-#top-section {
-	background: url( https://static.igem.org/mediawiki/2011/c/cc/Banner_bilkent.jpg) no-repeat top center fixed;
 }
 #globalWrapper {
@@ Line 147: / Line 150: @@
 	color: white;
 }
+#banner{
+	position:fixed;
+	z-index:24;
+}
 </style>
@@ Line 173: / Line 179: @@
 		<span class='tab_item'>
 			PROJECT
+                        <div class='sliding_menu'>
+					<span class='sliding_item'>
+					<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>
 		</span>
+                        </div>
+               </span>
 		<span class='tab_item'>
 			TEAM
@@ Line 180: / Line 194: @@
 					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Gallery">Gallery</a>
 				</span>
+                                        <span class='sliding_item'>
+					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Team">Team_Page</a>
 			</div>
 		</span>
 		<span class='tab_item'>
-			LAB WORKS
+			LABWORKS
 			<div class='sliding_menu'>
 				<span class='sliding_item'>
-					Protocols
+					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Protocols">Protocols</a>
 				</span>
 				<span class='sliding_item'>
-					Experiment
+					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Experiment">Experiment</a>
 				</span>
                                  <span class='sliding_item'>
-                                         <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'>
-			FUN PART
+			HUMAN PRACTICE
 			<div class='sliding_menu'>
 				<span class='sliding_item'>
-					Picnics
+					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/BBQ_Party">BBQ Party</a>
 				</span>
 				<span class='sliding_item'>
-					Human Practises
+					<a href="https://2011.igem.org/Team:Bilkent_UNAM_Turkey/Team_Meetup">Team Meetup</a>
                                  </span>
 				<span class='sliding_item'>
-                                         iGEM Everywhere
+                                         <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 229: / Line 248: @@
 <ul>
-	<li>
-<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>
-<p><span lang=3DTR>We aim for the genetic modification of the unicellular microalga <i
+<table width="880" height="225" cellpadding="5" cellspacing="0" style="background:transparent !important;">
-style=3D'mso-bidi-font-style:normal'>Chlamydomonas reinhardtii</i>  by introducing the
+<tr>
-<i style=3D'mso-bidi-font-style:normal'>nfsI</i> gene belonging to the bacterium <i
+       <td rowspan="2"> <img src="https://static.igem.org/mediawiki/2011/5/54/But.png" width="370" height="340"></td>
-style=3D'mso-bidi-font-style:normal'>Enterobacter cloacae</i> in order to
-investigate how nitroreductase expressing-microalgae respond to trinitrotoluene
+	<td><img src="https://static.igem.org/mediawiki/2011/e/eb/Nbt1201-1168-F1.gif" width="400"></td>
-(TNT) exposure. Our experimental design is as follows:
+</tr>
-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:
+     <tr><td>
-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
+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.
-biological degradation of TNT will be investigated.<b style=3D'mso-bidi-font-weight:normal'><o:p
+        </td>
-></o:p></b></span></p>
+       </tr>
-<p>Introduction:<p>
-TNT or 2,4,6-trinitrotoluene was produced in 1863 by Wilbrand, and then used as the primary explosive by military forces in the world for several decades. The storage, usage, and disposal of TNT is a worldwide problem. TNT can enter into biological systems and constitutes a significant risk to human health. The adverse effects of TNT were indicated for humans such as irritation of the skin, aplastic anemia, cataract or spermatozoa malformancy. Furthermore, there is a high risk of contamination of food and water resources by TNT leakage from the contaminated areas. Thus, removal of TNT is highly important.
+        </table>
 	</li>
 </ul>
 <ul>
 	<li>
-		I’m Ebuzer, graduated from the Middle East Technical University and I’ am starting my PhD in UNAM. My hobbies consist of football, squash, Dota, watching movies, pen spinning. My favourites are shawshank redemption (movie), Game of thrones (book), Dexter (series). At last I am really interested in biodiesel production and algal systems. This year we got a grateful team, working hard and getting fun are our basic rules.
+        <table width="880" height="225" cellpadding="5" cellspacing="0" style="background:transparent !important;">
+        <td><img src="https://static.igem.org/mediawiki/2011/a/a1/Untitled.png" width="400" height="380"></td>
+<td>
 	</li>
-	<p>
+        <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.
-		I’m Ufuk, sophomores of Bilkent University, Molecular Biology and Genetics Department. Playing squash and Dota are my favourite activities, if I win. Fantastic books are fascinates me. First book, I read was One Thousand and One Nights. In iGEM; I like its fun and working style. Everything happens together. I like to watch movies especially with friends. This is my first iGEM experience, I am thankful to my team members for sharing their fun.
+        </li>
-	<p>
+        </td>
-	<li>
+        </tr>
-		I am Tarkan and one of the member of the Bilkent – UNAM – Turkey team. I love watching and playing sports especially football and basketball just as usual Turkish guys do. I love dancing but generally too shy to start doing it in public. I like talking and meeting new people. Telling jokes and amuzing people is my style of communication, because that is the best way of telling your good intentions towards others. I participate volunteering action a lot in the campus and that actions target poor, rural and disabled children. I love them and enjoy spending time with. So, that is it for me now.
+        </table>
-	</li>
+</ul>
-	<li>
+<ul>
-		It is Burcu from Bilkent University, Institute of Material Science and Nanotechnology. I am very proud of being a member of Bilkent UNAM Turkey team because I think; here we reflect the real team spirit. Here is a brief information about me: I spent every minute of me by listening music! Nothing makes me happy like talking with people. I do love sports activities if I can bring down my laziness. Reading books is not for me but reading articles has become my pleasure for a long time. As many members of my team, it is my first IGEM participation. I hope we will rock the IGEM world with our endless energy and success!
-	</li>
-I am Ahmet Emin, just graduated from Molecular Biology and Genetics at Bilkent University in Ankara, Turkey. I am now a graduate student in Laboratory of Sustainable Technologies in UNAM, Institute of Material Science and Nanotechnology at Bilkent University. My current research interests are sustainable and environmental biotechnology, microbioengineering and vaccine science in immunology.
 	<li>
+<table width="880" height="225" cellpadding="5" cellspacing="0" style="background:transparent !important;">
+<tr>
+<td><img src="https://static.igem.org/mediawiki/2011/e/ee/01089.jpg" width="440" height="300"></td>
+<td>
+<p>
+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>
+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 <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.
+</p>
+</td>
+</tr>
+</table>
-	</li>
-</ul>
-<ul>
-	<li>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>
-When we are 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 has began.
-We added our protocols which are helpful to transform C.reinhartii and E.coli. Basic cloning protocols also added our protocol page. Experiments and safety questions also available from link at the top section.
 	</li>
 </ul>
 <ul>
 	<li>
-		This matches the fourth tab
+		<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 285: / Line 321: @@
-<a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2011&group=Bilkent_UNAM_Turkey">Addded genes</a>
+<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></b>
+<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></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></b>
+<img src="https://static.igem.org/mediawiki/2011/9/9f/DNA_submission_to_registry.JPG" width="700"><p>
 </ul>
 <ul>
 	<li>
-		This matches the sixth tab
+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.
+<h1>Sponsors</h1>
+<a href="http://www.bilkent.edu.tr"><img src="http://www.bilkent.edu.tr/~yayinbir/amblem/ing-amblem.jpg" height="100"></img></a>
+<a href="http://www.nano.org.tr/index1.html"><img src="http://www.nano.org.tr/files/Unam_logo.jpg" height="100"></img></a>
+<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>
 		</div>
@@ Line 311: / Line 393: @@
 }
+//this is for banner
+var tr1 = document.createElement('tr');
+var table1 = document.createElement('table');
+table1.setAttribute('id','banner');
+var image1 = document.createElement('img');
+image1.setAttribute('src', 'https://static.igem.org/mediawiki/2011/a/a1/Unam.gif');
+image1.setAttribute('style','border:0;');
+var image2 = document.createElement('img');
+image2.setAttribute('src', 'https://static.igem.org/mediawiki/2011/0/05/Igem.gif');
+image2.setAttribute('style','border:0;');
+var image3 = document.createElement('img');
+image3.setAttribute('src', 'https://static.igem.org/mediawiki/2011/0/06/But.gif');
+image3.setAttribute('style','border:0;');
+var image4 = document.createElement('img');
+image4.setAttribute('src', 'https://static.igem.org/mediawiki/2011/3/32/Bilkent.gif');
+image4.setAttribute('style','border:0;');
+var href1 = document.createElement('a');
+href1.setAttribute('href','http://www.nano.org.tr/index1.html');
+var href2 = document.createElement('a');
+href2.setAttribute('href','https://2011.igem.org/Main_Page');
+var href3 = document.createElement('a');
+href3.setAttribute('href','https://2011.igem.org/Team:Bilkent_UNAM_Turkey');
+var href4 = document.createElement('a');
+href4.setAttribute('href','http://www.bilkent.edu.tr');
+var td1 = document.createElement('td');
+var td2 = document.createElement('td');
+var td3 = document.createElement('td');
+var td4 = document.createElement('td');
+var td5 = document.createElement('td');
+td5.setAttribute('width','110');
+href1.appendChild(image1);
+href2.appendChild(image2);
+href3.appendChild(image3);
+href4.appendChild(image4);
+td1.appendChild(href1);
+td2.appendChild(href2);
+td3.appendChild(href3);
+td4.appendChild(href4);
+tr1.appendChild(td1);
+tr1.appendChild(td5);
+tr1.appendChild(td2);
+tr1.appendChild(td3);
+tr1.appendChild(td4);
+table1.appendChild(tr1);
+document.getElementById('top-section').appendChild(table1);
+//banner up to here
@@ Line 317: / Line 477: @@
-var flash = document.createElement("div");
-flash.setAttribute("id", "effect560621");
-flash.setAttribute("style", "width:975px;height:98px;");
-document.getElementById("top-section").appendChild(flash );
@@ Line 340: / Line 496: @@
 </script>
-<script type="text/javascript" src="http://www.effectgenerator.com/1.0.7/effect.php?id=560610&replace=effect560621"></script>
+<script type="text/javascript">var switchTo5x=true;</script><script type="text/javascript" src="http://w.sharethis.com/button/buttons.js"></script><script type="text/javascript">stLight.options({publisher:'fc7a483f-b897-4a2e-9b57-bb2baf6e43da'});</script>
 </html>