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| <div class="writeback"> | | <div class="writeback"> |
| <h3>Methan<b>E.COLI</b>c : Decreasing the Greenhouse effects and Saving the workers life in one system</h3> | | <h3>Methan<b>E.COLI</b>c : Decreasing the Greenhouse effects and Saving the workers life in one system</h3> |
- | <p>Firedamp explosions are frequently seen cases at all mines over the world. In Turkey every year, 50 miners lose their lives because of firedamp explosions. Firedamp is a flammable gas found in coal mines and it mainly contains methane. Beside its explosive property, methane is also the main contributor to global warming. However recent mine mechanisms release obtained methane into air. By offers of Synthetic biology, we aimed to design a device which will work on E.coli that provides solutions for side effects of methane. Device that we are planning to construct involves the genes of bacteria (Methylococcus capsulatus) and insect (Drosophilia melanogaster) Our compact system in E.coli is fabricated as sensation of methane, the conversion of methane to methanol and then entrapment of methanol to handle for biofuel and death of bacteria at 42 C by kill switch mechanism.</p> | + | <p>Firedamp explosions are frequently seen cases at all mines over the world. In Turkey every year, 50 miners lose their lives because of firedamp explosions. Firedamp is a flammable gas found in coal mines and it mainly contains methane. Beside its explosive property, methane is also the main contributor to global warming. However recent mine mechanisms release obtained methane into air. By offers of Synthetic biology, we aimed to design a device which will work on <i>E.coli</i> that provides solutions for side effects of methane. Device that we are planning to construct involves the genes of bacteria (<i>Methylococcus capsulatus</i>) and insect (<i>Drosophilia melanogaster</i>). Our compact system in <i>E.coli</i> is fabricated as sensation of methane, the conversion of methane to methanol and then entrapment of methanol to handle for biofuel and death of bacteria at 42 C by kill switch mechanism.</p> |
| <p>When project is analyzed in stepwise, there are successive 4 steps of our modelled system in modified organism. As mentioned in subtitles, methane is sensed, then converted to methanol and methanol is entrapped and to elute methanol the cells are dead. </p> | | <p>When project is analyzed in stepwise, there are successive 4 steps of our modelled system in modified organism. As mentioned in subtitles, methane is sensed, then converted to methanol and methanol is entrapped and to elute methanol the cells are dead. </p> |
| </div> | | </div> |
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| <img src="https://static.igem.org/mediawiki/2011/1/1c/Projectheader.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/1/1c/Projectheader.png" height="75px" width="890px"> |
| <h2>Introduction</h2> | | <h2>Introduction</h2> |
- | <p>Methan<b>E.COLIc</b> project is designed to solve one of the problems of Turkey on worker security in mines, by constructing the natural parts of organisms.The main reason for us to choose such a project is that in Turkey- and also in many countries- each year, huge numbers of workers in mines lost their life due to deficiencies and conditions in their working areas (mines). The release of Grizu gas leads to subsidence of mines and so death of workers.This project is also designed to solve one of universal problem; global warming. Methane gas is a potential greenhouse gas.This project focuses on sensing the ambient methane gas and converting to one of the bio-fuel sources, methanol. Methanol is entrapped by product of one of the constructs of project, and then cells are dead by kill switch device of project to elute methanosol.</p> | + | <p>Methan<b>E.COLIc</b> project is designed to solve one of the problems on worker security in mines of Turkey , by constructing the natural parts of organisms. The main reason for us to choose such a project is that in Turkey- and also in many countries- each year, huge numbers of workers in mines lost their life due to deficiencies and conditions in their working areas (mines). The release of Grizu gas leads to subsidence of mines and so death of workers.This project is also designed to solve one of universal problem; global warming. Methane gas is a potential greenhouse gas.This project focuses on sensing the ambient methane gas and converting to one of the bio-fuel sources, methanol. Methanol is entrapped by product of one of the constructs of project, and then cells are dead by kill switch device of project to elute methanol.</p> |
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| <img src="https://static.igem.org/mediawiki/2011/7/72/Teamheader.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/7/72/Teamheader.png" height="75px" width="890px"> |
| <h2>Team</h2> | | <h2>Team</h2> |
- | <p><b><i>Hello everyone!We are Metu Ankara IGEM team.Our team consists of high motivated,social and enjoyable “undergraduate and graduate scientists” from departments of physics, chemistry ,biology and computer education & instructional technology. We are such a team that complete each other so that we all experienced team spirit in IGEM. This makes us happy while doing experiences even in the hot summer.Our slogan is “ all for one, one for all”!!Then, who are we?</i></b></p> | + | <p><b><i>Hello everyone!We are Metu Ankara IGEM team.Our team consists of high motivated,social and enjoyable “undergraduate and graduate scientists” from departments of physics, chemistry ,biology, computer engineer and computer education & instructional technology. We are such a team that complete each other so that we all experienced team spirit in IGEM. This makes us happy while doing experiences even in the hot summer.Our slogan is “ all for one, one for all”!!Then, who are we?</i></b></p> |
| <br/> | | <br/> |
| <div id="slider"> | | <div id="slider"> |
- | <img alt="" width="640px" height="480px" src="http://img17.imageshack.us/img17/9489/dscn1067ll.jpg"> | + | |
- | <img alt="" src="https://static.igem.org/mediawiki/2011/9/96/Gokcan_01.jpg">
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- | <img alt="" src="https://static.igem.org/mediawiki/2011/7/73/Sibel_01.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/f/fb/12345.JPG"> |
- | <img alt="" src="https://static.igem.org/mediawiki/2011/2/2b/Simge_01.jpg">
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- | <img alt="" src="https://static.igem.org/mediawiki/2011/e/e8/Yunus_01.jpg">
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- | <img alt="" src="https://static.igem.org/mediawiki/2011/8/87/Ibrahimkut.jpg">
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- | <img alt="" src="https://static.igem.org/mediawiki/2011/1/1b/Humanpractice.png">
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- | <img alt="" src="https://static.igem.org/mediawiki/2011/1/1c/Projectheader.png">
| + | <img src="https://static.igem.org/mediawiki/2011/8/8d/1093.JPG"> |
- | <img alt="" src="https://static.igem.org/mediawiki/2011/4/4c/Softwaretoolheader.png">
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- | <img alt="" src="https://static.igem.org/mediawiki/2011/7/72/Teamheader.png">
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- | <img alt="" src="https://static.igem.org/mediawiki/2011/2/28/Wetlabheader.pn">
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| + | <img src="https://static.igem.org/mediawiki/2011/1/17/DSCN1910.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/0/0e/DSCN1915.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/5/5a/Ff.JPG"> |
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| </div> | | </div> |
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| <ul> | | <ul> |
| <li><a href="mailto:akkayams@metu.edu.tr">Prof. Dr. Mahinur S. Akkaya</a></li> | | <li><a href="mailto:akkayams@metu.edu.tr">Prof. Dr. Mahinur S. Akkaya</a></li> |
- | <li><a href="mailto:kursat@metu.edu.tr">Kürşat Çağıltay</a></li> | + | <li><a href="mailto:kursat@metu.edu.tr">Assoc. Prof. Dr.Kürşat Çağıltay</a></li> |
| </ul> | | </ul> |
| <h3><u>Advisors</u></h3> | | <h3><u>Advisors</u></h3> |
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| <div class="smallbox"> | | <div class="smallbox"> |
| <h2><a href="mailto:sibelataol8@gmail.com">Sibel Ataol</a></h2> | | <h2><a href="mailto:sibelataol8@gmail.com">Sibel Ataol</a></h2> |
- | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/d/d0/Sibel_011.jpg"> | + | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/a/a9/Sibel-01.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
| <p> Sibel is first semester student in Master's program of Biomedical engineering at Middle East | | <p> Sibel is first semester student in Master's program of Biomedical engineering at Middle East |
- | Technical University indeed she is graduated from Biology Department at METU. This is the second year of her in IGEM team from METU.she is one of the experienced in team and elder sister:) As a vice team lead, planing the experiments and cloning strategies and motivating team are the responsibilities of her. Studying in bioengineering and regenerative sciences is her desire | + | Technical University indeed she is graduated from Biology Department at METU. This is the second year of her in IGEM team from METU.She is one of the experienced in team and elder sister:) As a vice team lead, planing the experiments and cloning strategies and motivating team are the responsibilities of her. Studying in bioengineering and regenerative sciences is her desire |
| for future.</p> | | for future.</p> |
| </div> | | </div> |
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| <div class="smallbox"> | | <div class="smallbox"> |
| <h2><a href="mailto:e153564@metu.edu.tr">Funda Guzey</a></h2> | | <h2><a href="mailto:e153564@metu.edu.tr">Funda Guzey</a></h2> |
- | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/5/50/Funda01.jpg"> | + | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/9/93/Funda.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
| <p>She is a senior student of Biological Sciences at Middle East Technical University. This is her third year in iGEM competition. She gained a lot of experiences in this summer. One of the her interests is Synthetic Biology. However, her main interest is Biomedical and Tissue Engineering. She feels lucky to have such a wonderful team and is glad to share a wonderful summer with her team.</p> | | <p>She is a senior student of Biological Sciences at Middle East Technical University. This is her third year in iGEM competition. She gained a lot of experiences in this summer. One of the her interests is Synthetic Biology. However, her main interest is Biomedical and Tissue Engineering. She feels lucky to have such a wonderful team and is glad to share a wonderful summer with her team.</p> |
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| <div class="smallbox"> | | <div class="smallbox"> |
| <h2><a href="mailto:simgeyuz@gmail.com">G. Simge Yüz</a></h2> | | <h2><a href="mailto:simgeyuz@gmail.com">G. Simge Yüz</a></h2> |
- | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/2/2b/Simge_01.jpg"> | + | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/f/f6/Sibel_012-1.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
| <p>She is a recent graduate student of Chemistry and a fourth year student of Biological Sciences. This is the first year of her in iGEM team. She wants to study on neuropharmacology in the field of neuroscience. She is glad to join to METU-Ankara-iGEM team. She enjoys dancing especially Argentine tango and swimming. She is also a member of Flashmob Ankara Society</p> | | <p>She is a recent graduate student of Chemistry and a fourth year student of Biological Sciences. This is the first year of her in iGEM team. She wants to study on neuropharmacology in the field of neuroscience. She is glad to join to METU-Ankara-iGEM team. She enjoys dancing especially Argentine tango and swimming. She is also a member of Flashmob Ankara Society</p> |
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| </div> | | </div> |
| | | |
- | <div class="smallbox">
| + | |
- | <h2><a href="mailto:cihanefe@gmail.com">Cihan Efe KILIC</a></h2>
| + | |
- | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/a/a8/Cihan.jpg">
| + | |
- | <div class="smalltext">
| + | |
- | <p>I am a third year student at the Department of Chemistry at Middle East Technical University. This is the first year of mine in iGEM team. I faced synthetic biology on my Biochemistry course. I want to study on the Electrochemistry-Enzyme immobilization. I believe that synthetic biology will give some benefits for my future work. I like team working and sharing the success. I like to cool staff with liquid nitrogen J I enjoys playing musical instruments flute and martial arts.</p>
| + | |
- | </div>
| + | |
- | </div>
| + | |
| | | |
| <div class="smallbox"> | | <div class="smallbox"> |
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| <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2010/a/a2/Metu-burak.jpg"> | | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2010/a/a2/Metu-burak.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
- | <p>I am a recent graduate of METU Molecular Biology and Genetics department and now studying towards my masters degree on Molecular Bioengineering at METU. My interest in synthetic biology did start during my undergraduate years and after graduation I started up the Sentegen company which is the first biotechnology based company focused on synthetic biology in Turkey. I continue my research and training in synthetic biology while also contributing to the development of the field in my country. We need new scientific revolutions to solve huge problems of life and emerging field of synthetic biology is best candidate for biotechnological revolution. I am interested in synthetic biology applications, along with Lab-on-a-Chip devices for molecular biology techniques, and we are designing gene synthesis chips to produce biobricks - raw materials of garage biology- faster and cheaper. I enjoy snowboarding, cycling and writing poems.</p> | + | <p>He is a recent graduate of METU Molecular Biology and Genetics department and now studying towards his masters degree on Molecular Bioengineering at METU. His interest in synthetic biology did start during his undergraduate years and after graduation he started up the Sentegen company which is the first biotechnology based company focused on synthetic biology in Turkey. He continues his research and training in synthetic biology while also contributing to the development of the field in his country. He needs new scientific revolutions to solve huge problems of life and emerging field of synthetic biology is best candidate for biotechnological revolution. He is interested in synthetic biology applications, along with Lab-on-a-Chip devices for molecular biology techniques, and he is designing gene synthesis chips to produce biobricks - raw materials of garage biology- faster and cheaper. he enjoys snowboarding, cycling and writing poems.</p> |
| </div> | | </div> |
| </div> | | </div> |
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| <center><h3><u>Software Group</u></h3></center> | | <center><h3><u>Software Group</u></h3></center> |
| <div class="smallbox"> | | <div class="smallbox"> |
- | <h2><a href="mailto:miktat_aktas@hotmail.com">Miktat Aktaş</a></h2> | + | <h2><a href="mailto:agca1988@gmail.com">Muhammed Akif Ağca</a></h2> |
- | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/8/8d/Miktat.JPG"> | + | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2010/1/10/Metu-akif2.jpg"> |
| <div class="smalltext"> | | <div class="smalltext"> |
- | <p>He graduated from Computer Education & Instructional Technology Department of Middle East Technical University last semester and he contributes this genius team as a coder for website. He wants to be a successful academician in his department at METU. He likes swimming and everything related to computers and automobiles.</p>
| + | <p>Akif is a graduate of Computer Education and Instructional Technologies department. In bachelor he has worked on Software Development, Database Management, Instructional Technologies, and Bioinformatics.<br /> |
| + | He was software developer and team leader of BioGuide project and Synthetic Biology Online Lecture. |
| + | <br />Currently he is mastering in Software Engineering and developing scientific applications, he will continue to work on Science and Technology Management after becoming master of Software Engineering. |
| + | </p> |
| </div> | | </div> |
| </div> | | </div> |
| <div class="smallbox"> | | <div class="smallbox"> |
- | <h2><a href="mailto:agca1988@gmail.com">M. Akif Ağca</a></h2> | + | <h2><a href="mailto:miktat_aktas@hotmail.com">Miktat Aktaş</a></h2> |
- | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2010/1/10/Metu-akif2.jpg"> | + | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/8/8d/Miktat.JPG"> |
| <div class="smalltext"> | | <div class="smalltext"> |
- | <p>Kutay is a graduate of Molecular Biology and Genetics, and now doing his M.Sc. in Biotechnology department at METU. This is his first year in IGEM team. He is interested in plant-based drugs, plant-pathogen interaction, biofuel production and bioremediation. He enjoys playing basketball, watching movies, and listening to music.</p> | + | <p>He graduated from Computer Education & Instructional Technology Department of Middle East Technical University last semester and he contributes this genius team as a coder for website. He wants to be a successful academician in his department at METU. He likes swimming and everything related to computers and automobiles.</p> |
| </div> | | </div> |
| </div> | | </div> |
| + | |
| <div class="smallbox"> | | <div class="smallbox"> |
- | <h2>...</h2> | + | <h2>Ceyhun Kerimov</h2> |
- | <img src="...."> | + | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/4/4d/Ceyhunkerim.png"> |
| <div class="smalltext"> | | <div class="smalltext"> |
- | <p>...</p> | + | <p>Ceyhun was born in Azerbaijan. He is studying in METU Computer Engineering Department. <br /> |
| + | He is Java and Salesforce developer now. He was in web side of the project. He tried to help the team to manupilate and store the data. <br /> |
| + | He is working in web and cloud computing technologies. |
| + | </p> |
| </div> | | </div> |
| </div> | | </div> |
| <div class="smallbox"> | | <div class="smallbox"> |
- | <h2>...</h2> | + | <h2>Huseyin Lutin</h2> |
- | <img src="...."> | + | <img width="130px" height="180px" src="https://static.igem.org/mediawiki/2011/8/81/Husayinlut.png"> |
| <div class="smalltext"> | | <div class="smalltext"> |
- | <p>...</p> | + | <p>Huseyin is a senior student in METU Computer Engineering Department.<br /> |
| + | He was helping the team during software requirements specification step of the project.<br /> |
| + | He is working on computer graphics in this year. |
| + | </p> |
| | | |
| </div> | | </div> |
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| <img src="https://static.igem.org/mediawiki/2011/2/28/Wetlabheader.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/2/28/Wetlabheader.png" height="75px" width="890px"> |
| <h2>WET LAB</h2> | | <h2>WET LAB</h2> |
- | <p>Whole summer in lab work we aimed to design 7 new E.coli compatible Biobricks and 1 composite part from 2011 kit plate distributions, also we aimed to characterize each part by protein analysis and fluorescence protein measurements.</p> | + | <p>Whole summer in lab work we aimed to design 7 new <i>E.coli</i> compatible Biobricks and 1 composite part from 2011 kit plate distributions, also we aimed to characterize each part by protein analysis and fluorescence protein measurements.</p> |
| | | |
- | <p>We achieved design and compatibility of parts in E.coli, however not all parts’ characterization is achieved. Only the genes of designed composite part from kit plate is characterized by GFP measurements.</p> | + | <p>We achieved design and compatibility of parts in <i>E.coli</i>, however not all parts’ characterization is achieved. Only the genes of designed composite part from kit plate is characterized by GFP measurements.</p> |
| | | |
- | <p>In this section you can find out more details on all our wet lab works. You can also find our data under results subtitle and information about design of our parts-biobricks with explanations in literature. It also contains materials and protocols, and finally There is safety questions list on our safety considerations both in the lab and on a wider environmental scale.</p> | + | <p>In this section you can find out more details on all our wet lab works. You can also find our data under results subtitle and information about design of our parts-biobricks with explanations in literature. It also contains materials and protocols, and finally there is safety questions list on our safety considerations both in the lab and on a wider environmental scale.</p> |
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| <img src="https://static.igem.org/mediawiki/2011/1/1b/Humanpractice.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/1/1b/Humanpractice.png" height="75px" width="890px"> |
| <h2>Overview</h2> | | <h2>Overview</h2> |
- | <p>Methan<b>E.COLI</b>c project arises from sustainty and conservancy of human health and safety. Therefore while we were constructing the organismal device we also wanted to inform people from all age and we wanted to increase the public awareness on our project; methane gas based (firedamp) explosions and the greenhouse effect of methane gas.</p> | + | <p>Methan<b>E.COLI</b>c projec |
| + | t arises from sustainability and conservancy of human health and safety. Therefore while we were constructing the organismic device we also wanted to inform people from all age and we wanted to increase the public awareness on our project; methane gas based (firedamp) explosions and the greenhouse effect of methane gas.</p> |
| | | |
| <p>Our aim is to inform people in each age. After brainstorming and searching, we planned the content of information and activities according to following subtitles.</p> | | <p>Our aim is to inform people in each age. After brainstorming and searching, we planned the content of information and activities according to following subtitles.</p> |
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| <div class="text"> | | <div class="text"> |
| <img src="https://static.igem.org/mediawiki/2011/5/53/Futureplanheader.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/5/53/Futureplanheader.png" height="75px" width="890px"> |
- | <h2>Future Work</h2> | + | <h2>Future Plan</h2> |
| | | |
| + | <br /> |
| <center><iframe width="560" height="315" src="http://www.youtube.com/embed/XAkuG4Xjp2A" frameborder="0" allowfullscreen></iframe></center> | | <center><iframe width="560" height="315" src="http://www.youtube.com/embed/XAkuG4Xjp2A" frameborder="0" allowfullscreen></iframe></center> |
- | <p>Methane explosion is the main problem since the very beginning of the coal mines. All countries tried different systems to solve this methane problem. | + | <p>Methane explosions called as grisou are one of the main problems from the beginning of the coal mines. All countries have tried different systems to solve this methane problem. When we joined iGEM 2011 competition, our aim is to find a solution to that problem for humanity by cheaper and energy saving way. After a long literature research, we found how seriously dangerous the methane gas is and how people deal with this big problem on coal mines. Below are the countries that have faced with serious methane explosions throughout their history.</p> |
- | When we decided to join iGEM 2011 competition firstly, it was very hard to chose a project from our brainstorms. All member of this group come up with a very reasonable idea for our team and we evaluate them all were seemed very beneficial for humanity. | + | |
- | However, one day we face the problem of methane explosions on the news and at that time we decided to create new idea for this problem. After a long literature research, we found how seriously dangerous the methane gas and how people deal with this big problem on coal mines</p>
| + | |
| <ol> | | <ol> |
| | | |
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| | | |
| </ol> | | </ol> |
- | <p>These are the countries which have been faced with too big methane explosions true out their history. After a certain research we found that to deal up this problem, companies spent lots of money for effective solutions. | + | <p>Todays companies deal with this problem by; |
| <br /><i>Regenerative Thermal Oxidizer from MEGTEC capable of handling 60,000 scfm of VAM. At a methane concentration of about 0.7% a unit this size generates 50,000 carbon credits per year. This unit costs about US$ 1,5 million | | <br /><i>Regenerative Thermal Oxidizer from MEGTEC capable of handling 60,000 scfm of VAM. At a methane concentration of about 0.7% a unit this size generates 50,000 carbon credits per year. This unit costs about US$ 1,5 million |
| Elizabeth Obediente from CO2IMPACT at a methane upgrading facility at a coal mine in Alabama. The gas is stripped of impurities and upgraded to 96% methane per volume and then compressed and then sold to the natural gas pipeline.</i> | | Elizabeth Obediente from CO2IMPACT at a methane upgrading facility at a coal mine in Alabama. The gas is stripped of impurities and upgraded to 96% methane per volume and then compressed and then sold to the natural gas pipeline.</i> |
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| <li>Save the nature</li> | | <li>Save the nature</li> |
| <li>Process a new energy</li> | | <li>Process a new energy</li> |
- | <li>Cheap system</li> | + | <li>Obtain a cheap system</li> |
| </ul></p> | | </ul></p> |
| <h3><u>Save the coal workers’ life</u></h3> | | <h3><u>Save the coal workers’ life</u></h3> |
| | | |
- | <p>When we produce our project, we stop the search the worlds system and turn back to our country, so we saw that methane (CH3) is a big problem to get rid of our mines too. The way carry out on our county has some missing parts on safety. While we were proceeding our project, we focus on this part mainly and we have shaped it according to this. | + | <p>We aimed to collect the methane gas from coal mines to the tanks which are filled with water. When the methane passes the legal percent that is 1%, according to our project, the gas is dissolved in water in tanks. Then, inside the tablets containing our bacteria and that are already present on the tanks the molecular process for conversion of methane to methanol begins. |
- | <br />We aimed to collect the methane gas from coal mines to the tanks which are filled with water. When the methane passes the legal percent of %1, according to our project, we dissolve the gas on water tanks. After that we put tablets which include our bacteria on the tanks , so the methane and methanol process will begin with this step.</p>
| + | Below the number of workers dead by years are given according to Prof. Dr. Mustafa ÖZTÜRK’s research,Vice President of Parliamentary Commission for the Environment in Turkey: |
| + | |
| <br /> | | <br /> |
| <br /> | | <br /> |
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| </table></center> | | </table></center> |
| <br /> | | <br /> |
- | <p>According to Prof. Dr. Mustafa ÖZTÜRK’s research (Vice President of Parliamentary Commission for the environment on turkey), this the death workers amount since 1983 to 2008 on Turkey’s coal mines. | + | <center><h3>Methane explosions: </h3> |
- | <br />Our way, collecting all methane gas from the mine to tanks, not only make methane free working space for workers, but also could make the space more workable and safer.</p> | + | <iframe width="420" height="315" src="http://www.youtube.com/embed/25BE42PzZZc" frameborder="0" allowfullscreen></iframe></center> |
| + | |
| | | |
| <h3><u>Save the nature</u></h3> | | <h3><u>Save the nature</u></h3> |
| | | |
- | <p>During our research for safety systems for methane all over the world, we saw that in most ways, methane release to the atmosphere with or without some elements and chemicals. Just a few systems are used methane to produce new energy or something else.</p> | + | <p>Methane is one of the greenhouse gases in the atmosphere. Methane is continuously released from coal mining, livestock, landfills and natural gases to the atmosphere. The accumulation of these greenhouse gases causes one of the greatest problems of Earth: global warming. Our project aims to prevent release of methane gas by the conversion of it to methanol in bacterial system in coal mines. </p> |
- | <p>We noticed that methane gas is twenty four times harmful than the carbon monoxide gas for the atmosphere. According to our project, on the way that converting methane gas to methanol form, we prevent methane to make any damage to the nature on gas form. </p>
| + | <center><h3>Greenhouse gases: </h3> |
| + | <iframe width="420" height="315" src="http://www.youtube.com/embed/tm-zZMiL58A" frameborder="0" allowfullscreen></iframe> |
| + | </center> |
| + | |
| | | |
| <h3><u>Process a new energy</u></h3> | | <h3><u>Process a new energy</u></h3> |
| | | |
- | <p>During the research process for our project, we also realized that energy is the most important thing on today and future life. Today, all energy sources are almost over including petroleum. People are searching new energy source. As the last news from china, everyone saw that nuclear energy is not a secure and trustable way to get energy.</p> | + | <p>After the conversion of methane to methanol, methanol can be used as a precursor of bio-fuel so that accumulated methanol can be recovered. Ethanol is used as biofuel, also; however, methanol is more cheaper to obtain and use as a biofuel. According to Dr. Robert Zubrin, Methanol is cheaper than ethanol. It can also be made from a broader variety of biomass material, as well as from coal and natural gas. And methanol is the safest motor fuel.(American enterprise, February 13th, 2006).</p> |
| | | |
- | <p>On this century, people understand the nature’s value for human life. Now renewable energy systems are built all around the world like wind turbines and sun batteries.</p>
| |
| | | |
- |
| |
- | <p>According to our project, we planed that methanol could be used for making bio-fuel instead of ethanol. For the bio-fuel, ethanol is collecting from especially from the corps. However, on this way, we use corps unnecessarily. Studies suggest that vehicles that run on 85 per cent methanol blends, as well as petrol, actually have performance capabilities that equal or surpass vehicles running on petrol alone.</p>
| |
- |
| |
- | <p>Also, according to Dr. Robert Zubrin,<i> Methanol is cheaper than ethanol. It can also be made from a broader variety of biomass material, as well as from coal and natural gas. And methanol is the safest motor fuel.</i>(American enterprise, February 13th, 2006)</p>
| |
| | | |
| <h3><u>Cheap system</u></h3> | | <h3><u>Cheap system</u></h3> |
| | | |
- | <p>There are lots of system use now for methane gas and the gas explosions on mines. However, when we look closer to them, they are too expensive to build for a mine. If we notice also there are global economic problems nowadays, it seems not possible that companies may not be to get enough precaution for their workers, even their own life especially on the developing countries.</p> | + | <p>There are many systems used to prevent or minimize methane explosions. However, they are so expensive to use and none of them are based on a biological system. The biological system that we build contains a bacterial cell having a molecular process of conversion of methane to methanol is completely harmless and cheaper since expensive equipments are not needed.</p> |
| | | |
- | <p>On the other hand, we put all the bacteria that we produce in a capsule tablet. They are totally harmless on this form. When we put them in the water tanks, they will come to life and start their work.
| |
- |
| |
- | <p>This process does not cost million dollars or does not get a lot of time for building very big facilities. It is very cheap and has very easy process time.</p>
| |
- |
| |
- | <p> Our project is open for research and development. For the future of it, we planned to put smelling part to our bacteria for making workers area more fresh and comfortable. In addition, we can design a system for our bacteria to send it in the mine and maybe start the process inside the mine. Furthermore, we put also biosensor part the bacteria and the bacteria measure the percent of the gas level with itself.</p>
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| <img src="https://static.igem.org/mediawiki/2011/f/f8/Partnershipheader.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/f/f8/Partnershipheader.png" height="75px" width="890px"> |
| <h2>PartnerShip</h2> | | <h2>PartnerShip</h2> |
- |
| + | <ul> |
- |
| + | <li><a href="#partnership2">Collaboration</a></li> |
| + | <li><a href="#partnership3">Sponsors</a></li> |
| + | <li><a href="#partnership4">METU</a></li> |
| + | <li><a href="#partnership5">Acknowledgements</a></li> |
| + | <ul> |
| </div> | | </div> |
| </div> | | </div> |
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| <img src="https://static.igem.org/mediawiki/2011/f/f4/Extraheader.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/f/f4/Extraheader.png" height="75px" width="890px"> |
| <h2>Extras</h2> | | <h2>Extras</h2> |
- | <p></p>
| + | |
- |
| + | <br /> |
| + | <br /> |
| + | <center><p><img src="https://static.igem.org/mediawiki/2011/7/70/COLLY.jpg"></p><center> |
| + | <br /> |
| + | <br /> |
| + | <div id="slider2"> |
| + | <img src="https://static.igem.org/mediawiki/2011/d/d7/IMG_0788.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/c/c9/IMG_0793.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/f/fd/DSCN2037.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/4/45/DSCN1102.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/1/1a/IMG_0794.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/9/9f/IMG_0148.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/2/2a/IMG_0796.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/d/d0/DSCN1905.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/8/84/DSCN1786.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/1/12/DSCN1797.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/a/af/DSCN1812.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/3/31/DSCN1895.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/9/90/DSCN1917.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/d/d4/IMG_0210.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/3/34/DSCN1818.JPG"> |
| + | </div> |
| + | <br /> |
| + | <br /> |
| + | <center><h3>Hands on show!</h3></center> |
| + | <center><iframe width="560" height="315" src="http://www.youtube.com/embed/_b50ti5L1_M" frameborder="0" allowfullscreen></iframe></center> |
| + | <br /> |
| + | <br /> |
| + | <p><div class="extra"><iframe width="646px" height="350px" src="http://www.metu.edu.tr/~e172018/metu-bin/self-evaluation.html"></iframe></div></p> |
| + | <br /> |
| + | <br /> |
| + | <center><h3>Photos</h3> |
| + | <br /> |
| + | <br /> |
| + | <p><img src="https://static.igem.org/mediawiki/2011/2/26/Background.png"></p> |
| + | <p><img src="https://static.igem.org/mediawiki/2011/d/df/Bannergiris2.png"></p> |
| + | <p><img src="https://static.igem.org/mediawiki/2011/d/d1/Bannergiris.png"></p> |
| + | <p><img src="https://static.igem.org/mediawiki/2011/3/3f/Bioguide.png"></p> |
| + | <p><img src="https://static.igem.org/mediawiki/2011/4/4a/Labguardrulez_copy.jpg"></p> |
| + | <p><img src="https://static.igem.org/mediawiki/2011/4/45/Methanecanavar%C4%B1.jpg"></p> |
| + | |
| </div> | | </div> |
| </div> | | </div> |
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| <center><p><img src="https://static.igem.org/mediawiki/2011/1/10/Sensingesas.gif" height="454px" width="640px"></center></p> | | <center><p><img src="https://static.igem.org/mediawiki/2011/1/10/Sensingesas.gif" height="454px" width="640px"></center></p> |
| <h3>i) Introduction </h3> | | <h3>i) Introduction </h3> |
- | <p>In our methane.colic project, the first critical point is to sense the ambient methane gas. While in literature search, we have focused on the methane and DNA or methane and regulator protein interaction which binds to DNA after binding to methane. In structure, methane consists of one carbon atom and four hydrogen atom which means it is smaller in size and weight. Therefore it is hard to find any study based on methane interaction with DNA or protein to regulate transcription. This made us search for carbon hydrogen bond interaction with any oligo or protein to trigger transcription of any metabolite product. So that we also searched the literature for any organism which utilizes any alkane chain and alkane which regulates the transcription of organismal metabolites by interaction with DNA or protein. Since bacteria are environmental adapting organisms, it is possible to find any alkane to regulate the transcription of degradation metabolism. Then we have found the organism, Pseudomonas oleovorans to analyze the alkane degradation of organism for its carbon source.</p> | + | <p>In our methanE.COLIc project, the first critical point is to sense the ambient methane gas. While in literature search, we have focused on the methane and DNA or methane and regulator protein interaction which binds to DNA after binding to methane. In structure, methane consists of one carbon atom and four hydrogen atom which means it is smaller in size and weight. Therefore it is hard to find any study based on methane interaction with DNA or protein to regulate transcription. This made us search for carbon hydrogen bond interaction with any oligo or protein to trigger transcription of any metabolite product. So that we also searched the literature for any organism which utilizes any alkane chain and alkane which regulates the transcription of organismal metabolites by interaction with DNA or protein. Since bacteria are environmental adapting organisms, it is possible to find any alkane to regulate the transcription of degradation metabolism. Then we have found the organism, <i>Pseudomonas oleovorans</i> to analyze the alkane degradation of organism for its carbon source.</p> |
| | | |
| <h3>ii) Background </h3> | | <h3>ii) Background </h3> |
- | <p> Many microorganisms live in the environments where the conditions changing frequently and so the evolution is inevitable for mechanisms to withstand unfavorable situations. Therefore microorganisms can use their specific and sensitive mechanisms for sensing the required nutrients for them or any pollution to affect their sustainity. Otherwise they can expose to mutations which change the gene expression and gain new functionalities. In case they have ability to survive in such conditions. </p> | + | <p> Many microorganisms live in the environments where the conditions changing frequently and so the evolution is inevitable for mechanisms to withstand unfavorable situations. Therefore microorganisms can use their specific and sensitive mechanisms for sensing the required nutrients for them or any pollution to affect their sustainability. Otherwise they can expose to mutations which change the gene expression and gain new functionalities. In case they have ability to survive in such conditions. </p> |
| <p>While we were scanning the literature based on methane and alkane degrading organisms we have found some organisms that sensitive to methane presence and have mechanisms to activate transcription of related gene clusters.</p> | | <p>While we were scanning the literature based on methane and alkane degrading organisms we have found some organisms that sensitive to methane presence and have mechanisms to activate transcription of related gene clusters.</p> |
- | <p>We analyzed the soil bacteria, Pseudomonas oleovorans. This strain can assimilate the alkane for its carbon source and one of the microbial whole cell –biosensor. They have a gene cluster which codes for degradative pathway and includes the activator which interacts especially with linear alkanes. This activator protein, AlkS, in the presence of alkanes, induces the transcription from PalkB promoter which initiates the expression of genes code for assimilation of alkanes. We have analyzed the related articles in which the promoter region is studied and showed that it is expressed in E.coli correctly because of the corresponding RNA polymerase binding regions.</p> | + | <p>We analyzed the soil bacteria, <i>Pseudomonas oleovorans</i>. This strain can assimilate the alkane for its carbon source and one of the microbial whole cell –biosensor. They have a gene cluster which codes for degradative pathway and includes the activator which interacts especially with linear alkanes. This activator protein, AlkS, in the presence of alkanes, induces the transcription from PalkB promoter which initiates the expression of genes code for assimilation of alkanes. We have analyzed the related articles in which the promoter region is studied and showed that it is expressed in <i>E.coli</i> correctly because of the corresponding RNA polymerase binding regions.</p> |
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| <b><p>REFERENCE:</p></b> | | <b><p>REFERENCE:</p></b> |
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| <h3>iii) Modelling </h3> | | <h3>iii) Modelling </h3> |
- | <p> Since the parts that we have found belongs to yeast organism, it was hard to us to manipulate it in bacteria E.coli. We designed the tests of this part by characterizing one of the subunits of methane monooxgenase (MMo). For the functional activity of monooxygenase enzyme, there are required 3 subunits as A,B and C. The A subunit of methane monooxygenase is 210 kDa protein that is supposed as the methane binding active site of monoxygenase complex. This protein consists of non-haem iron and contains p-hydroxo bridge structure. We planned the experiments of this step as characterization of protein A by PCR amplification with specific primers of full construct device to obtained the sequence of protein A. The methane gas is applied to cell culture with our modelled device then the cells were centrifuged and the gas concentration is measured from supernatant.</p> | + | <p> Since the parts that we have found belongs to yeast organism, it was hard to us to manipulate it in bacteria <i>E.coli</i>. We designed the tests of this part by characterizing one of the subunits of methane monooxgenase (MMo). For the functional activity of monooxygenase enzyme, there are required 3 subunits as A,B and C. The A subunit of methane monooxygenase is 210 kDa protein that is supposed as the methane binding active site of monoxygenase complex. This protein consists of non-haem iron and contains p-hydroxo bridge structure. We planned the experiments of this step as characterization of protein A by PCR amplification with specific primers of full construct device to obtained the sequence of protein A. The methane gas is applied to cell culture with our modelled device then the cells were centrifuged and the gas concentration is measured from supernatant.</p> |
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| Larger tubes or bottles can be used to centrifuge cells if volumes of all subsequent solutions are increased in direct proportion. </em> </p> | | Larger tubes or bottles can be used to centrifuge cells if volumes of all subsequent solutions are increased in direct proportion. </em> </p> |
| </li> | | </li> |
- | <li>Centrifuge cells 7 min at 1600 g (3000 rpm in JS -5.2), 4 C.</li> | + | <li>Centrifuge cells 7 min at 1600 g, 4 C.</li> |
| <p>Allow centrifuge to decelerate without breake.<br /> | | <p>Allow centrifuge to decelerate without breake.<br /> |
| <em>We have not attempted to determine whether deceleration without braking is critical to this procedure. However, we do not use the breake for this step or for the subsequent centrifugation steps. </em> </p> | | <em>We have not attempted to determine whether deceleration without braking is critical to this procedure. However, we do not use the breake for this step or for the subsequent centrifugation steps. </em> </p> |
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| </ol> | | </ol> |
| </li> | | </li> |
- | <li><strong>Transformation</strong> <br />
| + | <li><strong>Transformation</strong> <br /> |
| <br /> | | <br /> |
| </li> | | </li> |
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| <li> Centrifuge at 4000 rpm for 5 min at 4 C .</li> | | <li> Centrifuge at 4000 rpm for 5 min at 4 C .</li> |
| <li> Discard the supernatant and keep pellet.</li> | | <li> Discard the supernatant and keep pellet.</li> |
- | <li> Resuspended the pellet with 250 ul Resuspension solution. (Bacteria should be resuspended completely by vortexing until no cell clumps remain)</li> | + | <li> Resuspend the pellet with 250 ul Resuspension solution. (Bacteria should be resuspended completely by vortexing until no cell clumps remain)</li> |
| <li>Transfer the cell suspension to eppendorf.</li> | | <li>Transfer the cell suspension to eppendorf.</li> |
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| <p><em>Do not vortex!</em><br /> | | <p><em>Do not vortex!</em><br /> |
| <em>Do not incubate for more than 5 min. (To avoid denaturation of supercoiled plasmid DNA!)</em></p> | | <em>Do not incubate for more than 5 min. (To avoid denaturation of supercoiled plasmid DNA!)</em></p> |
- | <li>Add 350 uL Neutralization solutionand mix immediately and throughly by inverting the tube 4-6 times.</li> | + | <li>Add 350 uL Neutralization solution and mix immediately and thoroughly by inverting the tube 4-6 times.</li> |
- | <p><em>(The neutralized bacterial lysate is cloudy and viscous) ("throughly" to avoid localized precipitation of bacterial cell debris)</em></p> | + | <p><em>(The neutralized bacterial lysate is cloudy and viscous) ("thoroughly" to avoid localized precipitation of bacterial cell debris)</em></p> |
| <li>Centrifuge at 13000 rpm for 5 min to precipitate cell debris and chromosomal DNA.</li> | | <li>Centrifuge at 13000 rpm for 5 min to precipitate cell debris and chromosomal DNA.</li> |
| <li>Transfer the supernatant to spin column (about 600 uL).</li> | | <li>Transfer the supernatant to spin column (about 600 uL).</li> |
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| 1 uL EcorI-HF<br /> | | 1 uL EcorI-HF<br /> |
| 1 uL Spe I<br /> | | 1 uL Spe I<br /> |
- | 5 uL 10*NE Buffer 2<br /> | + | 5 uL 10XNE Buffer 2<br /> |
- | 0.5 uL 100* BSA<br /> | + | 0.5 uL 100X BSA<br /> |
| To 50 uL add dH2O<br /> | | To 50 uL add dH2O<br /> |
| <br /> | | <br /> |
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| 500 ng Downstream Part Plasmid<br /> | | 500 ng Downstream Part Plasmid<br /> |
| 1 ul XbaI<br /> | | 1 ul XbaI<br /> |
- | 5 uL 10*NE Buffer 2<br /> | + | 5 uL 10X NE Buffer 2<br /> |
- | 0.5 uL 100* BSA<br /> | + | 0.5 uL 100X BSA<br /> |
| To 50 uL add dH2O<br /> | | To 50 uL add dH2O<br /> |
| <br /> | | <br /> |
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| 1 uL EcorI- HF<br /> | | 1 uL EcorI- HF<br /> |
| 1 uL PstI<br /> | | 1 uL PstI<br /> |
- | 15 uL 10* NE Buffer 2<br /> | + | 15 uL 10X NE Buffer 2<br /> |
- | 0.5 uL 100*BSA<br /> | + | 0.5 uL 100X BSA<br /> |
| To 50 uL add dH2O<br /> | | To 50 uL add dH2O<br /> |
| <br /> | | <br /> |
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| <ul><li>EtBr stains only dsDNA. You cannot see ssDNA on gel</li> | | <ul><li>EtBr stains only dsDNA. You cannot see ssDNA on gel</li> |
| <li>Minimum amount of DNA load:</li> | | <li>Minimum amount of DNA load:</li> |
- | <p>200 ng (Aysu)<br /> | + | <p>300 ng <br /> |
- | • Each band of 1kb ladder is approx. 125 ng (2.5 ul loaded) and can be seen on gel</p> | + | • Each band of 1kb ladder is approximately 125 ng (2.5 ul loaded) and can be seen on gel</p> |
| </ul> | | </ul> |
| | | |
- | <h3>Preparetion</h3> | + | <h3>Preparation</h3> |
| <ul><li>50X TAE (Tris-Acetate) Buffer<br /> | | <ul><li>50X TAE (Tris-Acetate) Buffer<br /> |
| | | |
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| <li>DNA standards | | <li>DNA standards |
| <ul> | | <ul> |
- | <li> [Aysu]: Promega 1.0 kb (1.0-10Kbp), 100 bp (0.1-1.0 Kbp)</li> | + | <li> Promega 1.0 kb (1.0-10Kbp), 100 bp (0.1-1.0 Kbp)</li> |
| </ul> | | </ul> |
| </li> | | </li> |
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| <li> Dynamic integration, auto exposure, 10 frames</li> | | <li> Dynamic integration, auto exposure, 10 frames</li> |
| <li> 50/50 brigthness/contrast</li> | | <li> 50/50 brigthness/contrast</li> |
- | <li> 0/0 hue/saturation</li> | + | |
| </ul> | | </ul> |
| </li> | | </li> |
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| <li> 2 uL Downstream Part Digestion</li> | | <li> 2 uL Downstream Part Digestion</li> |
| <li> 2 uL Desination Plasmid Digestion</li> | | <li> 2 uL Desination Plasmid Digestion</li> |
- | <li> 2 uL 10* T4 DNA ligase bufferl</li> | + | <li> 2 uL 10X T4 DNA ligase bufferl</li> |
| <li> 2 uL T4 DNA ligase buffer</li> | | <li> 2 uL T4 DNA ligase buffer</li> |
| <li>11 uL dH2O</li> | | <li>11 uL dH2O</li> |
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| - TB (Terrific Broth)<br /> | | - TB (Terrific Broth)<br /> |
| <br /> | | <br /> |
- | Reference:<a href="http://www.embl.de/pepcore/pepcore_services/protein_expression/ecoli/"> http://www.embl.de/pepcore/pepcore_services/protein_expression/ecoli/</a><br /> | + | Reference:<a href="http://www.embl.de/pepcore/pepcore_services/protein_expression/ecoli/" target="_blank"> http://www.embl.de/pepcore/pepcore_services/protein_expression/ecoli/</a><br /> |
| <br /> | | <br /> |
| <br /> | | <br /> |
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- | - store @ 24 C | + | - store at 24 C |
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| <br /> | | <br /> |
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- | - store @ room temp. | + | - store at room temp. |
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| <br /> | | <br /> |
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| - store at -20 C | | - store at -20 C |
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- | <br />
| + | |
- | - kullanirken cok iyi vortexlemek gerekir
| + | |
- |
| + | |
| <br /> | | <br /> |
| | | |
| <br /> | | <br /> |
- | <strong>30% Acrylimid 1% Bis-acrylimide </strong> <br /> | + | <strong>30% Acrylamide 1% Bis-acrylimide </strong> <br /> |
| - prepare in laminar flow | | - prepare in laminar flow |
| | | |
| <br /> | | <br /> |
- | - 30 g acrylimide and 1 g bis-acrylimide in 100 ml (toz stock kimyasal icin) | + | - 30 g acrylimide and 1 g bis-acrylimide in 100 ml |
| | | |
| <br /> | | <br /> |
- | - 75 mL acrylimide solution ( 40% stock, Apllichem) and 25 mL bis-acrylimide solution ( 2% stock, Apllichem)to final volume 100 ml (sıvı stock kimyasal icin) | + | - 75 mL acrylimide solution ( 40% stock, Apllichem) and 25 mL bis-acrylimide solution ( 2% stock, Apllichem)to final volume 100 ml |
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| <br /> | | <br /> |
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| <br /> | | <br /> |
- | - aliquot 10 x 600 ul and store @ -20 C | + | - aliquot 10 x 600 ul and store at -20 C |
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| <br /> | | <br /> |
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| <br /> | | <br /> |
- | - 600 ml running buffer is required for each run (runing buffer seviyesi “max filled” cizgisini gecmemesi lazim. yoksa volt degeri power supply dan ayarlansa bile deger olarak o seviyeye ulasamiyor) | + | - 600 ml running buffer is required for each run |
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| <center><p><iframe width="420" height="315" src="http://www.youtube.com/embed/g6RICJsKQAI" frameborder="0" allowfullscreen></iframe></p></center> | | <center><p><iframe width="420" height="315" src="http://www.youtube.com/embed/g6RICJsKQAI" frameborder="0" allowfullscreen></iframe></p></center> |
| | | |
- | <h3>Here is Our Online Lecture, Click the picture to go;</h3> | + | <h3>Here is our Online Lecture, Click the picture to go;</h3> |
| <center><p><a href="http://ocw.metu.edu.tr/course/view.php?id=137" target="_blank" alink="red" vlink="red" ><img src="https://static.igem.org/mediawiki/2011/5/50/Syntheticbiol.png" height="115px" width="632px" alt="Click picture to reach Online Lectures" ></a></center></p> | | <center><p><a href="http://ocw.metu.edu.tr/course/view.php?id=137" target="_blank" alink="red" vlink="red" ><img src="https://static.igem.org/mediawiki/2011/5/50/Syntheticbiol.png" height="115px" width="632px" alt="Click picture to reach Online Lectures" ></a></center></p> |
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| <img src="https://static.igem.org/mediawiki/2011/f/f8/Partnershipheader.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/f/f8/Partnershipheader.png" height="75px" width="890px"> |
| <h2>Collaboration</h2> | | <h2>Collaboration</h2> |
- | <h3>Collaboration with Turk teams in iGEM 2011 </h3><br /> | + | <h3>Collaboration with Turkish teams in iGEM 2011 </h3><br /> |
| <br /> | | <br /> |
- | 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;<b>Fatih Turkey, Bilkent_UNAM, METU-BIN</b> 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 <b>scott.??</b> 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. <br /> | + | 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;<b>Fatih Turkey, Bilkent_UNAM, METU-BIN</b> 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. <br /> |
| <br /> | | <br /> |
- | Except from this, we established a collaboration with <b>METU-BIN Software iGEM 2011</b> team on their software program. This year their project, <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/">M4B: Mining for BioBricks</a> 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.<br /> | + | Except from this, we established a collaboration with <b>METU-BIN Software iGEM 2011</b> team on their software program. This year their project, <a href="http://dayhoff.ii.metu.edu.tr:8080/m4b/" target="_blank">M4B: Mining for BioBricks</a> 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.<br /> |
| <br /> | | <br /> |
| “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.” <br /> | | “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.” <br /> |
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| <br /> | | <br /> |
| <br /> | | <br /> |
- | <h3>Helping to other new Turk teams in the future</h3> <br /> | + | <h3>Helping to other new Turkish teams in the future</h3> <br /> |
| <br /> | | <br /> |
| 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. <br /> | | 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. <br /> |
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| <h2>Software Tool</h2> | | <h2>Software Tool</h2> |
| <p>BioGuide is a Biological System Design tool. It has been developed in 2010 by the team METU TURKEY SOFTWARE. You can check the page for detailed information about the project :<br /> <a href="https://2010.igem.org/Team:METU_Turkey_Software" target="_blank">https://2010.igem.org/Team:METU_Turkey_Software</a></p> | | <p>BioGuide is a Biological System Design tool. It has been developed in 2010 by the team METU TURKEY SOFTWARE. You can check the page for detailed information about the project :<br /> <a href="https://2010.igem.org/Team:METU_Turkey_Software" target="_blank">https://2010.igem.org/Team:METU_Turkey_Software</a></p> |
- | <h3>Here is rough draft of BioGuide Paper you can read for technical details;</h3> | + | |
| + | |
| + | <h3>Here is rough draft and setup of BioGuide Paper you can read for technical details and download the software;</h3> |
| + | |
| <p><a href="https://static.igem.org/mediawiki/2011/d/db/BioGuide.pdf" target="_blank">BioGuide.pdf</a> | | <p><a href="https://static.igem.org/mediawiki/2011/d/db/BioGuide.pdf" target="_blank">BioGuide.pdf</a> |
| + | <p><a href="http://sourceforge.net/projects/bioguidesetup/files/BioGuideSetup.rar/download" target="_blank">Download the Software</a> |
| | | |
| <h3>This year;</h3> | | <h3>This year;</h3> |
| <p>We have completed biological system design part of BioGuide and enabled wet lab teams to use it.</p> | | <p>We have completed biological system design part of BioGuide and enabled wet lab teams to use it.</p> |
| | | |
- | <h3>You can watch the how to video of BioGuide to see what and how you can do with it;</h3> | + | <h3>You can watch the "how to" video of BioGuide to see what and how you can do with it;</h3> |
| | | |
| <center><iframe width="425" height="349" src="http://www.youtube.com/embed/P4pMri0bAMc?hl=en&fs=1" frameborder="0" allowfullscreen></iframe></center> | | <center><iframe width="425" height="349" src="http://www.youtube.com/embed/P4pMri0bAMc?hl=en&fs=1" frameborder="0" allowfullscreen></iframe></center> |
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| <p><i>This year we are using it while building one of our devices, kill switch composite. Kill switch composite consists of 4 main parts which are in 2011 kit plate distributions; T7 promoter, RNA thermometer, GFP and lysis casette. The upstream part of this composite is T7 promoter (BBa_I712074) which is strong promoter from T7 bacteriophage mostly used expression system and so for strong transcription T7 promoter expression system is chosen.</p> | | <p><i>This year we are using it while building one of our devices, kill switch composite. Kill switch composite consists of 4 main parts which are in 2011 kit plate distributions; T7 promoter, RNA thermometer, GFP and lysis casette. The upstream part of this composite is T7 promoter (BBa_I712074) which is strong promoter from T7 bacteriophage mostly used expression system and so for strong transcription T7 promoter expression system is chosen.</p> |
| <p>We also tried the inducible promoters (pLac-IPTG inducer) to design and express the lysis casette. We desired to use a promoter that could be induced and enhance the expression to control and manipulate the translation of device. When we typed IPTG on input box of Bioguide we had reached the possible promoters that could be induced by IPTG. This program gave their standard biobrick codes and finally we got these parts by knowing their location in kit plate.</p> | | <p>We also tried the inducible promoters (pLac-IPTG inducer) to design and express the lysis casette. We desired to use a promoter that could be induced and enhance the expression to control and manipulate the translation of device. When we typed IPTG on input box of Bioguide we had reached the possible promoters that could be induced by IPTG. This program gave their standard biobrick codes and finally we got these parts by knowing their location in kit plate.</p> |
- | <p>In downstream of promoter there is RNA thermometer(ROSE) coding region which determines the transcription of our lysis composite part. We had reached this part by coding the temperature 42 in input box of BioGuide. RNA thermometer (BBa_K115001) is temperature sensitive at which 42C translation initiates. </p> | + | <p>In downstream of promoter there is RNA thermometer(ROSE) coding region which determines the transcription of our lysis composite part. We had reached this part by coding the temperature 42 C in input box of BioGuide. RNA thermometer (BBa_K115001) is temperature sensitive at which 42 C translation initiates. </p> |
| <p>In downstream of RNA thermometer, green fluorescence protein(BBa_E0040) is ligated. This ligation is done to measure expression level and to comment on RNA thermometer efficiency. We typed GFP in output box since we wanted to measure fluorescence.</p> | | <p>In downstream of RNA thermometer, green fluorescence protein(BBa_E0040) is ligated. This ligation is done to measure expression level and to comment on RNA thermometer efficiency. We typed GFP in output box since we wanted to measure fluorescence.</p> |
- | <p>We had designed this composite and it's parts mostly by processing the BioGuide program that made our job easier in intense lab works. We reached the shortest path with our input and output parameters for this device to construct by BioGuide</i></p> | + | <p>We had designed this composite and it's parts mostly by processing the BioGuide program that made our job easier in intense lab works. We reached the shortest path with our input and output parameters for this device to construct by BioGuide.</i></p> |
| | | |
| </div> | | </div> |
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| <h3>i) Introduction </h3> | | <h3>i) Introduction </h3> |
| | | |
- | <p>When examined in order, conversion is the second step of device system. While in literature searches, it is found that methanotrophs which live in either extreme conditions or in deep oceans, the process is the same, methane is converted to methanol which is the oxygenated form of hydrocarbon group. The searches directed us to organism Methylococcus capsulatus which is one of the mostly studied organisms among methanotrophs. We designed the conversion part of this organism and modified coding operon according to E.coli strain to enhance the expression. The monoxygenase coding part with protein A, B and C products are designed for conversion step of this project.</p> | + | <p>When examined in order, conversion is the second step of device system. While in literature searches, it is found that methanotrophs which live in either extreme conditions or in deep oceans, the process is the same, methane is converted to methanol which is the oxygenated form of hydrocarbon group. The searches directed us to organism <i>Methylococcus capsulatus</i> which is one of the mostly studied organisms among methanotrophs. We designed the conversion part of this organism and modified coding operon according to <i>E.coli</i> strain to enhance the expression. The monoxygenase coding part with protein A, B and C products are designed for conversion step of this project.</p> |
| | | |
| <h3>ii) Background </h3> | | <h3>ii) Background </h3> |
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| | | |
| <h4>a) Soluble Methane Monooxygenase </h4> | | <h4>a) Soluble Methane Monooxygenase </h4> |
- | <p> In contrast to pMMO, sMMO has extremely broad substrate specificity and can oxidise a wide range of non-growth substrates such as alkanes, alkenes and aromatic compounds thus making it the more attractive enzyme for co-oxidation reactions. sMMO is expressed only under conditions in which the copper-to-biomass ratio is low, i.e. under “low-copper” growth conditions, when copper ions are omitted from the trace elements solution of a standard mineral salts medium or cells are grown in a fermentor to high cell densities.There is also some evidence that copper ions inhibit the activity of sMMO (Jahng and Wood 1996). Like many other multi-component oxygenase systems, sMMO contains a component of approximately 16 kDa, Protein B, which serves an “effector” or regulatory role. The activity of Protein B may be regulated by proteolysis at its amino terminus (Lloyd et al. 1997). At low concentrations, Protein B converts the hydroxylase from an oxidase and stabilizes intermediates necessary for oxygen activation. Saturating amounts of Protein B dramatically increase the rates of formation of intermediates and accelerate catalysis of methane to methanol by sMMO (Lee and Lipscomb 1999). When analyzed, the most extensively characterised sMMO enzymes are those from Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b (reviewed in Lipscomb 1994; Deeth and Dalton 1998). Therefore we preferred to study on Methylococcus capsulatus (Bath) for monooxygenase.The sMMO is a non-haem iron-containing enzyme complex consisting of three components. The hydroxylase consists of three subunits of 60, 45 and 20 kDa arranged in an α2 β2 γ2 configuration. sMMO genes are clustered on the chromosome of Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b. mmoX, mmoY and mmoZ encode the α-, β- and γ-subunits respectively of the hydroxylase. mmoB and mmoC code for Protein B and the reductase component. Interestingly, mmoB lies between mmoY and mmoZ; an ORF of unknown function, designated orfY, with a coding capacity of 12 kDa, lies between mmoZ and mmoC in all genes clusters analysed to date (McDonald et al. 1997).</p> | + | <p> In contrast to pMMO, sMMO has extremely broad substrate specificity and can oxidise a wide range of non-growth substrates such as alkanes, alkenes and aromatic compounds thus making it the more attractive enzyme for co-oxidation reactions. sMMO is expressed only under conditions in which the copper-to-biomass ratio is low, i.e. under “low-copper” growth conditions, when copper ions are omitted from the trace elements solution of a standard mineral salts medium or cells are grown in a fermentor to high cell densities.There is also some evidence that copper ions inhibit the activity of sMMO (Jahng and Wood 1996). Like many other multi-component oxygenase systems, sMMO contains a component of approximately 16 kDa, Protein B, which serves an “effector” or regulatory role. The activity of Protein B may be regulated by proteolysis at its amino terminus (Lloyd et al. 1997). At low concentrations, Protein B converts the hydroxylase from an oxidase and stabilizes intermediates necessary for oxygen activation. Saturating amounts of Protein B dramatically increase the rates of formation of intermediates and accelerate catalysis of methane to methanol by sMMO (Lee and Lipscomb 1999). When analyzed, the most extensively characterised sMMO enzymes are those from <i>Methylococcus capsulatus</i> (Bath) and <i>Methylosinus trichosporium</i> OB3b (reviewed in Lipscomb 1994; Deeth and Dalton 1998). Therefore we preferred to study on <i>Methylococcus capsulatus</i> (Bath) for monooxygenase.The sMMO is a non-haem iron-containing enzyme complex consisting of three components. The hydroxylase consists of three subunits of 60, 45 and 20 kDa arranged in an α2 β2 γ2 configuration. sMMO genes are clustered on the chromosome of <i>Methylococcus capsulatus</i> (Bath) and <i>Methylosinus trichosporium</i> OB3b. mmoX, mmoY and mmoZ encode the α-, β- and γ-subunits respectively of the hydroxylase. mmoB and mmoC code for Protein B and the reductase component. Interestingly, mmoB lies between mmoY and mmoZ; an ORF of unknown function, designated orfY, with a coding capacity of 12 kDa, lies between mmoZ and mmoC in all genes clusters analysed to date (McDonald et al. 1997).</p> |
| | | |
| <p> <b>REFERENCE:</b></p> | | <p> <b>REFERENCE:</b></p> |
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| <div class="content2"> | | <div class="content2"> |
| <div class="text"> | | <div class="text"> |
- | <img src="https://static.igem.org/mediawiki/2011/2/28/Wetlabheader.png" height="175px" width="890px"> | + | <img src="https://static.igem.org/mediawiki/2011/2/28/Wetlabheader.png" height="75px" width="890px"> |
- | <h2>Biobricks</h2> | + | <h2>Biobricks</h2> |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/f/f1/Lush.PNG"> <strong>LUSH protein coding device / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593002" target="_blank">BBa_K593002</a></div> |
| + | |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/d/d8/Composite.PNG" height="75px" > <strong>ROSE regulated kill-switch / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593000" target="_blank">BBa_K593000</a></div> |
| + | <br /> |
| + | <br /> |
| + | <br /> |
| + | <br /> |
| + | <br /> |
| + | <br /> |
| + | <br /> |
| + | <br /> |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/3/3a/Untitled1.PNG"> <strong>Lush protein / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593003" target="_blank">BBa_K593003</a></div> |
| + | |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/3/3a/Untitled1.PNG"> <strong>mmo X / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593004" target="_blank">BBa_K593004</a></div> |
| + | |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/3/3a/Untitled1.PNG"> <strong>mmo Y / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593005" target="_blank">BBa_K593005</a></div> |
| + | |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/3/3a/Untitled1.PNG"> <strong>mmo Z / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593006" target="_blank">BBa_K593006</a></div> |
| + | |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/3/3a/Untitled1.PNG"> <strong>mmo B / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593007" target="_blank">BBa_K593007</a></div> |
| + | |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/3/3a/Untitled1.PNG"> <strong>mmo C / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593008" target="_blank">BBa_K593008</a></div> |
| + | |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/3/3a/Untitled1.PNG"> <strong>mmo D / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593010" target="_blank">BBa_K593010</a></div> |
| + | |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/f/fa/Untitled12.PNG"> <strong>ROSE regulated kill switch / </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593009" target="_blank">BBa_K593009</a></div> |
| + | |
| + | <div class="biobir"><img src="https://static.igem.org/mediawiki/2011/c/c0/Rosebr.png"> <strong>ROSE regulated GFP generator/ </strong><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K593011" target="_blank">BBa_K593011</a></div> |
| </div> | | </div> |
| </div> | | </div> |
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| <h2>Public Awareness</h2> | | <h2>Public Awareness</h2> |
| <h3>5-10 year old group</h3> | | <h3>5-10 year old group</h3> |
- | <p>For this age group, we prepared and modified one of the national child game. In this game there is a circle of group of child, one is not included in that circle. It runs around the circle and labels one of the participants in circle. When recognizes, it chases that one with singing that special song. In our modified game, the one that out of circle was our restriction enzyme due to our group in video, we assigned the enzymes into two,also they are double digestion enzymes. These ones wore white caps in video. And we have three insert groups which wore red, green and yellow caps. The blue capped ones were our backbone.<br /> During (By this game and at the begining of) this game we told to kids what is DNA, enzyme and insert, and what we have done as Synthetic Biology.</p> | + | <center><iframe width="560" height="315" src="http://www.youtube.com/embed/DemmlqdfPnk" frameborder="0" allowfullscreen></iframe></center> |
| + | <p>For this age group, we prepared and modified one of the national child game. In this game there is a circle of group of child, one is not included in that circle. He/she runs around the circle and labels two of the participants in the circle. When the labelled kids realized that, they leave the circle and new kids join the circle. The video below shows our modified game in which four kids that out of circle are our restriction enzymes wearing white caps. Moreover, we have three insert groups which wear red, green and yellow caps. The blue capped ones are our backbone.<br /> During the game we explained kids what DNA, enzyme and insert are, and what we have done as a Synthetic Biology research group.</p> |
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- | <div id="slider2"> | + | <div id="slider4"> |
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- | <img alt="" src="http://img189.imageshack.us/img189/148/dscn1645s.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/4/4e/DSCN1645.JPG"> |
- | <img alt="" src="http://img713.imageshack.us/img713/7315/dscn1646b.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/d/d6/DSCN1651.JPG"> |
- | <img alt="" src="http://img683.imageshack.us/img683/6892/dscn1647k.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/d/d2/1682.JPG"> |
- | <img alt="" src="http://img854.imageshack.us/img854/2563/dscn1648q.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/9/9b/IMG_0084.JPG"> |
- | <img alt="" src="http://img594.imageshack.us/img594/2087/dscn1650r.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/0/04/IMG_0087.JPG"> |
- | <img alt="" src="http://img801.imageshack.us/img801/3709/dscn1651e.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/c/cb/IMG_0092.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/6/65/IMG_0106.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/f/f2/IMG_0122.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/8/81/IMG_0134.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/1/17/IMG_0136.JPG"> |
| + | |
| </div> | | </div> |
| | | |
| <h3>10-17 year old group</h3> | | <h3>10-17 year old group</h3> |
- | <p>This group consists of high school aged children groups.Through out the workshop, we have paired them as two groups. Firstly we have explained Synthetic Biolgy and what Synthetic Biology is able to do. After these training, we told them our project and taught them basic molecular biology procedures and what are required for basic synthetic biology based experiments. We have done the experiments(cloning procedures) together and also they did individually. We also encouraged them to join iGEM High School division.</p> | + | <p>This group consists of high school aged children groups.Through out the workshop, we have paired them in doubles. Firstly, we have explained Synthetic Biolgy and what Synthetic Biology is able to do. After these training, we explained them our project and taught them basic molecular biology procedures and what are the requirements of basic synthetic biology based experiments. We have done the experiments (cloning procedures) together and also they did individually. We also encouraged them to join iGEM High School division.</p> |
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- | <div id="slider3">
| + | <h3> Official Announcement To All Universities For Introduction Of Synthetic Biology and iGEM Competetion</h3> |
- |
| + | |
- | <img alt="" src="http://img189.imageshack.us/img189/148/dscn1645s.jpg">
| + | <p>For the last human practice approach, we believed that we should inform especially students from other universities about synthetic biology as students in universities are the ones who can improve this field for further generations. For that purpose, we published an official message from our instructor, Prof. Dr. Mahinur Akkaya, with this message, students from other universities –regardless of their department that they’re studying in- will be aware of the field synthetic biology and may not only consider about learning more but also consider about creating an iGEM team for coming years. Here is the original official message and its brief translation for you to read:<br /> |
- | <img alt="" src="http://img713.imageshack.us/img713/7315/dscn1646b.jpg">
| + | Dean Office of Arts and Science Department<br /> |
- | <img alt="" src="http://img683.imageshack.us/img683/6892/dscn1647k.jpg">
| + | Synthetic biology is a field where natural sciences and engineering sciences go together hand in hand. It is an emerging science that requires the literature search, knowledge of natural sciences and methods of engineering sciences. Synthetic biology is the engineering of organisms to give them desired properties, except their regular metabolic activities. These desired properties are entegrated into genome of the organism with molecular cloning procedures.<br /> |
- | <img alt="" src="http://img854.imageshack.us/img854/2563/dscn1648q.jpg">
| + | There are lots of studies going on to introduce this newly emerging science field to people from all age groups and producing an information repository and improving it at the same time. One of this studies is the iGEM (International Genetically Engineered Machines) competition.<br /> |
- | <img alt="" src="http://img594.imageshack.us/img594/2087/dscn1650r.jpg">
| + | We, as METU iGEM teams, are attending this competition for four years. For this newly emerging science field to improve more, we believe that it should be spread out to other universities and more and more people should attend this competiton. We are sending you our study about the videos of lab protocols that are mainly used in synthetic biology and references that you can search for more information. We feel honored to tell that these sources are available for everyone who would like to reach them. Links for the sources are as follows:<br /> |
- | <img alt="" src="http://img801.imageshack.us/img801/3709/dscn1651e.jpg">
| + | <a href="http://ocw.metu.edu.tr/course/view.php?id=137">http://ocw.metu.edu.tr/course/view.php?id=137</a> <br /> |
- | </div>
| + | <a href="http://www.youtube.com/user/Metuankara">http://www.youtube.com/user/Metuankara</a> |
| + | <br /> |
| + | <br /> |
| + | <p><img width="900px" src="https://static.igem.org/mediawiki/2011/b/bc/Imagetif.png"></p> |
| + | <br /> |
| + | <br /> |
| | | |
| <h3>18-24 year old group</h3> | | <h3>18-24 year old group</h3> |
- | <p>This group consists of METU students. We arranged the Physics lectures in METU by contacting with instructor. To give an effective presentation (Due to physics is an service course in METU), we have reached to students in several departments. We had told our project individually and told them what is Synthetic Biology, we gained many volunteers to join METU-iGEM team for the following years. Also in METU we have an online lecture application as METU open course ware. For this web page, we have prepare the course notes and they were uploaded to reach many students from all around to inform and contact for further relations about Synthetic Biology. | + | <p>This group consists of METU students. We arranged the Physics lectures in order to reach students from several departments. We explained the miracle of Synthetic Biology and our project. At the end of the presentation, we gained many volunteers to join METU-iGEM team for the following years. Also, we have an online lecture application as METU open course ware. For this web page, we have prepare the course notes and they were uploaded to reach many students from all around to inform and contact for further relations about Synthetic Biology. |
| <br /> | | <br /> |
- | Moreover, we distributed hand outs about our project and synthetic biology at METU campus, when the new students registrations were done. We aimed to inform students about our project and synthetic biology to attract their attention on the issue.</p>
| + | In addition, we distributed hand outs about our project and Synthetic Biology at METU campus, when the registration of new students were done. We aimed to inform students about our project and about Synthetic Biology to attract their attention on the issue.</p> |
| <p>Online lecture link: : <a href="http://ocw.metu.edu.tr/course/view.php?id=137" target="_blank">http://ocw.metu.edu.tr/course/view.php?id=137</a> | | <p>Online lecture link: : <a href="http://ocw.metu.edu.tr/course/view.php?id=137" target="_blank">http://ocw.metu.edu.tr/course/view.php?id=137</a> |
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- | <br /><div id="slider4"> | + | <br /> |
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- | <img alt="" src="http://img189.imageshack.us/img189/148/dscn1645s.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/8/82/DSCN1576.JPG"> |
- | <img alt="" src="http://img713.imageshack.us/img713/7315/dscn1646b.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/e/e3/DSCN1577.JPG"> |
- | <img alt="" src="http://img683.imageshack.us/img683/6892/dscn1647k.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/5/51/DSCN1578.JPG"> |
- | <img alt="" src="http://img854.imageshack.us/img854/2563/dscn1648q.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/5/57/DSCN1580.JPG"> |
- | <img alt="" src="http://img594.imageshack.us/img594/2087/dscn1650r.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/4/49/DSCN1581.JPG"> |
- | <img alt="" src="http://img801.imageshack.us/img801/3709/dscn1651e.jpg">
| + | <img src="https://static.igem.org/mediawiki/2011/f/f8/DSCN1585.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/1/1b/DSCN1587.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/a/ab/DSCN1589.JPG"> |
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| + | <img src="https://static.igem.org/mediawiki/2011/2/2b/DSCN2089.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/e/ee/DSCN2091.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/f/f4/DSCN2092.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/9/92/DSCN2097.JPG"> |
| + | <img src="https://static.igem.org/mediawiki/2011/6/60/DSCN2099.JPG"> |
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| </div> | | </div> |
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- | <p>For this group of people we met with group of engineers in Turkey who work in mining fields in Turkey. We have told our project in details and we have consulted them on background of our project. What are the conditions in mines, what are the general regulations for worker safety and what are the rooted controls for any gas release are the points which we asked and discussed on.</p> | + | <p>For this group of people we met with group of engineers who work in mining fields in Turkey. We explained our project in details and consulted them on background of our project. What the conditions in mines are, what the general regulations for worker safety are and what the rooted controls for any gas release are the main points which we discussed on.</p> |
| <h3>List of Engineers:</h3> | | <h3>List of Engineers:</h3> |
| <h3>Turkish Architects and Engineers Association members:</h3> | | <h3>Turkish Architects and Engineers Association members:</h3> |
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| <p><img src="https://static.igem.org/mediawiki/2011/8/8c/Sacem.png" height="100px" width="200px"></p></center></div> | | <p><img src="https://static.igem.org/mediawiki/2011/8/8c/Sacem.png" height="100px" width="200px"></p></center></div> |
| <div class="sponsors"><center><h3>Metu</h3> | | <div class="sponsors"><center><h3>Metu</h3> |
- | <p><img src="https://static.igem.org/mediawiki/2011/2/2d/Odtu.png" height="50px" width="75px"></p></center></div> | + | <p><img src="https://static.igem.org/mediawiki/2011/8/8a/Metud.png" height="100px" width="200px"></p></center></div> |
| </div> | | </div> |
| </div> | | </div> |
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| <center><p><img src="https://static.igem.org/mediawiki/2011/c/c2/Entrapment.gif" height="454px" width="640px"></center></p> | | <center><p><img src="https://static.igem.org/mediawiki/2011/c/c2/Entrapment.gif" height="454px" width="640px"></center></p> |
| <h3>i) Introduction</h3> | | <h3>i) Introduction</h3> |
- | <p>After conversion of methane to methanol, the successive step is the entrapment of methanol. Methanol is an alcohol form of hydrocarbon methane and includes hydroxyl group. Hydroxyl radical groups are highly reactive and, and so short-lived; however, they form an important part of radical chemistry. Hydroxyl groups are especially important in biological systems and their chemistry because free radicals tend to form hydrogen bonds both as donor and acceptor. This property is also related to their ability to increase hydrophilicity and water solubility. Therefore hydroxyl free radicals cause damage to oxidative cells and cellular membranes. In order to produce the methanol for further industrial manufacturing in cellular organism, the organismal conditions should be adjusted. In the light of this, for our bacterial system we transferred the protein coding sequence(named as LUSH) of Drosophilia melanogaster to attack to free methanols and hydroxyl group. Here is some structural information about protein LUSH.</p> | + | <p>After conversion of methane to methanol, the successive step is the entrapment of methanol. Methanol is an alcohol form of hydrocarbon methane and includes hydroxyl group. Hydroxyl radical groups are highly reactive and, and so short-lived; however, they form an important part of radical chemistry. Hydroxyl groups are especially important in biological systems and their chemistry because free radicals tend to form hydrogen bonds both as donor and acceptor. This property is also related to their ability to increase hydrophilicity and water solubility. Therefore hydroxyl free radicals cause damage to oxidative cells and cellular membranes. In order to produce the methanol for further industrial manufacturing in cellular organism, the organismic conditions should be adjusted. In the light of this, for our bacterial system we transferred the protein coding sequence(named as LUSH) of <i>Drosophilia melanogaster</i> to attack to free methanols and hydroxyl group. Here is some structural information about protein LUSH.</p> |
| | | |
| <h3>ii) Background</h3> | | <h3>ii) Background</h3> |
- | <p>LUSH is an alcohol-sensitive odorant binding protein expressed in the olfactory organs of Drosophila melanogaster, and it is used as a model system to investigate the biophysical nature of | + | <p>LUSH is an alcohol-sensitive odorant binding protein expressed in the olfactory organs of <i>Drosophila melanogaster</i>, and it is used as a model system to investigate the biophysical nature of |
| alcohol-protein interactions at alcohol concentrations that produce intoxication in humans. In this study, by using NMR spectroscopy, they have identified the regions of LUSH that show increased conformational stability on binding alcohols. These residues primarily line the alcohol-binding pocket. A direct measure of the degree of stability that alcohol imparts on LUSH has been provided. LUSH was originally identified as responsible for mediating an avoidance response to short-chain n-alcohols.</p> | | alcohol-protein interactions at alcohol concentrations that produce intoxication in humans. In this study, by using NMR spectroscopy, they have identified the regions of LUSH that show increased conformational stability on binding alcohols. These residues primarily line the alcohol-binding pocket. A direct measure of the degree of stability that alcohol imparts on LUSH has been provided. LUSH was originally identified as responsible for mediating an avoidance response to short-chain n-alcohols.</p> |
| <p>The general structure of odorant binding proteins consists of six α-helices surrounding a hydrophobic ligand- binding pocket which differs in size and shape between each protein. All these odorant binding proteins have a set of six cysteines that form three conserved disulfide bonds. In the study, by observing the X-ray crystal structures of LUSH-alcohol complexes, it was found that alcohol binds to a single site in the protein formed by a network of concerted hydrogen-binding residues located at one end of hyrophobic pocket. This binding site has some sequence and/or structural similarities to regions of several ligand gated ion channels (LGICs) that have previously been implicated in inferring sensitivity to alcohol. It is hypothesized in the study that the alcohol-binding site in LUSH may represent a more general structural motif for functionally relevant alcohol-binding sites in proteins. The characterization of the effects of n-alcohols on the structure and stability of LUSH is presented. Also, in the absence of ligand, LUSH exists in vitro in a partially unstructured state and binding of alcohols shifts the solution conformation to a more compact folded state which is accompanied by an increase in the overall protein stability. Those regions of the protein that show the largest changes in local dynamics on binding alcohol have been identified and it have been shown that these are predominantly associated with the residues that line the alcohol-binding pocket. The results provide a quantitative measure of the ability of short-chain alcohols to stabilize protein structure at physiological relevant concentrations. </p> | | <p>The general structure of odorant binding proteins consists of six α-helices surrounding a hydrophobic ligand- binding pocket which differs in size and shape between each protein. All these odorant binding proteins have a set of six cysteines that form three conserved disulfide bonds. In the study, by observing the X-ray crystal structures of LUSH-alcohol complexes, it was found that alcohol binds to a single site in the protein formed by a network of concerted hydrogen-binding residues located at one end of hyrophobic pocket. This binding site has some sequence and/or structural similarities to regions of several ligand gated ion channels (LGICs) that have previously been implicated in inferring sensitivity to alcohol. It is hypothesized in the study that the alcohol-binding site in LUSH may represent a more general structural motif for functionally relevant alcohol-binding sites in proteins. The characterization of the effects of n-alcohols on the structure and stability of LUSH is presented. Also, in the absence of ligand, LUSH exists in vitro in a partially unstructured state and binding of alcohols shifts the solution conformation to a more compact folded state which is accompanied by an increase in the overall protein stability. Those regions of the protein that show the largest changes in local dynamics on binding alcohol have been identified and it have been shown that these are predominantly associated with the residues that line the alcohol-binding pocket. The results provide a quantitative measure of the ability of short-chain alcohols to stabilize protein structure at physiological relevant concentrations. </p> |
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| <h2>Notebook</h2> | | <h2>Notebook</h2> |
- | <p><img src="https://static.igem.org/mediawiki/2011/8/87/Notebook-1.png" height="662px" width="524px"></p> | + | |
| + | <div id="slider6"> |
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| + | <img src="https://static.igem.org/mediawiki/2011/8/87/Notebook-1.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/c/c5/Week2.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/8/84/Week3.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/4/48/Week4.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/5/5d/Week5.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/8/8d/Week6.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/0/00/Week7.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/7/72/Week8.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/a/ab/Week9.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/1/12/Week10.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/8/8e/Week11.png"> |
| + | <img src="https://static.igem.org/mediawiki/2011/a/a4/Week13.png"> |
| + | </div> |
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| </div> | | </div> |
| </div> | | </div> |
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| <div class="text"> | | <div class="text"> |
| <img src="https://static.igem.org/mediawiki/2011/1/1b/Humanpractice.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/1/1b/Humanpractice.png" height="75px" width="890px"> |
- | <h2>Contact</h2> | + | <h2>Media Press</h2> |
- |
| + | |
| + | <center><p><iframe width="420" height="315" src="http://www.youtube.com/embed/Femv5f6V8UM" frameborder="0" allowfullscreen></iframe> |
| + | <p><img src="https://static.igem.org/mediawiki/2011/2/26/Untitled-ntvmsnbc.png"></p></center> |
| </div> | | </div> |
| </div> | | </div> |
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| <img src="https://static.igem.org/mediawiki/2011/f/f8/Partnershipheader.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/f/f8/Partnershipheader.png" height="75px" width="890px"> |
| <h2>Middle East Technical University</h2> | | <h2>Middle East Technical University</h2> |
- | <p><img src="https://static.igem.org/mediawiki/2011/2/2d/Odtu.png" height="50px" width="75px"></p> | + | <p><img src="https://static.igem.org/mediawiki/2011/8/8a/Metud.png" height="100px" width="200px"></p> |
| <p>Middle East Technical University is a pioneering university in education, research and community service in the country. In addition to being highly preferred by students, it is internationally recognized.Our country is successfully represented by METU academic staff in numerous scientific and professional institutions and committees.The wide variety of cultural, artistic and intellectual activities, and sports opportunities that are offered by our campuses are a part of the "education environment" of international quality. METU has been defined in national rankings as the university which has the "Richest Social Environment".Whatever your reason to visit METU is, you will find here an innovative, dynamic and exciting environment which offers diversity and variety of choices. Come and join us at METU where the most successful students of the country, the most outstanding teaching and research staff, and the most distinguished administrative-technical staff live, learn, and produce hand in hand...</p> | | <p>Middle East Technical University is a pioneering university in education, research and community service in the country. In addition to being highly preferred by students, it is internationally recognized.Our country is successfully represented by METU academic staff in numerous scientific and professional institutions and committees.The wide variety of cultural, artistic and intellectual activities, and sports opportunities that are offered by our campuses are a part of the "education environment" of international quality. METU has been defined in national rankings as the university which has the "Richest Social Environment".Whatever your reason to visit METU is, you will find here an innovative, dynamic and exciting environment which offers diversity and variety of choices. Come and join us at METU where the most successful students of the country, the most outstanding teaching and research staff, and the most distinguished administrative-technical staff live, learn, and produce hand in hand...</p> |
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| <h2>Contact</h2> | | <h2>Contact</h2> |
| + | <strong>Device Experiment Results</strong><br /> |
| + | <br /> |
| + | -<strong>Flask experiments</strong><br /> |
| + | <br /> |
| + | In characterization experiments, we choosed temperature sensitive RNA thermometer (BBa_K115001) and modelled the experiments on GFP measurements. RNA thermometer is a temperature sensitive DNA part that up to 42 C it forms a dimer. This dimer formation prevents polymerase readings that the translation is obstructed. At 42 C the linear form of part forms and translation initiates. This part is submitted to parts registry by iGEM 2008 TUDelft team and the experience of part is represented as none. We modelled the characterization of this part by planing two apart control groups.<br /> |
| + | <br /> |
| + | One pair group for characterization was T7 promoter,RNA thermometer and GFP from upstream to downstream at 37C and the same device at 42C. The aim of this control group was to control any expression of green fluorescence protein at 37 C to check RNA thermometer dimer formation. We prepared a flask experiments and from protein formation to folding range we measured the spectrophotometer and fluoresence spectrometer readings. It is showed the dimer formation of RNA thermometer at lower than 42 C caused inefficient binding of RBS to DNA. That means we measured the GFP readings at two temperatures however at 42 C the expression was observed in higher level. As seen at OD:0.6 reading there is a dramatic difference in expressions.<br /> |
| + | <br /> |
| + | Other pair group for characterization was T7 promoter with GFP at 37 C and T7 promoter,RNA thermometer and GFP from upstream to downstream at 42C. This control group was modelled in order to check and compare the expression levels of two devices. The expected result was to observe the similar readings. Because without RNA thermometer temperature switch off device express similar readings at 37C with RNA thermometer device at 42 C. In the data analysis we observed that there is deviation in readings between control T7 with GFP at 37C and to construct, T7 RNA thermometer and GFP at 42 C.<br /> |
| + | <br /> |
| + | <br /> |
| + | <center><h3>GFP Reading Data</h3> |
| + | <p><img src="https://static.igem.org/mediawiki/2011/d/db/Datapage.png"></p> |
| + | <br /> |
| + | <br/> |
| + | <p><img width="900px" src="https://static.igem.org/mediawiki/2011/3/34/Ans_paper.jpg"></center></p> |
| + | <br /> |
| + | <br /> |
| + | <p><strong>Assembly Results</strong><br /> |
| + | <br /> |
| + | According our clonning plan, we planned to ligate the coding sequences of methane monooxygenase as subunits and to express the functional monooxygenase enzyme. Since we synthesized the long coding sequence we did PCR experiments with specific primers we extracted the parts in each the gel electrophoresis results gave validation for successfully synthesied DNA fragments, then we digested and ligated each part with related promoters and vector (pSB1C3) again gel electrophoresis data gave us validation to correctly digest and ligated form. <br /> |
| + | <br /> |
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| + | <center><p><img src="https://static.igem.org/mediawiki/2011/2/28/1KB-Ladder-X-Lush.png"> |
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| + | <br /> |
| + | <br /> |
| + | <img src="https://static.igem.org/mediawiki/2011/e/ec/09%2C16-1kb-control-mmoB-D-Z-C.png"> |
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| + | <br /> |
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| + | <img src="https://static.igem.org/mediawiki/2011/6/6c/Z-B-c3-c.png"> |
| + | <br /> |
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| + | <img src="https://static.igem.org/mediawiki/2011/a/a5/09%2C19-a3-d-lush.png"> |
| + | <br /> |
| + | <br /> |
| + | <br /> |
| + | <img src="https://static.igem.org/mediawiki/2011/e/e4/09%2C18-1k%C4%B1b-D-control-C-Z.png"></p></center> |
| + | <br /> |
| + | <br /> |
| + | <br /> |
| + | |
| + | <br /> |
| + | <br /> |
| + | <strong>-The device parts control experiments</strong></p> |
| + | <p>The synthesized methane monoxygenase construct was so long part that we had problems in synthesizing that we got genes so late. By the way the long sequence was divided into two sequences that one of the regions were splitted into two parts therefore we could not ligated the two parts of coding sequence due to unidentified restriction sites, and full construct unfortunately did not reach to us. The main methane interacting region of monooxygenase could not be expressed functionally. |
| + | We expressed the protein B and C of methane monoxygenase encoeded from mmo B and mmo C genes in protein expression host E.coli BL21 strain. We planned to characterize the proteins in their theoretical molecular weights by SDS-PAGE analysis. However due to technical problems in gel formation we lost samples that we could not reached the data. |
| + | We planned another part on kit plate distributions to check works or not. The bacteriophage 21 lysis casette S, R, and Rz (PVJ4) (BBa_K124003). This part was designed by 2008 iGEM Brown team which induces lysis in E.coli bacteria. We ligated this part with ROSE regulated GFP generator to induce the lysis of bacteria at 42C. Apart from this ligate, we ligated lysis casette with plac promoter and lacZ expressing gene to observe the blue colonies on plates. However we could not observe any blue colony on plates. |
| + | |
| + | </p> |
| + | |
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| </div> | | </div> |
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| <br /> | | <br /> |
- | <center><iframe width="560" height="315" src="http://www.youtube.com/embed/DemmlqdfPnk" frameborder="0" allowfullscreen></iframe></center> | + | <center><p><iframe width="560" height="315" src="http://www.youtube.com/embed/gdRz8IICg5E" frameborder="0" allowfullscreen></iframe></p></center> |
| <br /> | | <br /> |
- | <p>In order to reach to huge amounts of people who are in several age groups, we have designed a flashmob related with our project- in molecular level- .(A flash mob (or flashmob) is a group of people who assemble suddenly in a public <a href="http://en.wikipedia.org/wiki/Public_place " target="_blank">place</a>, perform an unusual and sometimes seemingly pointless act for a brief time, then disperse, often for the purposes of entertainment, satire, artistic expression or—in rare cases—violence. Flash mobs are organized via <a href="http://en.wikipedia.org/wiki/Telecommunications" target="_blank">telecommunications</a>, <a href="http://en.wikipedia.org/wiki/Social_media" target="_blank">social media</a>, or <a href="http://en.wikipedia.org/wiki/Viral_email " target="_blank">viral emails</a> ).One of our group member who is a member of Flashmob society helped us for arrangements.. We use Flashmob in order to explain what is our project and increase the public awareness about Synthetic biology and particularly our project. Flashmob event took place at one of the biggest shopping malls in Ankara where people often strolled around. Afterwards, we had interviewed with people who watched our sketch and informed people about nearly limitless capabilities of synthetic biology. Indeed we had prepared hand outs that contains interesting statistical data about methane and it’s side effects, also information about iGEM</p> | + | <p>In order to reach more people from several age groups, we have organized a flashmob activity which is related with our project -in molecular level-. (A flashmob is an activity done by a group of people who assemble suddenly in a public <a href="http://en.wikipedia.org/wiki/Public_place " target="_blank">place</a>, perform an unusual and sometimes seemingly pointless act for a brief time, then disperse, often for the purposes of entertainment, satire, artistic expression. Flashmob activities are organized via <a href="http://en.wikipedia.org/wiki/Telecommunications" target="_blank">telecommunications</a>, <a href="http://en.wikipedia.org/wiki/Social_media" target="_blank">social media</a>, or <a href="http://en.wikipedia.org/wiki/Viral_email " target="_blank">viral emails</a> ).One of our group member who is also a member of Flashmob society in Ankara helped us for arrangements. We use flashmob activity in order to explain what our project is and to increase the public awareness about Synthetic Biology and especially about our project. Flashmob event took place at one of the biggest shopping malls in Ankara where people often strolled around. Afterwards, we had interviewed with people who watched our sketch and informed people about nearly limitless capabilities of synthetic biology. Indeed we prepared handouts that contains interesting statistical data about methane and its side effects, also information about iGEM and about our project.</p> |
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| </div> | | </div> |
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| <img src="https://static.igem.org/mediawiki/2011/f/f8/Partnershipheader.png" height="75px" width="890px"> | | <img src="https://static.igem.org/mediawiki/2011/f/f8/Partnershipheader.png" height="75px" width="890px"> |
- | <h2>Contact</h2> | + | <h2>Acknowledgements</h2> |
| + | We are grateful to;</p> |
| + | |
| + | <i><p>Gönenç Gürsoy, for helping in modelling, being our travel agent and ordering the best potato chips for us (with beer of course)...</p> |
| + | |
| + | <p>Duygu Yıldız, for being a mother and bringing delicious food for our breaks, being our light graffiti maker...</p> |
| + | |
| + | <p>Gence Bektaş for being a methane molecule...</p> |
| + | |
| + | <p>Önder Alparslan, for helping in modelling and ending our desperate search for a graphic tablet :)...</p> |
| + | |
| + | <p>Mustafa Türkkan for being the best lipid bilayer member ever :) even though being a civil engineer...</p> |
| + | |
| + | <p>Efe Köksal for being our moviemaker...</p> |
| + | |
| + | <p>Demir Berkay Yılmaz for our second moviemaker and being in lab with us most of the time... </p> |
| + | |
| + | <p>Ankara Flashmob society for being with us in our presentations and making it real fun...</p> |
| + | |
| + | <p>Tufan Öz, Burcu Tefon, Aslıhan Kurt and Çiğdem Yılmaz for their incredible patience to our questions and supplying chemicals at speed of light!</p> |
| + | |
| + | <p>As a team, we’d like to thank our instructor Professor Dr. Mahinur S. Akkaya for her patience, love, support and all of her solutions to our unending problems. :)</p></i> |
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| </div> | | </div> |
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| <li>While device training experiments we planned to use <b>methane gas CH4</b> and <b>methanol CH3OH</b>. Methane is inactive biologically and essentially nontoxic.Methane is not listed in the IARC, NTP or by OSHA as a carcinogen or potential carcinogen. When inhaled in high concentrations, so as to exclude an adequate supply of oxygen to the lungs causes dizziness, deeper breathing due to air hunger, possible nausea and eventual unconsciousness. In case of protection, we adjusted the progressing the steps for methane in glove boxes in order to provide the respiratory protection. The ventilation is supported by hood. However due to methane gas is potent for greenhouse effect for doing experiments, special hood system is designed that could be used which has its own gas container for storage of gases is used. Thus, emission of methane gas is controlled. Later on, filled gas container is taken by department of chemistry to empty with certain procedures. We arranged the conditions in department for possible experiments with methane gas. And protective gloves and goggles are equiped for personal safety.Out of the experiments for storage the gas tanks were saved in area where is cool enough and never used open flames.</li> | | <li>While device training experiments we planned to use <b>methane gas CH4</b> and <b>methanol CH3OH</b>. Methane is inactive biologically and essentially nontoxic.Methane is not listed in the IARC, NTP or by OSHA as a carcinogen or potential carcinogen. When inhaled in high concentrations, so as to exclude an adequate supply of oxygen to the lungs causes dizziness, deeper breathing due to air hunger, possible nausea and eventual unconsciousness. In case of protection, we adjusted the progressing the steps for methane in glove boxes in order to provide the respiratory protection. The ventilation is supported by hood. However due to methane gas is potent for greenhouse effect for doing experiments, special hood system is designed that could be used which has its own gas container for storage of gases is used. Thus, emission of methane gas is controlled. Later on, filled gas container is taken by department of chemistry to empty with certain procedures. We arranged the conditions in department for possible experiments with methane gas. And protective gloves and goggles are equiped for personal safety.Out of the experiments for storage the gas tanks were saved in area where is cool enough and never used open flames.</li> |
| </ol> | | </ol> |
- | <p>REFERENCE:<a href="http://www.isocinfo.com/DocumentRoot/13/Methane.pdf">http://www.isocinfo.com/DocumentRoot/13/Methane.pdf</a> <br /> | + | <p>REFERENCE:<a href="http://www.isocinfo.com/DocumentRoot/13/Methane.pdf" target="_blank">http://www.isocinfo.com/DocumentRoot/13/Methane.pdf</a> <br /> |
| For the steps with <b>methanol t</b>he characterization tests for LUSH protein, methanol is used. Methanol is hazardous in case of skin contact, eye contact, ingestion and inhalation. It is flammable liquid.The safety for this chemical is provided by experimenting in hood with high ventilation and and so much exposed because it pose a health risk to anyone in lab. <br /> | | For the steps with <b>methanol t</b>he characterization tests for LUSH protein, methanol is used. Methanol is hazardous in case of skin contact, eye contact, ingestion and inhalation. It is flammable liquid.The safety for this chemical is provided by experimenting in hood with high ventilation and and so much exposed because it pose a health risk to anyone in lab. <br /> |
- | REFERENCE :<a href="http://www.sciencelab.com/msds.php?msdsId=9927227">http://www.sciencelab.com/msds.php?msdsId=9927227</a> </p> | + | REFERENCE :<a href="http://www.sciencelab.com/msds.php?msdsId=9927227" target="_blank">http://www.sciencelab.com/msds.php?msdsId=9927227</a> </p> |
| <p>We had studied with ANS; 1-Anilino-8-Naphthalene Sulfonate as protein conformational tightening agent for LUSH protein folding experiments. We searched on safety of this chemical and we found that it is non hazardous chemical according to Directive 67/548/EE Following reference belongs to Sigma Aldrich MSDS report.<br /> | | <p>We had studied with ANS; 1-Anilino-8-Naphthalene Sulfonate as protein conformational tightening agent for LUSH protein folding experiments. We searched on safety of this chemical and we found that it is non hazardous chemical according to Directive 67/548/EE Following reference belongs to Sigma Aldrich MSDS report.<br /> |
- | <a href="http://www.sigmaaldrich.com/catalog/DisplayMSDSContent.do">http://www.sigmaaldrich.com/catalog/DisplayMSDSContent.do</a></p> | + | <a href="http://www.sigmaaldrich.com/catalog/DisplayMSDSContent.do" target="_blank">http://www.sigmaaldrich.com/catalog/DisplayMSDSContent.do</a></p> |
| <p><b>b. Risks to the safety and health of the general public if released by design or accident?</b></p> | | <p><b>b. Risks to the safety and health of the general public if released by design or accident?</b></p> |
| <ol> | | <ol> |
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| <b>a. Does your institution have its own biosafety rules and if so what are they? Provide a link to them online if possible.</b><br /> | | <b>a. Does your institution have its own biosafety rules and if so what are they? Provide a link to them online if possible.</b><br /> |
| Yes, there is general laboratory biosafety rules for lab security and researcher security obeyed in Biology and Chemistry departments. In research laboratories the students are provided with general lab security and rules which are compilation of general and international procedures for individual safety. These procedures are the compilation of several links as<br /> | | Yes, there is general laboratory biosafety rules for lab security and researcher security obeyed in Biology and Chemistry departments. In research laboratories the students are provided with general lab security and rules which are compilation of general and international procedures for individual safety. These procedures are the compilation of several links as<br /> |
- | <a href="http://oba.od.nih.gov/oba/rac/guidelines_02/NIH_Gdlnes_lnk_2002z.pdf">http://oba.od.nih.gov/oba/rac/guidelines_02/NIH_Gdlnes_lnk_2002z.pdf</a></p> | + | <a href="http://oba.od.nih.gov/oba/rac/guidelines_02/NIH_Gdlnes_lnk_2002z.pdf" target="_blank">http://oba.od.nih.gov/oba/rac/guidelines_02/NIH_Gdlnes_lnk_2002z.pdf</a></p> |
| <p> </p> | | <p> </p> |
| <p><b>b. Does your institution have an Institutional Biosafety Committee or equivalent group? If yes, have you discussed your project with them? Describe any concerns or changes that were made based on this review.</b></p> | | <p><b>b. Does your institution have an Institutional Biosafety Committee or equivalent group? If yes, have you discussed your project with them? Describe any concerns or changes that were made based on this review.</b></p> |
| <p>Yes there is biosafety and ethical research center in METU until 2000. This committee helds many conferences about ethics, environmental ethics in studies and the medicinal ethics based on human researchs. The below link belongs to this committee however in Turkish language.<br /> | | <p>Yes there is biosafety and ethical research center in METU until 2000. This committee helds many conferences about ethics, environmental ethics in studies and the medicinal ethics based on human researchs. The below link belongs to this committee however in Turkish language.<br /> |
- | <a href="http://www.ueam.metu.edu.tr/">http://www.ueam.metu.edu.tr</a></p> | + | <a href="http://www.ueam.metu.edu.tr/" target="_blank">http://www.ueam.metu.edu.tr</a></p> |
| <p> Indeed in Biology department at METU one of our professors, Prof.Dr Huseyin Avni Oktem was one of the members of National Biosafety Coordinating Committee. He is our pioneer for biosafety and security issues. In the case of any safety issues, he is the one to consult the critical safety points in our project and also discussed the project based on safety. </p> | | <p> Indeed in Biology department at METU one of our professors, Prof.Dr Huseyin Avni Oktem was one of the members of National Biosafety Coordinating Committee. He is our pioneer for biosafety and security issues. In the case of any safety issues, he is the one to consult the critical safety points in our project and also discussed the project based on safety. </p> |
| <p><b> c. Will / did you receive any biosafety and/or lab training before beginning your project? If so, describe this training.</b></p> | | <p><b> c. Will / did you receive any biosafety and/or lab training before beginning your project? If so, describe this training.</b></p> |
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| <p><b> </b></p> | | <p><b> </b></p> |
| <p>In Turkey, biosafety regulations are organized by the Biosafety Information Exchange Mechanism of Turkey, facility of Ministry of Agriculture and Rural Affair.<br /> | | <p>In Turkey, biosafety regulations are organized by the Biosafety Information Exchange Mechanism of Turkey, facility of Ministry of Agriculture and Rural Affair.<br /> |
- | <a href="http://www.tbbdm.gov.tr/en/Home.aspx">http://www.tbbdm.gov.tr/en/Home.aspx</a></p> | + | <a href="http://www.tbbdm.gov.tr/en/Home.aspx" target="_blank">http://www.tbbdm.gov.tr/en/Home.aspx</a></p> |
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| </div> | | </div> |